Seasonal variation of storage substances in stem cells of Diapensia lapponica. A light microscopic study

Owerwintering strategy of the sub-arctic evergreen Diapensia lapponica has been studied by examining storage substances in the stem cells throughout different seasons. Stem segments were taken from 5 and 20 mm behind the shoot tip, fixed in glutaraldehyde/formaldehyde and embedded in Epon. Semithin sections were stained with Toluidine blue for general observation, Sudan black for lipids, Amido black for proteins and periodic acid-Schiff s reagent (PAS) for carbohydrates. Lipids occurred abundantly throughout the year and seem to be the main storage substances. They were particularly common in mid-winter in the lower part of the shoot. The highest lipid content was found in the pith cells and parenchyma cells of the conductive tissues. Large amyloplasts appeared in mid-summer in higher amounts in the cortex than in the pith of the upper shoot, but vice versa in the lower stem. Starch was almost entirely lacking from November to April. Amido black staining did not indicate presence of protein bodies at any season.
The occurrence of lipids and starch grains in the stem of Diapensia is in general similar to the occurrence of these substances in the leaves throughout the annual cycle.     

Comparison of the formation of benzo[a]pyrene diolepoxide-DNA adducts in vitro by rat and human microsomes: evidence for the involvement of P-450IA1 and P-450IA2

The involvement of cytochrome P-450 isozymes in the activation of benzo[a]pyrene (BP) by human placental and liver microsomes was studied in vitro using monoclonal antibodies (Mab) toward the major 3-methylcholanthrene (MC)-inducible and phenobarbital-inductible rat liver P-450 isozymes (Mab 1-7-1 and Mab 2-66-3, respectively). Microsomes from human placenta and liver and rat liver were incubated with BP and DNA, and BP-diolepoxide-DNA (BPDE-DNA) adducts were measured by synchronous fluorescence spectrophotometry (SFS). The only BP metabolite giving the same fluorescence peak as chemically modified BPDE-DNA was BP-7,8-dihydrodiol. Five (smokers) out of 29 human placentas (smokers and nonsmokers), and five out of nine human livers were able to metabolically activate BP to BPDE-DNA adducts in this system. The Mab 1-7-1 totally inhibited the formation of BPDE-DNA adducts in placental microsomal incubations. Inhibition using rat or human liver microsomes was 50-60% and about 90%, respectively. The Mab 2-66-3 had no effect in any of the microsome types. Adduct formation was inhibited more strongly and at lower concentrations of Mab 1-7-1 compared with the inhibition of AHH activity. This study is a clear indication of the major role of P-450IA1 (P-450c) in human placenta and probably P-450IA2 (P-450d) in human liver in BP activation, while other isozymes also take part in the activation in rat liver. Furthermore, this clearly indicates that AHH activity and BP activation are not necessarily associated.     

Totipotency, somatic embryogenesis, and Harry Waris (1893–1973)

F. C. Steward and Jakob Reinert in the late 1950s, independently and with different degrees of scientific exactness, demonstrated that somatic cells of cultivated carrot can produce embryo-like structures in aseptic culture. Growth substances in the nutrient medium were viewed as central to the process. The now classic papers of Steward and Reinert have found a special and enduring place in the literature of plant development. But Harry Waris also deserves credit for his observation that vegetative cells sloughed off from aseptically germinated seedlings reared in liquid nutrient medium can produce 'embryos'. In his studies, seedlings of Oenanthe aquatica (Umbelliferae) were maintained in culture for protracted periods under nutrient conditions designed to foster imbalance in protein metabolism, but without exogenous growth hormones. Seedlings placed in media with high concentrations of glycine grew normally for 3–4 months; after this a "period of morbidity" occurred, followed by production of new plants from the root tips. These new plants, later called "neomorphs", in turn reproduced by colorless outgrowths of leaf epidermis. Such outgrowths, and "nodules" formed in a callus produced by the original seedlings, passed through stages described as "nodule", "fusiform", and a stage with two or more "lobes". Transfer of the neomorphs to a medium lacking glycine resulted in the development of normal plants. We show that Waris was among the first, if not the first, to observe and recognize somatic embryo production in aseptic culture, and indeed to call them "embryos". We also discuss his investigations in the context of understanding development at the cellular level, then and now.     

Contemporaneous Alnus decline and the beginning of Iron Age cultivation in pollen stratigraphies from southern Finland

Declines in Alnus coinciding with the first signs of Iron Age (a.d. 0–1150) human activities were found in the pollen stratigraphies of five small lakes in southern Finland. One lake did not show a clear minimum. Three of the lakes were investigated with close-interval analyses which showed that the Alnus minimum lasted for several centuries. The results were compared with 41 previously published pollen diagrams with evidence of Iron Age human activity from southern Finland. These diagrams were classified in three ways: (1) showing no Alnus minimum; (2) cases where a minimum was unclear; (3) showing a clear minimum in Alnus. The different types were found randomly scattered around southern Finland suggesting that Alnus minima were a local phenomenon. In most cases the Alnus minimum took place between ca. a.d. 600 and ca. a.d. 1000, a.d. 1300 being the latest date for the end of the minimum. The results do not suggest a pathogen outbreak over the entire area. The beginning of the minimum clearly coincides with the onset of Iron Age anthropogenic activities suggesting that these were the probable cause. Pollen analysis provides little information as to why trees were felled thus archaeological evidence is needed. However, the Alnus decline may prove a new and useful indicator of the onset of Iron Age anthropogenic activity in pollen diagrams.     

TopBP1 localises to centrosomes in mitosis and to chromosome cores in meiosis

Topoisomerase IIbeta binding protein 1 (TopBP1), previously shown to localise to sites of DNA damage and to stalled replication forks, has been implicated in DNA replication and in DNA damage response. In this work we showed that TopBP1 was localised in structures other than stalled replication forks. In late mitosis TopBP1 localises to centrosomes in a manner similar to other DNA damage response proteins such as BRCA1 and p53. Spindle checkpoint activation does not affect this centrosomal localisation. Moreover, in the testis, we detected high levels of TopBP1 associated with meiotic prophase chromosome cores and the X-Y pair. Together, these data suggest a direct role of TopBP1 during both mitosis and meiotic prophase I.     

Bacteria Contribute to Sediment Nutrient Release and Reflect Progressed Eutrophication-Driven Hypoxia in an Organic-Rich Continental Sea

In the sedimental organic matter of eutrophic continental seas, such as the largest dead zone in the world, the Baltic Sea, bacteria may directly participate in nutrient release by mineralizing organic matter or indirectly by altering the sediment’s ability to retain nutrients. Here, we present a case study of a hypoxic sea, which receives riverine nutrient loading and in which microbe-mediated vicious cycles of nutrients prevail. We showed that bacterial communities changed along the horizontal loading and vertical mineralization gradients in the Gulf of Finland of the Baltic Sea, using multivariate statistics of terminal restriction fragments and sediment chemical, spatial and other properties of the sampling sites. The change was mainly explained by concentrations of organic carbon, nitrogen and phosphorus, which showed strong positive correlation with Flavobacteria, Sphingobacteria, Alphaproteobacteria and Gammaproteobacteria. These bacteria predominated in the most organic-rich coastal surface sediments overlain by oxic bottom water, whereas sulphate-reducing bacteria, particularly the genus Desulfobacula, prevailed in the reduced organic-rich surface sediments in the open sea. They correlated positively with organic nitrogen and phosphorus, as well as manganese oxides. These relationships suggest that the bacterial groups participated in the aerobic and anaerobic degradation of organic matter and contributed to nutrient cycling. The high abundance of sulphate reducers in the surficial sediment layers reflects the persistence of eutrophication-induced hypoxia causing ecosystem-level changes in the Baltic Sea. The sulphate reducers began to decrease below depths of 20 cm, where members of the family Anaerolineaceae (phylum Chloroflexi) increased, possibly taking part in terminal mineralization processes. Our study provides valuable information on how organic loading affects sediment bacterial community compositions, which consequently may maintain active nutrient recycling. This information is needed to improve our understanding on nutrient cycling in shallow seas where the dead zones are continuously spreading worldwide.     

Cyanobactins—ribosomal cyclic peptides produced by cyanobacteria

Cyanobactins are small cyclic peptides that are produced by a diverse selection of cyanobacteria living in symbioses as well as terrestrial, marine, or freshwater environments. They include compounds with antimalarial, antitumor, and multidrug reversing activities and potential as pharmaceutical leads. Cyanobactins are produced through the proteolytic cleavage and cyclization of precursor peptides coupled with further posttranslational modifications such as heterocyclization, oxidation, or prenylation of amino acids. Cyanobactin gene clusters encode two proteases which cleave and cyclisize the precursor peptide as well as proteins participating in posttranslational modifications. The bioinformatic mining of cyanobacterial genomes has led to the discovery of novel cyanobactins. Heterologous expression of these gene clusters provided insights into the role of the genes participating in the biosynthesis of cyanobactins and facilitated the rational design of novel peptides. Enzymes participating in the biosynthesis of cyanobactins may prove useful as catalysts for producing novel cyclic peptides in the future. The recent discovery of the cyanobactin biosynthetic pathway in cyanobacteria extends our knowledge of their potential as producers of interesting metabolites.     

Nostophycin biosynthesis is directed by a hybrid polyketide synthase-nonribosomal peptide synthetase in the toxic cyanobacterium Nostoc sp. strain 152

Cyanobacteria are a rich source of natural products with interesting pharmaceutical properties. Here, we report the identification, sequencing, annotation, and biochemical analysis of the nostophycin (npn) biosynthetic gene cluster. The npn gene cluster spans 45.1 kb and consists of three open reading frames encoding a polyketide synthase, a mixed polyketide nonribosomal peptide synthetase, and a nonribosomal peptide synthetase. The genetic architecture and catalytic domain organization of the proteins are colinear in arrangement, with the putative order of the biosynthetic assembly of the cyclic heptapeptide. NpnB contains an embedded monooxygenase domain linking nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) catalytic domains and predicted here to hydroxylate the nostophycin during assembly. Expression of the adenylation domains and subsequent substrate specificity assays support the involvement of this cluster in nostophycin biosynthesis. Biochemical analyses suggest that the loading substrate of NpnA is likely to be a phenylpropanoic acid necessitating deletion of a carbon atom to explain the biosynthesis of nostophycin. Biosyntheses of nostophycin and microcystin resemble each other, but the phylogenetic analyses suggest that they are distantly related to one another.     

Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria

Background

Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the pharmaceutical and biotechnological industries. Many of these compounds are the products of non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways. However, current understanding of the diversification of these pathways is largely based on the chemical structure of the bioactive compounds, while the evolutionary forces driving their remarkable chemical diversity are poorly understood.

Results

We carried out a phylum-wide investigation of genetic diversification of the cyanobacterial NRPS and PKS pathways for the production of bioactive compounds. 452 NRPS and PKS gene clusters were identified from 89 cyanobacterial genomes, revealing a clear burst in late-branching lineages. Our genomic analysis further grouped the clusters into 286 highly diversified cluster families (CF) of pathways. Some CFs appeared vertically inherited, while others presented a more complex evolutionary history. Only a few horizontal gene transfers were evidenced amongst strongly conserved CFs in the phylum, while several others have undergone drastic gene shuffling events, which could result in the observed diversification of the pathways.

Conclusions

Therefore, in addition to toxin production, several NRPS and PKS gene clusters are devoted to important cellular processes of these bacteria such as nitrogen fixation and iron uptake. The majority of the biosynthetic clusters identified here have unknown end products, highlighting the power of genome mining for the discovery of new natural products.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-977) contains supplementary material, which is available to authorized users.