Effects of Selective Logging on Populations of Two Tropical Understory Herbs in an Amazonian Forest1

This study examined the effects of (1) rime elapsed after logging and (2) logging intensity on the total, juvenile, and adult densities, and on reproduction of Calathea altissima and Ischnosiphon amuma (Matantaceae), two monocot herb species in the understory of Central Amazonian forests. Logging was carried out experimentally at various intensities in eight plots (4 ha each) during 1987 and three plots in 1993. Five plots were left as experimental controls. In 1998, total and adult densities of the two species were greater in the plots logged 11 years before than in controls. For I. arouma, total and adult densities were also higher in the plots logged 5 years before; however, juvenile densities were less affected. The intensity of logging influenced adult density of both species but not total or juvenile densities. Densities of reproductive individuals of both species were higher in the logged areas and increased with logging intensity. The effects of time after logging and logging intensity on reproduction were indirect due to the greater number of adult plants in those areas. The observed effects were probably mediated by changes in canopy cover in logged areas. Greater light intensities in logging gaps, roads, and their margins may lead to increased reproduction, recruitment, growth, and survival, which in turn can lead to increased plant density. These results indicate that logging has long–term effects on understory plant populations.     

PHYLOGENETIC RELATIONSHIPS AMONG STREPTOPHYTES AS INFERRED FROM CHLOROPLAST SMALL AND LARGE SUBUNIT rRNA GENE SEQUENCES1

To gain insights into the phylogeny of charophytes and into their relationships with other green algae and bryophytes, we analyzed the chloroplast small and large subunit rRNA sequences of charophytes belonging to five orders (Charales, Coleochaetales, Desmidiales, Klebsormidiales, and Zygnematales), of chlorophytes from the four remaining classes of green algae, and of bryophytes representing the three classes reported in this group of land plants. We also probed the gene organization and intron content of the chloroplast rDNA operon in charophytes and bryophytes. The organization of this operon proved to be highly conserved, except in members of the Desmidiales and Zygnematales. Homologous group II introns were identified in the trnA(UGC) gene of all charophyte groups examined and in the trnI(GAU) gene of charophytes from all orders except the Desmidiales and Zygnematales. Phylogenetic analyses of concatenated rDNA sequences consistently placed the prasinophyte Mesostigma viride Lauterborn at the base of the Streptophyta and Chlorophyta, although alternative topologies positioning Mesostigma within the Streptophyta could not be rejected. A sister group relationship was unambiguously established between Chaetosphaeridium globosum (Nordstedt) Klebahn and members of the Coleochaetales. The Charales, Coleochaetales, Desmidiales, and Zygnematales were found to be monophyletic, and a sister group relationship was observed for the Desmidiales and Zygnematales. Although our analyses failed to resolve the branching order of the Coleochaetales, Charales, Desmidiales/Zygnematales, and bryophytes, they revealed that the problematic charophyte taxon Entransia fimbriata Hughes strongly clusters with Klebsormidium flaccidum (Kützing) Silva, Mattox et Blackwell to form a basal lineage relative to the other charophyte orders examined.     

DNA Methylation and Carcinogenesis

The hypothesis of the exclusively genetic origin of cancer (cancer is a disease of genes, a tumor without any damage to the genome does not exist) dominated in the oncology until recently. A considerable amount of data confirming this hypothesis was accumulated during the last quarter of the last century. It was demonstrated that the accumulation of damage of specific genes lies at the origin of a tumor and its following progression. The damage gives rise to structural changes in the respective proteins and, consequently, to inappropriate mitogenic stimulation of cells (activation of oncogenes) or to the inactivation of tumor suppressor genes that inhibit cell division, or to the combination of both (in most cases). According to an alternative (epigenetic) hypothesis that was extremely unpopular until recently, a tumor is caused not by a gene damage, but by an inappropriate function of genes (cancer is a disease of gene regulation and differentiation). However, recent studies led to the convergence of these hypotheses that initially seemed to be contradictory. It was established that both factors–genetic and epigenetic–lie at the origin of carcinogenesis. The relative contribution of each varies significantly in different human tumors. Suppressor genes and genes of repair are inactivated in tumors due to their damage or methylation of their promoters (in the latter case an epimutation, an epigenetic equivalent of a mutation, occurs, producing the same functional consequences). It is becoming evident that not only the mutagens, but various factors influencing cell metabolism, notably methylation, should be considered as carcinogens.     

Water use by perennial plants in the transition zone between river oasis and desert in NW China

The study aimed at establishing the role of two possible water sources (inundation, ground water) for the water supply to the perennial plant species Alhagi sparsifolia, Calligonum caput-medusae, Populus euphratica and Tamarix ramosissima growing in the transition zone between a river oasis and the open desert at the southern fringe of the Taklamakan desert (Xinjiang province, NW China). The basic hypothesis was that inundations, which normally occur in summer when rivers from a nearby mountain range carry high water, contribute significantly to the plants’ water supply. When, in the first summer, inundations did not occur, four sites, each of which covered by a relatively dense stand of one species, were artificially flooded. Soil and plant water relations as well as meteorological variables were measured during two growing seasons. Water use efficiency of production (WUE_P) was calculated by relating biomass production, which was determined using allometric regressions, to water use.The effects of artificial flooding on the plant water relations were negligible. Water use was relatively high, especially in the A. sparsifolia and the P. euphratica stands and in a dense stand of T. ramosissima (up to approx. 500 kgH₂O m⁻² year⁻¹). Using the total above-ground biomass in the calculation, WUE_P was highest in C. caput-medusae and P. euphratica, and lowest, in A. sparsifolia. From soil and plant water relations, and against the background of the climate and the productivity of the vegetation, it is concluded that all perennial plants in the transition zone between oases and desert in that region must have sufficient access to ground water to ensure long-term survival. Management of ground water such that it remains continuously accessible to the perennial plants is a prerequisite for the conservation and sustainable use of the vegetation in the transition zone.     

Genome analysis of Agrobacterium tumefaciens: construction of physical maps for linear and circular chromosomal DNAs, determination of copy number ratio and mapping of chromosomal virulence genes.

The phytopathogenic bacterium Agrobacterium tumefaciens is unique in that it possesses both linear and circular DNA chromosomes in addition to a plant-tumor-inducing (Ti) plasmid. We analyzed the two chromosomal DNA molecules in strain MAFF301001, whose Ti plasmid has already been sequenced completely. Physical maps of the chromosomal DNAs were constructed by Southern hybridization experiments using Pme I and Swa I fragments and short fragments bridging the Swa I fragments with special care to avoid any missing fragment. Hybridization with 16S rDNA probe showed one rDNA locus on the linear chromosome and two loci on the circular chromosome. For this bacterium to be pathogenic, not only Ti plasmid but also chromosomal genes are required. The chromosomal virulence (chv) genes (chvA, chvB, chvD, chvE, chvG, chvH, and chvI) and the chromosomal genes affecting the virulence [acvB, pgm(exoC), glgP, miaA, and ros] were successfully mapped onto 5 different regions in the chromosomal physical maps. These chv genes and the chromosomal genes affecting the virulence other than pgm and glgP were found on the circular chromosome, whereas the pgm and glgP genes were located on the linear chromosome. In contrast to the large terminal inverted repeats of Streptomyces linear chromosomal DNA, no hybridization signal was detected between left and right terminal fragments of the linear A. tumefaciens chromosome. Quantitative analysis of DNA fragments indicated that the copy numbers of the two chromosomal DNAs and the Ti plasmid are identical.     

Clades within the ‘higher land birds’, evaluated by nuclear DNA sequences

In this study we investigated the phylogenetic relationships within the ‘higher land birds’ by parsimony analysis of nucleotide DNA sequences obtained from the two nuclear, protein-coding genes, c- myc and RAG-1. Nuclear genes have not previously been used to address this phylogenetic question. The results include high jackknife support for a monophyletic Apodiformes (including the Trochilidae). This arrangement was further supported by the observation of an insertion of four amino acids in the c- myc gene in all apodiform taxa. Monophyly was also inferred for each of the two piciform groups Galbulae and Pici. Within Pici, the Capitonidae was found to be paraphyletic, with the New World barbets more closely related to the Ramphastidae than to the Old World barbets. Another clade with high jackknife support consists of the Upupidae, Phoeniculidae and Bucerotidae. The families Momotidae and Todidae, and Coraciidae and Brachypteraciidae, respectively, also form well supported monophyletic clades. The results are inconclusive regarding the monophyly of the orders Coraciiformes and Piciformes, respectively.     

Ribonucleases and their antitumor activity

The antitumor effect of ribonucleases was studied with animal ribonucleolytic enzymes, bovine pancreatic RNase A, bovine seminal RNase (BS-RNase), onconase and angiogenin. While bovine pancreatic RNase A exerts a minor antitumor effect, BS-RNase and onconase exert significant effects. Angiogenin, as RNase, works in an opposite way, it initiates vascularization of tumors and subsequent tumor growth. Ribonunclease inhibitors are not able to inhibit the antitumor effectiveness of BS-RNase or onconase. However, they do so in the case of pancreatic RNases. Conjugation of BS-RNase with antibodies against tumor antigens (preparation of immunotoxins) like the conjugation of the enzyme with polymers enhances the antitumor activity of the ribonuclease. After conjugation with polymers, the half-life of BS-RNase in blood is extended and its immunogenicity reduced. Recombinant RNases have the same functional activity as the native enzymes. The synthetic genes have also been modified, some of them with gene sequences typical for the BS-RNase parts. Recent experimental efforts are directed to the preparation of ‘humanized antitumor ribonuclease’ that would be structurally similar to human enzyme with minimal immunogenicity and side effects. The angiogenesis of tumors is attempted to be minimized by specific antibodies or anti-angiogenic substances.     

Genotype and phenotype associations with drought tolerance in barley tested in North Africa

A review is presented of genetic strategies deployed in a 3-yr project on drought tolerance in barley. Data were collected on genetic, physiological and agronomic traits in non-irrigated and irrigated field trials in Egypt, Morocco and Tunisia. A wide range of barley germplasm (developed from African and European cultivars, adapted landraces and wild barleys) was tested, and positive traits were found in each gene pool. The contrasting environments of the three North African countries had major effects on plant/genotype performance. Genetic effects were also detected, as were genotype × environment interactions. A range of strategies were deployed to investigate the physiology and genetics of quantitative traits associated with field performance. Quantitative trait locus (QTL) analysis was performed using backcross lines, recombinant inbred lines and doubled haploid mapping populations. A detailed genetic map was generated in the Tadmor × (ER/Apm) recombinant inbred lines, an important mapping population specifically developed by ICARDA (Centre for Agricultural Research in Dry Areas) and CIMMYT (International Maize and Wheat Improvement Center) to study drought. Quantitative trait loci (QTLs) for grain yield and other important morphological and physiological traits were also identified in a population of doubled haploids derived from F2BCj plants from a cross between a cultivar and a wild barley accession. Significantly, the wild parental line was found to contribute a number of positive alleles for yield. Effects of major developmental genes could explain many of the responses observed. QTLs were found to cluster around major genes controlling flowering time (sghI), plant stature (sdwI and arie.GP) and ear type (vrsl), and it is highly likely that the associations represent pleiotropic effects. Some QTLs were associated with candidate genes such as dehydrins and rubisco activase. One of the most significant results was the identification and generation of material that out performed the best local standards in the three participating North African countries; the selected lines have now entered local breeding programmes. The strategies adopted provided information on physiological traits, genotypes and genetic markers that could be used for marker-assisted selection. Target QTLs and their associated genetic markers may be deployed in marker assisted selection programmes to match crop phenology to the field environment.     

Reproductive biology of the threatened golden galaxias Galaxias auratus Johnston and the influence of lake hydrology

Golden galaxias Galaxias auratus (31–235 mm fork length, L _F) were collected monthly from littoral habitats in Lakes Crescent and Sorell, Tasmania, Australia, between July 2000 and December 2002. Spawning habitats were identified and monitored in both lakes, and surveyed in Lake Crescent. Trends in gonado-somatic indices and reproductive stages of development indicated that gonad development in both sexes begins in midsummer and peaks in late autumn to early winter. Males mature at smaller sizes (50% at 52 mm L _F) than females (50% at 76 mm L _F), larger individuals are predominately females (95% of fish ≥138 mm L _F), and overall male to female ratios are female biased ( c . 1:2). Spawning occurs late autumn to early spring (water temperatures = 1·4–9·7° C) with peaks in spawning activity in winter (mean water temperatures <5° C). Demersal adhesive eggs ( c. 1·5 mm diameter) were found on cobble substrata ( c. 20–250 mm diameter) in littoral areas ( c. 0·2–0·6 m deep) and fecundity of fish 71–181 mm L _F ranged from 619 to 14 478 eggs. The rate of change in water level over the 20 days prior to monthly sampling was important in explaining the occurrence of spent fish and this accounted for temporal differences in spawning between the populations. Lake hydrology influences the reproductive cycle of G. auratus by possibly providing a stimulus for spawning and it controls the availability of spawning habitat in Lake Crescent. Seasonal hydrological cycles ( i.e. rises during late autumn to winter) and a minimum water level of 802·20 m Australian Height Datum in Lake Crescent during autumn (above which littoral areas of cobble substratum are inundated) are critical to G. auratus populations.     

The role of major histocompatibility complex diversity in vigour of fish males (Abramis brama L.) and parasite selection

The major histocompatibility complex (MHC) presents a group of genes with highly polymorphic loci involved in specific immune responses. The factors maintaining extensive MHC polymorphism have been questioned, considering three possible hypotheses of parasite‐mediated selection driving an extensive MHC diversity (i.e. heterozygote advantage, rare‐allele advantage, and favouring optimal MHC diversity). The patterns of MHC diversity of class IIB genes were investigated following two noncontradicting hypotheses, parasite‐driven selection and MHC‐based mating preferences, using males of common bream collected in the spawning period. Two allelic groups DAB1 and DAB3 were recognized from the phylogenetic analyses. Individuals expressed one or two alleles of the same or different allelic groups. Several individuals shared identical alleles; however, the presence of parasite species was not associated with the occurrence of a particular allele. The presence of different allelic groups (only DAB1, only DAB3, or both DAB1 and DAB3) in individuals was not associated with parasite presence or diversity. The expression of two DAB1 alleles was associated with higher endoparasite abundance. Moreover, nucleotide diversity in individuals expressing a single type of alleles (DAB1 or DAB3) increased with the abundance of ectoparasitic Dactylogyrus spp. (Monogenea) and Ergasilus sp. (Crustacea). This suggests that the expression of two alleles of a single allelic type is related to high metazoan parasite infection whereas no significant influence of parasitism on the combined allelic form (the presence of both DAB1 and DAB3 alleles) was found. Moreover, the expression of two alleles of a single allelic type was related to decreased immunocompetence measured by spleen size. The condition factor was higher in fish expressing the combined allelic type. Thus, the presence of alleles of different lineages in individuals appears to be advantageous for individual male fitness. The expression of a single allelic type was related to higher sexual ornamentation, which could support the role of MHC in the hypothesis of the sexual selection of ‘good genes’. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90 , 525–538.