bluuebunny/crossref_metadata_2025_split huggingface dataset:
Foraminiferal evolution as revealed by β‐tubulin data
Authors: HABURA ANDREA , WEGENER LAURA , TRAVIS JEFFREY L. , BOWSER SAMUEL S. 
Published: April 2005

Foraminiferal taxonomy is traditionally based on morphological characteristics, particularly the structure and composition of the test (shell). Recently, a comprehensive SSU‐based molecular phylogeny confirmed some multi‐chambered foraminiferal groups while enhancing our understanding of the single‐chambered, or the so‐called “allogromiid”, taxa. However, some relationships, such as the origin of the foraminiferal order Miliolida, remain unresolved, suggesting an approach involving multiple data sources may improve understanding. Here, we discuss the evolutionary implications of β‐tubulin genes from several species of foraminifera. Foraminiferal β‐tubulin is highly divergent, possibly indicating a period of accelerated evolution of this gene at the base of the foraminiferal lineage, but it is well‐conserved within the group. We show its utility in helping to resolve the phylogenetic position of Miliammina fusca, a foraminiferan whose proper classification has been debated for 70 years. M. fusca is a morphological “chimera”, and we show that its placement in SSU trees is not particularly robust. However, β‐tubulin data assigns Miliammina to the Miliolida, some of whose members show a similar chamber coiling pattern. This placement agrees with an earlier observation that M. fusca's actin isoforms more closely resemble those of traditional milolids. This finding implies that test formation can revert from calcareous to agglutinated, suggesting a reexamination of some relationships inferred from the fossil record.Supported by NSF OPP0003639.
Cloning of mitichondrial cytochrome b gene from Pseudourostyla cristata by heat shock
Authors: LIU XINYING , MAO YONGZHEN , DANIEL LEE KAM‐LEN , JIN LIPEI 
Published: April 2005

The total RNA was extracted from Pseudourstyla cristata after 2 h of heat shock, and the cDNA was synthesized directly using Smart LD‐PCR. The amplified cDNA products showed a strong band around 1.5 kb. The products were purified, cloned and sequenced. The resulting full cDNA sequence had a total length of 1538 bp including 1068 bp of cytb gene and UTR at both sides and showed all of the expected features for a fully functional CYB. The predicted protein is 49% (30% identical) similar to Paramecium tetraurelia. The sequence predicts a UAA stop codon 207 nucleotides from the end of the transcript suggesting a 3′ UTR, unlike that of Paramecium tetraurelia. Prediction of transmembrane helices in the analysis of proteins indicates the expected eight transmembrane domains. The cytb gene expression profiles after heat shock and before heat shock were generated using quantitative real‐time PCR. After 2 h of heat shock, the cytb gene expression was significantly enhanced. This is the first report that shows complete cytb gene among hypotrichous ciliates. Currently, we are investigating whether the method of cloning cytb rapidly are fit for other hypotrichous ciliates so as to analyze their phylogenetic relationship.This work was supported by a grant from NSFC (No: 30370210) to L. P. JIN.
Phylogenetic position of the apostome ciliates tested using the small subunit rRNA gene sequence
Authors: LYNN DENIS H. , STRUEDER‐KYPKE MICHAELA , BRADBURY PHYLLIS C. 
Published: April 2005

Apostome ciliates are exclusively symbionts, typically of crustaceans. Their life cycles are complex, but show remarkable similarities to ophyroglenines and to other symbiotic oligohymenophoreans, particularly those that undergo microstome–macrostome transformations. The highly modified structures around the cytostome—the rosette and x, y, and z kineties—have made the assessment of homologies to other groups of ciliates difficult. A description of the apostome somatic kinetids with well‐developed overlapping kinetodesmal fibrils suggested affinities with hymenostomes (Bradbury 1966. J. Protozool., 13:591). Further analysis of the ultrastructural features of the oral region of the tomite of Hyalophysa demonstrated homologies to the paroral and adoral ciliature of hymenostomes, confirming these affinities (Bradbury 1989. J. Protozool., 36:95). To test this hypothesis, we proposed to sequence the small subunit rRNA (SSrRNA) genes of apostomes. Specimens of Gymnodinioides sp. were collected from molts of the amphipod Marinogammarus obtusatus collected off the coast of Eastport, ME. Seawater was decanted from the substrate upon which tomonts had settled, and the dish was flooded with 70% ethanol. The ethanol‐fixed ciliates were collected by a micropipette, rinsed with distilled water, and DNA was extracted using the modified Chelex® protocol. The SSrRNA genes were amplified by PCR, and sequences obtained in both directions. Initial BLAST searches of the GenBank databases clearly demonstrated affinities with oligohymenophorean ciliates, particularly scuticociliates. In preliminary phylogenetic analyses which use likelihood, distance and parsimony methods, this relationship was confirmed. However, the apostome sequence diverged basal to the Subclasses Astomatia and Scuticociliatia consistent with the assignment of a Subclass Apostomatia within the Class Oligohymenophorea. We have made collections of Hyalophysa chattoni and anticipate that the SSrRNA gene sequences of this genus will confirm the relationship of apostomes to the oligohymenophoreans.Funded by NSERC Canada Discovery Grant to D. H. L.
Two adjacent genes encoding copper‐induced‐type metallothioneins in Tetrahymena thermophila may have resulted from a relatively recent gene duplication
Authors: BAKSHANDEH ARTA , HAMILTON EILEEN P. , ORIAS EDUARDO 
Published: April 2005

Tetrahymena thermophila is a valuable model organism for the study of metallothioneins, which play important roles in the metabolism of essential metal ions and in heavy‐metal detoxification. Starting from a T. thermophila expressed sequence tag (EST) originally annotated as a Zn–Cu–Cd metallothionein (GenBank Acc #BM394105), we determined the genomic sequence corresponding to this EST and its flaking region. The sequence contains two adjacent genes encoding metallothioneins of the copper‐induced type: the MTT2 gene (submitted to GenBank by Boldrin et al. as Cu‐inducible while this work was in progress) and a second, novel gene (MTT4), located ∼1.4 kb downstream from and with same orientation as MTT2. Our entire sequenced segment is contained in the T. thermophila whole‐genome sequence recently completed at TIGR. Both MTT4 and MTT2 are intronless and encode two nearly identical proteins (two differences out of 108 amino acids). The 5′ and 3′‐flanking regions of both the metallothionein genes show significant sequence similarity as well, suggesting recent gene duplication. All glutamines use the CAA codon, reminiscent of codon usage observed in highly expressed Tetrahymena genes. MTT4 and MTT2 map to a 1.5‐Mb macronuclear chromosome from the right arm of micronuclear chromosome 2.Supported by NIH grant RR02931. Sequence data were obtained from The Institute for Genomic Research Tetrahymena website, http://www.tigr.org/tdb/e2k1/ttg/
The Tetrahymena thermophila genome sequence: 1. Genome‐wide uniformity of macronuclear chromosome copy number in spite of amitotic (random) copy distribution
Authors: ORIAS EDUARDO , SALZBERG STEVEN L. , DELCHER ARTHUR L. 
Published: April 2005

In Ciliates, the diploid, mitotic, genetically silent micronucleus is the cell's germline, while the macronucleus is the exclusive site of gene expression. Pre‐genomic studies in Tetrahymena thermophila have shown that

The macronucleus contains 250–300 chromosomes, derived from the five germline chromosomes;
G2 copies of each chromosome are distributed amitotically (randomly) during macronuclear division.

In heterozygotes, this results in the segregation of vegetative descendants expressing only one of the two alleles (assortment). Phenotypic assortment rate measurements for a handful of loci suggested a uniform macronuclear chromosome G1 copy number (∼45 per macronucleus; rDNA minichromosome excepted). The NIGMS/NSF‐supported, whole‐genome‐shotgun sequencing of the T. thermophila macronuclear genome was recently completed at TIGR. (Sequence and scaffold databases, and related resources, are publicly available for blasting or downloading without restriction at http://www.tigr.org/tdb/e2k1/ttg/). Analysis of the depth of sequence coverage shows that (rDNA excepted) at least 95%—and possibly all—of the macronuclear genome is in chromosomes with uniform copy number. This implies the existence of regulatory mechanisms that independently correct the number of copies of nearly 300 different chromosomes after random distribution at every cell cycle.Supported by NIH grant RR02931. Preliminary sequence data were obtained from The Institute for Genomic Research website.
Divergent β‐tubulins from foraminifera: Implications for microtubule assembly
Authors: WEGENER LAURA , TRAVIS JEFFREY L. , HABURA ANDREA , BOWSER SAMUEL S. 
Published: April 2005

Foraminifera utilize an unusual and very rapid microtubule assembly/disassembly system: a state transition between microtubules and helical filaments. The helical filament is an assembly polymorph that forms when the microtubule lattice uncoils into a ribbon of tubulin dimers connected only by lateral subunit/subunit bonds. An unusual β‐tubulin sequence, which may be implicated in this process, has previously been reported from the foraminiferan Reticulomyxa filosa. In order to determine the taxonomic distribution and possible significance of this tubulin isoform, we sequenced and analyzed β‐tubulin genes from a broad taxonomic range of foraminifera. These genes contain a large number of substitutions, conserved within the group, which may alter the biochemical properties of β‐tubulin, especially in regions involved in subunit/subunit binding between α‐ and β‐tubulin in the microtubule lattice. In particular, the M‐loop, which is intimately involved in lateral subunit binding, shows only 30% homology to the consensus sequence for eukaryotic β‐tubulins. Multiple regions identified to be involved in longitudinal contacts with α‐tubulin are also highly substituted. In contrast, the foraminiferal α‐tubulin is well conserved with its homologs in other organisms. We suggest that these alterations to the consensus eukaryotic β‐tubulin sequence may help to explain the unusual assembly properties of foraminiferal microtubules.This work was supported by NSF OPP0003639.
Diagnostics of Neospora caninum antibodies of bovine milk by ELISA
Authors: HURKOVÁ L. , HARAGÁLOVÁ D. , MODRY D. 
Published: April 2005

Neospora caninum (Apicomplexa: Sarcocystidae) is a coccidian parasite with a two‐host life‐cycle. Dogs and coyotes are definitive hosts. A wide spectrum of mammals serves as intermediate hosts (i.a. ruminants, horses, canids). The reproductive failures associated with abortion in cattle have an economic impact. A milk ELISA is a simple serological method for diagnostics of anti‐Neospora caninum antibodies in dairy herds. We used a commercial Neospora caninum iscom ELISA kit (Svanova, Sweden) designed to detect bovine Neospora‐specific antibodies in blood serum. We examined 332 dairy herds in the Czech Republic. Milk serum was examined at dilution 1:100 according to manufacturer's instructions. The number of milking cows in the examined herds varied, but never exceeded 200 per one bulk sample. Four out of 332 examined herds were significantly positive, the positive bulk milk samples were obtained from herds consisting of 7, 19, 35 and 98 cows. Hitherto, we have studied in detail the smallest herd. The milk and blood samples or only blood samples (in some animals, e.g. calves) were examined individually. We observed the correlation of positivity between milk and blood. Moreover, the mother‐descendant positivity/negativity was found. A dog living in the farm was examined, being coprologically negative but serologically positive (IFAT).This is the next proof of the occurrence of N. caninum in cattle in the Czech Republic. In addition, our results refer to an importance of transplacental transmission in cattle.
Oral hygiene: past history and future recommendations
Authors: Sgan‐Cohen Harold D 
Published: April 2005

Abstract:Review of the dental literature reveals a changing emphasis attached to maintenance of optimal oral hygiene among patients over time. Moreover, a different relationship to this topic has been evident in the USA, Britain and Scandinavia. These changes, differences, and the rationale behind them, are described. The age of initiating oral hygiene practice and the optimal frequency of dental cleaning is discussed. Finally, recommendations are offered concerning oral hygiene promotion, both at the individual and community levels.
Effects of Interaction Between Cadmium and Plumbum on Phytochelatins and Glutathione Production in Wheat (Triticum aestivum L.)
Authors: SUN Qin , WANG Xiao‐Rong , DING Shi‐Ming , YUAN Xin‐Fang 
Published: April 2005

Abstract: Phytochelatins (PCs) may function as a potential biomarker for metal toxicity. However, less attention has been paid to the effects of metal interactions on the production of PCs and glutathione (GSH), the most prominent cellular thiol. In the present study, the effects of interactions between cadmium (Cd) and plumbum (Pb) on the production of PCs and GSH were monitored over a period of 14 d in wheat (Triticum aestivum L.) tissues. The results showed that combination of Cd and Pb led to synergistic growth inhibition in wheat. Exposure to Cd or Pb increased levels of PCs in a concentration‐, tissue‐, and time‐dependent manner. Cadmium was more effective that Pb in increasing PCs production. Compared with the effects of Cd or Pb alone on the production of PCs, the combination of Cd and Pb acted synergistically, resulting in an enhanced production of PCs. Cadmium also stimulated GSH production in a concentration‐, tissue‐, and time‐dependent manner. However, Pb had no obvious effects on GSH levels. The combination of Pb and Cd antagonized GSH production over the course of the growth period. The results of the present study suggest that metal interactions should be considered in the application of PCs and GSH as potential biomarkers for the evaluation of metal toxicity.(Managing editor: Ping HE)
Effects of Exogenous Spermidine on Antioxidant System Responses of Typha latifolia L. Under Cd2+ Stress
Authors: TANG Chun‐Fang , LIU Yun‐Guo , ZENG Guang‐Ming , LI Xin , XU Wei‐Hua , LI Cheng‐Feng , YUAN Xing‐Zhong 
Published: April 2005

Abstract: The effects of foliar spraying with spermidine (Spd), ranging in concentration from 0.25 to 0.50 mmol/L, on the antioxidant system under Cd2+ stress (range 0.1–0.2 mmol/L Cd2+) in Typha latifolia L. grown hydroponically were investigated in order to offer a referenced evidence for an understanding of the mechanism by which polyamines (PAs) relieve the damage to plants by heavy metal and improve the phytoremediation efficiency of heavy metal‐contaminated water. The results showed that Cd2+ stress induced oxidative injury, as evidenced by an increase in the generation of superoxide anion (O2‐), as well as the hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents in both leaves and caudices. With the exception of superoxide dismutase (SOD) activity in the leaves, an increase in the activities of catalase (CAT), guaiacol peroxidase (GPX), and glutathione reductase (GR) was observed in both leaves and caudices, SOD activity was increased in caudices, and ascorbate peroxidase (APX) activity was increased in leaves following Cd2+ treatment. The reduced glutathione (GSH) content in both leaves and caudices and the reductive ascorbate content in leaves was obviously increased, which were prompted by the application of exogenous Spd. Spraying with Spd increased the activity of GR and APX in both leaves and caudices, whereas the activity of SOD, CAT, and GPX was increased only in caudices following spraying with Spd. The generation of O2 ‐. and the H2O2 and MDA content in both leaves and caudices decreased after spraying with Spd. The decrease in MDA was more obvious following the application of 0.25 than 0.50 mmol/L Spd. It is supposed that exogenous Spd elevated the tolerance of T. latifolia under Cd2+ stress primarily by increasing GR activity and the GSH level.(Managing editor: Ping HE)
Analysis of the Genetic Structure of Sclerotinia sclerotiorum (Lib.) de Bary Populations from Different Regions and Host Plants by Random Amplified Polymorphic DNA Markers
Authors: SUN Jun‐Ming , IRZYKOWSKI Witold , JEDRYCZKA Malgorzata , HAN Fen‐Xia 
Published: April 2005

Abstract: The genetic diversity and genetic structure of a population of isolates of Sclerotinia sclerotiorum (Lib.) de Bary from different regions and host plants were investigated using the random amplified polymorphic DNA (RAPD) method with 20 random decamer primer pairs in order to provide some information on the phylogenetic taxa and breeding for resistance to sclerotinia stem rot. A minimum of three and a maximum of 15 unambiguously amplified bands were generated, furnishing a total of 170 bands ranging in size from 100 to 3 200 bp, corresponding to an average of 8.5 bands per primer pair. One hundred and four of these 170 bands (61.2%) were polymorphic, the percentage of polymorphic bands for each primer pair ranging from 0.0% to 86.7%. The genetic relationships among the isolates, based on the results of RAPD analysis, were examined. The genetic similarity of all selected isolates was quite high. At the species level, the genetic diversity estimated by Nei's gene diversity (h) was 0.197 and Shannon's index of diversity (I) was 0.300. The unweighted pair‐group mean analysis (UPGMA) cluster analysis showed that most isolates from the same regions were grouped in the same cluster or a close cluster. The population of isolates from Hefei (Anhui Province, China) was more uniform and relatively distant to other populations. The Canadian population collected from carrot (Daucus carota var. sativa DC.) was relatively close to the Polish population collected from oilseed rape (Brassica napus L.) plants. There was no relationship between isolates from the same host plants. An analysis of molecular variance (AMOVA) revealed that the percentage of variance attributable to variation among and within populations was 50.62% and 49.38%, respectively. When accessions from China, Europe, and Canada were treated as three separate groups, the variance components among groups, among populations within groups, and within populations were −0.96%, 51.48%, and 49.47%, respectively. The genetic differentiations among and within populations were highly significant (P < 0.001). Similarly, the coefficient of gene differentiation (Gst) in total populations calculated by population genetic analysis was 0.229 4, which indicated that the genetic variation among populations was 22.94%. The gene flow (Nm) was 1.68, which indicated that the gene permutation and interaction among populations was relatively high.(Managing editor: Wei WANG)
Volatile Organic Compounds and Their Roles in Bacteriostasis in Five Conifer Species
Authors: GAO Yan , JIN You‐Ju , LI Hai‐Dong , CHEN Hua‐Jun 
Published: April 2005

Abstract: In order to make clear the functions of plant volatile organic compounds (VOCs) on bacteriostasis and air decontamination, we analyzed the composition and content of VOCs in Pinus tabulaeformis Carr., P. bungeana Zucc., Sabina chinensis Antoine, Picea koraiensis Nakai, and Cedrus deodara G. Don under near‐natural conditions using the thermal‐desorption cold trap gas chromatography/mass spectrometer technique. The effects of the VOCs on airborne microorganisms were investigated using the method of natural sedimentation. Results showed that the major VOCs were as follows: limonene, β‐pinene, α‐pinene, and α‐caryophyllene in Pinus tabulaeformis and P. bungeana; limonene, borneol acetate, β‐pinene, myrcene, and tricylene in S. chinensis; limonene, α‐pinene, myrcene, camphene, and β‐pinene in Picea koraiensis; and limonene, 2, (10)‐pinene, α‐pinene, and myrcene in C. deodara. These VOCs and the corresponding foliar extracts inhibited the growth of bacteria and stimulated the growth of fungi. Experimental data using monomers of the VOCs demonstrated that limonene, β‐pinene, and three aldehydes could significantly inhibit bacterial growth, suggesting an inhibitory effect of VOCs on the growth of airborne microorganisms in the five conifer species. The bacteriostasis and air‐decontaminating effects of plant VOCs are further discussed in terms of their chemical composition.(Managing editor: Wei WANG)
Vitamins A, C, and E and β‐Carotene Content in Seeds of Seven Species of Vicia L.
Authors: SAHIN Ahmet , KIRAN Yasar , KARATAS Fikret , SONMEZ Senem 
Published: April 2005

Abstract: To determine the vitamins A, C, and E and β‐carotene content of Vicia species that can be used in animal feed, a high performance liquid chromatography (HPLC) method was used to investigate the vitamin and β‐carotene content in mature and immature seeds of seven Vicia species (Vicia anatolica Turrill., V. ervilia (L.) Willd., V. michauxii Sprengel, V. mollis Boiss. et Hausskn. ex Boiss., V. noeana Reuter ex Boiss., V. peregrina L., and V. sericocarpa Fenzl.), which are useful plants in animal feed in the eastern Anatolia region in Turkey. The vitamin content was found to differ between mature and immature seeds. The levels of vitamins A, C, and E and β‐carotene were higher in mature seeds than in immature seeds (P < 0.01).(Managing editor: Wei WANG)
Dimethyl Sulfoxide Is Feasible for Plant Tubulin Assembly In vitro: A Comprehensive Analysis
Authors: XU Chun‐Hua , HUANG Shan‐Jin , YUAN Ming 
Published: April 2005

Abstract: It is much more difficult for tubulin from plant sources to polymerize in vitro than tubulin from animal sources. Taxol, a most widely used reagent in microtubule studies, enhances plant microtubule assembly, but hinders microtubule dynamics. Dimethyl sulfoxide (DMSO), a widely used reagent in animal microtubule studies, is a good candidate for the investigation of plant microtubule assembly in vitro. However, proper investigation is lacking about the effects of DMSO on plant microtubule assembly in vitro. In the present study, DMSO was used to establish optimal conditions for the polymerization of plant tubulin. Tubulin, purified from lily pollen, polymerizes into microtubules at a critical concentration of 1.2 mg/mL in the presence of 10% DMSO. The polymers appear to have a normal microtubule structure, as revealed by electron microscopy. In the presence of 10% DMSO, microtubule polymerization decreases when the pH of the medium is increased from 6.5 to 7.4. Both the polymerization rate and the mass of the polymers increase as temperature increases from 25 to 40 °C. Tubulin polymerizes and depolymerizes along with cycling of temperature, from 37 to 4 °C, or following the addition to or the removal of Ca2+ from the medium. When incubated with nuclei isolated from tobacco BY‐2 suspension cells, tubulin assembles onto the nuclear surface in the presence of 10% DMSO. Labeling lily pollen tubulin with 5‐ (and 6‐) carboxytetramethyl‐rhodamine succinimidyl ester (NHS‐rhodamine) was performed successfully in the presence of 10% DMSO. Labeled tubulin assembles into a radial structure on the surface of BY‐2 nuclei. The polymerization of lily pollen tubulin is also enhanced by microtubule‐associated proteins from animal sources in the presence of 10% DMSO. All the experimental results indicate that plant tubulin functions normally in the presence of DMSO. Therefore, DMSO is an appropriate reagent for plant tubulin polymerization and investigation of plant microtubules in vitro.(Managing editor: Li‐Hui ZHAO)