Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae)

Polymerase chain reaction (PCR) products corresponding to 803 bp of the cytochrome oxidase subunits I and II region of mitochondrial DNA (mtDNA COI-II) were deduced to consist of multiple haplotypes in three Sitobion species. We investigated the molecular basis of these observations. PCR products were cloned, and six clones from one individual per species were sequenced. In each individual, one sequence was found commonly, but also two or three divergent sequences were seen. The divergent sequences were shown to be nonmitochondrial by sequencing from purified mtDNA and Southern blotting experiments. All seven nonmitochondrial clones sequenced to completion were unique. Nonmitochondrial sequences have a high proportion of unique sites, and very few characters are shared between nonmitochondrial clones to the exclusion of mtDNA. From these data, we infer that fragments of mtDNA have been transposed separately (probably into aphid chromosomes), at a frequency only known to be equalled in humans. The transposition phenomenon appears to occur infrequently or not at all in closely related genera and other aphids investigated. Patterns of nucleotide substitution in mtDNA inferred over a parsimony tree are very different from those in transposed sequences. Compared with mtDNA, nonmitochondrial sequences have less codon position bias, more even exchanges between A, G, C and T, and a higher proportion of nonsynonymous replacements. Although these data are consistent with the transposed sequences being under less constraint than mtDNA, changes in the nonmitochondrial sequences are not random: there remains significant position bias, and probable excesses of synonymous replacements and of conservative inferred amino acid replacements. We conclude that a proportion of the inferred change in the nonmitochondrial sequences occurred before transposition. We believe that Sitobion aphids (and other species exhibiting mtDNA transposition) may be important for studying the molecular evolution of mtDNA and pseudogenes. However, our data highlight the need to establish the true evolutionary relationships between sequences in comparative investigations.      

Initial verification of the resistance management strategy for Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) in Australia

Shortly after the initial detection of western flower thrips (WFT), Frankiniella occidentalis (Pergande), in Australia during 1993 a resistance management strategy based on the alternation of chemical groups was implemented. This study aimed to verify this strategy by field testing α-cypermethrin against WFT with and without chemical alternation. Up to 114 times α-cypermethrin resistance (at LC50) was detected and resistance increased with and without chemical alternation; however, chemical alternation did significantly reduce numbers of thrips compared with a nonalternation strategy. Resistance has the potential to undermine the sustainable use of those chemicals to which there is no current detectable resistance. Consequently, chemicals with a high frequency and level of resistance against WFT need to be identified through monitoring and quickly eliminated from WFT chemical control recommendations.     

A simple method for studying whole sections of rice grain

We developed a new and simple method to collect sections of a whole brown rice kernel for investigation of histological properties. A single kernel of rice was dehydrated through a graded ethanol series, transferred to xylene, and embedded in paraffin. During sectioning of the blocks using a rotary microtome, we used a special adhesive tape to collect and place the sections on slides so they remained flat. The use of the adhesive tape technique combined with autofluorescence characteristics allowed us to visualize cell walls throughout an entire longitudinal or transverse section of a whole rice kernel. We obtained scanning electron microscopy images of the sections to determine section quality.     

Discriminating lymphomas and reactive lymphadenopathy in lymph node biopsies by gene expression profiling

Background

Diagnostic accuracy of lymphoma, a heterogeneous cancer, is essential for patient management. Several ancillary tests including immunophenotyping, and sometimes cytogenetics and PCR are required to aid histological diagnosis. In this proof of principle study, gene expression microarray was evaluated as a single platform test in the differential diagnosis of common lymphoma subtypes and reactive lymphadenopathy (RL) in lymph node biopsies.

Methods

116 lymph node biopsies diagnosed as RL, classical Hodgkin lymphoma (cHL), diffuse large B cell lymphoma (DLBCL) or follicular lymphoma (FL) were assayed by mRNA microarray. Three supervised classification strategies (global multi-class, local binary-class and global binary-class classifications) using diagonal linear discriminant analysis was performed on training sets of array data and the classification error rates calculated by leave one out cross-validation. The independent error rate was then evaluated by testing the identified gene classifiers on an independent (test) set of array data.

Results

The binary classifications provided prediction accuracies, between a subtype of interest and the remaining samples, of 88.5%, 82.8%, 82.8% and 80.0% for FL, cHL, DLBCL, and RL respectively. Identified gene classifiers include LIM domain only-2 (LMO2), Chemokine (C-C motif) ligand 22 (CCL22) and Cyclin-dependent kinase inhibitor-3 (CDK3) specifically for FL, cHL and DLBCL subtypes respectively.

Conclusions

This study highlights the ability of gene expression profiling to distinguish lymphoma from reactive conditions and classify the major subtypes of lymphoma in a diagnostic setting. A cost-effective single platform "mini-chip" assay could, in principle, be developed to aid the quick diagnosis of lymph node biopsies with the potential to incorporate other pathological entities into such an assay.

     

Altered predation susceptibility of mosquitofish infected with Eustrongylides ignotus

Eustrongylides ignotus is a parasitic nematode whose definitive hosts are often piscivorous wading birds (Ciconiiformes). Several species of small fishes are intermediate hosts, while larger predatory fish may be paratenic (transport) hosts. We examined predation susceptibility of infected mosquitofish (Gambusia holbrooki) to three species of predatory fishes, including juvenile largemouth bass (Micropterus salminoides), warmouth (Lepomis gulosus), and bluegill (Lepomis macrochirus). A 250 L aquarium with removable plexiglass divider and remote observation windows was constructed. Aquatic macrophytes were placed in the tank to provide refuge for the fishes. Predatory fish were allowed to acclimate to one half of the tank, while one infected and one uninfected mosquitofish were placed in the other. The divider was removed and an observer recorded the number of capture attempts and time required for capture. Predators were observed for behavioral alterations for 4 days after ingestion of infected mosquitofish, then examined at necropsy. Infected prey were selected preferentially in 31 of 38 (82%) trials. The number of capture attempts was 2.7+/-0.2 (x +/- SE) for infected fish and 3.9+/-0.4 for uninfected fish. Mean time of capture was 12.4+/-1.6 min for infected fish and 21.7+/-2.9 for uninfected fish. Because of these differences, infected mosquitofish were more susceptible to predation (P < 0.01) than uninfected fish. Aberrant behavior including lethargy, convulsions, and buoyancy abnormalities was observed in eight (67%) predatory fish. At necropsy, larvae of E. ignotus were found in the coelomic cavity, viscera, and swim bladders of predators. Parasite-induced behavior modification of intermediate hosts may predispose them to predation by wading birds and thereby facilitate the transmission of this nematode in natural populations.     

Epizootiology of Eustrongylides ignotus in Florida: transmission and development of larvae in intermediate hosts

Under laboratory conditions, 2 modes of transmission of Eustrongylides ignotus (Nematoda: Dioctophymatoidea) to fish were identified. Eastern mosquitofish (Gambusia holbrooki) became infected after ingestion of either eggs of E. ignotus containing first-stage larvae or aquatic oligochaetes (Limnodrilus hoffmeisteri) containing third-stage larvae of E. ignotus. After removal from the uterus of gravid E. ignotus females and incubation for 17-28 days, depending on temperature, it was found that parasite eggs contained first-stage larvae that were infective to fish and oligochaetes. Larvae developed to the third stage in oligochaetes and were infective to fish 35-77 days postinfection (PI) and when fed to fish, developed to the fourth stage between 127 and 184 days PI. Eggs containing first-stage larvae fed directly to fish developed to the fourth stage between 84 and 105 days PI. The amount of time for development from the undifferentiated egg to the fourth-stage larva was 78-156 days shorter when fish ingested eggs containing first-stage larvae than when fish ingested oligochaetes containing third-stage larvae. Three species of large piscivorous fish, including black crappie (Pomoxis nigromaculatus), largemouth bass (Micropterus salmoides), and warmouth (Lepomis gulosus), were fed mosquitofish containing fourth-stage larvae. At necropsy, live E. ignotus larvae were recovered from all 3 species. Several fish had multiple infections after ingesting > 1 larva, indicating that bioaccumulation of the parasite in the food chain may occur.     

Tyrosine phosphorylation of myosin heavy chain during skeletal muscle differentiation: an integrated bioinformatics approach

Background  

Previously it has been shown that insulin-mediated tyrosine phosphorylation of myosin heavy chain is concomitant with enhanced association of C-terminal SRC kinase during skeletal muscle differentiation. We sought to identify putative site(s) for this phosphorylation event.     

Tyrosine phosphorylation of myosin heavy chain during skeletal muscle differentiation: an integrated bioinformatics approach

Previously it has been shown that insulin-mediated tyrosine phosphorylation of myosin heavy chain is concomitant with enhanced association of C-terminal SRC kinase during skeletal muscle differentiation. We sought to identify putative site(s) for this phosphorylation event. A combined bioinformatics approach of motif prediction and evolutionary and structural analyses identified tyrosines163 and 1856 of the skeletal muscle heavy chain as the leading candidate for the sites of insulin-mediated tyrosine phosphorylation. Our work is suggestive that tyrosine phosphorylation of myosin heavy chain, whether in skeletal muscle or in platelets, is a significant event that may initiate cytoskeletal reorganization of muscle cells and platelets. Our studies provide a good starting point for further functional analysis of MHC phosphor-signalling events within different cells.     

Hybridization and asymmetric introgression across a narrow zone of contact between Neotoma fuscipes and N. macrotis (Rodentia: Cricetidae)

When lineages diverge in allopatry and come into secondary contact, we have a unique opportunity to examine the degree to which they have become reproductively isolated from one another and the mechanisms that contribute to rates of interspecific gene flow. If hybridization and introgression have occurred in the past or are ongoing, examining patterns of variation in differentially inherited genetic markers can provide insight into underlying mechanisms determining interspecific reproductive interactions. We investigated genetic variation in a recently discovered contact zone between two species of woodrats (Neotoma fuscipes and N. macrotis) in central coastal California. Previous studies have found evidence of historic hybridization between these species, but an active site of sympatry had yet to be discovered. Here, we describe the first known area of sympatry between the two species and present evidence of ongoing hybridization at this site. We intensively sampled throughout the narrow area of interspecific contact and continuously into the adjacent areas where each taxon existed largely in isolation of the other. We genotyped 851 individuals sampled in a single year at 15 nuclear microsatellite loci and sequenced a portion of the cytochrome b gene in a subset of these to examine patterns of introgression. We find that the area of sympatry is less than 1 km in length, but hybridization appeared to be fairly common, with 15% of the woodrats being of hybrid origin. At least some hybrids are fertile because introgression was evident. However, introgression appeared to be asymmetric with backcrosses toward N. macrotis being more common, a pattern we suspect is due in part to directional mate choice related to differential body size. This study adds to our growing understanding of the nature of species boundaries, especially between lineages that are far along the continuum towards speciation. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 162–172.