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.      

Trace elements as fingerprint of lake of provenance and of species of some native and exotic fish of northern Patagonian lakes

A survey of trace element contents in fish muscle and liver was performed in different lakes of two northern Patagonian national parks: Nahuel Huapi and Los Alerces national parks. The aim of the work was to obtain the first set of reference data on elements that are not liable to be disturbed by human activities and to identify compositional patterns related to the species and site of collection. The species studied are native creole perch and velvet catfish and exotic brown trout, rainbow trout, and brook trout. The elements analyzed are Br, Cs, Fe, Rb, Se, Na, and Zn. Trace elements in muscle of brown trout, rainbow trout, and creole perch showed statistical patterns that allow one to identify the national park of origin, as well as which of the lakes (Traful, Espejo Chico, or the Nahuel Huapi-Moreno system) of the Nahuel Huapi National Park from which they come. Contents in the liver provide similar but less clear patterns than contents in muscle; however, in some particular cases, they provide additional information. Trace element contents in muscle are also good indicators of the species collected within a lake.     

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.     

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.     

Heavy metal and other trace elements in native mussel Diplodon chilensis from Nothern Patagonia Lakes, Argentina

Native mussels, Diplodon chilensis, were sampled from four lakes in Nahuel Huapi National Park, Northern Patagonia, Argentina in order to evaluate heavy-metal distribution in the region and to assess the contribution of this compartment of the trophic web to their circulation in the food chain. The concentration of potential pollutants Ag, As, Cr, Hg, Sb, and Se, and other nine elements of interest (Ba, Br, Ca, Co, Cs, Fe, Na, Sr, and Zn) were determined in Diplodon chilensis pooled samples. Digestive glands were analyzed separately from soft tissues. Geological tracers Sc, Ta, Th, and rare earth elements were also determined in order to discriminate lithophile contributions. Elemental concentrations of Ba, Br, Fe, Sr, Se, and Zn in total soft tissues samples do not show significant differences among sampling sites. Arsenic and Cr contents in total soft tissues and digestive gland pooled samples are higher in sampling points close to zones with human settlements. Silver contents in samples collected in Lake Nahuel Huapi were higher than in the other lakes studied, and up to 50-fold higher than the sample collected in Lake Traful, considered as the reference. Mercury highest concentration values measured in total soft tissues pooled samples from lakes Nahuel Huapi and Moreno were found to be similar to those observed in other reported Hg contamination situations, and they are three to five times higher than those of the reference samples collected in Lake Traful.     

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.

     

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.     

Rb-Cs ratio as an indicator of fish diet in lakes of the Patagonia, Argentina

The ratios of Rb to Cs contents were studied in five fish species from seven lakes located in the Patagonia Andean Range, Argentina in order to trace fish diet. The species studied were native velvet catfish (Diplomistes viedmensis) and creole perch (Percichthys trucha), and exotic brown trout (Salmo trutta), rainbow trout (Oncorhynchus mykiss), and brook trout (Salvenilus fontinalis). Rainbow trout specimens from two farms were also studied, as well as fish food items and native mussels (Diplodon chilensis). Rb and Cs concentrations were determined by instrumental neutron activation analysis. A positive correlation of Cs concentration in the muscle of velvet catfish with fish length was observed, probably associated with the long biological half-life of this element in this species, whereas the Rb concentration remained constant, hence inhibiting the use of Rb-Cs ratios as a tracer in this case. Seasonal variations observed for rainbow trout and Cs concentration background bias in one of the lakes studied are also a limiting factor to the use of Rb-Cs ratios as a diet tracer. Rb-Cs ratios allowed clear differentiation of rainbow trout raised in farms from the natural specimens that lived in the same environment, in agreement with Rb-Cs ratios determined in both diets. Rb-Cs ratios in rainbow trout showed significant differences between Rivadavia and Futalaufquen lakes compared to Moreno and Nahuel Huapi lakes, which could be associated with a higher participation of plankton in the diet in the first case. No relevant variations in Rb-Cs ratios of brown trout were observed, probably because of the similarity in the diet.