Complete mtDNA of the Meretrix lamarckii (Bivalvia: Veneridae) and molecular identification of suspected M. lamarckii based on the whole mitochondrial genome

The complete nucleotide sequence of the mitochondrial genome of the clam Meretrix lamarckii (Bivalvia: Veneridae) was determined. It contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding region. We also sequenced the mitochondrial genome of the sample collected from Zhejiang province, which showed morphologic discrepancy compared with classic M. lamarckii. Comparison of two complete mitochondrial DNA data demonstrated that the two sequences have a similarity as high as 99%. The complete mitochondrial genome of M. lamarckii from Hainan is 20,965nts in length and the sample from Zhejiang is 21,209nts in length. We therefore record one new locality for the M. lamarckii and thus the geographic distribution of M. lamarckii stretches from the south coast of Guangdong China to more north, arriving at the south coast of Zhejiang China.     

Probing the Drosophila retinal determination gene network in Tribolium (II): The Pax6 genes eyeless and twin of eyeless

The Pax6 genes eyeless (ey) and twin of eyeless (toy) are upstream regulators in the retinal determination gene network (RDGN), which instructs the formation of the adult eye primordium in Drosophila. Most animals possess a singleton Pax6 ortholog, but the dependence of eye development on Pax6 is widely conserved. A rare exception is given by the larval eyes of Drosophila, which develop independently of ey and toy. To obtain insight into the origin of differential larval and adult eye regulation, we studied the function of toy and ey in the red flour beetle Tribolium castaneum. We find that single and combinatorial knockdown of toy and ey affect larval eye development strongly but adult eye development only mildly in this primitive hemimetabolous species. Compound eye-loss, however, was provoked when ey and toy were RNAi-silenced in combination with the early retinal gene dachshund (dac). We propose that these data reflect a role of Pax6 during regional specification in the developing head and that the subsequent maintenance and growth of the adult eye primordium is regulated partly by redundant and partly by specific functions of toy, ey and dac in Tribolium. The results from embryonic knockdown and comparative protein sequence analysis lead us further to conclude that Tribolium represents an ancestral state of redundant control by ey and toy.     

On shortcomings of using mtDNA sequence divergence for the systematics of hares (genus Lepus): An example from cape hares

Despite the well-known fact that evolutionary patterns of single genes or sequences are not necessarily paralleled by organismic evolution, using mitochondrial sequence divergence for inferring phylogenetic relationships among hare species is not uncommon. Earlier studies reported interspecific introgression in the genus Lepus that may slur systematic conclusions drawn exclusively from mtDNA data. We examined pairwise divergence in partial mtHV-1 sequences and nuclear gene pools based on microsatellite and allozyme loci separately in a South and North African population of cape hares, Lepus capensis, and did not find significant correspondence on the individual level within either population. Also, the former population had a significantly higher level of mtHV-1 sequence divergence compared to the latter, but levels of individual nuclear gene pool divergence did not differ significantly between the two populations. Hence, the absence of correspondence between mtHV-1 sequence divergence and nuclear gene pool divergence among individuals within a population might be independent of the population-specific level of differentiation among individuals. Our results complement earlier findings in hares, and strongly recommend to include nuclear gene pool evidence for systematic inferences within this genus, even under the absence of mitochondrial introgression.     

Expression of Zkrml2, a homologue of the Krml1/val segmentation gene, during embryonic patterning of the zebrafish (Danio rerio)

We have identified Zkrml2, a novel homologue of the segmentation gene Krml/val in zebrafish (Danio rerio). Zkrml2 shows 72% and 92% identity in its basic leucine zipper domain with mouse Krml1 and zebrafish val, respectively. Zkrml2 is expressed coincident with MyoD throughout the somites starting at the three somite stage, becomes restricted to the dermomyotome, and subsequently disappears. Transient expression is also detected in the reticulospinal and oculomotor neurons. Zkrml2 maps to the Oregon linkage group 11 (Boston Linkage group 14) with no mapped zebrafish mutations nearby.     

Interleukin-8 gene polymorphism is associated with acute coronary syndrome in the Chinese Han population

Background

Acute coronary syndrome (ACS) is one of the most common forms of heart disease. Recent studies have shown that interleukin (IL)-8 plays a key role in the development of atherosclerotic plaques, but the relationship between the common genetic variants of IL-8 and ACS has not been extensively studied.

Methods

This case-control study in the Chinese Han population included 675 patients with ACS and 636 age- and sex-matched controls. We investigated IL-8 polymorphisms and their association with susceptibility to ACS. The investigation was replicated in the second study comprising 360 cases and 360 control subjects. The plasma concentration of IL-8 was measured by enzyme-linked immunosorbent assay.

Results

IL-8 −251 A/T polymorphism was associated with increased susceptibility to ACS (P = 0.004; odds ratio = 1.30; 95% confidence interval: 1.12–1.53). The second study yielded similar results. An increased IL-8 level was found in the plasma of acute myocardial infarction patients, suggesting that IL-8 −251 A/T may affect the expression of IL-8.

Conclusion

IL-8 −251 A/T polymorphism is associated with ACS risk in the Chinese Han population and the A allele of IL-8 −251 A/T may be an independent predictive factor for ACS.     

A multicopy suppressor ofnin1-1 of the yeastSaccharomyces cerevisiae is a counterpart of theDrosophila melanogaster diphenol oxidase A2 gene,Dox-A2

NIN1 is an essential gene for growth of the yeastSaccharomyces cerevisiae and was recently found to encode a component of the regulatory subunit of the 26S proteasome. Thenin1-1 mutant is temperature sensitive and its main defect is in G₁/S progression and G₂/M progression at non-permissive temperatures. One of the two multicopy suppressors ofnin1-1, SUN2 (SUppressor of Nin1-1), was found to encode a protein of 523 amino acids whose sequence is similar to those ofDrosophila melanogaster diphenol oxidase A2 and the mouse mast-cell Tum^– transplantation antigen, P91A. The C-terminal half of Sun2p was found to be functional as Sun2p at 25° C, 30° C, and 34° C but not at 37° C. The open reading frame (ORF) of theDrosophila diphenol oxidase A2 gene (Dox-A2) was obtained from a lambda phage cDNA library using the polymerase chain reaction technique. TheDox-A2 ORF driven by theTDH3 promoter complemented the phenotype of a strain deleted forsun2. ThisDox-A2-dependent strain was temperature sensitive and accumulated dumb-bell-shaped cells, with an undivided nucleus at the isthmus, after temperature upshift. This morphology is similar to that ofnin1-1 cells kept at a restrictive temperature. These results suggest thatSUN2 is a functional counterpart ofDox-A2 and that these genes play a pivotal role in the cell cycle in each organism.     

Suitability of Aphis fabae, Myzus persicae (Homoptera: Aphididae) and Aleyrodes proletella (Homoptera: Aleyrodidae) as prey for Coccinella undecimpunctata (Coleoptera: Coccinellidae)

The suitability of Aphis fabae Scopoli, Myzus persicae Sulzer and Aleyrodes proletella L. as food sources for Coccinella undecimpunctata L. was evaluated by studying the impact of prey consumption on the predator’s population growth parameters and feeding parameters. Unlike A. proletella, A. fabae and M. persicae supported the development and reproduction of C. undecimpunctata. A. fabae and M. persicae were considered to be essential prey, whereas A. proletella was considered to be an alternative prey. Aphid species showed different degrees of suitability: M. persicae significantly decreased the pre-oviposition period and increased adult longevity, fecundity and fertility compared with A. fabae. Moreover, A. fabae represents a suitable diet for larval development, but is not a suitable food source for adult reproduction. The predator’s population growth parameters, R₀, r_m and λ were increased with M. persicae, whereas T decreased. We found that the 4th instar larvae were the most voracious, particularly when fed on M. persicae; nevertheless, with this prey daily weight gain and feeding efficiency of 4th instar larvae were similar to that of individuals fed with A. fabae.     

Retrotransposon-induced ectopic expression of the Om(2D) gene causes the eye-specific Om(M) phenotype in Drosophila ananassae

Optic morphology (Om) mutations in Drosophila ananassae map to at least 22 loci, which are scattered throughout the genome. Om mutations are all semidominant, neomorphic, nonpleiotropic, and associated with the insertion of a retrotransposon, tom. We have found that the Om(2D) gene encodes a novel protein containing histidine/proline repeats, and is ubiquitously expressed during embryogenesis. The Om(2D) RNA is not detected in wild-type eye imaginal discs, but is abundantly found in the center of the eye discs of Om(2D) mutants, where excessive cell death occurs. D. melanogaster flies transformed with the Om(2D) cDNA under control of the hsp70 promoter display abnormal eye morphology when heat-shocked at the third larval instar stage. These results suggest that the Om(2D) gene is not normally expressed in the eye imaginal discs, but its ectopic expression, induced by the tom element, in the eye disc of third instar larvae results in defects in adult eye morphology.     

Phylogenetic relationships of Ceratitis fruit flies inferred from nuclear CAD and tango/ARNT gene fragments: Testing monophyly of the subgenera Ceratitis (Ceratitis) and C. (Pterandrus)

Systematic studies of Ceratitis (Tephritidae) fruit flies using molecular (i.e., COI, ND6, and period genes) and morphological (plus host-use characters) data have recently challenged the monophyly of the subgenera Ceratitis (Ceratitis) and Ceratitis (Pterandrus). In this paper, we report on the phylogenetic utility of three single-copy nuclear gene regions (two non-overlapping fragments of the carbamoylphosphate synthetase, CPS, locus of CAD, and a fragment of tango) within these taxa and investigate evolutionary relationships based on a concatenated ca. 3.4 kb data set that includes the six protein encoding gene regions. Results indicate that the CAD and tango genes provide useful phylogenetic signal within the taxa and are compatible with the previously studied genes. The two subgenera, as currently classified, are not monophyletic. Our molecular phylogenetic analyses support a revised classification in which (1) the subgenus C. (Pterandrus) comprises two lineages called A and B, (2) the C. (Pterandrus) B species should be included in C. (Ceratitis), and (3) the newly defined subgenera C. (Pterandrus) (=Pterandrus section A) and C. (Ceratitis) [=C. (Ceratitis) + C. (Pterandrus) section B] are reciprocally monophyletic.     

AtBS14a and AtBS14b, two Bet1/Sft1-like SNAREs from Arabidopsis thaliana that complement mutations in the yeast SFT1 gene

SNAREs are membrane-associated proteins that play a central role in vesicle targeting and intra-cellular membrane fusion reactions in eukaryotic cells. Here we describe the identification of AtBS14a and AtBS14b, putative SNAREs from Arabidopsis thaliana that share 60% amino acid sequence identity. Both AtBS14a and BS14b are dosage suppressors of the temperature-sensitive growth defect in sft1-1 cells and over-expression of either AtBS14a or AtBS14b can support the growth of sft1Δ cells but not bet1Δ cells. These data together with structure–function and biochemical studies presented herein suggest that AtBS14a and AtBS14b share properties that are consistent with them being members of the Bet1/Sft1 SNARE protein family.     

Morphological variation of Juniperus oxycedrus subsp. oxycedrus (Cupressaceae) in the Mediterranean region

The intra- and inter-population variation of Juniperus oxycedrus subsp. oxycedrus were examined biometrically on the basis of morphological characters of needles, seeds and cones. Cluster analysis of Euclidean distances and discriminant analysis were performed to verify the hypothesis of geographic differentiation and origin from the West- and East-Mediterranean Pleistocene refugial regions. The West-Mediterranean populations of J. oxycedrus subsp. oxycedrus differed from the eastern ones. The intra-populational differentiation of three of the West-Mediterranean populations was significantly higher than within the other West- and all the East-Mediterranean ones.Results confirm the hypothesis of probable different origins of the East- and West-Mediterranean populations of the taxon.     

Characterization of the pyruvate kinase-encoding gene (pki1) of Trichoderma reesei

The pyruvate kinase-encoding gene (pki1) from Trichoderma reesei was isolated by hybridization to the corresponding Aspergillus nidulans pkiA gene. The 1614-bp nucleotide (nt) sequence of the cloned gene codes for a 538-amino-acid protein. The coding sequence contains a single intron of 246 nt at a position identical to that of intron E in the A. nidulans gene. The PKI protein shows extensive homology to the PKIs of A. nidulans and A. niger (67%) and Saccharomyces cerevisiae (59%). The 5' non-coding sequence contains a number of motifs typical for yeast glycolytic genes, but so far only rarely found in filamentous fungi.     

Molecular phylogeny of the Acre clade (Crassulaceae): Dealing with the lack of definitions for Echeveria and Sedum

The phylogenetic relationships within many clades of the Crassulaceae are still uncertain, therefore in this study attention was focused on the “Acre clade”, a group comprised of approximately 526 species in eight genera that include many Asian and Mediterranean species of Sedum and the majority of the American genera (Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Villadia, and Thompsonella). Parsimony and Bayesian analyses were conducted with 133 species based on nuclear (ETS, ITS) and chloroplast DNA regions (rpS16, matK). Our analyses retrieved four major clades within the Acre clade. Two of these were in a grade and corresponded to Asian species of Sedum, the rest corresponded to a European–Macaronesian group and to an American group. The American group included all taxa that were formerly placed in the Echeverioideae and the majority of the American Sedoideae. Our analyses support the monophyly of three genera – Lenophyllum, Thompsonella, and Pachyphytum; however, the relationships among Echeveria, Sedum and the various segregates of Sedum are largely unresolved. Our analyses represents the first broad phylogenetic framework for Acre clade, but further studies are necessary on the groups poorly represented here, such as the European and Asian species of Sedum and the Central and South American species of Echeveria.     

Mitochondrial DNA phylogeography reveals the existence of an Evolutionarily Significant Unit of the sand goby Pomatoschistus minutus in the Adriatic (Eastern Mediterranean)

The sand goby Pomatoschistus minutus is a major component of marine shelf and estuarine food webs and an important study organism in behavioural research. Yet, despite the sand goby’s significance, its past and present patterns of migration and gene flow are poorly understood. Here we use the mtDNA control region and parts of the flanking tRNA genes of 63 fish from six localities in the Adriatic (Eastern Mediterranean), Western Mediterranean, Atlantic, and North Sea to investigate the phylogeography of this gobiid. Phylogenetic analyses and population genetics statistics reveal the existence of an Evolutionarily Significant Unit, sensu Moritz (1994), in the Adriatic and another in the Western Mediterranean, Atlantic, and North Sea. A possible biogeographical scenario for the separation of the ancestral population is that sand gobies in the Adriatic and Western Mediterranean split between 10,000 and 5000 years ago when due to the rise in sea temperature they migrated northwards and were bisected by the Italian peninsula. A testable prediction of this scenario is that sand gobies from the Western Mediterranean, Adriatic, and Aegean form three reciprocally monophyletic groups which are the descendants of a three-way diversification event.