Chrysosporum ovalisporum is synonymous with the true-branching cyanobacterium Umezakia natans (Nostocales/Aphanizomenonaceae)

True branching is a facultative characteristic only known from two cyanobacteria in the Aphanizomenonaceae, Umezakia natans and Dolichospermum brachiatum. In both cases, its expression has been associated with environmental stress, and its practical use as a diacritical feature has been previously evaluated. In this study, we undertook further evaluation of the phylogeny of Umezakia natans and its relationship to Chrysosporum ovalisporum as a previous study suggested the two were potentially congeneric. We used combined morphological, phylogenetic, and phylogenomic approaches to determine their relatedness using new strains available from a broad geographic range. Phylogenetic analysis based on 16S rRNA gene sequences showed that Australian C. ovalisporum and Japanese U. natans strains clustered together with accessions of C. ovalisporum originating from Australia, Israel, and Spain, with high p-distance similarity values (99.5%–99.9%). Additionally, differences between the two species in the 16S–23S ITS region was low (0%–2.5%). The average nucleotide identity of the U. natans and C. ovalisporum strains was also high (ANI of > 99.5 and AF > 0.9) and supported a genus-level separation from Chrysosporum bergii (83 ANI between clusters). Furthermore, in culture, strains of both species grown in vitamin-free media showed facultative true branching, a feature not previously known in C. ovalisporum. Collectively, the results support unification of C. ovalisporum and U. natans according to the principle of priority as Umezakia ovalisporum.     

Tadpole fingerprinting: Using tail venation patterns to photo-identify tadpole individuals of a threatened frog

Traditional methods for identifying individual amphibians in capture–mark–recapture (CMR) studies have been primarily confined to post-metamorphic stages, using artificial markers that come with a variety of limitations. An alternative that may open CMR studies to earlier life stages involves the use of a species' natural external markers in photo-based identification. In this study, we investigated whether it was possible to distinguish tadpoles of the threatened green and golden bell frog (Litoria aurea) at the individual level based on tail venation patterns. We collected photographs of the tails of captive-raised tadpoles using a smartphone over a 4-week period. This photo-library was used to create an electronic survey where participants were asked to detect matches for query tadpoles from small image pools. We found that most participants agreed on a match for each query, with perfect consensus achieved for most queries (83%). We detected a 14% decline in perfect consensus when participants were asked to match images of tadpoles separated by longer time intervals, suggesting that it is more difficult to visually identify recapture events of L. aurea tadpoles over extended periods due to changes to tail appearance. However, consensus was obtained by participants for all queries, with all matches verified as being correct by the primary researcher. The strength of agreement among participants with no prior experience in matching tadpole tails suggests that there is sufficient inter-individual variation in this feature for individuals to be manually identified. We thus propose that photo-identification is likely to be a valid, non-invasive technique that can be used for short-term studies on tadpole populations that display tail venation. This offers an alternative to artificial markers that may not allow for individual identification, while also opening up tadpole monitoring programmes to citizen scientists who can be recruited online to process image data from home.     

Evolution of Associative Learning in Chemical Networks

Organisms that can learn about their environment and modify their behaviour appropriately during their lifetime are more likely to survive and reproduce than organisms that do not. While associative learning – the ability to detect correlated features of the environment – has been studied extensively in nervous systems, where the underlying mechanisms are reasonably well understood, mechanisms within single cells that could allow associative learning have received little attention. Here, using in silico evolution of chemical networks, we show that there exists a diversity of remarkably simple and plausible chemical solutions to the associative learning problem, the simplest of which uses only one core chemical reaction. We then asked to what extent a linear combination of chemical concentrations in the network could approximate the ideal Bayesian posterior of an environment given the stimulus history so far? This Bayesian analysis revealed the ‘memory traces’ of the chemical network. The implication of this paper is that there is little reason to believe that a lack of suitable phenotypic variation would prevent associative learning from evolving in cell signalling, metabolic, gene regulatory, or a mixture of these networks in cells.     

A mechanism for gene-environment interaction in the etiology of congenital scoliosis

Congenital scoliosis, a lateral curvature of the spine caused by vertebral defects, occurs in approximately 1 in 1,000 live births. Here we demonstrate that haploinsufficiency of Notch signaling pathway genes in humans can cause this congenital abnormality. We also show that in a mouse model, the combination of this genetic risk factor with an environmental condition (short-term gestational hypoxia) significantly increases the penetrance and severity of vertebral defects. We demonstrate that hypoxia disrupts FGF signaling, leading to a temporary failure of embryonic somitogenesis. Our results potentially provide a mechanism for the genesis of a host of common sporadic congenital abnormalities through gene-environment interaction.     

Characterization of the catalytically active Mn(II)-loaded argE -encoded N -acetyl-l -ornithine deacetylase from Escherichia coli

The catalytically competent Mn(II)-loaded form of the argE-encoded N-acetyl-l-ornithine deacetylase from Escherichia coli (ArgE) was characterized by kinetic, thermodynamic, and spectroscopic methods. Maximum N-acetyl-l-ornithine (NAO) hydrolytic activity was observed in the presence of one Mn(II) ion with k _cat and K _m values of 550 s⁻¹ and 0.8 mM, respectively, providing a catalytic efficiency (k _cat/K _m) of 6.9 × 10⁵ M⁻¹ s⁻¹. The ArgE dissociation constant (K _d) for Mn(II) was determined to be 0.18 μM, correlating well with a value obtained by isothermal titration calorimetry of 0.30 μM for the first metal binding event and 5.3 μM for the second. An Arrhenius plot of the NAO hydrolysis for Mn(II)-loaded ArgE was linear from 15 to 55 °C, suggesting the rate-limiting step does not change as a function of temperature over this range. The activation energy, determined from the slope of this plot, was 50.3 kJ mol⁻¹. Other thermodynamic parameters were ΔG ^‡ = 58.1 kJ mol⁻¹, ΔH ^‡ = 47.7 kJ mol⁻¹, and ΔS ^‡ = –34.5 J mol⁻¹ K⁻¹. Similarly, plots of lnK _m versus 1/T were linear, suggesting substrate binding is controlled by a single step. The natural product, [(2S,3R)-3-amino-2-hydroxy-4-phenylbutanoyl]leucine (bestatin), was found to be a competitive inhibitor of ArgE with a K _i value of 67 μM. Electron paramagnetic resonance (EPR) data recorded for both [Mn(II)_(ArgE)] and [Mn(II)Mn(II)(ArgE)] indicate that the two Mn(II) ions form a dinuclear site. Moreover, the EPR spectrum of [Mn(II)Mn(II)(ArgE)] in the presence of bestatin indicates that bestatin binds to ArgE but does not form a μ-alkoxide bridge between the two metal ions.     

Cytotoxic and mutagenic effects of tobacco-borne free fatty acids

Tobacco smoke contains substances capable of binding iron in an aqueous medium and transferring the metal into both organic solvents and intact mammalian red cells. This iron-binding activity is due to free fatty acids which are abundant in tobacco smoke and form 2:1 (free fatty acid:iron) chelates with ferrous iron. These earlier observations suggested that smoke-borne free fatty acids and the associated delocalization of iron within the lung might contribute to both the chronic pulmonary inflammation and the carcinogenesis associated with smoking. We now report that micromolar concentrations of iron or free fatty acid are not toxic to cultured human lung fibroblasts. However, when combined, the same low concentrations of iron and free fatty acid exert synergistic toxicity. Furthermore, the combination of free fatty acid and iron is highly mutagenic, inducing almost as many selectable mutations in the gene for hypoxanthine/guanine phosphoribosyl transferase as does benzo[a]pyrenediolepoxide, a class I carcinogen generated from benzo[a]pyrene present in cigarette smoke. The combination of free fatty acid and iron also promotes transformation of NIH 3T3 cells into an anchorage-independent phenotype. We conclude that free fatty acids in tobacco smoke may be important contributors to both the pulmonary damage and the carcinogenesis associated with smoking.     

Wasps, beetles and the beginning of the ends

Recent papers investigating the genes regulating early embryogenesis in the wasp Nasonia vitripennis and the beetle Tribolium castaneum have provided us with important clues as to how early development is controlled in insects other than higher dipterans such as Drosophila melanogaster. The results of these studies demonstrate that in insects that do not have bicoid, anterior patterning is regulated by a combination of maternal orthodenticle and hunchback. Furthermore, during the evolution of long-germ-band development, Nasonia and Drosophila may have evolved different mechanisms to pattern posterior segments, marginalising the important role of the terminal system in short-germ-band embryos.     

Abnormal, Error-Prone Bypass of Photoproducts by Xeroderma Pigmentosum Variant Cell Extracts Results in Extreme Strand Bias for the Kinds of Mutations Induced by UV Light

Xeroderma pigmentosum (XP) is a rare genetic disease characterized by a greatly increased susceptibility to sunlight-induced skin cancer. Cells from the majority of patients are defective in nucleotide excision repair. However, cells from one set of patients, XP variants, exhibit normal repair but are abnormally slow in replicating DNA containing UV photoproducts. The frequency of UV radiation-induced mutations in the XP variant cells is significantly higher than that in normal human cells. Furthermore, the kinds of UV-induced mutations differ very significantly from normal. Instead of transitions, mainly C→T, 30% of the base substitutions consist of C→A transversions, all arising from photoproducts located in one strand. Mutations involving cytosine in the other strand are almost all C→T transitions. Forty-five percent of the substitutions involve thymine, and the majority are transversions. To test the hypothesis that the UV hypermutability and the abnormal spectrum of mutations result from abnormal bypass of photoproducts in DNA, we compared extracts from XP variant cells with those from HeLa cells and a fibroblast cell strain, MSU-1.2, for the ability to replicate a UV-irradiated form I M13 phage. The M13 template contains a simian virus 40 origin of replication located directly to the left or to the right of the target gene, lacZα, so that the template for the leading and lagging strands of DNA replication is defined. Reduction of replication to ~37% of the control value required only 1 photoproduct per template for XP variant cell extracts, but ~2.2 photoproducts for HeLa or MSU-1.2 cell extracts. The frequency of mutants induced was four times higher with XP variant cell extracts than with HeLa or MSU-1.2 cell extracts. With XP variant cell extracts, the proportion of C→A transversions reached as high as 43% with either M13 template and arose from photoproducts located in the template for leading-strand synthesis; with HeLa or MSU-1.2 cell extracts, this value was only 5%, and these arose from photoproducts in either strand. With the XP variant extracts, 26% of the substitutions involved thymine, and virtually all were T→A transversions. Sequence analysis of the coding region of the catalytic subunit of DNA polymerase delta in XP variant cell lines revealed two polymorphisms, but these do not account for the reduced bypass fidelity. Our data indicate that the UV hypermutability of XP variant cells results from reduced bypass fidelity and that unlike for normal cells, bypass of photoproducts involving cytosine in the template for the leading strand differs significantly from that of photoproducts in the lagging strand.