Complete nucleotide sequence and gene organization of the mitochondrial genome of Paa spinosa (Anura: Ranoidae)

The mt genome of Paa spinosa (Anura: Ranoidae) is a circular molecule of 18,012 bp in length, containing 38 genes (including an extra copy of tRNA-Met gene). This mt genome is characterized by three distinctive features: a cluster of rearranged tRNA genes (LTPF tRNA gene cluster), a tandem duplication of tRNA-Met gene (Met1 and Met2), and distinct repeat regions at both 5′ and 3′-sides in the control region. Comparing the locations and the sequences of all tRNA-Met genes among Ranoidae, and constructing NJ tree of the nucleotide of those tRNA-Met genes, we suggested a tandem duplication of tRNA-Met gene can be regarded as a synapomorphy of Dicroglossinae. To further investigate the phylogenetic relationships of anurans, phylogenetic analyses (BI, ML and MP) based on the nucleotide dataset and the corresponding amino acid dataset of 11 protein-coding genes (except ND5 and ATP8) arrived at the similar topology.     

Mitochondrial sequence data reveals the phylogeny of the Asian Helice group of crabs (Decapoda: Brachyura: Varunidae)

The taxonomy of the Helice s. l. crabs has been recently revised, subdividing the Asian species in three genera, Helice , Helicana and Pseudohelice . The last one is widespread throughout the Indo-West Pacific Ocean and a single species, Pseudohelice subquadrata , is found in Asia. The other two genera appear to be endemic to Asia. However, phylogenetic affinities among the Asian representatives of Helice s. l. are poorly understood, and different morphology-based hypotheses of relationships remain untested. In this study, we used sequence data from a mitochondrial gene-block spanning three different genes [16S rDNA- trnL ₁ - IGS -nad1 ] to perform phylogenetic analyses. The results provide independent molecular evidence supporting the splitting of the Asian species into Helice and Helicana . Helice is suggested to be paraphyletic with respect to P. subquadrata . In addition, the heterogeneity of the genus Pseudohelice is shown when including the East Asian and East African counterparts. We propose that the two genera, Helice and Pseudohelice , are not monophyletic in their current composition.     

Hydroxylation of thiacloprid by bacterium Stenotrophomonas maltophilia CGMCC1.1788

Chloropyridinyl neonicotinoid insecticides play a major role in crop protection and flea control on cats and dogs. Imidacloprid, thiacloprid and acetamiprid have in common the 6-chloro-3-pyridinylmethyl group but differ in the nitroguanidine or cyanoamidine substituent on an acyclic or cyclic moiety. Our previous study found that Stenotrophomonas maltophilia CGMCC 1.1788 could hydroxylate imidacloprid to 5-hydroxy imidacloprid, and 5-hydroxy imidacloprid was easily converted to 10–19 times higher insecticidal olefin imidacloprid against aphid or whitefly. Acetamiprid could be transformed by S. maltophilia to form N-demethylation product(IM 2-1). In this paper, we examined S. maltophilia CGMCC 1.1788’s ability of transformation of thiacloprid. S. maltophilia CGMCC 1.1788 can hydroxylate thiacloprid to 4-hydroxy thiacloprid characterized by HPLC-MS/MS and NMR analysis, however 4-hydroxy thiacloprid could not be converted to olefin thiacloprid under acid conditions like imidacloprid, whereas oxidized and decyonated simultaneously to form 4-ketone thiacloprid imine in alkaline solution. Bioassays indicated that 4-hydroxy thiacloprid had 156 times lower insecticidal activity than thiacloprid, and the ketone-imine derivative almost had no toxicity towards aphid. Though both imidacloprid and thiacloprid are hydroxylated by S. maltophilia CGMCC 1.1788 at the same carbon atom position, however the structural difference between in imidacloprid and thiacloprid, originate the entire discrepancy in bioefficacy of metabolite and its further degrading pathway. These results explain that why thiacloprid is classified as not relevant grade for soil and seed applications, whereas imidacloprid is recommended and acetamiprid is limited.     

A novel C-type lectin (Cflec-3) from Chlamys farreri with three carbohydrate-recognition domains

C-type lectins are a superfamily of carbohydrate-recognition proteins which play crucial roles in the innate immunity. In this study, the gene of a C-type lectin with multiple carbohydrate-recognition domains (CRDs) from scallop Chlamys farreri (designated as Cflec-3) was cloned by rapid amplification of cDNA ends (RACE) approach based on expression sequence tag (EST) analysis. The full-length cDNA of Cflec-3 was of 2256 bp. The open reading frame encoded a polypeptide of 516 amino acids, including a signal sequence and three CRDs. The deduced amino acid sequence of Cflec-3 showed high similarity to members of C-type lectin superfamily. By fluorescent quantitative real-time PCR, the Cflec-3 mRNA was mainly detected in hepatopancreas, adductor, mantle, and marginally in gill, gonad and hemocytes of healthy scallops. After scallops were challenged by Listonella anguillarum, the mRNA level of Cflec-3 in hemocytes was up-regulated and was significantly higher than that of blank at 8 h and 12 h post-challenge. The function of Cflec-3 was investigated by recombination and expression of the cDNA fragment encoding its mature peptide in Escherichia coli BL21 (DE3)-pLysS. The recombined Cflec-3 (rCflec-3) agglutinated Gram-negative bacteria Pseudomonas stutzeri. The agglutinating activity was calcium-dependent and could be inhibited by d-mannose. These results collectively suggested that Cflec-3 was involved in the immune response against microbe infection and contributed to nonself-recognition and clearance of bacterial pathogens in scallop.     

Purification and characterization of a small cationic protein from the tobacco hornworm Manduca sexta

The prophenoloxidase (proPO) activation system is an important defense mechanism in arthropods, and activation of proPO to active phenoloxidase (PO) involves a serine proteinase cascade. Here, we report the purification and characterization of a small cationic protein CP8 from the tobacco hornworm, Manduca sexta, which can stimulate proPO activation. BLAST search showed that Manduca CP8 is similar to a fungal proteinase inhibitor-1 (AmFPI-1), an inducible serine proteinase inhibitor-1 (ISPI-1), and other small cationic proteins with unknown functions. However, we showed that Manduca CP8 did not inhibit proteinase activity, but stimulated proPO activation in plasma. When small amount (0.1 μg) of purified native CP8 or BSA was added to cell-free plasma samples and incubated for 20 min, low PO activity was observed in both groups. But significantly higher PO activity was observed in the CP8-group than in the BSA-group when more proteins (0.5 μg) were added and incubated for 20 min. However, when the plasma samples were incubated with proteins for 30 min, high PO activity was observed in both the CP8 and BSA groups regardless of the amount of proteins added. Moreover, when PO in the plasma was pre-activated with Micrococcus luteus, addition of CP8 did not have an effect on PO activity, and CP8/bacteria mixture did not stimulate PO activity to a higher level than did BSA/bacteria. These results suggest that CP8 helps activate proPO more rapidly at the initial stage. CP8 mRNA was specifically expressed in fat body and its mRNA level decreased when larvae were injected with saline or bacteria. However, CP8 protein concentration in hemolymph did not change significantly in larvae injected with saline or microorganisms.     

Meprin A and meprin α generate biologically functional IL-1β from pro-IL-1β

The present study demonstrates that both oligomeric metalloendopeptidase meprin A purified from kidney cortex and recombinant meprin α are capable of generating biologically active IL-1β from its precursor pro-IL-1β. Amino-acid sequencing analysis reveals that meprin A and meprin α cleave pro-IL-1β at the His¹¹⁵-Asp¹¹⁶ bond, which is one amino acid N-terminal to the caspase-1 cleavage site and five amino acids C-terminal to the meprin β site. The biological activity of the pro-IL-1β cleaved product produced by meprin A, determined by proliferative response of helper T-cells, was 3-fold higher to that of the IL-1β product produced by meprin β or caspase-1. In a mouse model of sepsis induced by cecal ligation puncture that results in elevated levels of serum IL-1β, meprin inhibitor actinonin significantly reduces levels of serum IL-1β. Meprin A and meprin α may therefore play a critical role in the production of active IL-1β during inflammation and tissue injury.     

Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales

Background  

The phylogeny of Cetacea (whales) is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins) underestimates its diversity. To remedy these problems, we sequenced the complete mitochondrial genomes of seven dolphins and analyzed these data with partitioned Bayesian analyses. Moreover, we incorporate a newly-developed "relaxed" molecular clock to model heterogenous rates of evolution among cetacean lineages.     

Fifteen polymorphic microsatellite markers for the giant spiny frog, Paa spinosa

We characterized 15 polymorphic microsatellite loci for the giant spiny frog, Paa spinosa. These loci were highly polymorphic when screened in 38 individuals from two different populations, with nine to 23 alleles per locus. The range of observed and expected heterozygosities was 0.231-0.916 and 0.296-0.944, respectively. These polymorphic loci will be useful for assessing genetic diversity, population structure, gene flow, population assignment and determining paternity in the giant spiny frog.     

Polymorphic microsatellite DNA markers for the ark shell Scapharca subcrenata (bivalve: Arcidae)

We have isolated and characterized twelve novel polymorphic microsatellite loci from Scapharca subcrenata to analyse the population structure. The number of observed alleles per locus ranged from 3 to 17. Observed heterozygosity (H _O) ranged from 0.321 to 0.929. Cross-species amplification was tested successfully in three other bivalve species. These microsatellite markers will be useful for genetic diversity studies of S. subcrenata and other Lamellibranchia species.     

Isolation and characterization of microsatellite markers from reed parrotbill, Paradoxornis heudei (Aves: Timaliidae)

Eleven microsatellite markers were obtained from reed parrotbill, Paradoxornis heudei, using the fast isolation by AFLP of sequences containing repeats (FIASCO) method as part of an effort to compare levels of genetic diversity in different populations of China. Polymorphism levels ranged form 5 to 11 alleles (mean = 9.27) using 32 reed parrotbills, with the observed heterozygosity ranging from 0.037 to 0.80. Six loci were significant deviated from HWE and nine loci showed linkage equilibrium. The utility of these loci on two other Passeriformes species, vinous-throated parrotbill (P. webbianus) and oriental great reed warbler (Acrocephalus orientalis), were also tested.