bluuebunny/crossref_metadata_2025 huggingface dataset:
Site fidelity and homing behaviour of some kelp‐bed fishes
Authors: Hartney K. B.
Published: April 2005

Common species of kelp‐bed fishes including adult blacksmith Chromis punctipinnis, adult senorita Oxyjulis californica, and sub‐adult kelp bass Paralabrax clathratus were collected from two separate and isolated rocky reefs at Santa Catalina Island, California, U.S.A. where giant kelp Macrocystis pyrifera was present. After tagging, groups of fishes were either returned to their initial collection site or displaced to an alternative kelp‐bed site to measure site fidelity and homing behaviour. No tagged fishes that were returned to their initial collection sites and subsequently resighted, exhibited any movement to another reef suggesting that these fishes have a limited home range, and handling during capture and tagging had no effect on site fidelity. Of fishes translocated to alternative kelp‐bed sites, up to 80% of tagged senorita and 100% of tagged blacksmith that were resighted had returned to the site of their initial collection, indicating that these species are motivated and able to relocate previously utilized areas when displaced. However, when young‐of‐the‐year and juvenile kelp bass were displaced, none were ever seen again suggesting that disruption of the relationship between a young kelp bass and its home site may influence its survival.
Migratory behaviour of post‐smolt Atlantic salmon during initial stages of seaward migration
Authors: Lacroix G. L. , McCurdy P.
Published: April 2005

The movements of 24 hatchery‐reared Atlantic salmon Salmo salar smolts, with miniature acoustic transmitters (pingers) implanted surgically, were determined after release in the coastal waters of Passamaquoddy Bay (mean tide range 6 m), New Brunswick, Canada, to describe the first stages of seaward migration. Automated pinger detection at fixed sites, and pinger location and tracking by boat were used. Post‐smolts left the release area rapidly, and the majority moved to open waters of the bay within several tidal cycles. Initially, post‐smolts moved with a seaward orientation on ebb tides and held positions on flood tides. Their movements into open waters were diurnal, and the timing corresponded with the state of the tide during which they moved through a narrow channel. Post‐smolts moved preferentially through this passageway with the aid of the tidal stream. Successful movements out through the channel occurred during ebb tides and any movements back in were during flood tides. Ground speed of fish moving through the channel was 4·2 body lengths s−1 and faster than the tidal stream velocities in the channel. The relative velocity of fish swimming through the channel was 2 body lengths s−1. Post‐smolt movement was indicative of active, directed swimming with a reliance on ebb‐tide transport for migration through a coastal area with strong tidal currents. Some post‐smolts moved seaward directly with no apparent period of acclimation for the transfer to the marine environment, whereas others delayed their departure. These differences in behaviour were probably related to asynchrony in smolting when fish were released.
The use of pigmentation and morphological characters to identify Italian mullet fry
Authors: Serventi M. , Harrison I. J. , Torricelli P. , Gandolfi G.
Published: April 2005

Mullet fry from Italian coastal waters are examined to ascertain ontogenetic changes in pigmentation, external morphology, anal‐fin ray counts, and morphology of the pyloric caeca and pharyngobranchial organ. The taxonomic utility of these characters is assessed. Intraspecific and ontogenetic variation in anal‐fin ray numbers do not make this a consistently reliable character for identification purposes. Pharyngobranchial morphology can assist diagnoses of larger fry or juveniles; however, pigmentation patterns are the most reliable characters for smaller fry. Pigmentation characters, which can be used in laboratory‐ and field‐based studies, require minimal manipulation of the fish and enable rapid identification of large numbers of specimens. These techniques are valuable for aquaculturists and fish biologists requiring more information on the identification, distribution and life history of mugilids.
Short‐term thermal acclimation induces adaptive changes in the inner mitochondrial membranes of fish skeletal muscle
Authors: Kilarski W. M. , Romek M. , Kozlowska M. , Gorlich A.
Published: April 2005

In the oxidative muscles (musculi laterales superficiales) of crucian carp Carassius carassius acclimated for 6 weeks to either 5 or 25° C, the volume density and the surface density of fibres per tissue did not differ significantly between the control and experimental groups. The correlation ratio (μ2) for these values was below 50, 39·3 and 43·9 respectively. After acclimation to 5° C, the surface density of outer mitochondrial membrane per fibre increased significantly from 0·93 to 1·23m2 cm−3 in the summer population but dropped from 0·94 to 0·67 m2 cm−3 in the winter population. The surface density of outer mitochondrial membrane per mitochondrion increased from 3·24 to 4·52 m2 cm−3 in summer fish. After acclimation to 25° C, the surface density of inner mitochondrial membranes per muscle fibre decreased from 4·04 to 1·79 m2 cm−3 in summer fish and from 3·86 to 1·07 m2 cm−3 in winter fish. The surface density of inner mitochondrial membranes per mitochondrion increased from 14·17 to 15·60 m2cm−3 in summer fish but dropped from 13·91 to 10·67 m2 cm−3 in winter fish. Correlation matrices demonstrate a negative correlation of the surface density of outer mitochondrial membrane per mitochondrion with the volume density of mitochondria per fibre and temperature, suggesting cold‐induced proliferation of small mitochondria. It was concluded that short‐term cold acclimation increased surface area of the inner mitochondrial membranes in summer fish.
A UGT2B17‐positive donor is a risk factor for higher transplant‐related mortality and lower survival after bone marrow transplantation
Authors: Terakura Seitaro , Murata Makoto , Nishida Tetsuya , Emi Nobuhiko , Akatsuka Yoshiki , Riddell Stanley R. , Morishima Yasuo , Kodera Yoshihisa , Naoe Tomoki
Published: April 2005

We recently identified a human minor histocompatibility (H) antigen, encoded by UDP glycosyltransferase 2 family, polypeptide B17 (UGT2B17), whose immunogenicity results from differential expression in donor and recipient cells as a consequence of a homozygous deletion of the UGT2B17 gene. UGT2B17 is highly expressed in the liver and colon, which are major targets for graft‐versus‐host disease (GVHD). To assess the significance of homozygous UGT2B17 gene deletion in allogeneic haematopoietic stem cell transplantation (HSCT), we analysed DNA from 435 stem cell transplant recipients with a haematological malignancy and their human leucocyte antigen‐identical unrelated bone marrow donors using sequence‐specific primer polymerase chain reaction. Homozygous deletion of the UGT2B17 gene was observed in 85% of normal donors and in 82% of patients. The analysis showed no significant association between UGT2B17 mismatch in the GVHD direction and the incidence of acute GVHD, chronic GVHD, relapse, or survival. However, the use of a UGT2B17‐positive donor was an independent risk factor for higher transplant‐related mortality and lower survival after transplantation. UGT2B17 is a metabolic enzyme for hormones, drugs, and potentially toxic exogenous compounds and is expressed in subsets of haematopoietic cells. Thus, the enzyme function of UGT2B17 in donor cells may affect the outcome of allogeneic HSCT.
Serum thymus and activation‐regulated chemokine, macrophage‐derived chemokine and eotaxin as markers of severity of atopic dermatitis
Authors: Jahnz‐Rozyk K. , Targowski T. , Paluchowska E. , Owczarek W. , Kucharczyk A.
Published: April 2005

Background:  Expression of CCR4 ligands, such as thymus and activation‐regulated chemokine (TARC) and macrophage‐derived chemokine (MDC), leads to preferential influx of T‐helper (Th) 2‐type lymphocytes to the lesional skin in atopic dermatitis (AD). Eotaxin, like the CCR3 ligand, is an important contributor of eosinophils recruitment in the course of AD. These chemokines are assumed to play an important role in the patomechanism of AD.

Methods:  In this study, the serum concentration of TARC, MDC, eotaxin and total immunoglobulin E (IgE) in AD patients and healthy people were compared. Correlation between the studied indices and activity of AD was established. Severity of AD was assessed according to the SCORAD score. The study comprised 44 healthy people and 43 patients with AD. The serum concentrations of TARC, MDC, eotaxin and IgE were measured with the use of enzyme‐linked immunosorbent assay kits.

Results:  The serum levels of TARC, MDC, eotaxin and IgE appeared to be significantly higher in patients with AD than in healthy people. A strong positive correlation was revealed between the levels of TARC, MDC, total IgE in serum of patients with AD and SCORAD. In contrast, no significant relationship was found for the serum eotaxin concentration and TARC, MDC, IgE or disease severity.

Conclusion:  Our findings indicate that TARC and MDC are actively involved in the pathogenesis of AD and their expression, opposite to that of eotaxin, is strongly associated with clinical picture of atopic dermatitis.
Current issues regarding the use of pneumococcal conjugate and polysaccharide vaccines in Australian children
Authors: Mackenzie Grant A , Carapetis Jonathan R , Morris Peter S , Leach Amanda Jane
Published: April 2005

Objective:  To present the results of child pneumococcal vaccination studies in the setting of current Australian disease epidemiology and immunization policy, and issues that clinicians should consider in discussions with families.

Methods:  This paper includes a narrative review of randomized, controlled, double blind studies and systematic reviews which evaluated the efficacy of child pneumococcal vaccination.

Results:  7PCV is expected to prevent >80% of childhood invasive pneumococcal disease (IPD, includes meningitis, septicaemia/bacteraemia) and the associated mortality. 7PCV may prevent 6% of all pneumonia, 18% of radiographically‐defined pneumonia, 6% of all otitis media (OM) and 20%–40% of tympanostomy tube procedures. It may also reduce IPD due to antibiotic‐resistant pneumococci, and prevent IPD in unvaccinated individuals. The impact of replacement disease caused by non‐vaccine serotypes is not yet known. Pneumococcal polysaccharide vaccines given to 2‐year‐old children may prevent approximately 19% of all and 26% of recurrent OM.

Conclusion:  The Australian Standard Vaccination Schedule recommends universal infant immunization with seven‐valent pneumococcal conjugate vaccine (7PCV). Universal infant 7PCV will prevent pneumococcal diseases and deaths. The potential for its impact to be reduced in the long‐term by serotype replacement must be closely monitored. Information concerning disease epidemiology, vaccine efficacy and safety, disease risk perception and national costs may prove useful in discussions with families.
Hepatic failure in a child with anti‐epileptic hypersensitivity syndrome
Authors: Li Albert M , Nelson Edmund AS , Hon Ellis KL , Cheng Frankie WT , Chan Dorothy FY , Sin Ngai Chuen , Ma Kwok Chiu , Cheung Kam Lau , Fok Tai Fai
Published: April 2005

Abstract:  An 11‐year‐old boy developed severe hypersensitivity reaction to phenobarbitone resulted in fulminant hepatic failure. During the course of illness, he developed clinical features compatible with severe acute respiratory syndrome (SARS) that may have complicated the recovery of his underlying hypersensitivity reaction, which was subsequently controlled with intravenous immune globulin and corticosteroids.
Cerebral thrombosis in childhood nephrosis
Authors: Gangakhedkar Arun , Wong William , Pitcher Lydia A
Published: April 2005

Abstract: Sinovenous thrombosis is an uncommon but serious complication associated with nephrotic syndrome in children. We describe a 9‐year‐old Caucasian boy who presented with dehydration, vague neurological symptoms and seizures. A diagnosis of nephrotic syndrome was made during the course of hospitalization. The serum antithrombin III level was decreased and brain imaging showed cerebral sinovenous thrombosis. Anticoagulant therapy with heparin was commenced and the patient made a slow but gradual clinical, as well as radiological recovery. We describe this case and review available literature to highlight the importance of suspecting and recognizing this potentially life threatening complication and initiating early treatment.
Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing
Authors: Larue Ross , Yu Zhongtang , Parisi Victoria A. , Egan Adrian R. , Morrison Mark
Published: April 2005

It is well recognized that a dynamic biofilm develops upon plant biomass in the herbivore gastrointestinal tract, but this component of the microbiome has not previously been specifically sampled, or directly compared with the biodiversity present in the planktonic fraction of digesta. In this study, the digesta collected from four sheep fed two different diets was separated into three fractions: the planktonic phase, and the microbial populations either weakly or tightly adherent to plant biomass. The community DNA prepared from each fraction was then subjected to both ribosomal intergenic spacer analysis (RISA) and denaturing gradient gel electrophoresis (DGGE). Both types of analysis showed that dietary factors influence community structure, and that the adherent fractions produced more complex profiles. The RIS‐clone libraries prepared from the planktonic and adherent populations were then subjected to restriction fragment length polymorphism (RFLP) and DNA sequence analyses, which resulted in a far greater degree of discrimination among the fractions. Although many of the sequenced clones from the adherent populations were assigned to various clusters within the low G+C Gram‐positive bacteria, the clone libraries from animals consuming an all‐grass diet were largely comprised of novel lineages of Clostridium, while in animals consuming the starch‐containing diet, Selenomonas and Ruminococcus spp. were the dominant low G+C Gram‐positive bacteria. Additionally, the libraries from hay‐fed animals also contained clones most similar to asaccharolytic Clostridia, and other Gram‐positive bacteria that specialize in the transformation of plant phenolic compounds and the formation of cinnamic, phenylacetic and phenylpropionic acids. These results reveal, for the first time, the phylogeny of adherent subpopulations that specialize in the transformation of plant lignins and other secondary compounds, which potentiate polysaccharide hydrolysis by other members of the biofilm.
Phenotypic characterization of Rice Cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture
Authors: Kemnitz Dana , Kolb Steffen , Conrad Ralf
Published: April 2005

A so far uncultured member of the Euryarchaeota was enriched from an anoxic riparian soil and phenotypically characterized using quantitative polymerase chain reaction (qPCR; ‘real‐time PCR’). The microorganism is related to the Thermoplasmatales and belongs to Rice Cluster III (RC‐III). Enrichment cultures utilized yeast extract (YE) by transiently accumulating acetate as major fermentation product, which was subsequently converted to methane. The abundance of RC‐III archaea within the enrichment cultures was quantified by analysis of the terminal restriction fragment length polymorphism (T‐RFLP) and by qPCR. We developed qPCR assays targeting the 16S rRNA genes (16S rDNA) specific for RC‐III as well as for the Archaea in general. The enrichment cultures consisted of a mixed methanogenic community of Bacteria and Archaea, the latter consisting of up to 60% of members of RC‐III. The other archaea belonged to Methanosarcinaceae, Methanomicrobiaceae and Methanobacteriaceae. The enriched RC‐III archaea were represented by two sequences (LL25A, LL37A) that were highly similar to each other and to those detected in the soil inoculum (>98% similarity). However, the 16S rDNA copy numbers of RC‐III archaea were about 1000‐fold lower than those of Bacteria. Nevertheless, we were able to estimate growth parameters and physiological properties of one of the enriched RC‐III archaea (LL25A) by measuring the increase of 16S rDNA copy numbers specific for this group under different growth conditions. The enriched RC‐III archaeon grew optimally at temperatures between 20 and 30°C and neutral pH using YE, meat extract, peptone or tryptone under anoxic conditions. Doubling time was approximately 3 days. No proliferation was detected on carbohydrates, amino acids, fatty acids, glycerol, alcohols, aromatic compounds, purine and pyrimidine bases or pyruvate. Various exogenous electron acceptors (e.g. ferric iron, S0) did not support growth on YE. Proliferation of  the  enriched  RC‐III  archaeon  was  hardly  affected by the antibiotics ampicillin, kanamycin and streptomycin. These findings suggest that the enriched archaeon is a mesophilic anaerobe, which can grow heterotrophically on peptides. Further enrichment on peptone and kanamycin eventually allowed the microscopic detection of coccoid cells stained by fluorescence in situ hybridization (FISH).
Adult non‐biting midges: possible windborne carriers of Vibrio cholerae non‐O1 non‐O139
Authors: Broza Meir , Gancz Hanan , Halpern Malka , Kashi Yechezkel
Published: April 2005

Vibrio cholerae is a waterborne bacterium native to the aquatic environment. There are over 200 known serogroups yet only two cause cholera pandemics in humans. Direct contact of human sewage with drinking water, sea‐born currents and marine transportation, represent modes of dissemination of the bacteria and thus the disease. The simultaneous cholera outbreaks that occur sometimes in distant localities within continental landmasses are puzzling. Here we present evidence that flying, non‐biting midges (Diptera; Chironomidae), collected in the air, carry viable non‐O1 non‐O139 serogroups of V. cholerae. The association of V. cholerae with chironomid egg masses, which serve as a V. cholerae reservoir, was further confirmed. In simulated field experiments, we recorded the transfer of environmental V. cholerae by adult midges from the aquatic environment into bacteria‐free water‐pools. In laboratory experiments, flying adult midges that emerged from V. cholerae (O1 or O139) contaminated water transferred the green fluorescent protein (GFP)‐tagged pathogenic bacteria from one laboratory flasks to another. Our findings show that aerial transfer by flying chironomids may play a role in the dissemination of V. cholerae in nature.
Morphological and Molecular Investigations of Tubulinosema ratisbonensis gen. nov., sp. nov. (Microsporidia: Tubulinosematidae fam. nov.), a Parasite Infecting a Laboratory Colony of Drosophila melanogaster (Diptera: Drosophilidae)
Authors: FRANZEN CASPAR , FISCHER SUSANNE , SCHROEDER JOSEF , SCHÖLMERICH JÜRGEN , SCHNEUWLY STEPHAN
Published: April 2005

Abstract. A new species of microsporidia from Drosophila melanogaster was investigated by light and electron microscopy and by ribosomal RNA (rRNA) sequencing. This microsporidium and the previously described Nosema kingi and Nosema acridophagus have been transferred to the new genus Tubulinosema gen. nov. with the following characters: nuclei are in diplokaryotic arrangement during the life cycle. All stages are in direct contact with the host cell cytoplasm, slightly anisofilar polar tube with the last coils being smaller in diameter arranged in one or two rows on both sides of the diplokaryon and small tubuli on the surface of late meronts. Spores are oval or slightly pyriform. Thick endospore wall, thinner over anchoring disc. This new genus and the genus Brachiola have been placed in a new family Tubulinosematidae fam. nov. Phylogenetic analysis of small subunit rRNA sequences by different methods placed Tubulinosema spp. in one clade with the genus Brachiola forming its sister clade, which is distant from the clade containing the true Nosema spp. including Nosema bombycis.
A molecular perspective on the phylogeny of amoeboid protists
Authors: BERNEY CÉDRIC , PAWLOWSKI JAN
Published: April 2005

The origin of amoeboid protists is one of the greatest enigmas of eukaryotic phylogeny. Although it has long been accepted that amoeboid protists are polyphyletic, the lack of molecular data for many amoeboid taxa impeded their placement in the tree of life. We have sequenced the small‐subunit ribosomal RNA and actin genes from a broad taxonomic sampling of amoeboid protists, including three lineages of heliozoans (Actinophryida, Desmothoracida, and Taxopodida) and one lineage of radiolarians (Phaeodarea) for which no molecular data were available yet. Phylogenetic analyses of our data show that (1) all lobose amoebae sequenced to date belong to the recently defined phylum Amoebozoa and (2) Heliozoa and Radiolaria both represent polyphyletic assemblages, as suggested by previous ultrastructural studies. However, although axopodia evolved at least five times independently during the evolution of eukaryotes, our study also reveals that most protists possessing filopodia, reticulopodia, and/or axopodia are closely related, and constitute a new supergroup of amoeboid protists, the Rhizaria.
Genotypic identification and species names in Acanthamoeba: correlation and conflict
Authors: BOOTON GREGORY C. , KELLY DARYL J. , FUERST PAUL A.
Published: April 2005

Many named isolates of Acanthamoeba, e.g. isolates designated Acanthamoeba polyphaga, are used widely in studies of pathogenicity, and other biological characters. However, molecular analyses show that isolates designated A. polyphaga are polyphyletic. Isolates may be very dissimilar at the molecular level, but share a species name, leading investigators to believe that they should share biological characteristics. Here, we present a summary of the correlation in Acanthamoeba between genotypes and the named species of this genus. Analyses of sequences of the nuclear small subunit ribosomal RNA gene (ssu rDNA) have identified at least fifteen genotypes of the free‐living ameba genus Acanthamoeba. Genotype determination has been defined by a sequence dissimilarity of five percent or greater in pairwise sequence comparisons. The ssu rDNA genotypes correlate well with many of the named species of Acanthamoeba. However, in some cases a species name exists as an invalid synonym of other species names within monophyletic genotypic clades. In addition, numerous species names are associated with the large and widely distributed Acanthamoeba genotype T4. Using molecular examination, some of these species designations are shown to be polyphyletic. The genotypes identified by nuclear ssu rDNA are supported by the addition of data from the mitochondrial ssu rDNA, which also provide some resolution of clades within genotype T4. Some lineages within the T4 genotype are associated with named species. Robust identification of Acanthamoeba isolates, including molecular data such as genotypic designation, is required so that data from studies on physiology or pathology may be correctly interpreted.
Protistan diversity in the Ross Sea, Antarctica: linking genotype, morphology and physiology
Authors: GAST REBECCA J. , MORAN DAWN M. , DENNETT MARK R. , ROSE JULIE M. , CARON DAVID A.
Published: April 2005

Traditional microscope‐based studies of protistan assemblages in the Ross Sea, Antarctica have contributed significantly to our understanding of the microbial biogeography and food web structure in this extreme cold‐water environment. However, these investigations have neither been able to characterize the genetic diversity of the communities, nor have they necessarily determined the abundances or trophic contribution of the dominant organisms. Resolution of the latter issue is hindered by the fact that physiological studies are often conducted on opportunistic species that respond to enrichment culture rather than species truly representative of intact communities. Therefore, we sought to determine the genetic diversity of microbial eukaryotes in ice, water and slush samples from the Ross Sea, and establish both morphologic and physiologic links between enrichment cultures and the genetic data. Denaturing gradient gel electrophoresis and ribosomal clone library analyses indicate that the protistan communities are very diverse, but those present in similar habitats are more alike than those in different habitats at the same site. We have been able to identify several protists from our enrichment cultures as being genetically represented in the original samples. General studies of their physiology have been initiated and methods for determining their abundances are being developed.
A high percentage of Euplotes genes require a +1 translational frameshift for expression
Authors: KLOBUTCHER LAWRENCE A. , MOLLENBECK MATTHIAS , GAVIN MICHAEL C. , FARABAUGH PHILIP J.
Published: April 2005

A previous survey of Euplotes genes available in GenBank indicated that >5% required a +1 translational frameshift for expression, much higher than observed in other organisms. Because this sample of sequences was non‐random and biased towards highly expressed genes, we have randomly selected and sequenced 25 Euplotes crassus macronuclear DNA molecules to more accurately assess the frequency of frameshifting. Three new +1 frameshift genes were identified, and all have sequence features similar to the previously postulated frameshift sites. The results indicate that the frequency of Euplotes+1 frameshift genes is indeed high, and likely >10%. We have also examined the evolution of one of two frameshift sites present in the telomerase reverse transcriptase (TERT) genes of E. crassus. TERT gene segments were isolated from five additional Euplotes species. FS2 was found only in E. crassus and the closely related E. vannus, and phylogenetic analyses indicate that the site arose late in the evolution of the Euplotes group. Moreover, a novel frameshift site (FS3) was identified solely in the TERT gene of E. minuta. These results indicate that frameshift sites have arisen within genes during the recent history of Euplotes, and that it may be an ongoing process. Overall, the data suggest to us that the appearance of a frameshift site in a Euplotes gene is selectively neutral, or near‐neutral. This would require an efficient mechanism of frameshifting in Euplotes. A model will be presented linking frequent frameshifting to a second unusual genetic feature of Euplotes, stop codon reassignment.
Protistan communities of the the Great Barrier Reef
Authors: LANGLOIS G. A.
Published: April 2005

Studies conducted at the Heron Island Research Station, located on the Capricorn region of the Great Barrier Reef, characterized complex protistan communities. Heron Reef is home to around 72 percent of the coral species found on the Great Barrier Reef. The paper will emphasize the diversity of ciliates found in benthic and epiphytic samples and will focus on the interactive role of the protistan component of the reef, including ciliates implicated in coral diseases that occur following bleaching episodes. Samples were taken by direct capture, observed with phase contrast and epifluorescent microscopy, and recorded by video and photomicrographic methods.
Gene expression in the dinoflagellate Karenia brevis: Analysis of an expressed sequence tag (EST) library and development of an oligonucleotide microarray
Authors: LIDIE KRISTY B. , RYAN JAMES C. , VAN DOLAH FRANCES M.
Published: April 2005

Karenia brevis (Davis) is a unicellular dinoflagellate responsible for nearly annual “red tides” in the Gulf of Mexico. Insight into the molecular mechanisms that control growth, toxicity, and adaptive mechanisms in K. brevis is critical to understanding the formation and persistence of these toxic blooms. However, little information is available on the molecular biology K. brevis. Therefore, we constructed a cDNA library from which to gain insight into its expressed genome and to develop tools for studying gene expression. Large‐scale sequencing of 9728 clones yielded 7001 high‐quality expressed sequence tags (ESTs) for further analysis. The highest expressed gene accounts for only 1% of the total ESTs. Approximately 29% of ESTs were found to have homology to known sequences in other organisms after BLASTx similarity comparisons to the Genbank nonredundant database (p<10−4). Using a minimum identity of 95% within a 50‐bp region of overlap, the 7001 ESTs were assembled into 5054 contigs. Of the 5054 contigs, 4399 contained only a single sequence. Of those containing >2 ESTs, approximately 40% displayed single nucleotide polymorphisms, suggesting the presence of multiple gene copies in this haploid organism. Gene‐specific 60‐mer oligonucleotides were then designed for each of the 5054 contigs using a Parcel clustering package, version 2.2.8 (Agilent). The resulting oligonucleotides and controls were printed on glass slides to yield an 8000 feature array using inkjet printing technology (Agilent). The 8000 features included 5054 unique features and 2946 secondary probes. Validation experiments to assess system noise, reproducibility, log ratio accuracy, and differential gene expression are underway using Agilent Feature Extraction tools and Rosetta Luminator Gene Expression Analysis software.
Food uptake in the mixotrophic Dinophysis acuminata
Authors: MARANDA LUCIE , GRASON EMILY W. , RINES JAN E.
Published: April 2005

Evidence of food uptake in the photosynthetic genus Dinophysis comes solely from the presence of food vacuoles, as no photosynthetic cells have ever been observed in the act of feeding. We examined the feeding ecology of D. acuminata in natural populations and under laboratory conditions. Using depth‐integrated sampling of the water column, we determined the frequency of food vacuolated cells at 2‐h intervals over a 24‐h period in a shallow marine embayment. Food vacuoles in preserved cells were enumerated using Nomarski differential interference contrast microscopy; ultrastructural characters were recorded by transmission electron microscopy. A peak in the feeding activity was observed toward dusk for an abundant June population, with 26% of cells with at least one food vacuole. Mechanisms of concurrent carbon acquisition were evident from the presence of chloroplasts with starch grains and food vacuoles within the same cell. Vacuole content could not be identified. In a preliminary 2‐wk long simulated grazing experiment, a mixture of two hypothesized preys, Rhodomonas salina and Dunaliella tertiolecta, was offered to D. acuminata; the Dinophysis populations decreased steadily and at the same rate, whether food was present or not. The evaluation of the food vacuole frequency will be repeated in the coming season to verify the observed pattern, while grazing experiments will include a variety of food items and incubation conditions. Our current inability to successfully culture any photosynthetic Dinophysis limits ecophysiological approaches, either at the population or cellular level, to manipulation of field samples.

Supported by National Institutes of Health Grant GM62126‐01A1.
In the land of the blind, one‐eye is king: ecology of the mixotrophic ciliates Strombidium oculatum and Strombidium stylifer
Authors: MCMANUS GEORGE , ZHANG HUAN , LIN SENJIE , KATZ LAURA , PIROG KATARZYNA A.
Published: April 2005

Strombidium oculatum and Strombidium stylifer live in tide pools at mid‐latitudes on both sides of the North Atlantic Ocean. These “green” ciliates obtain chloroplasts from macroalgae, in particular from members of the Ulvophyceae, which they use for photosynthesis. Both ciliates also contain orange‐pigmented granules that are organized into an eyespot. These granules are probably also obtained from their prey, the motile swarmer cells of the algae. Strombidium stylifer has been cultivated in our laboratory on pieces of Ulva, as well as a variety of microalgae. Strombidium oculatum has resisted cultivation to date. S. stylifer is an obligate mixotroph, incapable of sustained growth either starved in the light or fed in the dark. The presence in the ciliates of algal‐derived organelles of photosynthesis and photodetection raises interesting questions about the behavior of both predator and prey, with light possibly being a critical integrating cue for their interaction.
Genetically mapping a Tetrahymena cloned and sequenced gene: ASI1
Authors: BARBEAU REBECCA A. , ORIAS EDUARDO , KARRER KATHLEEN M. , HAMILTON EILEEN
Published: April 2005

The Tetrahymena thermophila ASI1 gene encodes a leucine zipper protein that is upregulated during post‐zygotic development (Udani and Karrer 2002). AT‐rich sequence flanking chromosome breakage junctions in T. thermophila frequently contain insertion/deletion polymorphisms between inbred strains B and C3 that are amenable to genetic mapping. ASI1 contains one intron, which likewise is AT‐rich and presumably not under stringent selection. PCR‐amplification with intron‐flanking primers revealed a B‐C3 PCR product size polymorphism. The segregation pattern of B and C3 alleles of ASI1 in meiotic segregant panels showed that it maps to the linkage group JO6 on micronuclear chromosome 3R. The segregation pattern in a terminal assortant panel showed that ASI1 does not co‐assort with any previously mapped polymorphism. Comparison of the ASI1 sequence with the genome sequence database at TIGR showed that this locus is carried on a 0.98‐Mb sequence scaffold. Therefore mapping the ASI1 polymorphism has identified one additional genetically mapped and sequence‐tagged macronuclear chromosome and the corresponding sequence scaffold. DNA polymorphism‐tagged MAC chromosomes and sequence scaffolds should accelerate the co‐assortment mapping of mutant genes with interesting phenotypes to known sequence scaffolds, which will facilitate positional cloning and candidate gene identification.

Supported by NIH grant RR02931. Preliminary sequence data were obtained from The Institute for Genomic Research website.
Microzooplankton grazing on harmful dinoflagellate blooms: Are ciliates or heterotrophic dinoflagellates important?
Authors: STOECKER DIANE K. , JOHNSON MATTHEW D. , REAUGH MATTHEW , GUSTAFSON DANIEL E.
Published: April 2005

Microzooplankton grazing can be important in regulating growth of dinoflagellate populations, including species responsible for harmful algal blooms. In the Chesapeake Bay region, microzooplankton community grazing coefficients on small cell‐size dinoflagellates are often greater than potential gross growth coefficients of dinoflagellates, and thus grazing may prevent bloom formation. Who are the major microzooplankton grazers on small dinoflagellates? Ciliates or other dinoflagellates? Data from Chesapeake Bay and its tributaries indicate both; sometimes ciliates and sometimes dinoflagellates are the major grazers. The importance of ciliates and heterotrophic dinoflagellates varies with season and location, but often one group dominates the microzooplankton assemblage. Specific clearance and division rates of ciliates are higher than that of heterotrophic dinoflagellates, thus it could be expected that ciliates would be the dominant microzooplankton grazers. However, during summer, small heterotrophic dinoflagellates are often the dominant grazers on small dinoflagelllates in the mesohaline Bay. Differential predation by copepods on ciliates may be responsible for this pattern. When microzooplankton community grazing is less than dinoflagellate cell division, red tides may result. Thus, it is important to understand the factors controlling both ciliate and heterotrophic dinoflagellate populations and their grazing impacts.
A TFIIH Homologue Controls the Mutually Exclusive Expression of the Stage‐Specific Antigens of Trypanosoma brucei
Authors: LECORDIER L. , DEVAUX S. , WALGRAFFE D. , POELVOORDE P. , VANHAMME L. , PAYS E.
Published: April 2005

Antigenic variation in Trypanosoma brucei relies on a mono‐allelic control of the multiple variant surface glycoprotein (VSG) expression sites (ESs). A single ES is active in bloodstream forms (BF) and none are in insect‐specific procyclic forms (PF), where procyclin replaces the VSG. In PF, disrupting TbTFIIH by conditional RNAi of any of the Tbp44, TbXPD or TbXPB subunits, or by over‐expression of a TbXPD mutant, led to strong transcriptional stimulation in the beginning of the ESs. Both RNA elongation and mRNA production were up‐regulated. This effect was linked to inhibition of procyclin, and occurred irrespective of the various cellular phenotypes, some of which were lethal due to cell cycle arrest. In BF, stimulation of procyclin was linked to inhibition of the active ES. Thus, TbTFIIH is involved in the mutually exclusive expression of the VSG and procyclin transcription units, both of which are transcribed by RNA Pol I.
Functional Genomics of Plasmodium falciparum: a new approach for identifying therapeutic targets against malaria
Authors: LE ROCH K. G. , ZHOU Y. , JOHNSON J. R , YOUNG J. , KIDGELL C. , WINZELER E.
Published: April 2005

In 1996, an international consortium was established to determine the sequence of the 26 Mb Plasmodium falciparum genome. Six years later, the genome sequence was published with an estimation of 5,268 genes. However, 60% of these predicted genes encode hypothetical proteins that share little or no sequence similarity with proteins from other organisms. Elucidation of function using traditional forward and reverse genetic techniques with these hypothetical P. falciparum genes is proving challenging and time consuming. As a result, high‐throughput genomic and proteomic techniques have emerged as important tools to elucidate gene function more rapidly and cost‐effectively. Despite the major challenges posed by the wealth of data generated by high‐throughput genomics and proteomics, we have developed methods to optimize the analysis of these large data sets. Here, we describe how we interpret the data to generate biologically relevant conclusions, which will improve the general understanding of the biology of the malaria parasite as well as lead to the identification of new promising targets for drug and vaccine developments.
Identification of a Novel Basal Body Protein of Trypanosoma brucei: a Role in the Cell Cycle?
Authors: PRADEL L. , BONHIVERS M. , ROBINSON D. R.
Published: April 2005

All eukaryote cells have cell cycle stages through which they must pass in order to undergo growth, development and division (e.g. G1, S, G2, M, and C). Transition through these stages is controlled by numerous proteins, including cyclin‐dependent kinases. Trypanosoma brucei is a parasitic protozoan of global, medical and agricultural importance that does not have many of the classical cell cycle checkpoints found in other eukaryotes such as cell arrest when mitosis is blocked. However, previous work has identified flagellum basal body separation as a novel cell cycle checkpoint in this organism. Essentially, if basal bodies do not separate cell division is blocked. From in silico database searches we have identified a T. brucei protein (we have named TbNEK1), with high homology to NIMA‐related kinase family of proteins of Aspergillus nidulans. We have cloned, expressed and made antibodies to this protein, which is located to the basal bodies. In vivo over‐expression of TbNEK1 in T. brucei induces cell cycle modifications resulting in the formation of multiple basal bodies, loss of kinetoplast segregation, multinuclated cells and cell division block. These results suggest the role of TbNEK1 is, in part, to modulate basal body replication or function, which subsequently leads to secondary effects that block progression through the cell cycle.
Characterization and Functional Analysis of HMG Proteins in Plasmodium falciparum
Authors: BRIQUET S. , GISSOT M. , BOSCHET C. , TISSANDIE E. , VAQUERO C.
Published: April 2005

Little is known about regulation of gene expression in Plasmodium. Indeed, only few regulatory elements and no clearly defined transcription factors have been reported, so far. In order to evaluate the interplay between cis‐ and trans‐acting elements controlling the regulation of transcription, we annotated several High Mobility Group proteins of the HMGB superfamily containing one or two HMG‐box(es) of 80 aa consisting of three α‐helices arranged in L‐shaped configuration. These computational analyses suggest that the Plasmodium proteins (PfHMG1‐4) might function as architectural factors through their ability to bind DNA in a structure‐specific manner and to induce bending of DNA. PfHMG1 (97 aa) was cloned from the genomic DNA of the 3D7 clone. The protein was expressed in E. coli and antibodies were raised in mice. A messenger of 1.3 kb was characterised by Northern blotting of 3D7 total RNA. Temporal expression of the transcript and protein was examined in two Plasmodium clones, 3D7 and F12 its gametocyte‐less derivative. The transcript appeared to be developmentally regulated throughout the erythrocytic cycle of Plasmodium as well as the protein present in the nuclear extracts. The functional analysis of the recombinant PfHMG1 via EMSA with synthetic fourway DNA junctions and ligase‐mediated circularisation assays showed that the factor is a genuine architectural protein. In addition, the functional analyses of two other factors PfHMG3 and PfHMG4 are underway. The sequences of PfHMG1 and PfHMG3 are quite similar; however, pfhmg1 transcript is mainly expressed during erythrocytic asexual cycle in contrast to pfhmg3 preferentially expressed in the gametocytes.
The hyrax (Procavia capensis) is reservoir host of Leishmania tropica in northern Israel
Authors: SVOBODOVA M. , VOTYPKA J. , KRAVCHENKO V. , ASHFORD R. W. , WARBURG A.
Published: April 2005

In order to identify a reservoir host of Leishmania tropica, we have trapped mammals in a cutaneous leishmaniasis focus in the Galilee region of Northern Israel. During May 2003, racoon traps (in total 275 in 11 nights) and Sherman traps (in total 170 in 8 nights) were put in boulders surrounding four endemic villages. In total, 34 hyraxes (Procavia capensis), 32 spiny mice (Acomys cahirinus) andone house mouse (Mus domesticus) were caught. Biopsies were taken from anaesthesized animals, which were released after recovery. Parasites were isolated from the nose of one hyrax. The strain was typed as L. tropica and was identical with previous isolates from patients and sand flies originating from the focus. Biopsies from other hyraxes and mice (ear biopsy) were culture and PCR negative, while PCR from the infected hyrax was positive. Previously, L. tropica DNA was detected in two hyraxes trapped in the focus but parasites were not isolated. Thus, we have confirmed the potential of hyraxes to serve as reservoir hosts. After inoculation of the hyrax strain into the ear of spiny mice, 2/4 animals were culture‐positive, and 5/5 were PCR positive. Moreover, parasite DNA was detected not only in the inoculation site, but also in the nose and hind foot of one Acomys. L. tropica is thus able to disseminate in its host. Differences in biology between the two most abundant mammals in the focus are probably the reason why the hyrax, and not the spiny mouse, is a suitable reservoir of L. tropica.
The effect of heavy metals on the rumen ciliate Entodinium caudatum
Authors: MIHALIKOVÁ K. , JAVORSKY P. , VÁRADYOVÁ Z. , KISIDAYOVÁ S.
Published: April 2005

The effect of three heavy metals on the growth of the rumen ciliate Entodinium caudatum was studied in vitro. The Entodinium caudatum (E.c.) cells were treated with mercury (HgCl2), copper (CuCl2) and chromium (K2Cr2O7) for a period of 4–5 days. The tested concentrations of mercury and copper were 1, 5, 10, 20, 50 mg/l1 and concentrations of chromium were 2, 10, 20, 40, 100 mg/l. All experiments were performed under two different conditions: either in presence of intact bacterial population in culture or reduced bacterial population, when culture was treated by antibiotics. Concentration of Hg of 5–20 mg/l1 significantly decreased the concentration of E.c. cells at the end of experiment. The dose of 50 mg/l was lethal. Copper caused significant decrease in the E.c. cell concentration after exposure to 10–50 mg/l. No tested concentrations of copper resulted in culture death. Chromium was the most toxic metal. Concentration of 2–20 mg/l caused significant decrease in cell growth and concentrations of 40 and 100 mg/l were lethal. Cultures treated by antibiotics were more sensitive to tested heavy metals. It could be concluded that all heavy metals decreased the cell growth of E.c. at concentration from 5 mg/l.

The study was supported by funds from grant Agency for Science of the Slovak Academy of Sciences (2/3058/23, 2/3064/23) and funds from APVT grant (51012602).
Critical analysis of the topology and rooting of the parabasalian 16S rRNA tree
Authors: HAMPL V. , CEPICKA I. , FLEGR J. , TACHEZY J. , KULDA J.
Published: April 2005

The morphological classification of the protozoan phylum Parabasala is not in absolute agreement with the 16S rRNA phylogeny. However, there are strong indications that tree‐construction artifacts play a considerable role in the shaping of the 16S rRNA tree. We have performed rigorous analyses designed to minimize such artifacts using the slow–fast and taxa‐exclusion methods. The analyses, which included new sequences from the genera Monocercomonas and Hexamastix, in most respects confirmed the previously suggested tree topology and polyphyly of order Hypermastigida and family Monocercomonadidae but detected one artificial cluster of long branches (Trichonymphidae, Pseudotrichonymphidae, Hexamastix and Tricercomitus). The analyses also indicated that the rooting of the phylum Parabasala on the trichonymphid branch, as widely accepted, is doubtful and that reliable rooting on the basis of current data is likely impossible.
Effects of Time‐Variant Extremely‐Low‐Frequency (ELF) Electromagnetic Fields (EMF) on Cholinesterase Activity in Dictyostelium discoideum
Authors: AMAROLI ANDREA , TRIELLI FRANCESCA , BIANCO BRUNO , GIORDANO STEFANO , MOGGIA ELSA , DELMONTE CORRADO MARIA U.
Published: April 2005

Recently, we have shown the presence of molecules belonging to the cholinergic signalling system in the ciliate Paramecium primaurelia and in the sarcodine Dictyostelium discoideum. Propionylcholinesterase (PrChE) activity has been detected in single‐cell amoebae of D. discoideum, using cytochemical, electrophoretic, and spectrophotometric methods (Falugi et al., Chemosphere, 48:407–414, 2002; Amaroli et al., Europ. J. Protistol., 39:213–222, 2003). It has been suggested that this enzyme activity is involved in cell–cell and cell–environment interactions, as its inhibition by xenobiotic compounds affects cell migration and aggregation. In this work, we have spectrophotometrically evaluated the effect of an ELF‐EMF of 300 T, 50 Hz, on PrChE activity after exposure of single‐cell amoebae from 1 h up to 48 h at 22°C. The enzyme activity was inhibited significantly by 1‐h‐ and 3‐h exposures, whereas it was similar to the control value after a 4‐h exposure. A significant increase in PrChE activity was found after 5‐ and 24‐h exposures, while a decrease in PrChE activity appeared in 48‐h‐exposed samples. The increased PrChE activity detected in 24‐h‐exposed cells returned to the control value 24 h after transferring the amoebae to standard conditions. A delay in both migration and aggregation processes was observed in 3 h‐exposed cells, corresponding to a decreased PrChE activity. After a 24‐h exposure, a decrease in the fission rate and an increase in the cell size were found.