Phylogeography of the Rhabditis (Pellioditis) marina species complex: evidence for long-distance dispersal, and for range expansions and restricted gene flow in the northeast Atlantic.

Pinpointing processes that structure the geographical distribution of genetic diversity of marine species and lead to speciation is challenging because of the lack of obvious dispersal barriers and the likelihood of substantial (passive) dispersal in oceans. In addition, cryptic radiations with sympatric distributions abound in marine species, challenging the allopatric speciation mechanism. Here, we present a phylogeographical study of the marine nematode species complex Rhabditis (Pellioditis) marina to investigate processes shaping genetic structure and speciation. Rhabditis (P.) marina lives on decaying macroalgae in the intertidal, and may therefore disperse over considerable distances. Rhabditis (P.) marina consists of several cryptic species sympatrically distributed at a local scale. Genetic variation in the COI gene was screened in 1362 specimens from 45 locations around the world. Two nuclear DNA genes (ITS and D2D3) were sequenced to infer phylogenetic species. We found evidence for ten sympatrically distributed cryptic species, seven of which show a strong genetic structuring. A historical signature showed evidence for restricted gene flow with occasional long-distance dispersal and range expansions pre-dating the last glacial maximum. Our data also point to a genetic break around the British Isles and a contact zone in the Southern Bight of the North Sea. We provide evidence for the transoceanic distribution of at least one cryptic species (PmIII) and discuss the dispersal capacity of marine nematodes. The allopatric distribution of some intraspecific phylogroups and of closely related cryptic species points to the potential for allopatric speciation in R. (P.) marina.

Apparent uncoupling of energy production and consumption in long-lived Clk mutants of Caenorhabditis elegans.

Clk mutants of Caenorhabditis elegans are characterised by an overall slow down of temporal processes and increase in life span. It was hypothesised that Clk mutations slow down the pace of many cellular functions and lower the rate of energy metabolism, possibly resulting in slower production of reactive oxygen species which in turn could result in slower ageing. We tested this hypothesis by measuring respiration rates, light production capacities (a measure of metabolic potential) and ATP levels in various strains harbouring mutant alleles of the Clk genes clk-1 and gro-1 and of three other genes that interact with the Clk genes. We found a mild reduction of oxygen consumption rates but little alteration of metabolic capacities in the single Clk mutants during the first 4-5 days of their adult lives, relative to the wild-type strain. This difference tended to fade away with increasing age, however, and aged Clk mutants eventually retained higher metabolic capacities than the wild-type control strain N2. These profiles are suggestive of physiological time being retarded, relative to chronological time in Clk mutants. Ageing clk-1 and gro-1 mutants also retained substantially elevated ATP levels relative to the N2 strain, and the simultaneous presence of mutations in daf-2 or age-1 - genes that affect longevity - boosted this effect. Thus, energy production and consumption appear to be uncoupled in these mutants. Mutation in the transcription factor daf-16 suppressed the Age and ATP phenotypes, but not the reduction of respiration rate imparted by mutation in clk-1.

Neuroglobin and cytoglobin as potential enzyme or substrate.

The possible enzymatic activities of neuro- and cytoglobin as well as their potential function as substrates in enzymatic reactions were studied. Neuro- and cytoglobin are found to show no appreciable superoxide dismutase, catalase, and peroxidase activities. However, the internal disulfide bond (CD7-D5) of human neuroglobin can be reduced by thioredoxin reductase. Furthermore, our in vivo and in vitro studies show that Escherichia coli cells contain an enzymatic reducing system that keeps the heme iron atom of neuroglobin in the Fe(2+) form in the presence of dioxygen despite the high autoxidation rate of the molecule. This reducing system needs a low-molecular-weight compound as co-factor. In vitro tests show that both NADH and NADPH can play this role. Furthermore, the reducing system is not specific for neuroglobin but allows the reduction of the ferric forms of other globins such as cytoglobin and myoglobin. A similar reducing system is present in eukaryotic tissue protein extracts.

Very high resolution structure of a trematode hemoglobin displaying a TyrB10-TyrE7 heme distal residue pair and high oxygen affinity.

Monomeric hemoglobin from the trematode Paramphistomum epiclitum displays very high oxygen affinity (P(50)<0.001 mm Hg) and an unusual heme distal site containing tyrosyl residues at the B10 and E7 positions. The crystal structure of aquo-met P. epiclitum hemoglobin, solved at 1.17 A resolution via multiwavelength anomalous dispersion techniques (R-factor=0.121), shows that the heme distal site pocket residue TyrB10 is engaged in hydrogen bonding to the iron-bound ligand. By contrast, residue TyrE7 is unexpectedly locked next to the CD globin region, in a conformation unsuitable for heme-bound ligand stabilisation. Such structural organization of the E7 distal residue differs strikingly from that observed in the nematode Ascaris suum hemoglobin (bearing TyrB10 and GlnE7 residues), which also displays very high oxygen affinity. The oxygenation and carbonylation parameters of wild-type P. epiclitum Hb as well as of single- and double-site mutants, with residue substitutions at positions B10, E7 and E11, have been determined and are discussed here in the light of the protein atomic resolution crystal structure.

Alignment of 700 globin sequences: extent of amino acid substitution and its correlation with variation in volume.

Seven-hundred globin sequences, including 146 nonvertebrate sequences, were aligned on the basis of conservation of secondary structure and the avoidance of gap penalties. Of the 182 positions needed to accommodate all the globin sequences, only 84 are common to all, including the absolutely conserved PheCD1 and HisF8. The mean number of amino acid substitutions per position ranges from 8 to 13 for all globins and 5 to 9 for internal positions. Although the total sequence volumes have a variation approximately 2-3%, the variation in volume per position ranges from approximately 13% for the internal to approximately 21% for the surface positions. Plausible correlations exist between amino acid substitution and the variation in volume per position for the 84 common and the internal but not the surface positions. The amino acid substitution matrix derived from the 84 common positions was used to evaluate sequence similarity within the globins and between the globins and phycocyanins C and colicins A, via calculation of pairwise similarity scores. The scores for globin-globin comparisons over the 84 common positions overlap the globin-phycocyanin and globin-colicin scores, with the former being intermediate. For the subset of internal positions, overlap is minimal between the three groups of scores. These results imply a continuum of amino acid sequences able to assume the common three-on-three alpha-helical structure and suggest that the determinants of the latter include sites other than those inaccessible to solvent.

Mechanisms of life span determination in Caenorhabditis elegans.

Molecular analysis of several gerontogenes of Caenorhabditis elegans has led to the discovery of at least two life span-controlling pathways. An insulin-like signaling cascade consisting of proteins encoded by the genes daf-2, age-1, akt-1, akt-2, daf-16 and daf-18 regulates dauer diapause, reproduction, and longevity. This pathway regulates all three processes systemically. daf-12 interacts with it, affecting dauer diapause and longevity. Life span extension mediated by this pathway probably results from the activation of an enhanced life-maintenance program, which is normally operative during dauer diapause. A different mechanism is specified by the clock genes clk-1, clk-2, clk-3 and gro-1, which regulate metabolic activity and the pace of many temporal processes including longevity. There is some controversy as to whether the life span extension observed in these mutants requires the activity of daf-16. All known gerontogenes appear to confer resistance to environmental stress, usually multiple stress factors, including oxidative stress, high temperature, and exposure to ultraviolet radiation. Caloric restriction extends longevity substantially, and may act by activating the enhanced life-maintenance program.

The primary structure of histone H3 from the nematode Caenorhabditis elegans.

The complete amino acid sequence of histone H3 (135 residues) from the nematode Caenorhabditis elegans has been established. Microheterogeneity occurs at positions 96 and 100 of the chain. The sequences of the nematode H3 isoforms are very similar to the major chain of calf thymus H3 with which they show 4 substitutions in total. The major variant has cysteine in position 96. This is the first report of cysteine in this position in H3 from non-mammalian tissue. An exceptional methylation site has been detected at position 79. Various other sites of secondary modification are of a conservative nature.

The histones of Caenorhabditis elegans: no evidence of stage-specific isoforms. An overview.

The nematode Caenorhabditis elegans expresses one species of H2A and one species of H4 molecules, at least two species of H1 (H1.1, H1.2), two species of H2B (H2B.1, H2B.2) and 2-4 species of H3 (H3.1 and H3.3 and an unassigned Ile/Leu microheterogeneity in H3). The study of their primary structures has been completed now and all of them, with the exception of the Ile/Leu microheterogeneity in H3, have been assigned to protein spots on two-dimensional gels. One spot, previously designated H3.2, probably represents C-terminally cleaved H3.1. The relative abundance of the isohistones was essentially the same when derived from either eggs, gravid adults or postreproductive, senescent worms. The degree of post-translational modification, however, particularly acetylation of H2A, H2B and H3 histone species, was reduced at old age.

Unexpected intron location in non-vertebrate globin genes.

The Caenorhabditis elegans and Artemia T4 globin sequences are highly homologous with other invertebrate globins. The intron/exon patterns of their genes display a single intron in the E and G helices respectively. Precoding introns in multirepeat globins are inserted in homologous positions. Comparison of the intron/exon patterns in the known globin gene sequences demonstrates that they are more diverse than first expected but nevertheless can be derived from an ancestral pattern having 3 introns and 4 exons.

Nuclease digestion of DNA and RNA in nuclei from young adult and senescent Caenorhabditis elegans (Nematoda).

Nuclei prepared from young adult and senescent Caenorhabditis elegans (Nematoda) were subjected to digestion by micrococcal nuclease and DNaseI. The kinetics of digestion of nuclei by micrococcal nuclease showed no change with age. There was, however, an age-related increase of acid-soluble deoxyribonucleotides released by DNaseI, suggesting that subtle alterations of chromatin conformation occur in aged nematodes. The ratio of nuclear RNA to DNA decreased and the nuclear RNA became more susceptible to enzymatic degradation as the worms grew old. These findings appear to indicate that nuclear RNA is less protected by protein in old nematodes. The decline of the nuclear RNA/DNA ratio with age is in good agreement with the generally accepted idea that there is a reduced level of RNA and protein synthesis in old animals.

Insulin-like signaling, metabolism, stress resistance and aging in Caenorhabditis elegans.

The nervous system acts as a major regulator of the life span of Caenorhabditis elegans. Temperature and chemical stimuli from the environment are integrated with internal signals from the reproductive system to specify adult longevity. An insulin-like signaling cascade acts in neurons and coordinates control of senescence of the entire organism by regulating metabolism and a stress response mechanism. Caloric restriction extends life span, possibly by activation of the stress response program.

Peptide mapping and microsequencing of proteins separated by SDS-PAGE after limited in situ acid hydrolysis.

A method is described for the isolation of peptide fragments from proteins separated by polyacrylamide gel electrophoresis. After completion of the electrophoresis step, gels are stained with Ponceau S or Coomassie Blue. Gel portions containing protein stained with Ponceau S are excised and transferred to borosilicate glass digestion tubes containing 0.9 ml of 1 mM NaOH or 5 mM Na2HPO4. After complete dissociation of the dye from the protein, 0.1 ml of 20% formic acid is added and the protein is hydrolyzed in situ at 112 degrees C for four hours. Subsequently the acid solution is made 10% in acetonitrile and chromatographed as such on a C18 (C4) reversed-phase column using an appropriate large-volume sample loading syringe and injection loop. Proteins stained with Coomassie Blue can be hydrolyzed in situ after complete removal of the dye with an aqueous solution containing 40% acetone, 10% triethylamine and 5% acetic acid. The gel slices are next washed with HPLC-grade water and protein is hydrolyzed in 2% formic acid under standard conditions. Gel-related contaminants do not interfere with the peptide separation under the proper conditions of HPLC analysis.

Modulation of kinase activities in dauers and in long-lived mutants of Caenorhabditis elegans.

Mutant alleles of the genes age-1 and daf-2 that lengthen life span (Age phenotype) of Caenorhabditis elegans cause higher protein kinase (PKA, PKC, PTK) activity levels in senescing worms relative to wild-type. Elevated levels of PKA and PTK were also present in dauer larvae, developmentally arrested juveniles specialized for long-term survival, relative to L3 larvae, the alternative developmental stage. PKC activity was downregulated in dauers of a non-Age control strain and in age-1 mutant dauers, compared to L3 larvae, but similar activities were measured in dauers and L3 larvae of a daf-2 mutant strain. Thus, age-1 and daf-2 mutant worms may express distinct elements of a dauer-specific survival program during adult life.

Two-parameter logistic and Weibull equations provide better fits to survival data from isogenic populations of Caenorhabditis elegans in axenic culture than does the Gompertz model.

We have fitted Gompertz, Weibull, and two- and three-parameter logistic equations to survival data obtained from 77 cohorts of Caenorhabditis elegans in axenic culture. Statistical analysis showed that the fitting ability was in the order: three-parameter logistic > two-parameter logistic = Weibull > Gompertz. Pooled data were better fit by the logistic equations, which tended to perform equally well as population size increased, suggesting that the third parameter is likely to be biologically irrelevant. Considering restraints imposed by the small population sizes used, we simply conclude that the two-parameter logistic and Weibull mortality models for axenically grown C. elegans generally provided good fits to the data, whereas the Gompertz model was inappropriate in many cases. The survival curves of several short- and long-lived mutant strains could be predicted by adjusting only the logistic curve parameter that defines mean life span. We conclude that life expectancy is genetically determined; the life span-altering mutations reported in this study define a novel mean life span, but do not appear to fundamentally alter the aging process.

Age-specific modulation of light production potential, and alkaline phosphatase and protein tyrosine kinase activities in various age mutants of Caenorhabditis elegans.

Previous work has shown that reduction-of-function mutations in the genes daf-2 and age-1 can increase adult life (Age phenotype) of Caenorhabditis elegans and that certain daf-12 alleles considerably amplify this effect in daf-2; daf-12 doubles. We have measured the light production potential (LPP) and alkaline phosphatase (ALP) and protein tyrosine kinase (PTK) activity levels as suitable biochemical markers to further investigate genetic interactions between these genes. The light production assay measures superoxide anion production by freeze-thawed worms in assay medium containing sufficient amounts of nicotineamide adenine dinucleotide, reduced form (NADH) and nicotineamide adenine dinucleotide phosphate, reduced form (NADPH) to drive the chemiluminescent reaction at maximal speed, and 5 mM cyanide to fully repress cytosolic superoxide dismutase (SOD). This assay thus provides an estimate of the maximum output of the metabolic pathways involved at the instant of freeze-fixation, and under the condition of the assay. LPP and PTK activities decreased similarly in daf-12(m20), and a control strain that had wild-type alleles of daf-12, age-1, and daf-2. The age-dependent decrease of LPP and PTK was reduced in age-1(hx542) and age-1(hx542); daf-2(e1370), and virtually absent in daf-2(e1370) and daf-2(e1370); daf-12(m20) mutant worms. ALP activity increased with age in non-Age genotypes and showed little, if any, age-dependent alteration in daf-2(e1370) and daf-2(e1370); daf-12(m20) mutant worms. Mutation in both age-1 and daf-2 caused no stronger phenotype than a single mutation as estimated by LPP, PTK, and ALP. We propose that (a) daf-2 is the major effector of metabolic activity during adult life, (b) daf-2 downregulates metabolic activity with increasing age, and (c) daf-12 stimulates oxygen consumption independently of daf-2.

Chromatographic recovery of polypeptides from copper-stained sodium dodecyl sulfate polyacrylamide gels.

A procedure of preparative electrophoresis is described in which proteins separated on sodium dodecyl sulfate gels, stained with copper and eluted by simple diffusion, are highly concentrated on a fluorocarbon packing and freed of small molecular weight substances, including sodium dodecyl sulfate and buffer components and gel-related substances. This method can be used for microscale preparations or it can be scaled up to recover milligram amounts of protein. The purified polypeptides, however denatured, are suitable for amino acid sequencing.

Three Biological Species Closely Related to Rhabditis (Oscheius) pseudodolichura Körner in Osche, 1952.

The Oscheius subgenus (Nematoda: Rhabditidae) comprises several common free-living hermaphroditic species. Morphological identification is difficult due to a lack of reliable characters to discriminate species. We studied 32 strains that are closely related to Rhabditis (Oscheius) pseudodolichura and R. (O.) tipulae. We present results from mating experiments between the strains and sequence data from the internal transcribed spacer region of ribosomal RNA, allowing discrimination of three closely related biological species.

Fabrication and functionalization of PCB gold electrodes suitable for DNA-based electrochemical sensing.

The request of high specificity and selectivity sensors suitable for mass production is a constant demand in medical research. For applications in point-of-care diagnostics and therapy, there is a high demand for low cost and rapid sensing platforms. This paper describes the fabrication and functionalization of gold electrodes arrays for the detection of deoxyribonucleic acid (DNA) in printed circuit board (PCB) technology. The process can be implemented to produce efficiently a large number of biosensors. We report an electrolytic plating procedure to fabricate low-density gold microarrays on PCB suitable for electrochemical DNA detection in research fields such as cancer diagnostics or pharmacogenetics, where biosensors are usually targeted to detect a small number of genes. PCB technology allows producing high precision, fast and low cost microelectrodes. The surface of the microarray is functionalized with self-assembled monolayers of mercaptoundodecanoic acid or thiolated DNA. The PCB microarray is tested by cyclic voltammetry in presence of 5 mM of the redox probe K3Fe(CN6) in 0.1 M KCl. The voltammograms prove the correct immobilization of both the alkanethiol systems. The sensor is tested for detecting relevant markers for breast cancer. Results for 5 nM of the target TACSTD1 against the complementary TACSTD1 and non-complementary GRP, MYC, SCGB2A1, SCGB2A2, TOP2A probes show a remarkable detection limit of 0.05 nM and a high specificity.