The origin of Cretaceous black shales: a change in the surface ocean ecosystem and its triggers

Black shale is dark-colored, organic-rich sediment, and there have been many episodes of black shale deposition over the history of the Earth. Black shales are source rocks for petroleum and natural gas, and thus are both geologically and economically important. Here, we review our recent progress in understanding of the surface ocean ecosystem during periods of carbonaceous sediment deposition, and the factors triggering black shale deposition. The stable nitrogen isotopic composition of geoporphyrins (geological derivatives of chlorophylls) strongly suggests that N₂-fixation was a major process for nourishing the photoautotrophs. A symbiotic association between diatoms and cyanobacteria may have been a major primary producer during episodes of black shale deposition. The timing of black shale formation in the Cretaceous is strongly correlated with the emplacement of large igneous provinces such as the Ontong Java Plateau, suggesting that black shale deposition was ultimately induced by massive volcanic events. However, the process that connects these events remains to be solved.     

Harnessing the Evolvability of Tricyclic Microviridins To Dissect Protease–Inhibitor Interactions

Understanding and controlling proteolysis is an important goal in therapeutic chemistry. Among the natural products specifically inhibiting proteases microviridins are particularly noteworthy. Microviridins are ribosomally produced and posttranslationally modified peptides that are processed into a unique, cagelike architecture. Here, we report a combined rational and random mutagenesis approach that provides fundamental insights into selectivity‐conferring moieties of microviridins. The potent variant microviridin J was co‐crystallized with trypsin, and for the first time the three‐dimensional structure of microviridins was determined and the mode of inhibition revealed.     

Impact of diazotrophy on N stable isotope signatures of nitrate and particulate organic nitrogen: case studies in the north-eastern tropical Atlantic Ocean

During two independent cruises in the north-eastern tropical Atlantic Ocean, we applied two different approaches to investigate the impact of diazotrophy on nitrogen stable isotope signatures in nitrate and particulate organic nitrogen (PON) of the food-web constituents. The first approach, used during the Poseidon cruise 348 in the Mauritanian upwelling, investigated the long-term influence of diazotrophy on the natural abundance of δ¹⁵N-NO^? ₃ and PON. The second approach, adopted during the Cape Verde field cruise, applied stable isotope tracer addition experiments. These served to determine the instantaneous transfer of diazotrophic N to the higher trophic level. Both approaches showed that N₂ fixation was compatible with the pattern and the magnitude of the isotopic depletion of dissolved NO^? ₃ during the Mauritanian upwelling cruise, as well as PON in zooplankton and phytoplankton during the Cape Verde cruises. An N-budget using ¹⁵N incorporation rates and diazotrophic N₂ fixation rates showed that 6 % of the daily N₂ fixation was potentially taken up by the mesozooplankton community. Direct grazing accounted for 56 % of gross mesozooplanktonic N incorporation, while 46 % occurred due to channelling through the microbial loop.     

Leader Peptide‐Free In Vitro Reconstitution of Microviridin Biosynthesis Enables Design of Synthetic Protease‐Targeted Libraries

Microviridins are a family of ribosomally synthesized and post‐translationally modified peptides with a highly unusual architecture featuring non‐canonical lactone as well as lactam rings. Individual variants specifically inhibit different types of serine proteases. Here we have established an efficient in vitro reconstitution approach based on two ATP‐grasp ligases that were constitutively activated using covalently attached leader peptides and a GNAT‐type N‐acetyltransferase. The method facilitates the efficient in vitro one‐pot transformation of microviridin core peptides to mature microviridins. The engineering potential of the chemo‐enzymatic technology was demonstrated for two synthetic peptide libraries that were used to screen and optimize microviridin variants targeting the serine proteases trypsin and subtilisin. Successive analysis of intermediates revealed distinct structure–activity relationships for respective target proteases.     

Structural Elucidation of the Bispecificity of A Domains as a Basis for Activating Non‐natural Amino Acids

Many biologically active peptide secondary metabolites of bacteria are produced by modular enzyme complexes, the non‐ribosomal peptide synthetases. Substrate selection occurs through an adenylation (A) domain, which activates the cognate amino acid with high fidelity. The recently discovered A domain of an Anabaenopeptin synthetase from Planktothrix agardhii (ApnA A₁) is capable of activating two chemically distinct amino acids (Arg and Tyr). Crystal structures of the A domain reveal how both substrates fit into to binding pocket of the enzyme. Analysis of the binding pocket led to the identification of three residues that are critical for substrate recognition. Systematic mutagenesis of these residues created A domains that were monospecific, or changed the substrate specificity to tryptophan. The non‐natural amino acid 4‐azidophenylalanine is also efficiently activated by a mutant A domain, thus enabling the production of diversified non‐ribosomal peptides for bioorthogonal labeling.     

Detection of total microcystin in fish tissues based on lemieux oxidation and recovery of 2-methyl-3-methoxy-4-phenylbutanoic acid (MMPB) by solid-phase microextraction gas chromatography-mass spectrometry (SPME-GC/MS)

Microcystins (MCs) are widespread cyanobacterial toxins in freshwater systems, and have been linked to both acute and chronic health effects. A growing number of studies suggest that MC can bioaccumulate in food webs. Although, several methods (i.e. ELISA, LC-MS) have been developed for analysis of MC in water, extraction (for subsequent analysis) of the toxin from biological matrices (i.e. animal tissues) is impeded owing to covalent binding of toxins and active sites of their cellular targets, i.e. protein phosphatases. As an alternative approach, chromatographic methods for analysis of a unique marker, 2-methyl-3-methoxy-4-phenylbutanoic acid (MMPB), the product of the Lemieux oxidation of MCs, have been previously developed, and shown to measure total (bound and unbound) MC. Application, however, has been limited by poor recovery of the analyte. An improved recovery method is proposed – specifically the use of solid-phase microextraction (SPME). The MMPB analogue, 4-phenylbutanoic acid (4PB), and oxidized MC, were used to develop methods, and we specifically investigated several SPME fibres, and post-oxidation steps. Specifically, a method employing post-oxidation methyl esterification, followed by headspace SPME recovery of MMPB, was developed, and subsequently applied to analysis of environmental samples (i.e. fish tissues) previously shown to contain MCs. The method shows high linearity for both water and tissues spiked with MC, and an improved limit of quantitation of approximately 140?ng?g^?1. Evaluation of field samples by SPME-GC/MS detected considerably higher levels of MC, than detected by conventional methods (i.e. ELISA), and it is proposed that this technique reveals MC (particularly in the bound form) that is not detected by these methods. These results indicate that the developed method provides improved detection capability for MC in biological matrices, and will enhance our ability to understand bioaccumulation in freshwater food webs, as well as monitor exposure.     

Ceramides from the Taiwan Red Alga Ceratodictyon Spongiosum and Symbiotic Sponge Sigmadocia Symbiotica

The structure of a mixture of ceramides ( 1 ) de rived from 2‐amino‐4(E)‐alkene‐1,3‐diol sphingenines with C₂₂, C₂₃, and C₂₄ saturated fatty acid residues from red alga Ceratodictyon spongiosum ZANARDINI (Rhodymeniaceae) containing the symbiotic sponge Sigmadocia symbiotica has been elucidated on the basis of spectroscopic and chemical evidence. In addition, one new sterol, n‐nonadecanoic acid 24‐ methylenecholesteryl ester ( 2 ), and six known sterols were also isolated from the marine organisms.     

Phosphotransacetylase as a key factor in biological production of polyhydroxybutyrate

Phosphotransa cetylase (Pta) catalyzes the reversible conversion of, acetyl-coenzyme A (CoA) to acetyl phosphate. Polyhydroxybutyrate (PHB) synthase and accumulation were compared between a Pta-deficient mutant and the wild-type Escherichia coli, which were transformed with pAE100, coding for 3-ketothiolase, NADPH-dependenta cetoacetyl-CoA reductase, and PHB synthase from Ralstonia eutropha. During the growth period, PHB synthase activity in the Pta-deficient mutant was lower than that in the wild type. PHB accumulation in the Pta-deficient mutant, however, was higher than that in wild-type cells grown in Luria-Bertani (LB) medium containing 1% glucose (high C:N ratio). The Pta-deficient mutant showed PHB accumulation even in LB medium (low C:N ratio), whereas wild-type cells showed no PHB accumulation. These data suggest the activation of PHB synthase by acetyl phosphate that is synthesized by Pta. A decrease in Pta activity probably causes some increase in acetyl-CoA as substrate for the PHB synthesis pathway, resulting in increased PHB accumulation.     

Contribution of the Malpighian tubules for the maintenance of symbiotic microorganisms in cephalotes ants

Given the physiological importance of the Malpighian tubules to homeostasis in ants, this study aimed to characterize the enzymology, histology, histochemistry, and ultramorphology of the Malpighian tubules of Cephalotes atratus, C. clypeatus, and C. pusillus, as a contribution for the understanding of this organ, as well as to examine its role in the maintenance of symbiontic microorganisms in the ileum of these ants.