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At least 163 records · Page 9Linked to original sources
PubMed2006

Contrasting soil ciliate species richness and abundance between two tropical plant species: a test of the plant effect.

We still have a rudimentary understanding about the mechanism by which plant roots may stimulate soil microbial interactions. A biochemical model involving plant-derived biochemical fractions, such as exudates, has been used to explain this "rhizosphere effect" on bacteria. However, the variable response of other soil microbial groups, such as protozoa, to the rhizosphere suggests that other factors could be involved in shaping their communities. Thus, two experiments were designed to: (1) determine whether stimulatory and/or inhibiting factors associated with particular plant species regulate ciliate diversity and abundance and (2) obtain a better understanding about the mechanism by which these plant factors operate in the rhizosphere. Bacterial and chemical slurries were reciprocally exchanged between two plant species known to differ in terms of ciliate species richness and abundance (i.e., Canella winterana and plantation Tectona grandis). Analysis of variance showed that the bacteria plus nutrients and the nutrients only treatment had no significant effect on overall ciliate species richness and abundance when compared to the control treatment. However, the use of only colpodean species increased the taxonomic resolution of treatment effects revealing that bacterial slurries had a significant effect on colpodean ciliate species richness. Thus, for particular rhizosphere ciliates, biological properties, such as bacterial diversity or abundance, may have a strong influence on their diversity and possibly abundance. These results are consistent with a model of soil bacteria-mediated mutualisms between plants and protozoa.

Plants↗
PubMed2006

Molecular discrimination of Perna (Mollusca: Bivalvia) species using the polymerase chain reaction and species-specific mitochondrial primers.

This work was prompted by the need to be able to identify the invasive mussel species, Perna viridis, in tropical Australian seas using techniques that do not rely solely on morphology. DNA-based molecular methods utilizing a polymerase chain reaction (PCR) approach were developed to distinguish unambiguously between the three species in the genus Perna. Target regions were portions of two mitochondrial genes, cox1 and nad4, and the intergenic spacer between these that occurs in at least two Perna species. Based on interspecific sequence comparisons of the nad4 gene, a conserved primer has been designed that can act as a forward primer in PCRs for any Perna species. Four reverse primers have also been designed, based on nad4 and intergenic spacer sequences, which yield species-specific products of different lengths when paired with the conserved forward primer. A further pair of primers has been designed that will amplify part of the cox1 gene of any Perna species, and possibly other molluscs, as a positive control to demonstrate that the PCR is working.

Animals↗
PubMed2006

"Minute" species of Cochliopodium (Himatismenida): Description of three new fresh- and brackish-water species with a new diagnosis for Cochliopodium minus Page, 1976.

Only two species of Cochliopodium below 20mum in size are currently known. These are the recently described marine Cochliopodium gallicum Kudryavtsev and Smirnov, 2006 and a freshwater C. minutum West, 1901, an incompletely described species that has never been re-isolated since its initial description. In this paper, the descriptions of three independent species of similar size below 20microm, C. minutoidum, C. kieliense, and C. maeoticum are presented. In the light microscope they all resemble the description of C. minutum, C. minutoidum being most similar to this species. However, the available description of C. minutum is inadequate to permit the assignment of any strain to this species with confidence. Therefore, a status of nomen dubium is proposed for C. minutum. Furthermore, C. minutoidum appears to be very similar to a fish endobiont identified by Dyková et al. (1998. Cochliopodium minus, a scale-bearing amoeba isolated from organs of perch Perca fluviatilis. Dis. Aquat. Org. 34, 205-210) as C. minus. Direct comparison of my strain of C. minutoidum with the type strain of C. minus suggests that it is not identical to C. minus. The obtained data enabled me to add the ultrastructural features to the diagnosis of C. minus for more precise identification of this species.

Animals↗
PubMed2005

Species-specific PCR-based assays for the detection of Fusarium species and a comparison with the whole seed agar plate method and trichothecene analysis.

Species-specific PCR was used for the identification of nine Fusarium species in pure mycelial culture. A PCR-based method was compared with the whole seed agar plate method and trichothecene analysis for three toxin-producing Fusarium species using 85 grain samples of wheat, barley, oat, corn and rye. A simple SDS-based DNA extraction system followed by potassium acetate precipitation resulted in consistent PCR amplification of DNA fragments from cultures and grain samples. The species-specific PCR assays correctly identified pure cultures of Fusarium avenaceum ssp. avenaceum (9 isolates), Fusarium acuminatum ssp. acuminatum (12 isolates), Fusarium crookwellense (7 isolates), Fusarium culmorum (12 isolates), Fusarium equiseti (11 isolates), Fusarium graminearum (77 isolates), Fusarium poae (10 isolates), Fusarium pseudograminearum (23 isolates), and Fusarium sporotrichioides (10 isolates). Multiplex PCR was developed for the simultaneous detection of F. culmorum, F. graminearum and F. sporotrichioides, the three most important trichothecene producing species in Canada. In grain samples, results of PCR assays for these same three species related well with whole seed agar plate method results and determination of Fusarium trichothecenes. The PCR assay described in this study can be used for routine detection and identification of Fusarium spp. in Canada.

Colony Count, Microbial↗
PubMed2006

Differences in penetration routes and establishment rates of four entomopathogenic nematode species into four white grub species.

We compared the penetration of the entomopathogenic nematodes Steinernema scarabaei (AMK001 strain), S. glaseri (NC1 strain), Heterorhabditis zealandica (X1 strain), and H. bacteriophora (GPS11 strain) into third-instars of the scarabs Popillia japonica, Anomala orientalis, Cyclocephala borealis, and Rhizotrogus majalis. When larvae were exposed to nematodes for 6-72 h larval mortality and nematode establishment rate and occasionally speed of kill often showed the same pattern within nematode-white grub combinations. But no two nematodes or white grub species had the same pattern for these observations for all white grub or nematode species, respectively. Mortality, establishment, and speed of kill followed a similar pattern for H. zealandica, S. glaseri, and S. scarabaei, but there was no clear relationship for H. bacteriophora. Significant nematode establishment was only observed after at least 48 h exposure in most nematode-white grub combinations. Faster establishment was observed only for H. zealandica in A. orientalis and R. majalis (after 24 h) and for S. scarabaei in P. japonica and R. majalis (after 12 h). Nematode establishment after 72 h in the different scarab species was generally low for S. glaseri (<1.5%) and H. bacteriophora (<3%), higher for H. zealandica (2-5%), and the highest for S. scarabaei (1-14%). However, in another experiment establishment was generally higher after 96h exposure. Nematode penetration sites were determined by comparing nematode establishment in larvae with mouth, anus, mouth+anus, or none sealed with glue. The trends for each nematode species were very similar in the different white grub species. H. zealandica and H. bacteriophora showed excellent cuticular penetration ability but may also penetrate through mouth and/or anus. S. glaseri also penetrated through the cuticle but lower establishment in larvae with mouth or mouth+anus sealed suggested that the mouth is an important penetration site. S. scarabaei showed a preference for the mouth as a penetration site, but it showed some cuticular penetration ability and may also use the anus as a penetration site. The methodology used cannot exclude that cuticular penetration also included penetration through the spiracles. To fully understand the effect of nematode and white grub species on nematode virulence, future studies will have to compare host immune response to the penetrating IJs and the role of the symbiotic bacteria in these interactions.

Animals↗
PubMed2006

Cryptosporidium species found in cattle: a proposal for a new species.

Humans and animals are infected worldwide by apicomplexan parasites of the genus Cryptosporidium. Yet, parasitologists are continuously surprised by the expanding complexity of this genus. Over the past 20 years, cattle were identified as being a reservoir host for taxa transmitted from animals to humans. However, a remarkable assemblage of species affects cattle, including both cattle-specific, in addition to a zoonotic, species. To clarify species classification, Cryptosporidium pestis n. sp. is proposed for the species formerly recognized as the "bovine genotype" of C. parvum. The observed increasing complexity of Cryptosporidium species, along with recent advances in knowledge, should be reconsidered in the context of past records, and not vice versa. In this way, the gaps in our understanding of Cryptosporidium species can be identified and addressed in a scientific manner.

Animals↗
PubMed1998

Evidence for rodent-common and species-typical limb and digit use in eating, derived from a comparative analysis of ten rodent species.

Order Rodentia comprises a vast portion of mammalian species (1814 species), which occupy extremely diverse habitats requiring very distinct motor specializations (e.g. burrowing, hopping, climbing, flying and swimming). Although early classification of paw use ability suggests rodents are impoverished relative to primates and make little use of their paws, there have been no systematic investigations of paw use in rodents. The present study was undertaken to describe limb/paw movements in a variety of common rodents. The movements used for handling sunflower seeds and other foods were videorecorded and analyzed in the guinea pig (Cavia porcellus), Mongolian gerbil (Meriones unguiculatus), Syrian hamster (Mesocricetus auratus), laboratory mouse (Mus musculus), laboratory rat (Rattus norvegicus), gray squirrel (Sciurus carolinensis), red squirrel (Tamiasciurus hudsonicus), Richardson's ground squirrel (Spermophilus richardsonni), prairie dog (Cynomus parvidens), and Canadian beaver (Castor americanus). The results suggested five order-common movements of food handling: (1) locating food by sniffing, (2) grasping food by mouth, (3) sitting back on the haunches to eat, (4) grasping the food using an elbow-in movement, and (5) manipulate the food with the digits. Different species displayed species-typical specializations including (1) bilateral grasping with the paws (gerbil), (2) unilateral grasping with a paw (beaver), (3) unilateral holding (ground squirrels), (4) various grip and digit postures (all species), (5) unilateral object removal from the mouth (gerbil), (6) bilateral thumb holding (squirrels), and (7) simultaneous holding/manipulation of two objects (squirrels). Only the guinea pig did not handle food with its paws, suggesting its behavior is regressive. The existence of a core pattern of paw and digit use in rodents suggests that skilled limb and paw movements originate at least with the common ancestors of the rodent, and likely the common ancestor to rodent and primate lineages, while species-typical movements suggest specialization/regression of limb use has occurred in a number of mammalian orders.

Animals↗
PubMed2003

Pythium carbonicum, a new species isolated from a spoil heap in northern France, the ITS region, taxonomy and comparison with related species.

Pythium carbonicum (F-72) sp. nov. was found in soil samples taken on the top of a spoil heap in northern France. The morphology of this new species resembles that of a recently described species: Pythium megacarpum. However, the antheridial and oogonial characteristics of this new species are unique, and the comparison of its ITS region of the nuclear ribosomal DNA indicates that this species is also related to the genus Phytophthora. The fungus does not sporulate, the sporangia germinate directly into mycelium through germ tubes. The oogonia of P. carbonicum are smooth-walled and also papillated, and are provided with monoclinous and diclinous antheridia that wrap around, forming a complicated knot. Morphological features of this new species, together with the sequences of the ITS region of its nuclear ribosomal DNA and its comparison with related species are discussed here.

Base Sequence↗
PubMed1996

Species difference in the disposition of liposomes among mice, rats, and rabbits: allometric relationship and species dependent hepatic uptake mechanism.

PURPOSE: The species difference in the pharmacokinetics of liposomes was investigated in mice, rats and rabbits. METHODS: Liposomes were intravenously injected at doses of 1, 10 and 100 (nmol/g body weight), and the time courses of liposomes in blood, liver and spleen were measured. Pharmacokinetic parameters were regressed as a function of body weight (BW) and dose of liposomes (D). The uptake mechanism of liposomes was also examined with the isolated perfused liver between rats and mice. RESULTS: Mean residence time increased with the increase of BW and D of liposomes. This increase of mean residence time resulted from the decreased total body clearance, which was principally explained by the species difference in the hepatic uptake clearance (CLh) of liposomes. The parameter CLh was regressed well by a multiple regression as a function of BW and D. In this analysis, an exponent for BW was around 0.5, which clearly indicates that smaller animals have higher uptake clearance per unit BW. Immunohistochemical analysis revealed that there was no significant difference in the density of Kupffer cells among these species. This suggest that the species difference in CLh resulted not from the density of Kupffer cells but from the uptake ability of Kupffer cells among species. In the isolated perfused liver, the hepatic uptake of liposomes was mainly explained by opsonin dependent uptake in rats, while opsonin independent uptake in mice. CONCLUSIONS: These quantitative and qualitative information on the species difference of liposome disposition will provide an useful information for constructing a drug delivery system using liposomes.

Animals↗
PubMed1980

The antibody response to myoglobin is independent of the immunized species. Analysis in terms of replacements in the antigenic sites and in environmental residues of the cross-reactions of fifteen myoglobins with sperm-whale myoglobin antisera raised in different species.

The recent determination of the entire antigenic structure of sperm-whale myoglobin with rabbit and goat antisera has permitted the examination of whether the antigenic structure recognized by antibodies depends on the species in which the antisera are raised. Also, by knowledge of the antigenic structure, the molecular factors that determine and influence antigenicity can be better understood in terms of the effects of amino acid substitutions occurring in the antigenic sites and in the environmental residues of the sites. In the present work, the myoglobins from finback whale, killer whale, horse, chimpanzee, sheep, goat, bovine, echidna, viscacha, rabbit, dog, cape fox, mouse and chicken were examined for their ability to cross-react with antisera to sperm-whale myoglobin. By immunoadsorbent titration studies with radioiodinated antibodies, each of these myoglobins was able to bind antibodies to sperm-whale myoglobin raised in goat, rabbit, chicken, cat, pig and outbred mouse. It was found that the extent of cross-reaction of a given myoglobin was not dependent on the species in which the antisera were raised. This indicated that the antibody response to sperm-whale myoglobin (i.e. its antigenic structure) is independent of the species in which the antisera are raised and is not directed to regions of sequence differences between the injected myoglobin and the myoglobin of the immunized host. Indeed, in each antiserum from a given species examined, that antiserum reacted with the myoglobin of that species. The extent of this auto-reactivity for a given myoglobin was comparable with the general extent of cross-reactivity shown by that myoglobin with antisera raised in other species. The cross-reactivities and auto-reactivities (both of which are of similar extents for a given myoglobin) can be reasonably rationalized in terms of the effects of amino acid substitutions within the antigenic sites and within the residues close to these sites. These findings confirm that the antigenicity of the sites is inherent in their three-dimensional locations.

Amino Acid Sequence↗
PubMed2002

Presence of Anopheles culicifacies B in Cambodia established by the PCR-RFLP assay developed for the identification of Anopheles minimus species A and C and four related species.

A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay developed for identification of five species of the Anopheles minimus Theobald group and a related mosquito species of the Myzomyia Series (Diptera: Culicidae) was applied to morphologically identified adult female specimens collected in Ratanakiri Province, north-eastern Cambodia. In addition to finding An. aconitus Dönitz, An. minimus species A and An. pampanai Büttiker & Beales, some specimens showed a new restriction banding pattern. Siblings of specimens that exhibited this new PCR-RFLP pattern were morphologically identified as An. culicifacies James sensu lato. Based on nucleotide sequences of the ribonuclear DNA internal transcribed spacer 2 region (ITS2) and the mitochondrial cytochrome oxidase I gene (COI), these specimens were recognized as An. culicifacies species B (sensu Green & Miles, 1980), the first confirmed record of the An. culicifacies complex from Cambodia. This study shows that the PCR-RFLP assay can detect species not included in the initial set-up and is capable of identifying at least seven species of the Myzomyia Series, allowing better definition of those malaria vector and non-vector anophelines in South-east Asia.

Animals↗
PubMed2004

Molecular, morphological and behavioural data reveal the presence of a cryptic species in the widely studied Drosophila serrata species complex.

The Drosophila serrata species complex from Australia and New Guinea has been widely used in evolutionary studies of speciation and climatic adaptation. It is believed to consist of D. serrata, D. birchii and D. dominicana, although knowledge of the latter is limited. Here we present evidence for a previously undescribed cryptic member of the D. serrata species complex. This new cryptic species is widespread in far north Queensland, Australia and is likely to have been previously mistaken for D. serrata. It shows complete reproductive isolation when crossed with both D. serrata and D. birchii. The cryptic species can be easily distinguished from D. serrata and D. birchii using either microsatellite loci or visual techniques. Although it occurs sympatrically with both D. serrata and D. birchii, it differs from these species in development time, viability, wing size and wing morphology. Its discovery explains patterns of recently described mitochondrial DNA divergence within D. serrata, and may also help to clarify some ambiguities evident in early evolutionary literature on reproductive incompatibility within the D. serrata species complex.

Analysis of Variance↗
PubMed1992

Poly(ADP-ribose) polymerase activity in mononuclear leukocytes of 13 mammalian species correlates with species-specific life span.

Poly(ADP-ribosyl)ation is a eukaryotic posttranslational modification of proteins that is strongly induced by the presence of DNA strand breaks and plays a role in DNA repair and the recovery of cells from DNA damage. We compared poly(ADP-ribose) polymerase (PARP; EC 2.4.2.30) activities in Percoll gradient-purified, permeabilized mononuclear leukocytes from mammalian species of different maximal life span. Saturating concentrations of a double-stranded octameric oligonucleotide were applied to provide a direct and maximal stimulation of PARP. Our results on 132 individuals from 13 different species yield a strong positive correlation between PARP activity and life span (r = 0.84; P << 0.001), with human cells displaying approximately 5 times the activity of rat cells. Intraspecies comparisons with both rat and human cells from donors of all age groups revealed some decline of PARP activity with advancing age, but it was only weakly correlated. No significant polymer degradation was detectable under our assay conditions, ruling out any interference by poly(ADP-ribose) glycohydrolase activity. By Western blot analysis of mononuclear leukocytes from 11 species, using a crossreactive antiserum directed against the extremely well-conserved NAD-binding domain, no correlation between the amount of PARP protein and the species' life spans was found, suggesting a greater specific enzyme activity in longer-lived species. We propose that a higher poly(ADP-ribosyl)ation capacity in cells from long-lived species might contribute to the efficient maintenance of genome integrity and stability over their longer life span.

Age Factors↗
PubMed2006

Larval ecology, geographic range, and species survivorship in Cretaceous mollusks: organismic versus species-level explanations.

The observation that geographic range size in Cretaceous mollusks is correlated with species survivorship and is heritable at the species level has figured repeatedly in discussions of species selection over the past two decades. However, some authors have suggested that the relationship between mode of larval development and geographic range supports the reduction of this example to selection on organismic properties. Our reanalysis of Jablonski's work on heritability at the species level finds that geographic range is significantly heritable (using a randomization test) in both bivalves and gastropods, even within a single larval mode. Further, generalized linear models show that geographic range size is more important than larval mode in predicting extinction probability in both gastropods and bivalves. These results reaffirm the role and heritability of geographic range as a species-level property that can promote species selection; the model-based approach applied here may help to operationalize "screening off " and related approaches to evaluating hierarchical explanations in evolution.

Animals↗
PubMed1995

Developmental DNA rearrangements and micronucleus-specific sequences in five species within the Tetrahymena pyriformis species complex.

In Tetrahymena thermophila, the development of a transcriptionally active macronucleus from a transcriptionally inert micronucleus includes the elimination of many segments of DNA, the bulk of which belong to repetitive sequence families. Two approaches were used to study the interspecies variations in developmentally eliminated DNA segments. First, the occurrence of restriction fragments crosshybridizing to developmentally eliminated DNA segments isolated from T. thermophila was examined in other species of Tetrahymena. Most micronucleus-specific sequence families examined showed large differences in numbers and intensities of crosshybridizing bands in different species, indicating the possibility of gain or loss of repeats within each of the sequence families. Second, the presence of developmentally excisable DNA segments, i.e., of rearrangement sites, was examined in the same set of species at a number of unique loci. This was carried out by comparing the hybridization patterns of seven unique macronucleus-retained sequences in the micro- and macronuclei of each of the species. Essentially all of the loci displayed variability with respect to the presence of rearrangement sites among the species examined. Results from the two approaches indicate that generation or loss of developmental rearrangements can occur among the species examined here.

Animals↗
PubMed2002

Species boundaries, populations and colour morphs in the coral reef three-spot damselfish (Dascyllus trimaculatus) species complex.

Coloration patterns of tropical reef fishes is commonly used for taxonomic purposes, yet few studies have focused on the relationship between species boundaries and coloration types. The three-spot damselfish (Dascyllus trimaculatus) species complex comprises four species that vary both in geographical ranges and colour patterns making them an ideal model to study these relationships. We analysed the mitochondrial control region of 122 individuals from all four species collected from 13 localities. Individuals from two species (Dascyllus albisella and D. strasburgi) grouped into monophyletic clades, while the two other species (D. trimaculatus and D. auripinnis) were found to be paraphyletic. Coloration patterns were therefore not found to be good predictors of genetic isolation. In contrast, geographical origin was always consistent with the observed genetic pattern.

Animals↗
PubMed2006

The bacterial species dilemma and the genomic-phylogenetic species concept.

The number of species of Bacteria and Archaea (ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA-DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic-phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels.

Archaea↗
PubMed1996

Polymorphism at the dnaK locus of Brucella species and identification of a Brucella melitensis species-specific marker.

The dnaK gene and surrounding sequences from reference strains of the six Brucella species were amplified by the polymerase chain reaction (PCR) with primers chosen according to the published sequence of the B. ovis dnaK gene and studied for polymorphism with nine restriction endonucleases. The restriction patterns were identical for all species with all restriction endonucleases tested except for B. melitensis strain 16M that showed a different pattern with EcoRV, consistent with the presence of a single site instead of two for the other Brucella species. The absence of the second EcoRV site for B. melitensis 16M was confirmed by DNA sequence analysis. The second EcoRV site in other Brucella species was located in a 12-bp segment, which was missing from the published dnaK sequence of B. ovis, between the stop codon of the dnaK gene and its putative transcription terminator sequence. The difference between B. ovis strain 63/290 and B. melitensis 16M was due to an additional base-pair in B. melitensis 16M. Subsequently, 71 other field, vaccinal and reference strains of the six Brucella species and their different biovars were studied for restriction fragment length polymorphism (RFLP) of the dnaK locus with EcoRV. The presence of a unique EcoRV site was specific to B. melitensis strains. Southern blot analysis of whole genomic DNA digested with EcoRV and with the dnaK gene used as probe also detected a distinct pattern for B. melitensis. These results indicate that both PCR-RFLP and Southern blot analysis of the dnaK locus can be used to distinguish B. melitensis strains from the other Brucella species and may be useful for typing and diagnostic purposes as well.

Base Sequence↗