Phylogeny of theAsterales sensu lato based onrbcL sequences with particular reference to theGoodeniaceae

TherbcL gene of 25 taxa was sequenced and analyzed cladistically in order to define more precisely the orderAsterales s.l. and to reconstruct the phylogeny ofGoodeniaceae. The cladistic analyses show that theAsterales comprise the familiesAbrophyllaceae, Alseuosmiaceae, Argophyllaceae, Asteraceae, Calyceraceae, Campanulaceae s.l.,Donatiaceae, Goodeniaceae (includingBrunoniaceae),Menyanthaceae, Pentaphragmataceae, andStylidiaceae. Abrophyllaceae, Alseuosmiaceae, Brunoniaceae, andDonatiaceae have previously not been studied in this respect. Within theGoodeniaceae, four groups supported by therbcL data can be distinguished: the genusLechenaultia, theAnthotium-Dampiera-group, the genusBrunonia, and a group formed by the remaining genera, theScaevola-Goodenia-group.     

Abstract power structures (APS) and related bumping orders

Generalizing an idea of M. Richardson (Fundamentals of Mathematics, New York: Macmillan Co., 1958), an APS on a given populationP is a non-empty collection of non-empty subsets ofP such that ifA is in the collection andA⊆B, thenB is in the collection. From a structure of this kind a partial ordering ofP, called therelated bumping order, is derived. The question is raised as to what kinds of partial orderings can be so obtained. For structures determined by voting weights of the members of the population, a complete characterization of all possible bumping orders is obtained.     

Detection of loci in theleu region ofRhizobium meliloti chromosome

A multi-marked strain ofRhizobium meliloti was developed by the co-mutation method and employed to contribute to the genetic map ofR. meliloti chromosome. Seven loci were placed at 5 sites in theleu region in the orderman-aba, fix, leu-cro-azt, ost-thi.     

Naphthalene-utilizing and mercury-resistant bacteria isolated from an acidic environment

Soil samples were taken from areas of low pH (2.5–3.5) surrounding an outdoor coal storage pile. These samples were added to medium with naphthalene as the sole carbon source to enrich for organisms capable of degrading polycyclic aromatic hydrocarbons (PAH) at low pH. Five such bacterial strains were isolated. Sequencing of the 16S rDNA showed them to be members of the genera Clavibacter, Arthrobacter and Acidocella. These organisms were all capable of growth with naphthalene as a sole carbon source at low pH. The genes nahAc, nahAd, phnAc, nahH, xylE or GST, which are known to be associated with PAH degradation were not detected. Isolate 10, the Acidocella strain, tolerated high levels of mercury. PCR amplification and sequencing of genes from the mer operon from isolate 10 DNA suggested that mercury is transported into the bacterial cell and subsequently detoxified since the enzymes encoded by genes in this operon are involved in these processes.     

piggyBacis an effective tool for functional analysis of thePlasmodium falciparumgenome

Background  

Much of thePlasmodium falciparumgenome encodes hypothetical proteins with limited homology to other organisms. A lack of robust tools for genetic manipulation of the parasite limits functional analysis of these hypothetical proteins and other aspects of thePlasmodiumgenome. Transposon mutagenesis has been used widely to identify gene functions in many organisms and would be extremely valuable for functional analysis of thePlasmodiumgenome.     

Phylogenetic relationships in theCampanulales based onrbcL sequences

Phylogenetic relationships within the angiosperm orderCampanulales were investigated by comparative sequencing of the chloroplast generbcL. CompleterbcL sequences were obtained for ten species in six families within the order. These data were analyzed along with previously publishedrbcL sequences from other taxa (for a total of 117 species) within the subclassAsteridae and outgroups, producing 32 equally parsimonious trees. A subset consisting of 44 of these taxa was then chosen and more rigorous analyses performed, resulting in four equally parsimonious trees. Results indicate that two major clades roughly corresponding to traditionally circumscribedAsterales andCampanulales exist as sister taxa. In particular, therbcL trees indicate thatSphenoclea is not a member ofCampanulales orAsterales, thatPentaphragma is more closely allied toAsterales thanCampanulales, that theCyphiaceae are not monophyletic, thatCampanulaceae andLobeliaceae are not sister taxa, and thatStylidiaceae are correctly placed withinCampanulales.     

Phytosociological study of thePicea jezoensis forests of the far east

Forest communities dominated byPicea jezoensis (Yezo spruce) are described from across their entire distributional range in eastern Asia, including the territories of the Russian Far East and Japan. A total of 476 relevés are used representing the following dominant types of spruce forests: pureP. jezoensis, mixedP. jezoensis andAbies sachalinensis, mixedP. jezoensis andAbies nephrolepis, and purePicea glehnii communities. The vegetation is classified into 11 associations, 2 community types, 6 subassociations, 25 variants and 8 subvariants. Nine associations, including theAsaro heterotropoidis-Abietetum sachalinensis, Weigelo middendorffianae-Piceetum jezoensis, Lysichito-Piceetum glehnii, Swido albae-Piceetum obovatae, Oplopanaco elati-Piceetum jezoensis, Philadelpho tenuifolii-Piceetum jezoensis, Vaccinio-Piceetum jezoensis, Rhododendro aurei-Piceetum jezoensis, andMoneseto uniflorae-Piceetum jezoensis, are described for the first time. The ecology and structure of all communities are described and their syntaxonomy discussed. The communities are placed in three alliances,Piceion jezoensis, Abieti nephrolepidis-Piceion jezoensis andPino pumilae-Piceion jezoensis, all. nov. All of the communities described are considered to belong to the orderAbieti-Piceetalia of the classVaccinio-Piceetea.     

Isolation of keratinophilic fungi from soil in the vicinity of Bogota,Colombia

Soil collected from 54 areas in and around Bogota, Colombia were examined for the presence of keratinophilic fungi by theVanbreuseghem's hair baiting technique. The organisms isolated and frequency are indicated:Trichophyton terrestre, 33;T. ajelloi, 32;Chrysosporium keratinophilum, 30;Microsporon gypseum, 14; andM. fulvum, 1. The perfect stage,Nannizzia gypsea, 1; andArthroderma quadrifidum, 2; were observed growing on hair in three plates.The following organisms apparently have been reported for the first time from soil samples in Colombia:M. fulvum, T. ajelloi, T. terrestre, C. keratinophilum, N. gypsea, andA. quadrifidum.     

Omphalotaceae fam. nov. undPaxillaceae,ein chemotaxonomischer Vergleich zweier Pilzfamilien derBoletales

TheOmphalotaceae fam. nov., which include the generaOmphalotus andLampteromyces, are defined on the basis of characteristic sesquiterpenes and of their ability to cause white-rot. Anatomical and morphological features of the representatives of these genera support the creation of this new family. The occurrence of pigments, typical of theBoletales, and of cyanophilous spores, indicate membership of theOmphalotaceae in the orderBoletales. Relationships to the other families of this order — especially to thePaxillaceae — are discussed. The possible functional significance of fungal metabolites is considered.

Herrn Prof. Dr.J. Poelt zur Vollendung seines 60. Lebensjahres gewidmet.—Veränderte Fassung eines Vortrages auf der Tagung der Deutschen Botanischen Gesellschaft, Wien, September 1984.     

Genetic basis of microbial carotenogenesis

The synthesis of carotenoids begins with the formation of a phytoene from geranylgeranyl pyrophosphate, a well conserved step in all carotenogenic organisms and catalyzed by a phytoene synthase, an enzyme encoded by the crtB (spy) genes. The next step is the dehydrogenation of the phytoene, which is carried out by phytoene dehydrogenase. In organisms with oxygenic photosynthesis, this enzyme, which accomplishes two dehydrogenations, is encoded by the crtP genes. In organisms that lack oxygenic photosynthesis, dehydrogenation is carried out by an enzyme completely unrelated to the former one, which carries out four dehydrogenations and is encoded by the crtI genes. In organisms with oxygenic photosynthesis, dehydrogenation of the phytoene is accomplished by a ζ-carotene dehydrogenase encoded by the crtQ (zds) genes. In many carotenogenic organisms, the process is completed with the cyclization of lycopene. In organisms exhibiting oxygenic photosynthesis, this step is performed by a lycopene cyclase encoded by the crtL genes. In contrast, anoxygenic photosynthetic and non-photosynthetic organisms use a different lycopene cyclase, encoded by the crtY (lyc) genes. A third and unrelated type of lycopene β-cyclase has been described in certain bacteria and archaea. Fungi differ from the rest of non-photosynthetic organisms in that they have a bifunctional enzyme that displays both phytoene synthase and lycopene cyclase activity. Carotenoids can be modified by oxygen-containing functional groups, thus originating xanthophylls. Only two enzymes are necessary for the conversion of β-carotene into astaxanthin, using several ketocarotenoids as intermediates, in both prokaryotes and eukaryotes. These enzymes are a β-carotene hydroxylase (crtZ genes) and a β-carotene ketolase, encoded by the crtW (bacteria) or bkt (algae) genes. Electronic Publication     

Ultrastructure of sieve-element plastids inCaryophyllales (Centrospermae), evidence for the delimitation and classification of the order

The orderCaryophyllales (Centrospermae) was found to contain specific P-type sieve-element plastids which are characterized by protein inclusions composed of ring-shaped bundles of filaments and of central crystalloids. The sieve-element plastids of 14 families (140 species investigated) fit into this overall characterization, and more specific details are used to delimit the families and arrange them within the order.Phytolaccaceae, the basic family of the order display much diversity: the crystalloids inside their plastids are either globular (most genera) or polygonal (Stegnosperma), starch may also be present (Phytolacca).Nyctaginaceae, with starch inBougainvillea sieve-element plastids, can be derived directly fromPhytolacca. Globular crystalloids are present in most of the families, as inDidiereaceae, Cactaceae, Aizoaceae-Tetragoniaceae, Portulacaceae-Basellaceae-Halophytaceae-Hectorellaceae. Caryophyllaceae andLimeum ofMolluginaceae contain polygonal crystalloids (otherMolluginaceae with globular crystalloids). Crystalloids are entirely absent fromChenopodiaceae (incl.Dysphaniaceae) andAmaranthaceae. The probable relationships between these families are presented diagrammatically in Fig. 13. Bataceae, Gyrostemonaceae, Vivianiaceae, Theligonaceae, Polygonaceae, Plumbaginaceae, Fouquieriaceae, Frankeniaceae, andRhabdodendraceae—all at some time included into theCaryophyllales (Centrospermae) or doubtfully referred to them—develop S-type (or different P-type) sieve-element plastids. Their direct connection to theCaryophyllales therefore is excluded. Finally, evolutionary trends of theCaryophyllales are discussed.Presented in the Symposium Evolution of Centrospermous Families, during the XIIth International Botanical Congress, Leningrad, July 8, 1975.     

Isolation,sequencing and mutational analysis of a gene cluster involved in nitrite reduction inParacoccus denitrificans

By using the gene encoding the C-terminal part of thecd ₁-type nitrite reductase ofPseudomonas stutzeri JM300 as a heterologous probe, the corresponding gene fromParacoccus denitrificans was isolated. This gene,nirS, codes for a mature protein of 63144 Da having high homology withcd ₁-type nitrite reductases from other bacteria. Directly downstream fromnirS, three othernir genes were found in the ordernirECF. The organization of thenir gene cluster inPa. denitrificans is different from the organization ofnir clusters in some Pseudomonads.nirE has high homology with a S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase (uro'gen III methylase). This methylase is most likely involved in the hemed ₁ biosynthesis inPa. denitrificans. The third gene,nirC, codes for a small cytochromec of 9.3 kDa having high homology with cytochromec _55X ofPs. stutzeri ZoBell. The 4th gene,nirF, has no homology with other genes in the sequence databases and has no relevant motifs. Inactivation of either of these 4 genes resulted in the loss of nitrite and nitric oxide reductase activities but not of nitrous oxide reductase activity.nirS mutants lack thecd ₁-type nitrite reductase whilenirE, nirC andnirF mutants produce a small amount ofcd ₁-type nitrite reductase, inactive due to the absence of hemed ₁. Upstream from thenirS gene the start of a gene was identified which has limited homology withnosR, a putative regulatory gene involved in nitrous oxide reduction. A potential FNR box was identified between this gene andnirS.Abbreviations SDS sodium dodecyl sulfate - NBT nitroblue tetrazolium - PAGE polyacrylamide gel electrophoresis     

Optimal sequence alignment using affine gap costs

When comparing two biological sequences, it is often desirable for a gap to be assigned a cost not directly proportional to its length. If affine gap costs are employed, in other words if opening a gap costsv and each null in the gap costsu, the algorithm of Gotoh (1982,J. molec. Biol. 162, 705) finds the minimum cost of aligning two sequences in orderMN steps. Gotoh's algorithm attempts to find only one from among possibly many optimal (minimum-cost) alignments, but does not always succeed. This paper provides an example for which this part of Gotoh's algorithm fails and describes an algorithm that finds all and only the optimal alignments. This modification of Gotoh's algorithm still requires orderMN steps. A more precise form of path graph than previously used is needed to represent accurately all optimal alignments for affine gap costs.     

New classification of liverworts based on molecular and morphological data

Complete sequences for the 18S-rRNA gene of 22 bryophytes (12 completely new) were determined and used to construct phylogenetic trees. The evaluation of sequence data according to the maximum parsimony principle (PAUP 3.1.1) and the neighbor-joining method (MEGA) results in similar phylogenetic trees in which theBryopsida appear as a sister group to theJungermanniopsida, and both together as a sister group to theMarchantiopsida. Among theMarchantiopsida, theSphaerocarpales diverge early as a separate clade. TheMetzgeriales andJungermanniales are monophyletic. They belong to one clade and cannot be separated by either method of evaluation.     

Syntaxonomic analysis of theAndropogon-rich grasslands (Hyparrhenietalia hirtae) in the western Mediterranean region

Using the Braun-Blanquet approach, a syntaxonomical revision of the orderHyparrhenietalia hirtae in the western Mediterranean region was made. Various syntaxa were studied with relevés from the Iberian Peninsula, southern France, Sardinia, Sicily and adjacent islands, Balearic Islands, Canary Islands and Morocco. One alliance (Hyparrhenion hirtae), 8 associations (one of them new:Lotononido lupinifoliae-Hyparrhenietum sinaicae) and several subassociations and variants were distinguished. A complete classification of theHyparrhenietalia hirtae in the studied area with ecological and biogeographical diagnoses is given.     

Characterization of type II protein secretion (xcp) genes in the plant growth-stimulatingPseudomonas putida, strain WCS358

InPseudomonas aeruginosa, the products of thexcp genes are required for the secretion of exoproteins across the outer membrane. Despite structural conservation of the Xcp components, secretion of exoproteins via the Xcp pathway is generally not found in heterologous organisms. To study the specificity of this protein secretion pathway, thexcp genes of another fluorescent pseudomonad, the plant growth-promotingPseudomonas putida strain WCS358, were cloned and characterized. Nucleotide sequence analysis revealed the presence of at least five genes, i.e.,xcpP, Q, R, S, andT, with homology toxcp genes ofP. aeruginosa. Unlike the genetic organization inP. aeruginosa, where thexcp cluster consists of two divergently transcribed operons, thexcp genes inP. putida are all oriented in the same direction, and probably comprise a single operon. Upstream ofxcpP inP. putida, an additional open reading frame, with no homolog inP. aeruginosa, was identified, which possibly encodes a lipoprotein. Mutational inactivation ofxcp genes inP. putida did not affect secretion, indicating that no proteins are secreted via the Xcp system under the growth conditions tested, and that an alternative secretion system is operative. To obtain some insight into the secretory pathway involved, the amino acid sequence of the N-terminus of the major extracellular protein was determined. The protein could be identified as flagellin. Mutations in thexcpQ andR genes ofP. aeruginosa could not be complemented by introduction of the correspondingxcp genes ofP. putida. However, expression of a hybrid XcpR protein, composed of the N-terminal one-third ofP. aeruginosa XcpR and the C-terminal two-thirds ofP. putida XcpR, did restore protein secretion in aP. aeruginosa xcpR mutant.     

Characterization of intracellular polygalacturonic acidtrans-eliminase fromKlebsiella oxytoca,Yersinia enterocolitica,andErwinia chrysanthemi

Intracellular polygalacturonic acidtrans-eliminase (PATE) was purified and characterized fromKlebsiella oxytoca andYersinia enterocolitica, enterobacteria unable to macerate plant tissue. The well-studied PATE from a strain ofErwinia chrysanthemi, a phytopathogen able to macerate plant tissue and cause soft-rot disease, was included for comparison. PATE from all strains displayed endo-splitting activity with pH optima between pH 8.5 and 9.0E. chrysanthemi had three isozymes (pls at pH 9.4, 9.0, and 7.8),K. oxytoca had two isozymes (pIs at pH 5.9 and 5.3), andY. enterocolitica had one isozyme (pI at pH 5.8). Molecular weights for theKlebsiella andYersinia PATEs were 71,000 and 55,000, respectively, compared with 33,000 for theErwinia PATE. Unlike theErwinia enzyme, theKlebsiella andYersinia PATEs did not require divalent cations for activity and could not macerate plant tissue without addition of pectinmethylesterase. The polygalacturonic acid-degrading enzymes found inK. oxytoca andY. enterocolitica appear to represent a separate type of PATE enzyme. It is unlikely that these organisms are phytopathogens; however, their ability to degrade polygalacturonic acid is probably advantageous to their survival in environments containing decomposing plant residues.     

Trophic interactions in soils as they affect energy and nutrient dynamics. II. Physiological responses of selected rhizosphere bacteria

Comparative microbial functions in the plant root zone were studied by evaluating rhizosphere-derivedPseudomonas andArthrobacter growth in chemostat culture and responses to root-exudate-related nutrients after varied starvation periods. These organisms were chosen to represent zymogenous and autochthonous microbes, respectively. In chemostat culture, thePseudomonas isolate showed increased energy charge and decreased populations with higher growth rates, whereas theArthrobacter had lower energy charge and cell population values which did not change appreciably with growth rate. The responses of these two types of organisms also differed with starvation. ThePseudomonas lost its ability to respire efficiently in the presence of several known root exudate components, whereas theArthrobacter isolate, in comparison, maintained a lower but more consistent ability to utilize these nutrients with increased starvation. TheArthrobacter also showed increased utilization of several substrates after starvation, suggesting its potential ability to function under restricted nutrient availability conditions. These results suggest thatPseudomonas-type organisms in the rhizosphere may best function in periods of more intense exudate release, whereas organisms of theArthrobacter- type may be more efficient at nutrient utilization during periods of lesser nutrient flux. Based on these data the rhizosphere-derivedPseudomonas isolate was considered to be an appropriate bacterium to use in more complex rhizosphere microcosm experiments where nutrient flux dynamics would be emphasized.     

Characterization ofgari andfu-fu preparation procedures in Nigeria

Processes for the production ofgari, East Nigerianfu-fu and West Nigerianfu-fu are described. Changes in pH value, moisture content, microflora and sugar content of cassava duringgari andfu-fu preparation are reported. Mannitol accumulated during thegari fermentation but not in either of thefu-fu fermentations. During each stage ofgari andfu-fu production, lactic acid bacteria predominated. Homofermentative organisms occurred most frequently in the early stages of each process and heterofermenters in the latter ones. Of the 179 microorganisms that were isolated and characterized fromgari andfu-fu, 52% were able to hydrolyse linamarin and 14% starch.     

Development and structure of the comose seeds ofHillia (Rubiaceae)

The hairs at the apical end of the seeds ofHillia are pluriseriate, multicellular structures. The cells making up a hair are elongated exotesta cells and, consequently, also have secondary thickenings identical (H. parasitica) or similar (H. costanensis) to those found on the exotesta cells on the main body of the seeds. Hair formation already starts in bud stage: at and around the chalazal region of an ovule, integument epidermis cells are grouped together to form ± elongated packets of 4–7 cells. The cells of each packet undergo further elongation and anticlinal division so that a hair on a mature seed may be up to c. 30 mm long. Basally, the seeds have a tail- to ± wing-like appendage, made up of only two cell layers, the exotesta of the ab- and adaxial side of the seed. This basal appendage shows the same anatomical structure as the wings of various anemochorous rubiaceous seeds. Although seed hairs of this kind are unique in theRubiaceae and — from the point of development and structure — not homologous to exotesta wings, the presence of a basal wing-like appendage suggests thatHillia, previously often placed into a tribe of its own (Hillieae), can be accommodated in theCinchoneae, a tribe in which winged, anemochorous seeds predominate. The tufts of hairs of the comose seeds ofHillia look superficially similar to those of certainAsclepiadaceae andApocynaceae (like theRubiaceae belonging to the orderGentianales). Comparisons based on literature data, however, reveal that there are striking differences in the position, development and structure of the hairs (produced at the micropylar end, initiated after fertilization, hairs unicellular, etc.).