Production of methanethiol and volatile sulfur compounds by the archaeon “Ferroplasma acidarmanus”

Acidophiles are typically isolated from sulfate-rich ecological niches yet the role of sulfur metabolism in their growth and survival is poorly defined. Studies of heterotrophically grown “Ferroplasma acidarmanus” showed that its growth requires a minimum of 100 mM of a sulfate-containing salt. Headspace gas analyses by GC/MS determined that the volatile sulfur compound emitted by active “F. acidarmanus” cultures is methanethiol. In “F. acidarmanus” cultures grown either heterotrophically or chemolithotrophically, methanethiol was produced constitutively. Radiotracer studies with ³⁵S-labeled methionine, cysteine, and sulfate showed that all three were used in methanethiol production. Additionally, ³H-labeled methionine was incorporated into methanethiol and was probably used as a methyl-group donor. Methanethiol production in whole cell lysates supplied with SO₃²⁻ indicated that NADPH-dependant sulfite reductase and methyltransferase activities were present. Cell lysates also contained enzymatic activity for methionine-γ-lyase that cleaved the side chain of either methionine to form methanethiol or cysteine to produce H₂S. Since methanethiol was detected from the degradation of cysteine, it is likely that sulfide was methylated by a thiol methyltransferase. Collectively, these data demonstrate that “F. acidarmanus” produces methanethiol through the metabolism of methionine, cysteine, or sulfate. This is the first report of a methanethiol-producing acidophile, thus identifying a new contributor to the global sulfur cycle.     

Characterization of an ATP-dependent DNA ligase from the acidophilic archaeon “<Emphasis Type="Italic">Ferroplasma acidarmanus</Emphasis>” Fer1

Analysis of the genome of "Ferroplasma acidarmanus" Fer1, an archaeon that is an extreme acidophile, identified an open reading frame encoding a putative ATP-dependent DNA ligase, which we termed FaLig. The deduced amino acid sequence of FaLig contains 595 amino acids, with a predicted molecular mass of 67.8 kDa. "F. acidarmanus" Fer1 is classified as a Euryarchaeote, but phylogenetic analysis using amino acid sequences showed that FaLig is more similar to DNA ligases from Crenarchaeota, suggesting that lateral transfer of these genes has occurred among archaea. The gene sequence encoding FaLig was cloned into a bacterial expression vector harbouring an upstream His-tag to aid purification. Conditions for expression and purification from Escherichia coli were identified and recombinant FaLig was confirmed to be an ATP-dependent DNA ligase. Optimal conditions for nick-joining by the protein were pH 6-7, 0.5 mM ATP, in the presence of either Mg(2+) or Mn(2+). Using a range of nicked, double-stranded nucleic acids, ligation was detected with the same substrates as previously determined for other DNA ligases. Although FaLig is the DNA ligase from one of the most extreme acidophilic organism yet studied, this characterization suggests that its biochemical mechanism is analogous to that of enzymes from other cellular systems.     

A critical review of the ‘neugliederung’ concept in relation to the development of the vertebral column

Summary The literature on the early embryonic development of the vertebral column in various animal species was analyzed to evaluate so many unrelated or contradictory observations. The recurring problems are described. One of the first was the lack of correspondence between the metameric boundaries of the primitive vertebral bodies arising from the somites and those of the adult vertebral bodies, as presumably shown by their relationship to the vertebral processes and spinal nerves. A century ago, Remak introduced the concept of Neugliederung, according to which the ultimate vertebral body boundaries are determined by a shift of a half segment in comparison with the earlier segment boundaries.     

Towards determining details of anaerobic growth coupled to ferric iron reduction by the acidophilic archaeon ‘<Emphasis Type="Italic">Ferroplasma</Emphasis><Emphasis Type="Italic"> acidarmanus</Emphasis>’ Fer1

Elucidation of the different growth states of Ferroplasma species is crucial in understanding the cycling of iron in acid leaching sites. Therefore, a proteomic and biochemical study of anaerobic growth in ‘Ferroplasma acidarmanus’ Fer1 has been carried out. Anaerobic growth in Ferroplasma spp. occurred by coupling oxidation of organic carbon with the reduction of Fe³⁺; but sulfate, nitrate, sulfite, thiosulfate, and arsenate were not utilized as electron acceptors. Rates of Fe³⁺ reduction were similar to other acidophilic chemoorganotrophs. Analysis of the ‘F. acidarmanus’ Fer1 proteome by 2-dimensional polyacrylamide gel electrophoresis revealed ten key proteins linked with central metabolic pathways ≥4 fold up-regulated during anaerobic growth. These included proteins putatively identified as associated with the reductive tricarboxylic acid pathway used for anaerobic energy production, and others including a putative flavoprotein involved in electron transport. Inhibition of anaerobic growth and Fe³⁺ reduction by inhibitors suggests the involvement of electron transport in Fe³⁺ reduction. This study has increased the knowledge of anaerobic growth in this biotechnologically and environmentally important acidophilic archaeon.     

An insertion element of the extremely thermophilic archaeon Sulfolobus solfataricus transposes into the endogenous β-galactosidase gene

Three phenotypically stable mutants of the extremely thermophilic archaeon Sulfolobus solfataricus have been isolated by screening for β-galactosidase negative colonies on plates with X-Gal (5-bromo-4-chloro-3-indolyl-(3-d-galactopyranoside). From one of these mutants an insertion element, designated ISC1217, was isolated and characterized. Sequence analysis of ISC1217 and of the regions adjacent to the insertion site in the β-galactosidase gene revealed features typical of a transposable element: ISC1217 contained terminal inverted repeats and was flanked by a direct repeat of 6 bp. The 1147 by sequence contained an open reading frame encoding a putative protein of 354 amino acid residues and, overlapping this, two smaller open reading frames on the opposite strand. There were approximately 8 copies of the insertion element in the S. solfataricus genome. ISC1217 did not cross-hybridize with DNA of other Sulfolobus species. All three independently isolated β-galactosidase mutants of S. solfataricus arose by transposition of ISC1217 or a related element.     

Factors affecting the early gene transfer step in the development of transgenic ‘Fuji’ apple plants

This study was conducted to determine the optimal transformation conditions during early gene transfer steps necessary to improve the efficiency of transformation mediated by Agrobacterium tumefaciens in Fuji apple plants. The use of 200 μM acetosyringone in the co-culture medium resulted in 4.7% transformation efficiency, compared with different concentrations of 0–400 μM. A 4-day co-culture period gave 1.9% transformation efficiency, compared with different co-culture periods of 1–5 days. There was no significant difference in transformation efficiency with different explant placement orientations on co-culture medium. A comparison of young leaves from plants cultured in rooting medium for 4 weeks with those cultured for 8 weeks showed that an 8-week culture period resulted in higher transformation efficiency. We therefore concluded that the efficiency of Fuji apple transformation depends on improving factors related to the gene transfer step.     

Rethinking the ‘everyday’ in ‘ethnicity and everyday life’

While ‘ethnicity and everyday life’ is a familiar collocation, sociologists concerned with racism and ethnicity have not engaged very much with the extensive body of social theory that takes the ‘everyday’ as its central problematic. In this essay, I consider some of the ways in which the sociology of the everyday might be of use to those concerned with investigating ethnicity and racism. For its part, however, the sociology of the everyday has tended to be remarkably blind to the role played by racism and racialization in the modern world. It is thus no less crucial to consider how the experiences of racialized groups might help us rethink influential accounts of the everyday. To this end, I provide a discussion of pioneering texts by C. L. R. James and W. E. B. du Bois, both of whom were driven by their reflections on racism and resistance to recognize the everyday not as an unremarked context, but as, precisely, a problematic one.     

Accumulation of additive effects generates a strong photoperiod sensitivity in the extremely late-heading rice cultivar ‘Nona Bokra’

Many rice cultivars that originated from lower-latitude regions exhibit a strong photoperiod sensitivity (PS) and show extremely late heading under long-day conditions. Under natural day-length conditions during the cropping season in Japan, the indica rice cultivar ‘Nona Bokra’ from India showed extremely late heading (202 days to heading) compared to the japonica cultivar ‘Koshihikari’ (105 days), from Japan. To elucidate the genetic factors associated with such extremely late heading, we performed quantitative trait locus (QTL) analyses of heading date using an F₂ population and seven advanced backcross progeny (one BC₁F₂ and six BC₂F₂) derived from a cross between ‘Nona Bokra’ and ‘Koshihikari’. The analyses revealed 12 QTLs on seven chromosomes. The ‘Nona Bokra’ alleles of all QTLs contributed to an increase in heading date. Digenic interactions were rarely observed between QTLs. Based on the genetic parameters of the QTLs, such as additive effects and percentage of phenotypic variance explained, these 12 QTLs are likely generate a large proportion of the phenotypic variation observed in the heading dates between ‘Nona Bokra’ and ‘Koshihikari’. Comparison of chromosomal locations between heading date QTLs detected in this study and QTLs previously identified in ‘Nipponbare’ × ‘Kasalath’ populations revealed that eight of the heading date QTLs were recognized nearby the Hd1, Hd2, Hd3a, Hd4, Hd5, Hd6, Hd9, and Hd13. These results suggest that the strong PS in ‘Nona Bokra’ was generated mainly by the accumulation of additive effects of particular alleles at previously identified QTLs.     

Stages in the development of Parkinson’s disease-related pathology

The synucleinopathy, idiopathic Parkinsons disease, is a multisystem disorder that involves only a few predisposed nerve cell types in specific regions of the human nervous system. The intracerebral formation of abnormal proteinaceous Lewy bodies and Lewy neurites begins at defined induction sites and advances in a topographically predictable sequence. As the disease progresses, components of the autonomic, limbic, and somatomotor systems become particularly badly damaged. During presymptomatic stages 1–2, inclusion body pathology is confined to the medulla oblongata/pontine tegmentum and olfactory bulb/anterior olfactory nucleus. In stages 3–4, the substantia nigra and other nuclear grays of the midbrain and forebrain become the focus of initially slight and, then, severe pathological changes. At this point, most individuals probably cross the threshold to the symptomatic phase of the illness. In the end-stages 5–6, the process enters the mature neocortex, and the disease manifests itself in all of its clinical dimensions.Funding for this project was made available by the German Research Council (Deutsche Forschungsgemeinschaft)     

The ‘paradigm of extremes’: extremely low genetic diversity in an extremely narrow endemic species, Coristospermum huteri (Umbelliferae)

Low levels of genetic diversity in endemic species are generally attributable to the small size of their populations. This lack of genetic variability will, predictably, be more evident in those species that occur in only one or a very few localities with a total population consisting of a few dozen individuals, or sometimes fewer (i.e. ‘extremely narrow endemics’, ENEs). We used allozyme electrophoresis to survey the genetic variability of Coristospermum huteri, an endemic species from the island of Majorca (Balearic Islands, W. Mediterranean Basin) with a single natural population of about 100 individuals. As expected, allozyme variability was virtually nil for this species (P = 8.3 %, A = 1.08, H _e = 0.022), which seems to be a general rule for ENEs (mean H _e = 0.057). A founder effect associated with a dispersal event from the continent is probably behind the lack of genetic diversity in this highly threatened species. Preservation of the mountain summit where the plant is found (Puig Major) is essential for the survival of C. huteri, and would also guarantee the conservation of other ENEs and rare and threatened species.     

Oddity and the ‘confusion effect’ in predation

We report on two sets of experiments designed to clarify the roles of sensory ‘confusion’ and prey ‘oddity’ as they interact to influence the hunting success of a pursuit predator, the largemouth bass (Micropterus salmoides), on silvery minnows (Hybognathus nuchalis). Bass quickly captured solitary minnows, but performed many unsuccessful attacks and took much longer to make a capture as prey school size was increased. At school sizes of eight and above, bass were effectively stymied, demonstrating the ‘confusion effect’. The inclusion of one or two ‘odd’ (blue-dyed) minnows in a school of eight greatly increased the ability of bass to capture both normal and odd prey, but this effect of oddity disappeared at a school size of 15. The implications of these results for understanding the adaptive basis of mixed species flocks, herds and schools is discussed.     

MdCKS1 Expression Involved in Fruit Size in Apple Cultivar ‘Fuji’ and ‘Ralls’

Russian Journal of Plant Physiology - CKS (cyclin-dependent kinase subunit) is one of cell cycle genes, and cell cycle in apple (Malus × domestic Borkh.) fruit controlled cell number and fruit...