Investigation of diversity and isotypes of the beta-tubulin cDNA in several small strongyle (Cyathostominae) species

The diversity of the beta-tubulin cDNAs of the cyathostominae and the occurrence of further isotypes were examined in adult worms isolated from an anthelmintic-na?ve horse. cDNAs encoding beta-tubulin from Cyathostomum catinatum, Cylicocyclus nassatus, Cylicocyclus insigne, Cylicocyclus radiatus, Cylicocyclus elongatus, Cyathostomum coronatum, and Cyathostomum pateratum were characterized using specific primers developed from the cDNA sequence of Cc. nassatus. The cDNA sequences span 1,429 bp and show identities ranging from 95.6 to 100%. The deduced protein sequences span 448 amino acids and were 98-100% identical. The amino acid sequences of the 7 species varied within and between species at 10 positions. A 3' Rapid Amplification of cDNA ends using a degenerate forward primer was carried out with cDNA from Cy. pateratum, Cy. coronatum, Cy. catinatum, and Cc. nassatus to investigate the occurrence of further beta-tubulin isotypes. The expected polymerase chain reaction (PCR) product of 400 bp, including 306 bp of coding sequence, was amplified, as was an additional fragment of 600 nucleotides in the case of Cy. pateratum, Cy. coronatum, and Cy. catinatum. Sequencing of the PCR products revealed no evidence for the existence of a second beta-tubulin isotype in cyathostomes. The variation in size was caused by a length polymorphism within the 3' untranslated region, and 2 functional mRNAs seem to be transcribed from the same gene.     

Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR

With an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elucidate ambiguous genotypes. In this study, we have used SNP specific Locked Nucleic Acid (LNA) hybridization probes on a real-time PCR platform to genotype an association cohort and propose three criteria to address ambiguous genotypes. Based on the kinetic properties of PCR amplification, the three criteria address PCR amplification efficiency, the net fluorescent difference between maximal and minimal fluorescent signals and the beginning of the exponential growth phase of the reaction. Initially observed SNP allelic discrimination curves were confirmed by DNA sequencing (n = 50) and application of our three genotype criteria corroborated both sequencing and observed real-time PCR results. In addition, the tested Caucasian association cohort was in Hardy-Weinberg equilibrium and observed allele frequencies were very similar to two independently tested Caucasian association cohorts for the same tested SNP. We present here a novel approach to effectively determine ambiguous genotypes generated from a real-time PCR platform. Application of our three novel criteria provides an easy to use semi-automated genotype confirmation protocol.     

Allele-specific PCR genotyping of the HSP70 gene polymorphism discriminating the green and red color variants sea cucumber （Apostichopus japonicus）

Color variation is a well-known feature of sea cucumbers (Apostichopus japonicus),which are classified into three groups based on their colors of red,green and black.It is also one of the most important traits related to how they taste,and it thereby affects their market price.Attempts were made to identify single-nucleotide polymorphisms (SNPs) and to analyze differences associated with SNP genotypes between green and red color variants using HSP70 as the target gene.The HSP70 gene,which is found universally in organisms from bacteria to humans,is one of the most evolutionarily conserved genes and the most widely studied biomarker of stress response.DNA fragments of 1074 bp covering a partial sequence of the sea cucumber HSP70 gene,were amplified from both red and green variants,and subsequently analyzed for the presence of SNPs.Twenty-seven polymorphic sites in total,including heterozygous sites,were observed.Of these,six sites were found to be significantly different SNP genotypes between green and red variants.Furthermore,PCR with an internal primer designed to include an allelespecific SNP at the 3' end (site 443) showed differentiation between the two variants,100％ and 4.2％ amplification in green and red variants,respectively.The validated SNPs may serve as informative genetic markers that can be used to distinguish variants at the early developmental stage,prior to color differentiation.     

RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers

Background

The combinatorial library strategy of using multiple candidate ligands in mixtures as library members is ideal in terms of cost and efficiency, but needs special screening methods to estimate the affinities of candidate ligands in such mixtures. Herein, a new method to screen candidate ligands present in unknown molar quantities in mixtures was investigated.

Results

The proposed method involves preparing a processed-mixture-for-screening (PMFS) with each mixture sample and an exogenous reference ligand, initiating competitive binding among ligands from the PMFS to a target immobilized on magnetic particles, recovering target-ligand complexes in equilibrium by magnetic force, extracting and concentrating bound ligands, and analyzing ligands in the PMFS and the concentrated extract by chromatography. The relative affinity of each candidate ligand to its reference ligand is estimated via an approximation equation assuming (a) the candidate ligand and its reference ligand bind to the same site(s) on the target, (b) their chromatographic peak areas are over five times their intercepts of linear response but within their linear ranges, (c) their binding ratios are below 10%. These prerequisites are met by optimizing primarily the quantity of the target used and the PMFS composition ratio. The new method was tested using the competitive binding of biotin derivatives from mixtures to streptavidin immobilized on magnetic particles as a model. Each mixture sample containing a limited number of candidate biotin derivatives with moderate differences in their molar quantities were prepared via parallel-combinatorial-synthesis (PCS) without purification, or via the pooling of individual compounds. Some purified biotin derivatives were used as reference ligands. This method showed resistance to variations in chromatographic quantification sensitivity and concentration ratios; optimized conditions to validate the approximation equation could be applied to different mixture samples. Relative affinities of candidate biotin derivatives with unknown molar quantities in each mixture sample were consistent with those estimated by a homogenous method using their purified counterparts as samples.

Conclusions

This new method is robust and effective for each mixture possessing a limited number of candidate ligands whose molar quantities have moderate differences, and its integration with PCS has promise to routinely practice the mixture-based library strategy.     

Molecular forms of four aldolases from larval and adult stages of the blowfly Phormia regina (Meigen)

Fructose diphosphate ldolases in crude muscle extracts of larval and adult Phormia regina are indistinguishable by polyacrylamide gel electrophoresis (PAGE) in several buffer systems. By contrast, larval and adult fat body aldolases differ in electrophoretic mobility, a difference shown to be due to the inequality of their net charge. Phormia regina larval muscle and fat body isozymes are clearly distinguishable by PAGE, and by pH optima and Michaelis constants.     

Mortality of Apatania fimbriata (Insecta: Trichoptera) during embryonic, larval and adult life stages

1. Egg masses, oviposition site preferences, and abiotic and biotic factors causing mortality during embryonic, larval and adult life stages of Apatania fimbriata were studied. Laboratory investigations provided information on the temperature dependence of embryonic development, measured as an increase in egg volume.
2. A. fimbriata laid hemispherical egg masses, consisting of a transparent matrix containing a mean of 208 eggs. Egg masses were laid on stones situated just above the water surface in dark cavities in the stream bank.
3. Two hundred egg masses were mapped and individually monitored during embryonic development. There was no significant correlation between mortality during embryonic development and any of the abiotic parameters measured. First-instar larvae of Osmylus fulvicephalus consumed developing eggs, and chironomids preyed on newly hatched larvae.
4. A mean of seventy-two females emerged per metre of stream. Mortality during the 1993/94 life cycle was measured as a percentage of the potential number of eggs laid. Female mortality between emergence and oviposition was ≈ 80%. Eight per cent of individuals were lost during embryonic development. Larval mortality to emergence in 1994 was 11.3%. This indicates that the terrestrial life stage is probably decisive in the regulation of A. fimbriata populations.
5. Duration of embryogenesis at constant temperatures (4–20 °C) in the laboratory was described best by a negative exponential function. This species is cold stenothermal and there was no hatching success at 20 °C.
6. Egg volumes during embryonic development increased sigmoidally over time.     

Comparative anatomy of muscle sets in larval and adult stages ofZophobas morio (Coleoptera,Tenebrionidae)

Summary The muscles of the metathoracic segment are described for the larva and imago of the beetleZophobas morio. In the search for possible homonomous and ontogenetic persistent structures, we further employed muscles served by the first segmental nerve in the thoracic and abdominal segments. In the larva, eight muscles per hemisegment are associated with this nerve. Based on topological criteria they may be characterized as homonomous for all tested segments. In the adult, the topology of the dorsal muscles seems to be different compared to the larval situation, due to the complex structural remodelling during metamorphosis. However, a supplementary analysis employing the innervation pattern allows us to equate larval with adult muscles, even down to the level of individual motor units. Comparison of different orthopteran and coleopteran species provides some evidence that these muscles are homologous, apparently representing part of a basic pattern common in pterygote insects.     

Mortality of Apatania fimbriata (Insecta: Trichoptera) during embryonic, larval and adult life stages

1. Egg masses, oviposition site preferences, and abiotic and biotic factors causing mortality during embryonic, larval and adult life stages of Apatania fimbriata were studied. Laboratory investigations provided information on the temperature dependence of embryonic development, measured as an increase in egg volume.
2. A. fimbriata laid hemispherical egg masses, consisting of a transparent matrix containing a mean of 208 eggs. Egg masses were laid on stones situated just above the water surface in dark cavities in the stream bank.
3. Two hundred egg masses were mapped and individually monitored during embryonic development. There was no significant correlation between mortality during embryonic development and any of the abiotic parameters measured. First-instar larvae of Osmylus fulvicephalus consumed developing eggs, and chironomids preyed on newly hatched larvae.
4. A mean of seventy-two females emerged per metre of stream. Mortality during the 1993/94 life cycle was measured as a percentage of the potential number of eggs laid. Female mortality between emergence and oviposition was ≈ 80%. Eight per cent of individuals were lost during embryonic development. Larval mortality to emergence in 1994 was 11.3%. This indicates that the terrestrial life stage is probably decisive in the regulation of A. fimbriata populations.
5. Duration of embryogenesis at constant temperatures (4–20 °C) in the laboratory was described best by a negative exponential function. This species is cold stenothermal and there was no hatching success at 20 °C.
6. Egg volumes during embryonic development increased sigmoidally over time.     

Effects of lufenuron on Lobesia botrana (Lepidoptera: Tortricidae) egg, larval, and adult stages

The effect of the chitin synthesis inhibitor lufenuron was evaluated against different developmental stages of Lobesia botrana Den. & Schiff. (Lepidoptera: Tortricidae). Lufenuron fed to adults at 10 ppm reduced their fecundity and fertility, but it did not affect adult longevity. High activity was observed against L. botrana eggs with greater effect on 1-d-old eggs than on the other age classes and on eggs treated by direct contact rather than those laid on a previously treated surface. Eggs laid by treated adults showed the same effects during development as eggs treated by contact or those laid on a treated surface. Larvae that emerged from treated eggs could not perforate grape berries. Administered into the diet, lufenuron had a larvicidal effect, resulting in similar LC50 values for different instars: 0.07 ppm for first instars, 0.08 ppm for third instars, and 0.11 ppm for fifth instars. None of the larvae treated with sublethal concentrations throughout their life emerged as adults at the highest concentration (0.08 ppm), and only 70% emerged at the lowest concentration (0.0025 ppm).     

Aeromonas detection and characterization using genus-specific PCR and single-strand conformation polymorphism (SSCP)

Based on sequence alignment, oligonucleotide primers targeting the Aeromonas extracellular lipase gene were developed for PCR detection of member of the genus. A pair of primers designed for conserved regions of the gene amplified a 276?bp sequence in all Aeromonas species and tested strains, but did not have a positive result with other Gram-positive and Gram-negative bacteria, showing high specificity and sensitivity. Selective enrichment in alkaline peptone water, followed by centrifugation, and direct usage of cells suspension as template, detected initial populations of 10?c.f.u.?ml(-1). Single-strand conformation polymorphism analysis of the PCR products allowed the characterization of Aeromonas strains with a high discriminatory power (Simpson's index?=?0.988). The method presented here provides a useful tool for the rapid detection of Aeromonas and the characterization of Aeromonas isolates.     

Yeast communities of the cactusPilosocereus arrabidae as resources for larval and adult stages ofDrosophila serido

The feeding behavior ofDrosophila serido on the yeast communities of necrotic stem tissue ofPilosocereus arrabidae were studied in a sand dune ecosystem of Rio de Janeiro, Brazil. The prevalence of cactophilic yeasts includingPichia barkeri, Candida sonorensis andGeotrichum sp. in the crops and external surfaces ofD. serido reflected its association with the cactus habitat. The effective number of yeasts vectored on the surface of flies was higher than that in the crops. Also overlap between the yeasts from stems and from crops was partial suggesting selective feeding by the flies in the substrates visited. The females had a higher effective number of yeast species and a lower similarity than males with the yeast community ofP. arrabidae. This was probably related to the search for oviposition sites by females. The presence ofPichia thermotolerans-like andPichia amethionina varpachycereana in the flies, but not inP. arrabidae stems, indicated thatD. serido was not limited to this cactus species. The larvae and adults lived in different patches with the adults feeding in patches with higher yeast species richness. The larvae had a narrower feeding niche and higher overlap withP. arrabidae, and preferredP. barkeri andPichia cactophila as food. Adult flies fed on patches with the most frequent yeasts except forP. cactophila. Pichia caribaea was found in higher frequency in the adult crops than in the stems. Our data suggested that there was food selection and diet partitioning between adult and larval stages ofD. serido.     

Allele-specific PCR detection of sweet cherry self-incompatibility (S) alleles S1 to S16 using consensus and allele-specific primers

PCR-based identification of all 13 known self-incompatibility (S) alleles of sweet cherry is reported. Two pairs of consensus primers were designed from our previously published cDNA sequences of S₁ to S₆ S-RNases, the stylar components of self-incompatibility, to reveal length variation of the first and the second introns. With the exception of the first intron of S₁₃, these also amplified S₇ to S₁₄ and an allele previously referred to as S_x, which we now label S₁₆. The genomic PCR products were cloned and sequenced. The partial sequence of S₁₁ matched that of S₇ and the alleles were shown to have the same functional specificity. Allele-specific primers were designed for S₇ to S₁₆, so that allele-specific primers are now available for all 13 S alleles of cherry (S₈, S₁₁ and S₁₅ are duplicates). These can be used to distinguish between S alleles with introns of similar size and to confirm genotypes determined with consensus primers. The reliability of the PCR with allele-specific primers was improved by the inclusion of an internal control. The use of the consensus and allele-specific primers was demonstrated by resolving conflicting genotypes that have been published recently and by determining genotypes of 18 new cherry cultivars. Two new groups are proposed, Group XXIII (S₃S₁₆), comprising 'Rodmersham Seedling' and 'Strawberry Heart', and Group XXIV (S₆S₁₂), comprising 'Aida' and 'Flamentiner'. Four new self-compatibility genotypes, S₃S₃, S₄S₆, S₄S₉ and S₄S₁₃, were found. The potential use of the consensus primers to reveal incompatibility alleles in other cherry species is also demonstrated.Communicated by H.F. Linskens     

Growth and food consumption during the larval stages of Paropsis atomaria (Coleoptera: Chrysomelidae)

The relative gross efficiency of food utilization by the larvae of Paropsis atomaria was estimated on eight occasions during their development on shoots of their preferred host plant, Eucalyptus blakelyi. The overall conversion ratio of 0.200 is compared with the ratios determined by other authors for a range of phytophagous insects. The ratios obtained for the separate growth stages of P. atomaria suggest that conversion efficiency declines temporarily following each ecdysis, and as the final-instar larva approaches maturity.

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Zusammenfassung Die Käferlarven wurden im Laboratorium auf abgeschnittenen Trieben der bevorzugten Wirtspflanze, Eucalyptus blakelyi Maiden, gezüchtet. Außer während des ersten Larvenstadiums und während der letzten Tage des vierten Larvenstadiums vergrößerte sich der Zuwachs der Larven mit der Zeit geometrisch.Der große Futterausnützungs-Quotient oder die Umsatzrate (Lebendgewichtzuwachs der Larven/Frischgewicht des aufgenommenen Futters) wurde während der 18 Tage des Larvenlebens 8mal gemessen. Die Umsatzrate sank vorübergehend nach jeder Häutung und auch in den letzten Tagen des vierten Larvenstadiums. Während dieser letzten Periode nahm das Wachstum der Larven verhältnismäßig schneller ab als die Nahrungsaufnahme; gleichzeitig erhöhte sich der Wassergehalt im Kot.Die Umsatzraten von P. atomaria (0.200) und der ebenfalls Eucalyptus-Blätter fressenden Sägewespe Perga affinis (0.242) liegen in der Mitte des Bereichs des Quotienten, der von anderen Autoren für pflanzenfressende Insektenarten ermittelt wurde.

     

Phylogeny of Hydrophiloidea (Coleoptera: Staphyliniformia) using characters from adult and preimaginal stages

A phylogenetic analysis using characters from egg cases, larvae, pupae and adults was conducted; the outgroups included the beetle families Silphidae, Hydraenidae and Histeridae. Characters from the immature stages were obtained mostly from material reared in the laboratory, those from the adults were obtained from Hansen's generic revision for the superfamily. The results support the position of Hydraenidae within the Staphylinoidea, and not as part of Hydrophiloidea; Histeroidea is proposed as the sister group of Hydrophiloidea. At family level two clades are distinguished; the relationships within the first clade are ((Georissidae Epimetopidae) Helophoridae), those within the second are ((Hydrophilidae Spercheidae) Hydrochidae). Larval characters were most informative at the base of the tree, especially those associated with the spiracular atrium; adult characters were most informative at the apex of the tree.     

Functional response of larval and adult stages of Hippodamia variegata (Coleoptera: Coccinellidae) to different densities of Aphis fabae (Hemiptera: Aphididae)

We compare the efficiencies of different stages of Hippodamia variegata (Coleoptera: Coccinellidae) preying on Aphis fabae (Scolpoli) (Hemiptera: Aphididae) by estimating the functional responses of all stages. The experiments were carried out on leaf disks in petri dishes with 15-20 replicates. Our results revealed that all larval instars and adult males and females of H. variegata exhibited type II functional responses on different densities of prey. The rate of searching efficiency and handling time were estimated as 0.063 h(-1) and 6.933 h for first instar, 0.059 h(-1) and 3.343 h for second instar, 0.103 h(-1) and 1.909 h for third instar, 0.114 h(-1) and 0.455 h for fourth instar, 0.159 h(-1) and 1.194 h for male, 0.093 h(-1) and 0.409 h for female, respectively. Thus, handing time decreased from first instar to female. Handling times of males were significantly greater than those of females. The most effective stages of H. variegata were females, fourth instars, and males. The efficiency of females was nearly three times greater than that of males. The voracity of larval stages and male and female adults of H. variegata were estimated as 2.93, 5.85, 12.13, 45.13, 18.33, and 44.60 (aphids/d), respectively.