Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments

Background

In spite of considerable efforts over past decades we still know relatively little regarding the biogeography of rotifers of inland waters in México. To help rectify this we undertook an extensive survey of the rotifer fauna of 48 water bodies in the Chihuahuan Desert of México.

Results

Of the sites surveyed, 21 had salinities ≥ 2000 μS cm^-1 and in these we found 57 species of monogonont rotifers and several bdelloids. Species richness in the saline sites varied widely, with a range in species richness of 1 to 27 and a mean (± 1SD) = 8.8 (± 6.2). Collectively all sites possess relatively high percent single- and doubletons, 33.3 and 21.7%, respectively. Simpson's Asymmetric Index indicated that similarity in rotifer species composition varied widely among a set of 10 sites. These were selected because they were sampled more frequently or represent unusual habitats. These SAI values ranged from 0.00 (complete dissimilarity) to 1.00 (complete similarity). The Jaccard Index varied between 0.00 and 0.35. This observation probably reflects similarities and differences in water chemistry among these sites. Inland saline systems differed in their chemical composition by region. Conductivity was related to hardness and alkalinity. In addition, hardness was positively associated with chloride and sulfate. RDA showed that several species were positively associated with chloride concentration. Other factors that were significantly associated with rotifer species included the presence of macrophytes, nitrate content, oxygen concentration, TDS, latitude and whether the habitat was a large lake or reservoir.

Conclusion

This study illustrates the diversity of the rotiferan fauna of inland saline systems and the uniqueness among waterbodies. Conservation of these systems is needed to preserve these unique sources of biodiversity that include rotifers and the other endemic species found in association with them.     

P-transposable vectors expressing a constitutive and thermoinducible hsp82-neo fusion gene for Drosophila germline transformation and tissue-culture transfection

Three P-transposable vectors (approx. 16, 12, and 9 kb) were constructed containing a hsp82-neo fusion gene encoding a truncated heat-shock protein 82 of Drosophila pseudoobscura and the bacterial neomycin phosphotransferase (NPT). In transgenic Drosophila melanogaster, hsp82-neo exhibits high levels of housekeeping gene promoter and NPT activities in all cells in the absence of heat-shock and is further induced (fivefold) by elevated temperatures (35 degrees-36 degrees C). The hsp82-neo selection of transformants is possible from embryo to adulthood. The hsp82-neo insertion in a P-element plasmid carrying an alcohol-dehydrogenase-encoding gene (Adh) produced plasmids pHS22 (approx. 16 kb) and pHS24 (approx. 12 kb), in which both genes were expressed, as observed in 13 transgenic strains. Cloning of DNA fragments up to at least 16 kb in a third vector, pHS85 (approx. 9 kb), lacking the Adh cointegrate is facilitated by a 104-bp multiple cloning site (MCS) positioned downstream (3') from hsp82-neo. To accept inserts of nonselectable foreign genes, MCS provides 20 restriction sites, eight of them unique. The hsp82-neo-expressing vectors also function in cell-culture transfection assays. The hsp82-neo fusion gene (3.73 kb) may be of wide application as a dominant selection marker in other animal systems and plants.     

Regulatory potential of S/MAR elements in transient expression

S/MARs (scaffold/matrix attachment regions) are the DNA regions that are involved in the interaction with the nuclear matrix and are identified by in vitro methods. According to the available information, S/MARs possess an insulating activity, i.e., the ability to block the interaction between the enhancer and promoter in vivo, and are, probably, intact insulators or their fragments. Nevertheless, there is still no direct proof for this correspondence. To obtain additional information on the insulator activity of S/MARs, we selected five DNA fragments of different lengths and affinities for the nuclear matrix from the previously constructed library of S/MARs and tested their ability to serve as insulators. Two of five elements exhibited an insulator (enhancer-blocking) activity upon the transient transfection of CHO cells. None of the S/MARs displayed either promoter or enhancer/silencer activities in these cells.     

<Emphasis Type=Italic>Gammaproteobacteria</Emphasis> as a Possible Source of Eicosapentaenoic Acid in Anoxic Intertidal Sediments

Eicosapentaenoic acid (EPA; n-20:5ω3) was found to be a constituent of phospholipids in three mesophilic strains of Gammaproteobacteria, which were isolated from anoxic most probable number series prepared with sediments from an intertidal flat of the German North Sea coast. Their partial 16S rRNA gene sequences identified the isolates as close relatives of Shewanella colwelliana, Vibrio splendidus, and Photobacterium lipolyticum. So far, eicosapentaenoic acid has mainly been reported to occur in eukaryotes and some piezophilic or psychrophilic bacteria. With decreasing temperature, relative contents of EPA (up to 14% of total fatty acids) increased in all strains. Additionally, Shewanella and Vibrio spp. showed a significant increase in monounsaturated fatty acids with lower growth temperature. Analysis of the phospholipid compositions revealed that EPA was present in all three major phospholipid types, namely, phosphatidyl glycerol (PG), cardiolipin and phosphatidyl ethanolamine (PE). However, EPA was enriched in PG and cardiolipin relative to PE. In the tidal flat sediments from which the isolates were obtained, substantial amounts of EPA-containing PG were detected, whereas other typical microeukaryotic phospholipids—being also a possible source of EPA—were abundant at the sediment surface but were present in clearly lower amounts in the anoxic layers beneath 5 cm depth. Therefore, the EPA-containing PG species in the deeper layers in these sediments may indicate the presence of Gammaproteobacteria closely related to the isolates. These bacteria appear to be an important source of EPA in buried, anoxic sediments beneath the layers harboring significant populations of benthic eukaryotes.     

Digitomotography in Parkinson’s Disease: A Cross-Sectional and Longitudinal Study

Motor symptoms in Parkinson’s disease (PD) are usually assessed with semi-quantitative tests such as the Unified PD Rating Scale (UPDRS) which are limited by subjectivity, categorical design, and low sensitivity. Particularly bradykinesia as assessed e.g. with speeded index finger tapping exhibits low validity measures. This exploratory study set out to (i) assess whether force transducer-based objective and quantitative analysis of motor coordination in index finger tapping is able to distinguish between PD patients and controls, and (ii) assess longitudinal changes. Sixteen early-stage and 17 mid-stage PD patients as well as 18 controls were included in the cross-sectional part of the study; thirteen, 16 and 16 individuals of the respective groups agreed in a reassessment 12 months later. Frequency, force, rhythmicity, regularity and laterality of speeded and metronome paced tapping were recorded by digitomotography using a quantitative motor system ("Q-Motor"). Analysis of cross-sectional data revealed most consistent differences between PD patients and controls in variability of tap performance across modalities assessed. Among PD patients, variability of taps and the ability to keep a given rhythm were associated with UPDRS motor and finger tapping scores. After 12 months, laterality parameters were reduced but no other parameters changed significantly. This data suggests that digitomotography provides quantitative and objective measures capable to differentiate PD from non-PD in a small cohort, however, the value of the assessment to track PD progression has to be further evaluated in larger cohorts of patients.     

Chitosan-based hybrid immobilization in bienzymatic reactions and its application to the production of laminaribiose

A hybrid-immobilization method was developed to improve the long-term stability of laminaribiose phosphorylase immobilized on epoxy supports Sepabeads EC-EP/S. Entrapment in chitosan retained all of the enzyme activity depending on the amount of entrapped solid materials and increased half-life by a factor of 10–94.4 h. No enzyme activity loss was determined during 12 times reuse. The immobilization method is also applicable to sucrose phosphorylase immobilized on Sepabeads EC-EP/S. Up to 31.9 g/L laminaribiose were produced in bienzymatic batch experiments with reaction-integrated product separation by adsorption on zeolites.

     

Calcium-dependent homoassociation of E-cadherin by NMR spectroscopy: changes in mobility,conformation and mapping of contact regions

Cadherins are calcium-dependent cell surface proteins that mediate homophilic cellular adhesion. The calcium-induced oligomerization of the N-terminal two domains of epithelial cadherin (ECAD12) was followed by NMR spectroscopy in solution over a large range of protein (10 microM-5 mM) and calcium (0-5 mM) concentrations. Several spectrally distinct states could be distinguished that correspond to a calcium-free monomeric form, a calcium-bound monomeric form, and to calcium-bound higher oligomeric forms. Chemical shift changes between these different states define calcium-binding residues as well as oligomerization contacts. Information about the relative orientation and mobility of the ECAD12 domains in the various states was obtained from weak alignment and 15N relaxation experiments. The data indicate that the calcium-free ECAD12 monomer adopts a flexible, kinked conformation that occludes the dimer interface observed in the ECAD12 crystal structure. In contrast, the calcium-bound monomer is already in a straight, non-flexible conformation where this interface is accessible. This mechanism provides a rational for the calcium-induced adhesiveness. Oligomerization induces chemical shift changes in an area of domain CAD1 that is centered at residue Trp-2. These shift changes extend to almost the entire surface of domain CAD1 at high (5 mM) protein concentrations. Smaller additional clusters of shift perturbations are observed around residue A80 in CAD1 and K160 in CAD2. According to weak alignment and relaxation data, the symmetry of a predominantly dimeric solution aggregate at 0.6 mM ECAD12 differs from the approximate C2-symmetry of the crystalline dimer.     

Phylogeny and physiology of candidate phylum ‘Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics

The ‘Atribacteria'' is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species- to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the ‘Atribacteria'' inclusive of OP9 and JS1. Additional conserved features within the ‘Atribacteria'' were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the ‘Atribacteria'' are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate.