The Early Holocene treeline in the southern French Alps: new evidence from travertine formations

Aims The present paper concerns the analysis of macro‐remains (plant imprints) from high altitude travertine deposits dating back to the early Holocene (9800 BP ). Our results allow us to discuss treeline location and ecology, and to supplement previous data based on pollen from natural sediments and charcoal from natural soil. Location The travertine under study is located in the Queyras massif, in the southern French Alps, along the Italian border. The site is situated on a south‐facing slope. Methods The travertine deposit has been dated by ²³⁰Th/²³⁴U. Taxonomic identification of plant imprints was achieved by comparison of the morphology of fossil specimens with extant material. Results Imprints of Pinus uncinata (cones and needles), broad‐leaved trees (Betula cf. pubescens, Populus tremula and Salix spp.), and unidentified trunks have been found. The plant assemblage records the existence at a high altitude (2200 m) of shade‐intolerant vegetation at around 9800 BP. Our data indicate that the treeline limit was at least 100 m higher than previously thought. The morphological features of the travertine, the plant assemblage and trunk diameters indicate that during the travertinization process, vegetation around the site was probably dense with tall upright trees. Main conclusions Our data show that Pinus uncinata and broad‐leaved trees developed at 2200 m, while regional pollen analyses locate the treeline at lower altitudes. Different research methods appear to provide different results. Around 9800 BP tree regeneration and growth were made possible up to at least 2200 m a.s.l., probably as a result of warmer and wetter summers. Warmer conditions are inferred from the predicted increase in incoming solar radiation based on calculated orbital variations, and wetter conditions are inferred from the build‐up of the travertine.     

Vegetation development at a mountain settlement site in the Swedish Scandes during the late Holocene: palaeoecological evidence of human-induced deforestation

A palaeoecological study was conducted close to the forest limit in the northern Scandinavian mountain range. The aim was to elucidate the degree to which human impact has affected the vegetation at Hiednikvalta, a Stállo settlement site. Stállo settlements consist of round hut foundations that have a hearth in the middle and are surrounded by a low turf wall. They were probably established by Sámi people using the mountain areas for hunting and/or reindeer herding. In order to separate the effects of humans and climate on the vegetation, a reference area approach was adopted, i.e. the vegetation development at the Stállo settlement site Hiednikvalta was compared with the vegetation development in a forested reference area Avvuhatjåhkkå, at the same altitude as Hiednikvalta but with no archaeological remains of settlements. Peat stratigraphies were retrieved at the two sites and pollen analysis, loss-on-ignition (LOI), pollen accumulation rates (PAR), macrofossil analysis and Betula pollen size statistics were all examined. The results indicate that Hiednikvalta was forested with Betula trees prior to the Stállo settlement period, which occurred between the eighth and thirteenth centuries. Human activities resulted in a decrease in tree cover at the site, as found in a previous study at Adamvalta, another Stállo settlement site in the region. However, the magnitude of vegetation change, and the post-Stállo vegetation development differed between the two areas, suggesting that site-specific factors are important. The use of reference areas in palynological studies is also discussed.     

Fossil evidence for a herbaceous diversification of early eudicot angiosperms during the Early Cretaceous

Eudicot flowering plants comprise roughly 70% of land plant species diversity today, but their early evolution is not well understood. Fossil evidence has been largely restricted to their distinctive tricolpate pollen grains and this has limited our understanding of the ecological strategies that characterized their primary radiation. I describe megafossils of an Early Cretaceous eudicot from the Potomac Group in Maryland and Virginia, USA that are complete enough to allow reconstruction of important life-history traits. I draw on quantitative and qualitative analysis of functional traits, phylogenetic analysis and sedimentological evidence to reconstruct the biology of this extinct species. These plants were small and locally rare but widespread, fast-growing herbs. They had complex leaves and they were colonizers of bright, wet, disturbance-prone habitats. Other early eudicot megafossils appear to be herbaceous rather than woody, suggesting that this habit was characteristic of their primary radiation. A mostly herbaceous initial diversification of eudicots could simultaneously explain the heretofore sparse megafossil record as well as their rapid diversification during the Early Cretaceous because the angiosperm capacity for fast reproduction and fast evolution is best expressed in herbs.     

Pinus cembra L. (arolla pine), a common tree in the inner French Alps since the early Holocene and above the present tree line: a synthesis based on charcoal data from soils and travertines

Aim In this study, charcoal‐based data for Pinus cembra L. (arolla pine) were gathered from soil and travertine sequences in order to reconstruct its historical biogeography at the landscape level in the inner western Alps during the Holocene. Location The study sites are located between 1700 and 2990 m a.s.l., in the southern (Queyras Massif and Ubaye Valley) and the northern (Maurienne Valley) parts of the inner French Alps. Methods Charcoal fragments were extracted from sediments by water sieving, using meshes of 5, 2, 0.8 and 0.4 mm. The charcoal mass of P. cembra was determined in each charcoal assemblage. Accelerator mass spectrometry and conventional ¹⁴C measurements were used to date the fragments. Results Supported by 40 ¹⁴C datings, the fragments show that, over 2000 m a.s.l., P. cembra accounts for around 40% (mean value) of identified fragments. Data reveal that arolla pine once extended between 260 and 375 m above the present‐day local tree lines. It was established in the southern and the northern French Alps from at least c. 9000 and 6000 cal yr bp , respectively. Main conclusions While present‐day populations of P. cembra are very fragmented in the inner French Alps, charcoal records indicate large past occurrences of this tree since the early Holocene. Human disturbance since the Neolithic seems to be the main reason for the regression of the arolla pine woodlands. On the south‐facing slopes of the study sites, currently deforested, this species extended up to 2800 m a.s.l. In the northern areas, charcoal records of the P. cembra expansion are consistent with the regional pollen archives, but in the southern massifs charcoal records indicate its presence c. 2600 years earlier than other palaeobotanical studies suggest. This discrepancy highlights the necessity to crosscheck data using several different proxies in order to assess the validity of conclusions regarding tree development in space and time.     

The occurrence of apical labial sensilla in the Aleyrodidae and evidence for a contact chemosensory function

Scanning electron microscopy of the apex of the labium of six species of whitefly [Aleurothrixus floccosus (Maskell), Aleyrodes spiraeoides Quaintance, Bemisia tabaci (Gennadius), Dialeurodes citri (Ashmead), Parabemisia myricae (Kuwana), and Trialeurodes vaporariorum (Westwood)], revealed that all possess seven pairs of sensilla symmetrically positioned on either side of the labial groove. Transmission electron microscopy revealed that in P. myricae, sensilla 1, 5, 6 & 7 are innervated each by a single dendrite, sensilla 2 & 4 are innervated by three dendrites each, and sensillum 3 is innervated by four dendrites. Multiple innervation of sensilla 2, 3 & 4 suggests a chemosensory or mechano-chemosensory function. Longitudinal sections of sensilla 2 & 4 showed that the sensilla were hollow with an apical pore, providing further morphological evidence for a chemosensory function. One dendrite appeared to end at the base of sensillum 2, suggesting that at least sensillum 2 has a dual mechano-chemosensory function. The presence of contact chemoreceptors on the labial tip may help explain how P. myricae can discriminate between hosts before probing.

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Zusammenfassung Untersuchungen mit dem Rasterelektronenmikroskop an sechs Spezies von Weißen Fliegen [Aleurothrixus floccusus (Maskell), Aleyrodes spiraeoides Quaintance, Bemisia tabaci (Gennadius), Dialeurodes citri (Ashmead), Parabemisia myricae (Kuwana), und Trialeurodes vaporariorum (Westwood)] zeigten, daß bei allen Arten die Spitze des Labiums mit sieben Paaren von Sensillen versehen ist, die symmetrisch auf jeder Seite der Lippenspalte angeordnet sind. Die Sensillen sind klein (ca. 1–4 m lang, 0.1–0.6 m breit) und in beiden Geschlechtern aller Arten ähnlich gestaltet. Mittels Transmissionelektronenmikroskopie wurde gezeigt, daß in P. myricae die Sensillen 1, 5, 6 & 7 durch jeweils einen einzigen, die Sensillen 2 & 4 durch jeweils drei und die Sensille 3 durch vier Dendriten innerviert werden. Die multiple Innervierung der Sensillen 2, 3 & 4 läßt eine chemosensorische oder mechanisch-chemosensorische Funktion vermuten. Längsschnitte durch die Sensillen 2 & 4 lieferten weitere Hinweise auf eine chemosensorische Funktion: die Sensillen sind hohl und an der Spitze mit einer Pore versehen. Wir erhielten keine schlüssigen Beweise für die Existenz von apikalen Poren an den anderen Sensillen. Einer der Dendriten an der Sensille 2 scheint an der Sensillenbasis zu enden; dies deutet darauf hin, daß zumindest diese Sensille ein Rezeptor sowohl für mechanische als auch für chemische Reize ist. Die Existenz dieser Kontakt-Chemorezeptoren an der Labiumspitze könnte erklären, wie P. myricae bereits vor dem Probestich zwischen Wirtspflanzen zu unterscheiden vermag. Diese Ergebnisse lassen außerdem vermuten, daß die sensorischen Aspekte des Wirtsfindung bei Weißen Fliegen grundsätzlich verschieden sind von denjenigen bei Blattläusen, welche nur über mechanische Rezeptoren an der Spitze der Unterlippe verfügen.

     

Intra-specific diversity of the chemical composition of Ligularia lamarum in the Hengduan Mountains,China: The structures of four new eremophilanes and a new seco-eremophilane

Chemical compositions and internal transcribed spacer (ITS) sequences of five samples of Ligularia lamarum collected in Sichuan Province, China, were analyzed. Fourteen compounds, including four new eremophilanes and one new seco-eremophilane, were isolated and their structures were elucidated by spectroscopic methods. Intra-specific diversity in the chemical composition was found to be higher than previously known. The result of DNA analysis suggested that one of the samples was introgressed, although its chemical composition was typical of L. lamarum.     

The potential use of identification of skeletal remains for the early detection of Ammotragus: an exotic ungulate species in Southern Spain

The main aim of our work was to evaluate osteometry as a complementary tool for the early detection of Ammotragus lervia, an exotic ungulate, which currently shows an expanding trend in southeastern Spain. For this purpose, 142 metacarpi and 123 metatarsi from seven Iberian ungulate species were determined by means of a classification function. In a general way, this function works, but regarding related species (those very similar from a morphometrical view), correct determination was reached in only 44.4–90% of the cases. However, in these cases, we can use auxiliary criteria like sexually dimorphic traits, and reach 100% correct identification of bones.     

The genus Spathius Nees (Hymenoptera,Braconidae, Doryctinae) in Mexico: occurrence of a highly diverse Old World taxon in the Neotropics

Two new species of the parasitoid wasp genus Spathius Nees (Braconidae: Doryctinae) from Mexico, S. mexicanussp. n. and S. chamelaesp. n., are described and illustrated. These represent the second and third described species of this highly diverse Old World genus in the Neotropics, and the first described species recorded for the Mexican territory.     

Palaeobotanical evidence for agricultural activities in the Eifel region during the Holocene: plant macro-remain and pollen analyses from sediments of three maar lakes in the Quaternary Westeifel Volcanic Field (Germany, Rheinland-Pfalz)

As a part of the ELSA-project (Eifel Laminated Sediment Archive) new pollen and plant macro-remain analyses have been carried out on a series of Holocene lacustrine sediments from three open maar lakes of the Quaternary Westeifel Volcanic Field. In combination with already existing pollen analyses, the archaeological record and written sources, the present study casts new light on settlement activities and henceforth the development of agriculture from the prehistoric to historic times in this region. While there are clues that wood pasturing was practised in the Eifel region from the Michelsberg Culture onwards (c. 4300 cal. b.c.), the Vulkaneifel is a remote area with relatively poor soils and a humid climate and was not constantly settled until the Late Neolithic/Early Bronze Age, when cereal pollen was found regularly in the deposits. Plant macro-remains (chaff), which give us direct evidence for arable agriculture in the surroundings of the maars, were also found in layers belonging to the Early Bronze Age (c. 1900 cal. b.c.). At the same time we can observe the massive spread of Fagus sylvatica (beech) in all pollen diagrams, which was most probably caused by a combination of climatic, anthropogenic and competitive factors. Later impacts of agriculture were an abundance of crop weeds and pollen in the following Middle Bronze Age. Nevertheless human impact remained discontinuous until the Urnfield Culture (1200–800 cal. b.c.). A layer of weeds dating at the end of the Urnfield Culture was found and also flax (Linum usitatissimum) cultivation first becomes apparent. However, the subsequent Iron Age and Roman Period reveal only crop weeds and cereal pollen in slightly higher concentrations, but the abundance of Poaceae pollen at this time is most probably consistent with grazing activities. There follows compelling evidence of the importance of flax cultivation and processing at the maars from the Merovingian Period (5th century a.d.) onwards. A detailed insight into the agriculture of the High Medieval comes from flash flood layers of the 14th century a.d., where remains of Secale cereale (rye) and crop weeds reflect winter-sown cultivation of rye. Cannabis sativa (hemp) was also cultivated and processed during the medieval. Finally we can trace the Prussian reforestation in the 19th century a.d., with an increase in Pinus sylvestris (pine) and Picea abies (fir), by both pollen and plant macro-remains.     

Crop water availability in early agriculture: evidence from carbon isotope discrimination of seeds from a tenth millennium BP site on the Euphrates

The analysis of carbon isotope discrimination (Δ) in crop plant remains from archaeological sites may help to assess water availability for early agriculture. This study presents the analysis of Δ in seeds of naked wheat (Triticum aestivum/durum), lentil (Lens orientalis/culinaris), and flax (Linum sp.) found at the archaeological site of Tell Halula in the valley of the Middle Euphrates (Syria). This Neolithic site is the oldest in this region of the Fertile Crescent where the cultivation of domesticated plants has been reported, with seed remains ranging from 9550 to 8465 BP. Most of the seeds analysed showed Δ values greater than 16 ‰, reaching 20 ‰ for some samples of flax. For wheat, Δ values were much higher than those reported in present-day (1996) durum wheat crops cultivated under rainfed conditions in north-west Syria under environments with somewhat higher rainfall than Tell Halula. Similarly, grains of present-day (1997) barley cultivated in the archaeological site also showed lower values than those found in archaeological kernels. An empirical relationship between Δ of mature kernels and total precipitation (plus irrigation where applicable) from heading to maturity (r² = 0.82, n = 11) was established for durum wheat, currently cultivated in different environments of the Mediterranean basin. The resulting relationship was applied to the data on Δ of wheat fossil kernels from Tell Halula to estimate the accumulated water inputs during the time (about 6 weeks) the kernels were produced. Calculated water inputs for wheat during early agriculture were (over 110 mm) at least 5 times higher than current-day rainfall accumulated in Tell Halula during the same phenological period. These results strongly suggest that early agriculture wheat was cultivated at Tell Halula under much wetter conditions than are currently to be found in the area. The presence of flax and its very high Δ values also support this conclusion. Whether such humid conditions during cultivation were due to moister conditions prevailing at this time, by planting in alluvial areas or by irrigation works is discussed.     

Role of the B helix in early folding events in apomyoglobin: evidence from site-directed mutagenesis for native-like long range interactions

The folding pathways of four mutants in which bulky hydrophobic residues in the B helix of apomyoglobin (ApoMb) are replaced by alanine (I28A, L29A, I30A, and L32A) have been analyzed using equilibrium and kinetic methods employing NMR, CD, fluorescence and mass spectrometry. Hydrogen exchange pulse-labeling followed by mass spectrometry reveals detectable intermediates in the kinetic folding pathways of each of these mutants. Comparison of the quench-flow data analyzed by NMR for the wild-type protein and the mutants showed that the substitutions I28A, L29A and L32A lead to destabilization of the B helix in the burst phase kinetic intermediate, relative to wild-type apomyoglobin. In contrast, the I30A mutation apparently has a slight stabilizing effect on the B helix in the burst phase intermediate; under weak labeling conditions, residues in the C helix region were also relatively stabilized in the mutant compared to the wild-type protein. This suggests that native-like helix B/helix C packing interactions occur in the folding intermediate. The L32A mutant showed significantly lower proton occupancies in the burst phase for several residues in the G helix, specifically F106, I107, E109 and A110, which are in close proximity to L32 in the X-ray structure of myoglobin, providing direct evidence that native-like helix B/helix G contacts are formed in the apomyoglobin burst phase intermediate. The L29A mutation resulted in an increase in burst phase proton occupancies for several residues in the E helix. Since these regions of the B and E helices are not in contact in the native myoglobin structure, these effects suggest the possibility of non-native B/E packing interactions in the kinetic intermediate. The differing effects of these B helix mutations on the apomyoglobin folding process suggests that each side-chain plays a different and important role in forming stable structure in the burst phase intermediate, and points to a role for both native-like and non-native contacts in stabilization of the folding intermediate.     

Generation of the primary antibody repertoire in rabbits: expression of a diverse set of Igk-V genes may compensate for limited combinatorial diversity at the heavy chain locus

 In mouse and human, generation of combinatorial diversity through use of different heavy and light chain variable region genes in immunoglobulin rearrangements can be a major contributor to the primary antibody repertoire. In rabbits, the contribution of the combinatorial mechanism to heavy chain diversity is minimal, as only a few Igh-V genes are rearranged and expressed. To investigate the contribution of combinatorial diversity toward generation of the rabbit V_κ repertoire, we constructed five genomic libraries from rabbit kidney DNA and 1 cDNA library from the bone marrow of a 1-day-old rabbit using a series of polymerase chain reaction-based strategies. Our analyses indicate that most of the sequences that we recovered from our libraries belong to a single family and some are extremely similar. The actual number of germline Igk-V genes is potentially greater than our conservative estimate of at least 39, 28 of which we found expressed as mRNA. The germline Igk-V genes display different lengths of the coding region 3′ of Cys 88 ranging from 7 to 12 amino acids, resulting in CDR3 length heterogeneity among functional V_κJ_κ sequences ranging from 8 to 15 amino acids. Some of the V_κJ_κ junctions had N and P nucleotide additions. Thus, in contrast to limited combinatorial diversity of its heavy chain, the rabbit can draw upon a diverse set of germline Igk-V genes. The κ light chain has the potential to be a major contributor toward generation of the antibody specificities of the rabbit pre-immune repertoire. Received: 14 April 1999 / Revised: 8 June 1999     

Identification of early developing axon projections from spinal interneurons in the chick embryo with a neuron specific beta-tubulin antibody: evidence for a new 'pioneer' pathway in the spinal cord

The early development of interneurons in the chick embryo spinal cord was studied using a monoclonal antibody against a neuron-specific beta-tubulin isoform. Early developing interneurons were divided into two cell groups on the basis of their location and the pattern of growth of their axons. One group is composed of cells that establish a primitive longitudinal pathway (PL-cells), whereas the other group contains cells constituting a circumferential pathway (C-cells). The onset of axonal development in both cell groups occurs at stage (st.) 15 (embryonic day, (E), 2) in the branchial segments, which is prior to axonogenesis of motoneurons. PL-cells develop in the region between the floor plate and the motoneuron nucleus. Their axons are the first neuronal processes ('pioneer axons') to arrive in the ventrolateral marginal zone and they project both rostrally and caudally to establish a primitive longitudinal association pathway at the ventrolateral surface of the neural tube. This pathway is formed before axons of C-cells arrive in the ventrolateral region. The first C-cells are initially located in the most dorsal portion of the neural tube, whereas later appearing C-cells are also located in both intermediate and ventral regions of the neural tube. The axons of C-cells project ventrally, without fasciculating, along the lateral border of the neural tube. Some of their axons enter the ipsilateral ventrolateral longitudinal pathway at st. 17. We often observed apparent contacts and interactions between preexisting axons of PL-cells and newly arriving axons of C-cells. The axons of commissural C-cells first enter the floor plate at st. 17 and cross the midline at st. 18. Axons of C cells begin to join the contralateral ventrolateral longitudinal pathway at st. 18+ to st. 19. In the floor plate region, contacts between growth cones and axons were often observed. However, axons in the floor plate at these stages were not fasciculated. These observations establish the timing and pattern of growth of axons from two specific populations of early developing interneurons in the chick spinal cord. Additionally, we have identified an early and apparently previously undescribed 'pioneer' pathway that constitutes the first longitudinal pathway in the chick spinal cord.     

Waves of parthenogenesis in the desert: evidence for the parallel loss of sex in a grasshopper and a gecko from Australia

The rarity of parthenogenesis, reproduction without sex, is a major evolutionary puzzle. To understand why sexual genetic systems are so successful in nature, we must understand why parthenogenesis sometimes evolves and persists. Here we use DNA sequence data to test for similarities in the tempo and mode of the evolution of parthenogenesis in a grasshopper and a lizard from the Australian desert. We find spectacular congruence between genetic and geographic patterns of parthenogenesis in these distantly related organisms. In each species, parthenogenesis evolved twice and appears to have expanded in parallel waves across the desert, suggesting a highly general selective force against sex.     

The cultivation bias: different communities of arbuscular mycorrhizal fungi detected in roots from the field,from bait plants transplanted to the field,and from a greenhouse trap experiment

The community composition of arbuscular mycorrhizal fungi (AMF) was investigated in roots of four different plant species (Inula salicina, Medicago sativa, Origanum vulgare, and Bromus erectus) sampled in (1) a plant species-rich calcareous grassland, (2) a bait plant bioassay conducted directly in that grassland, and (3) a greenhouse trap experiment using soil and a transplanted whole plant from that grassland as inoculum. Roots were analyzed by AMF-specific nested polymerase chain reaction, restriction fragment length polymorphism screening, and sequence analyses of rDNA small subunit and internal transcribed spacer regions. The AMF sequences were analyzed phylogenetically and used to define monophyletic phylotypes. Overall, 16 phylotypes from several lineages of AMF were detected. The community composition was strongly influenced by the experimental approach, with additional influence of cultivation duration, substrate, and host plant species in some experiments. Some fungal phylotypes, e.g., GLOM-A3 (Glomus mosseae) and several members of Glomus group B, appeared predominantly in the greenhouse experiment or in bait plants. Thus, these phylotypes can be considered r strategists, rapidly colonizing uncolonized ruderal habitats in early successional stages of the fungal community. In the greenhouse experiment, for instance, G. mosseae was abundant after 3 months, but could not be detected anymore after 10 months. In contrast, other phylotypes as GLOM-A17 (G. badium) and GLOM-A16 were detected almost exclusively in roots sampled from plants naturally growing in the grassland or from bait plants exposed in the field, indicating that they preferentially occur in late successional stages of fungal communities and thus represent the K strategy. The only phylotype found with high frequency in all three experimental approaches was GLOM A-1 (G. intraradices), which is known to be a generalist. These results indicate that, in greenhouse trap experiments, it is difficult to establish a root-colonizing AMF community reflecting the diversity of these fungi in the field roots because fungal succession in such artificial systems may bias the results. However, the field bait plant approach might be a convenient way to study the influence of different environmental factors on AMF community composition directly under the field conditions. For a better understanding of the dynamics of AMF communities, it will be necessary to classify AMF phylotypes and species according to their life history strategies.     

Flexible mating system in a logged population of <Emphasis Type="Italic">Swietenia macrophylla</Emphasis> King (Meliaceae): implications for the management of a threatened neotropical tree species

Microsatellites were used to evaluate the mating system of the remaining trees in a logged population of Swietenia macrophylla, a highly valuable and threatened hardwood species, in the Brazilian Amazon. A total of 25 open pollinated progeny arrays of 16 individuals, with their mother trees, were genotyped using eight highly polymorphic microsatellite loci. Genotypic data analysis from the progeny arrays showed that 373 out of the 400 seedlings (93.25%) were unambiguously the result of outcrossed matings and that the remaining 6.75% had genotypes consistent with self-fertilisation. Apomixis could be ruled out, since none of the 400 seedlings analysed had a multi-locus genotype identical to its mother tree. The high estimate of the multi-locus outcrossing rate (t _m = 0.938 ± 0.009) using the mixed mating model also indicated that the population in this remnant stand of S. macrophylla was predominantly allogamous. The relatively large difference between the multi-locus and single-locus outcrossing estimates (t _m −t _s = 0.117 ± 0.011) provides evidence that, in spite of the high outcrossing rate, a considerable degree of biparental inbreeding has contributed to the genetic structure of this population. Levels of outcrossing were not evenly distributed among maternal trees (t _m ranging from 0.39 to 1.00), suggesting the occurrence of a variable degree of self-incompatibility and/or dichogamy among individual trees of this monoecious species. Due to its generalist pollination system and some level of tolerance for selfing, S. macrophylla seems to be resilient to environmental disturbances such as those caused by logging, since it sets fruits with predominantly outcrossed seeds even at low stand densities. Therefore, the remaining individuals in logged areas or in relict fragments may be very important for long-term population recovery and genetic conservation programmes.     

The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species

The evolution of the RecA protein was analyzed using molecular phylogenetic techniques. Phylogenetic trees of all currently available complete RecA proteins were inferred using multiple maximum parsimony and distance matrix methods. Comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. The RecA trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the , , , , proteobacteria, cyanobacteria, high-GC gram-positives, and the Deinococcus-Thermus group. However, there are interesting differences between the RecA trees and these other trees. For example, in all the RecA trees the proteins from gram-positive species are not monophyletic. In addition, the RecAs of the cyanobacteria consistently group with those of the high-GC gram-positives. To evaluate possible causes and implications of these and other differences phylogenetic trees were generated for small-subunit rRNA sequences from the same (or closely related) species as represented in the RecA analysis. The trees of the two molecules using these equivalent species-sets are highly congruent and have similar resolving power for close, medium, and deep branches in the history of bacteria. The implications of the particular similarities and differences between the trees are discussed. Some of the features that make RecA useful for molecular systematics and for studies of protein evolution are also discussed.     

Molecular evidence for the occurrence of Contracaecum rudolphii A (Nematoda: Anisakidae) in shag Phalacrocorax aristotelis (Linnaeus) (Aves: Phalacrocoracidae) from Sardinia (western Mediterranean Sea)

Specimens of Contracaecum rudolphii Hartwich, 1964 (Nematoda: Anisakidae) from Phalacrocorax aristotelis (Linnaeus) from the Archipelago of La Maddalena (Sardinia, western Mediterranean Sea) were characterised genetically and compared with C. rudolphii A sensu D’Amelio et al. 1990 and C. rudolphii B sensu D’Amelio et al. 1990 from Phalacrocorax carbo sinensis (Blumenbach) from north-eastern Italy, and with C. rudolphii C sensu D’Amelio et al. 2007 from Phalacrocorax auritus (Lesson) from west-central Florida, USA. The sequencing of the small subunit of the mitochondrial ribosomal RNA gene (rrnS) and by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of the same gene and of the internal transcribed spacers (ITS) of nuclear ribosomal DNA (rDNA) allowed the identification of all specimens of C. rudolphii from P. aristotelis as C. rudolphii A. The results confirmed that the definition of genetic markers, following the analysis of nuclear ribosomal and mitochondrial DNA, provides quick and practical diagnostic tools for the detection of the 3 sibling species of C. rudolphii. The occurrence of C. rudolphii in P. aristotelis is reported for the first time from the Mediterranean area, improving the picture of the dispersal patterns of the populations of these piscivorous birds, and confirming the existence of different and isolated populations between the North and South European waters.     

The energy-conserving nitric-oxide-reductase system in Paracoccus denitrificans. Distinction from the nitrite reductase that catalyses synthesis of nitric oxide and evidence from trapping experiments for nitric oxide as a free intermediate during denitrification

1. A Clark-type electrode that responds to nitric oxide has been used to show that cytoplasmic membrane vesicles of Paracoccus denitrificans have a nitric-oxide reductase activity. Nitrous oxide is the reaction product. NADH, succinate or isoascorbate plus 2,3,5,6-tetramethyl-1,4-phenylene diamine can act as reductants. The NADH-dependent activity is resistant to freezing of the vesicles and thus the NADH:nitric-oxide oxidoreductase activity of stored frozen vesicles provides a method for calibrating the electrode by titration of dissolved nitric oxide with NADH. The periplasmic nitrite reductase and nitrous-oxide reductase enzymes are absent from the vesicles which indicates that nitric-oxide reductase is a discrete enzyme associated with the denitrification process. This conclusion was supported by the finding that nitric-oxide reductase activity was absent from both membranes prepared from aerobically grown P. denitrificans and bovine heart submitochondrial particles. 2. The NADH: nitric-oxide oxidoreductase activity was inhibited by concentrations of antimycin or myxothiazol that were just sufficient to inhibit the cytochrome bc1 complex of the ubiquinol--cytochrome-c oxidoreductase. The activity was deduced to be proton translocating by the observations of: (a) up to 3.5-fold stimulation upon addition of an uncoupler; and (b) ATP synthesis with a P:2e ratio of 0.75. 3. Nitrite reductase of cytochrome cd1 type was highly purified from P. denitrificans in a new, high-yield, rapid two- or three-step procedure. This enzyme catalysed stoichiometric synthesis of nitric oxide. This observation, taken together with the finding that the maximum rate of NADH:nitric-oxide oxidoreductase activity catalysed by the vesicles was comparable with that of NADH:nitrate-oxidoreductase, is consistent with a role for nitric-oxide reductase in the physiological conversion of nitrate or nitrite to dinitrogen gas. 4. Intact cells of P. denitrificans also reduced nitric oxide in an antimycin- or myxothiazol-sensitive manner. However, nitric oxide was not detected by the electrode during the reduction of nitrate. Nitric-oxide synthesis from nitrate could be detected with cells in the presence of very low concentrations of Triton X-100 which selectively inhibits nitric-oxide reductase activity. 5. Nitric oxide was detected as an intermediate in denitrification by including haemoglobin with an anaerobic suspension of cells that was reducing nitrate. The characteristic spectrum of the nitric oxide derivative of haemoglobin was observed.(ABSTRACT TRUNCATED AT 400 WORDS)