Luminescence Literature

The journal provides comprehensive literature searches on all aspects of luminescence which will be published in most issues. These lists have been produced regularly since 1986—some by year and some by specialized topic. This survey of papers on Obelia, Renilla, Aequorea and Gonyaulax is drawn from the 2000 literature and covers the biology of these organisms and the applications of genes and proteins from these organisms in analysis.     

Is the German suspension of MON810 maize cultivation scientifically justified?

We examined the justifications invoked by the German government in April 2009 to suspend the cultivation of the genetically modified maize varieties containing the Bt insect-resistance trait MON810. We have carried out a critical examination of the alleged new data on a potential environmental impact of these varieties, namely two scientific papers describing laboratory force-feeding trials on ladybirds and daphnia, and previous data on Lepidoptera, aquatic and soil organisms. We demonstrate that the suspension is based on an incomplete list of references, ignores the widely admitted case-by-case approach, and confuses potential hazard and proven risk in the scientific procedure of risk assessment. Furthermore, we did not find any justification for this suspension in our extensive survey of the scientific literature regarding possible effects under natural field conditions on non-target animals. The vast majority of the 41 articles published in 2008 and 2009 indicate no impact on these organisms and only two articles indicate a minor effect, which is either inconsistent during the planting season or represents an indirect effect. Publications from 1996 to 2008 (376 publications) and recent meta-analyses do not allow to conclude on consistent effects either. The lower abundance of some insects concerns mainly specialized enemies of the target pest (an expected consequence of its control by Bt maize). On the contrary, Bt maize have generally a lower impact than insecticide treatment. The present review demonstrates that the available meta-knowledge on Cry1Ab expressing maize was ignored by the German government which instead used selected individual studies.     

Molecular Diversity among Communities of Freshwater Microchlorophytes

Current hypotheses on the distribution of freshwater microchlorophytes lead to predictions of low diversity and wide environmental tolerances. Thus, the same few species should be found worldwide in many different habitats. However, these hypotheses are based on a morphospecies concept, which precludes the possibility of numerous cryptic species among these organisms. In this study, we examined the diversity of coccoid green microalgae and chlamydomonads (Chlorophyta) isolated from sites in Minnesota and North Dakota (USA) using techniques of 18S rDNA sequence analysis. Of 93 distinct 18S rDNA sequences identified from among 273 isolates examined by molecular techniques, all but four are new to science. The spatial distribution of organisms represented by these 18S rDNA sequences was not uniform, because some lakes and ponds yielded distinct 18S rDNA types not found at other sites. In addition, organisms generally considered to be cosmopolitan, such as Chlamydomonas reinhardtii and Chlorella vulgaris, were not found. These results challenge predictions of low species number and wide environmental tolerances among these eukaryotic microorganisms.     

The In Vitro Growth Response of Giardia Trophozoites from the Rabbit*

SYNOPSIS. A visual technic has been developed for determining concentration of Giardia trophozoites in culture tubes. Such a technic is desirable because the nature of Giardia growth makes routine enumeration of these organisms by hemocytometer or electronic cell counter expensive in both time and material. The visual method of counting Giardia trophozoites was correlated with counts of the same suspensions of organisms using an electronic particle counter. As a part of the correlation, the growth response, as measured by electronic cell counter, was established for 8 primary axenic cultures of Giardia trophozoites from the rabbit. The average starting number of organisms was 3.7 ± 0.6 × 10³ per ml, the average number of organisms at the peak of logarithmic growth was 1.78 ± 0.2 × 10⁵ per ml, and the generation time was 18.1 ± 1.6 hr. These data are compared with the available literature data quantitating Giardia growth.     

Lessons learned from Sphingomonas species that degrade abietane triterpenoids

Abietane terpenoid-degrading organisms include Sphingomonas spp which inhabit natural environments and biological treatment systems. An isolate from the high Arctic indicates that these organisms occur far from trees which synthesize abietanes and suggests that some of these organisms can occupy a niche in hydrocarbon-degrading soil communities. Abietane-degrading Sphingomonas spp provide additional evidence that the phylogeny of this genus is independent of the catabolic capabilities of its members. Studies of Sphingomonas sp DhA-33 demonstrate that biological treatment systems for pulp mill effluents have the potential to mineralize abietane resin acids. On the other hand, these studies indicate that some chlorinated dehydroabietic acids are quite recalcitrant. Strain DhA-33 grows relatively well on some chlorinated dehydroabietic acids but transforms others to stable metabolites. Using strain DhA-33, a novel method was developed to measure the metabolic activity of an individual population within a complex microbial community. Oligonucleotide hybridization probes were used to assay the 16S rRNA:rDNA ratio of DhA-33 as it grew in an activated sludge community. However, this method proved not to be sufficiently sensitive to measure naturally occurring resin acid-degrading populations. We propose that the same approach can be modified to use more sensitive assays. Received 01 May 1999/ Accepted in revised form 19 July 1999     

Calorific and carbon values of marine and freshwater Protozoa

Calorific and carbon values were determined for a variety of marine and freshwater Protozoa (Noctiluca miliaris, Euplotes sp.,Eufolliculina sp. respectivelyTetrahymena pyriformis, Paramecium caudatum), their food sources(Bacteria, Dunaliella primolecta, Ceratium hirundinella), and for Protozoa-dominated plankton samples. Most calorific values lie close to the centre of the range covering organisms in general. Low values in some marine samples probably resulted from the retention of bound water in the dried material. When all results were combined with data selected from the literature, the dependence of calorific value on carbon content was highly significant. This relationship is probably also adequately described by an energy-carbon regression through the variety of organic compounds commonly found in organisms. Calorific value expressed per unit carbon is shown to vary little in Protozoa (mean conversion factor 46 J [mg C]^–1) or throughout the range of biological materials considered in this study (45 J [mg C]^–1).     

Analysis of Initial Fouling Process in Coastal Environment: Effects of Settlement, Attachment, and Metamorphosis Promoters

Effects of lumichrome, l-tryptophan, and curcumin on fouling organisms were examined on panels immersed in a near-shore aquatic environment. These products showed effective action in aquariums in preliminary screening tests for promoting different steps of fouling. Lumichrome showed metamorphosis-inducing activity for ascidian larvae (Halocynthia), l-tryptophan was a settlement-inducer for larvae of barnacles (Balanus), and curcumin showed attachment-promoting activity on the blue mussel (Mytilus). In order to establish that these tests are helpful in screening actual fouling or antifouling compounds, we examined the action of these three compounds in a coastal environment by following the first steps of biofouling, that is, by studying the quantity of chlorophyll, the number of bacterial cells, and the larvae settled. These experiments on the seashore indicated that these compounds did not act as promoters for the target organisms; however, they did show promoting effects on some nontarget organisms. Received September 30, 1998; accepted September 28, 1999     

Molecular analysis of the nitrogen cycle in deep-sea microorganisms from the Nankai Trough: genes for nitrification and denitrification from deep-sea environmental DNA

Nitrification and denitrification are bacterial functions, which are important for the global nitrogen cycle. Thus, it is important to study the diversity and distribution of bacteria in the environment, which are involved in the nitrogen cycle on the earth. Ammonia monooxygenase encoded by the amoA gene and nitrite reductase encoded by nirK or nirS are essential enzymes for nitrificaton and denitrification, respectively. These genes can be used as markers for the identification of organisms in the nitrogen cycle. In this study, we identified amoA (42 clones) and nirS (98 clones) genes in parallel from samples recovered from the deep-sea of the Nankai Trough. Genes for nirK could not be amplified from these samples. The obtained amoA sequences were not so closely related to those of amoA genes from previously isolated environmental organisms and those of genes from environmental DNAs. On the other hand, the nirS genes sequenced showed some relationship to some extent with the latter genes. However, some of the newly sequenced genes formed clusters, which contained no previously identified genes on a phylogenetic tree. These are likely present in specific denitrifiers from the deep-sea. The results of this study further suggest that nitrifiers and denitrifiers live in the same area of the Nankai Trough and the nitrogen cycle exists even in the deep-sea.     

Organisms of deep sea hydrothermal vents as a source for studying adaptation and evolution

It has been postulated that life originated in a similar environment to those of deep sea hydrothermal vents. These environments are located along volcanic ridges and are characterized by extreme conditions such as unique physical properties (temperature, pressure), chemical toxicity, and absence of photosynthesis. However, numerous living organisms have been discovered in these hostile environments, including a variety of microorganisms and many animal species which live in intimate and complex symbioses with sulfo-oxidizing and methanotrophic bacteria. Recent proteomic analyses of the endosymbiont ofRiftia pachyptila and genome sequences of some free living and symbiotic bacteria have provided complementary information about the potential metabolic and genomic capacities of these organisms. The evolution of these adaptive strategies is connected with different mechanisms of genetic adaptation including horizontal gene transfer and . various structural and functional mutations. Therefore, the organisms in this environment are good models for studying the evolution of prokaryotes and eukaryotes as well as different aspects of the biology of adaptation. This review describes some current research concerning metabolic and plausible genetic adaptations of organisms in a deep sea environment, usingRiftia pachyptila as model.     

Casein kinase 2, circadian clocks, and the flight from mutagenic light

Circadian clocks play a fundamental role in biology and disease. Much has been learned about the molecular underpinnings of these biological clocks from genetic studies in model organisms, such as the fruit fly, Drosophila melanogaster. Here we review the literature from our lab and others that establish a role for the protein kinase CK2 in Drosophila clock timing. Among the clock genes described thus far, CK2 is unique in its involvement in plant, fungal, as well as animal circadian clocks. We propose that this reflects an ancient, conserved function for CK2 in circadian clocks. CK2 and other clock genes have been implicated in cellular responses to DNA damage, particularly those induced by ultraviolet (UV) light. The finding of a dual function of CK2 in clocks and in UV responses supports the notion that clocks evolved to assist organisms in avoiding the mutagenic effects of daily sunlight.     

Phylogenetic positions of several amitochondriate protozoa

Several groups of parasitic protozoa, as represented by Giardia, Trichomonas, En-tamoeba and Microsporida, were once widely considered to be the most primitive extant eukaryotic group—Archezoa. The main evidence for this is their ‘lacking mitochondria’ and possessing some other primitive features between prokaryotes and eukaryotes, and being basal to all eukaryotes with mitochondria in phylogenies inferred from many molecules. Some authors even proposed that these organisms diverged before the endosymbiotic origin of mitochondria within eukaryotes. This view was once considered to be very significant to the study of origin and evolution of eukaryotic cells (eukaryotes). However, in recent years this has been challenged by accumulating evidence from new studies. Here the sequences of DNA topoisomerase II in G. lamblia, T. vaginalis and E. histolytica were identified first by PCR and sequencing, then combining with the sequence data of the microsporidia Encephalitozoon cunicul and other eukaryotic groups of different evolutionary positions from GenBank, phylogenetic trees were constructed by various methods to investigate the evolutionary positions of these amitochondriate protozoa. Our results showed that since the characteristics of DNA topoisomerase II make it avoid the defect of ‘long-branch attraction’ appearing in the previous phylogenetic analyses, our trees can not only reflect effectively the relationship of different major eukaryotic groups, which is widely accepted, but also reveal phylogenetic positions for these amitochondriate protozoa, which is different from the previous phylogenetic trees. They are not the earliest-branching eukaryotes, but diverged after some mitochondriate organisms such as kinetoplastids and mycetozoan; they are not a united group but occupy different phylogenetic positions. Combining with the recent cytological findings of mitochondria-like organelles in them, we think that though some of them (e.g. diplomonads, as represented by Giardia) may occupy a very low evolutionary position, generally these organisms are not as extremely primitive as was thought before; they should be polyphyletic groups diverging after the endosymbiotic origin of mitochondrion to adapt themselves to anaerobic parasitic life.     

Ribosome-Inactivating Proteins from Plants Inhibit Ribosome Activity of Trypanosoma and Leishmania1

Ribosomes from Trypanosoma brucei rhodesiense and from Leishmania infantum were isolated and optimal conditions for in vitro translation were established. The effect of ribosome-inactivating proteins extracted from several plants was then assessed in order to identify those suitable for the preparation of immunotoxins against these organisms. Ribosomes from both species were inactivated by some ribosome-inactivating proteins (dianthins, saporins, pokeweed antiviral proteins, and the ribosome-inactivating chain of abrin). The similarity of the effects on the ribosomes from the two species examined indicates that ribosome-inactivating proteins should also be effective in a similar way on ribosomes from other species of Trypanosoma and Leishmania.     

Fluid-mediated dispersal in streams: models of settlement from the drift

I propose proximal mechanisms that help explain, unify, and expand the predictions of widely accepted empirical models of settlement in streams. I separated the process that leads to settlement of a drifting particle into three stages: (1) initial contact with a substrate, (2) attachment, and (3) settlement sensu stricto. I used physical principles (height above the bed, sinking rate, current speed profile) to predict time until contact (stage 1). I compared these predictions with empirical measurements of settlement of individual black fly larvae (Simulium vittatum) in a laboratory flume. I developed models from empirical data for stages 2 and 3. Each of these models is individual-based and predicts the fate of a single individual. To obtain a population level prediction, models for the three stages were combined and used to simulate the settlement of a group of black fly larvae. The predictions of this simulation were qualitatively similar to population level data from the literature particularly after the incorporation of channel-wide spatial heterogeneity in current speed. The effect of flow heterogeneity on the model agrees with previous work on the lateral transport of stream invertebrates during drift events showing that many organisms settle preferentially in slower areas. By using proximal principles, the approach used in this study brings into focus basic parameters and processes that influence settlement at the scale of the organisms. It also provides a null hypothesis against which to study the effect of local flow heterogeneity on the settlement of stream invertebrates and the capacity of organisms to actively influence settlement. Water currents in streams and rivers commonly transport large numbers of organisms. Consequently, hydrodynamic factors that favor or hamper the settlement of these organisms can potentially influence distributions and abundance. Moreover, if settlement probabilities vary with flow characteristics, this can in turn influence foraging strategies that rely on fluid-mediated dispersal. Received: 9 January 1999 / Accepted: 8 June 1999     

Colony formation in Scenedesmus: a literature overview and further steps towards the chemical characterisation of the Daphnia kairomone

Semiochemicals play an important role in interactions between living organisms in aquatic environments. Although the presence of chemical cues is confirmed in more and more systems, the chemical structures remain predominantly elusive. To create more accurate prey–predator interaction models and to advance the research on chemical communication, it is essential to identify these compounds. A literature overview of cues involving Daphnia (either as producer or receiver) is given and the progress towards their isolation and structure elucidation is described. Most of the research so far has concentrated on the elucidation of kairomones produced by predators of Daphnia (especially Chaoborus and several species of fish). Although some progress has been made, these cues have not been isolated and identified yet. Additionally new results on the isolation and identification of the kairomone responsible for the colony formation in Scenedesmus using differential diagnosis and bioassay-directed fractionation of Daphnia exudates are presented. The importance of suitable and well performing bioassays herein cannot be underestimated. Some preliminary results with solid-phase extraction with C₁₈ proved to be reproducible for extracting the active compound from Daphnia water, although it was not possible to get the biological activity into a single fraction. The cue was not extractable with an anion exchanger (SAX). Subjecting the extract to HPLC led to one active fraction.     

Microarray analysis of Mu transposition in Salmonella enterica, serovar Typhimurium: transposon exclusion by high-density DNA binding proteins

All organisms contain transposons with the potential to disrupt and rearrange genes. Despite the presence of these destabilizing sequences, some genomes show remarkable stability over evolutionary time. Do bacteria defend the genome against disruption by transposons? Phage Mu replicates by transposition and virtually all genes are potential insertion targets. To test whether bacteria limit Mu transposition to specific parts of the chromosome, DNA arrays of Salmonella enterica were used to quantitatively measure target site preference and compare the data with Escherichia coli. Essential genes were as susceptible to transposon disruption as non‐essential ones in both organisms, but the correlation of transposition hot spots among homologous genes was poor. Genes in highly transcribed operons were insulated from transposon mutagenesis in both organisms. A 10 kb cold spot on the pSLT plasmid was near parS, a site to which the ParB protein binds and spreads along DNA. Deleting ParB erased the plasmid cold spot, and an ectopic parS site placed in the Salmonella chromosome created a new cold spot in the presence of ParB. Our data show that competition between cellular proteins and transposition proteins on plasmids and the chromosome is a dominant factor controlling the genetic footprint of transposons in living cells.     

Ontogenetic allometry of the bluemouth, <Emphasis Type="Italic">Helicolenus dactylopterus dactylopterus</Emphasis> (Teleostei: Scorpaenidae), in the Northeast Atlantic and Mediterranean based on geometric morphometrics

Since the emergence of the ‘microbial loop’ concept, heterotrophic flagellates have received particular attention as grazers in aquatic ecosystems. These microbes have historically been regarded incorrectly as a homogeneous group of bacterivorous protists in aquatic systems. More recently, environmental rDNA surveys of small heterotrophic flagellates in the pelagic zone of freshwater ecosystems have provided new insights. (i) The dominant phyla found by molecular studies differed significantly from those known from morphological studies with the light microscope, (ii) the retrieved phylotypes generally belong to well-established eukaryotic clades, but there is a very large diversity within these clades and (iii) a substantial part of the retrieved sequences cannot be assigned to bacterivorous but can be assigned instead to parasitic and saprophytic organisms, such as zoosporic true fungi (chytrids), fungus-like organisms (stramenopiles), or virulent alveolate parasites (Perkinsozoa and Amoebophrya sp.). All these microorganisms are able to produce small zoospores to assure dispersal in water during their life-cycles. Based on the existing literature on true fungi and fungus-like organisms, and on the more recently published eukaryotic rDNA environmental studies and morphological observations, we conclude that previously overlooked microbial diversity and related ecological potentials require intensive investigation (i) for an improved understanding of the roles of heterotrophic flagellates in pelagic ecosystems and (ii) to properly integrate the concept of ‘the microbial loop’ into modern pelagic microbial ecology.     

Utilization of aromatic compounds by phototrophic purple nonsulfur bacteria

Biodegradation of aromatic compounds byRhodopseudomonas blastica andRhodospirillum rubrum appears to be lacking in the literature. The above species grew phototrophically (illuminated anaerobic conditions) on a variety of organic compounds. They were found to degrade benzoate, benzyl alcohol, 4-hydroxy-3,5-dimethoxybenzoate (Syringate) and 4-hydroxy-3-methoxybenzoate (vanillate). The ability of the above species to photocatabolize aromatic compounds indicates that these organisms may be ecologically significant as scavengers of aromatic derivatives in illuminated anaerobic habitats in nature.     

Ediacaran developmental biology

Rocks of the Ediacaran System (635–541 Ma) preserve fossil evidence of some of the earliest complex macroscopic organisms, many of which have been interpreted as animals. However, the unusual morphologies of some of these organisms have made it difficult to resolve their biological relationships to modern metazoan groups. Alternative competing phylogenetic interpretations have been proposed for Ediacaran taxa, including algae, fungi, lichens, rhizoid protists, and even an extinct higher‐order group (Vendobionta). If a metazoan affinity can be demonstrated for these organisms, as advocated by many researchers, they could prove informative in debates concerning the evolution of the metazoan body axis, the making and breaking of axial symmetries, and the appearance of a metameric body plan. Attempts to decipher members of the enigmatic Ediacaran macrobiota have largely involved study of morphology: comparative analysis of their developmental phases has received little attention. Here we present what is known of ontogeny across the three iconic Ediacaran taxa Charnia masoni, Dickinsonia costata and Pteridinium simplex, together with new ontogenetic data and insights. We use these data and interpretations to re‐evaluate the phylogenetic position of the broader Ediacaran morphogroups to which these taxa are considered to belong (rangeomorphs, dickinsoniomorphs and erniettomorphs). We conclude, based on the available evidence, that the affinities of the rangeomorphs and the dickinsoniomorphs lie within Metazoa.     

Recent advances in genetic analyses of hyperthermophilic Archaea and Bacteria

Hyperthermophilic Archaea and Bacteria are an extraordinarily important class of organisms for which genetic tools remain to be developed. Unique technological obstacles to this goal are posed by the thermophilic and, in some cases, strictly anaerobic nature of these organisms. However, recent advances in the cultivation of hyperthermophiles, in the discovery of genetic elements for vector development, and in the construction of genetic markers point toward the achievement of this goal in the near future. Transformation protocols have already been reported for Sulfolobus and Pyrococcus, and plasmid-mediated conjugation was recently found in Sulfolobus. Plasmids are available for Sulfolobus, Pyrococcus, and the bacterial hyperthermophile Thermotoga, and these provide the bases for vector construction in these hosts. A Desulfurococcus mobile intron may provide a novel means to introduce genes into a variety of archaeal hosts. With full genome sequences of several hyperthermophiles available soon, genetic tools will allow full exploitation of this information to study these organisms in depth and to utilize their unique properties in biotechnological applications. Received: 27 January 1997 / Accepted: 24 April 1997     

Occurrence of the parasitic sea lamprey<Emphasis Type="Italic">Petromyzon marinus</Emphasis> on western North Atlantic right whales <Emphasis Type="Italic">Eubalaena glacialis</Emphasis>

Few data exist on the marine distribution and host organisms of the parasitic sea lamprey, Petromyzon marinus. Some observers have speculated that cetaceans serve as hosts for these fish based on scars, but few lamprey – cetacean interactions have been described in detail in the literature. Here we discuss 35 previously unreported records of sea lampreys that were observed while attached to western North Atlantic right whales, Eubalaena glacialis, during the period 1984 – 2002. Of these observations, 11 were photographically documented with images of sufficient quality to identify the lamprey as P. marinus based on morphological characteristics. The majority of the attachments were recorded in the Bay of Fundy during the summer months when P. marinus are preparing to spawn. It is unknown how lampreys might benefit from this association or what cost may be incurred by their right whale hosts. Feeding and transport are two possible reasons for the attachments.