A comparative description of mitochondrial DNA differentiation in selected avian and other vertebrate genera

Levels of mitochondrial DNA (mtDNA) sequence divergence between species within each of several avian (Anas, Aythya, Dendroica, Melospiza, and Zonotrichia) and nonavian (Lepomis and Hyla) vertebrate genera were compared. An analysis of digestion profiles generated by 13-18 restriction endonucleases indicates little overlap in magnitude of mtDNA divergence for the avian versus nonavian taxa examined. In 55 interspecific comparisons among the avian congeners, the fraction of identical fragment lengths (F) ranged from 0.26 to 0.96 (F = 0.46), and, given certain assumptions, these translate into estimates of nucleotide sequence divergence (p) ranging from 0.007 to 0.088; in 46 comparisons among the fish and amphibian congeners, F values ranged from 0.00 to 0.36 (F = 0.09), yielding estimates of P greater than 0.070. The small mtDNA distances among avian congeners are associated with protein-electrophoretic distances (D values) less than approximately 0.2, while the mtDNA distances among assayed fish and amphibian congeners are associated with D values usually greater than 0.4. Since the conservative pattern of protein differentiation previously reported for many avian versus nonavian taxa now appears to be paralleled by a conservative pattern of mtDNA divergence, it seems increasingly likely that many avian species have shared more recent common ancestors than have their nonavian taxonomic counterparts. However, estimates of avian divergence times derived from mtDNA- and protein-calibrated clocks cannot readily be reconciled with some published dates based on limited fossil remains. If the earlier paleontological interpretations are valid, then protein and mtDNA evolution must be somewhat decelerated in birds. The empirical and conceptual issues raised by these findings are highly analogous to those in the long-standing debate about rates of molecular evolution and times of separation of ancestral hominids from African apes.      

Improved Electrochemical Analysis of Neuropathy Target Esterase Activity by a Tyrosinase Carbon Paste Electrode Modified by 1-Methoxyphenazine Methosulfate

A graphite-paste tyrosinase biosensor was improved by adding 1-methoxyphenazine methosulfate as a mediator. Mediator modification enhanced sensitivity to phenol 4-fold and long-term stability 3-fold. Phenol could be detected at 25 nM (S/N=2) using an Ag/AgCl reference electrode. The biosensor was used to measure the activity of a toxicologically significant enzyme, neuropathy target esterase (NTE), which yields phenol by hydrolysis of the substrate, phenyl valerate. Using the new biosensor, blood and brain NTE inhibition by organophosphorus (OP) compounds with different neuropathic potencies were well correlated (r=0.990, n=7), supporting the use of blood NTE as a biochemical marker of exposure to neuropathic OP compounds.     

Cheap and Long‐Life Reusable Polymer for Asymmetric Organozinc Catalysis Based on Camphor‐Derived Hydroxyamides

Polystyrene grafted with a chiral zinc‐complexing camphor‐derived N,N‐disubstituted hydroxyamide is proposed as a new type of functional polymer of high reusability for the development of sustainable organozinc‐catalyzed asymmetric reactions. The main goal of this new functional polymer is the ease of the hydroxyamide‐moiety preparation (cheap chiral ligand obtained straightforwardly from an enantiopure starting material coming from the chiral pool), as well as its chemical robustness when compared with other related zinc‐complexing functional groups. The latter allows the polymer to be active after multiple applications, without significant loss of its catalytic activity. This fact is exemplified by the design and preparation of a polymer functionalized with a bis(hydroxyamide) proved previously as active in the homogeneous enantioselective addition of diethylzinc to aldehydes. The result is a cheap functional polymer with a very high reusability (the enantioselectivity and chemical yield are maintained practically constant after 20 applications). Additionally, a methodology for the multicycle use of these functional polymers is presented. Chirality, 2012. © 2012 Wiley Periodicals, Inc.     

Selection against genetic defects in conservation schemes while controlling inbreeding

We studied different genetic models and evaluation systems to select against a genetic disease with additive, recessive or polygenic inheritance in genetic conservation schemes. When using optimum contribution selection with a restriction on the rate of inbreeding (ΔF) to select against a disease allele, selection directly on DNA-genotypes is, as expected, the most efficient strategy. Selection for BLUP or segregation analysis breeding value estimates both need 1–2 generations more to halve the frequency of the disease allele, while these methods do not require knowledge of the disease mutation at the DNA level. BLUP and segregation analysis methods were equally efficient when selecting against a disease with single gene or complex polygene inheritance, i.e. knowledge about the mode of inheritance of the disease was not needed for efficient selection against the disease. Smaller schemes or schemes with a more stringent restriction on ΔF needed more generations to halve the frequency of the disease alleles or the fraction of diseased animals. Optimum contribution selection maintained ΔF at its predefined level, even when selection of females was at random. It is argued that in the investigated small conservation schemes with selection against a genetic defect, control of ΔF is very important.     

Distribution of ichthyoplankton in the eastern Peter the Great Bay,Sea of Japan,in June and July of 2007

Comparison of the results of ichthyoplankton surveys conducted at 97 stations in the eastern part of the Peter the Great Bay of the Sea of Japan, in June–July 2007 with the similar research data of the 1950s shows that at present, as was the case 50 years ago, flatfish eggs belonging mainly to the yellowfin sole Limanda aspera and brown sole Pleuronectes herzensteini prevail in the local ichthyoplankton (up to 86%). The highest concentrations of these species’ eggs were recorded in the Vostok Bay and Strelok Bay. The spawning activity of flatfish in 2007 is found to be lower than in the mid 1900s, but the significance of the eastern part of the Peter the Great Bay for flatfish reproduction remains large. The importance of long-term monitoring in this area, which is being subjected to steadily growing anthropogenic impacts, is also proven.     

Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae)

We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that are heterogeneity is correlated between loci at synonymous sites. At nonsynonymous sites, the pattern of rate heterogeneity is not correlated between loci, primarily due to an aberrant pattern of rate heterogeneity at nonsynonymous sites of rbcL. We compare patterns of synonymous rate heterogeneity to predictors based on the generation time effect and the speciation rate hypotheses. Although there is some evidence for generation time effects, neither generation time effects nor speciation rates appear to be sufficient to explain patterns of rate heterogeneity in the grass plastid sequences.      

Induction of catalytic activity of plasminogen by monoclonal antibody IV-Ic in the presence of divalent metal cations and α2-antiplasmin

Investigation of the influence of divalent metal cations on the induction of plasminogen catalytic activity by monoclonal antibody IV-Ic showed that the presence of metal cations in the reaction medium changes the induction by slowing down or accelerating the process. Ions of Zn²⁺, Mn²⁺, and Cu²⁺ completely inhibit activation. Ions of Co²⁺ and Ni²⁺ decrease the rate of the first and second phases of the reaction more than 2 times. Ca²⁺ ions do not have any effect on the activation rate. Ions of Mg²⁺, Ba²⁺, and Sr²⁺ increase the rate of the first phase of the reaction by 1.5, 2.0, and 2.0 times and the rate of the second phase by 2.0, 3.8, and 4.7 times, correspondingly. Sr²⁺ ions have the strongest stimulating effect on plasminogen activation by monoclonal antibody IV-Ic. Investigation of the dose dependent effect of Sr²⁺ on the rate of plasminogen activation by monoclonal antibody IV-Ic showed stimulating effect of Sr²⁺ at concentrations from 0.1 to 1.0 mM with half maximum at 0.6 mM. However, Sr²⁺ ions do not affect amidolytic activity of plasmin and activation of plasminogen by streptokinase. Sr²⁺ ions also do not affect monoclonal antibody IV-Ic binding to plasminogen. The effect of Sr²⁺ is specific and mediated by the IV-Ic component. The presence of metal cations affects conformational changes in the process of active site formation. Metal cations also affect structure of the plasminogen molecule active site in the complex with monoclonal antibody IV-Ic and enzyme-substrate interaction. The effect of α₂-antiplasmin on the induction of plasminogen catalytic activity by monoclonal antibody IV-Ic in range of concentrations from 5 to 30 nM has been studied. α₂-Antiplasmin at concentration 30 nM almost completely inhibits induction of plasminogen catalytic activity by monoclonal antibody IV-Ic at the ratio plasminogen/α₂-antiplasmin of 3:1. This can be explained by competition of α₂-antiplasmin and monoclonal antibody IV-Ic for the lysine-binding sites of plasminogen and inhibition of the active center in activated complex plasminogen*—mAB IV-Ic. Divalent metal cations and α₂-antiplasmin are important factors in induction of plasminogen catalytic activity by monoclonal antibody IV-Ic. Published in Russian in Biokhimiya, 2006, Vol. 71, No. 6, pp. 778–785.     

Genomic aberrations in lung adenocarcinoma in never smokers

Background

Lung cancer in never smokers would rank as the seventh most common cause of cancer death worldwide.

Methods and Findings

We performed high-resolution array comparative genomic hybridization analysis of lung adenocarcinoma in sixty never smokers and identified fourteen new minimal common regions (MCR) of gain or loss, of which five contained a single gene (MOCS2, NSUN3, KHDRBS2, SNTG1 and ST18). One larger MCR of gain contained NSD1. One focal amplification and nine gains contained FUS. NSD1 and FUS are oncogenes hitherto not known to be associated with lung cancer. FISH showed that the amplicon containing FUS was joined to the next telomeric amplicon at 16p11.2. FUS was over-expressed in 10 tumors with gain of 16p11.2 compared to 30 tumors without that gain. Other cancer genes present in aberrations included ARNT, BCL9, CDK4, CDKN2B, EGFR, ERBB2, MDM2, MDM4, MET, MYC and KRAS. Unsupervised hierarchical clustering with adjustment for false-discovery rate revealed clusters differing by the level and pattern of aberrations and displaying particular tumor characteristics. One cluster was strongly associated with gain of MYC. Another cluster was characterized by extensive losses containing tumor suppressor genes of which RB1 and WRN. Tumors in that cluster frequently harbored a central scar-like fibrosis. A third cluster was associated with gains on 7p and 7q, containing ETV1 and BRAF, and displayed the highest rate of EGFR mutations. SNP array analysis validated copy-number aberrations and revealed that RB1 and WRN were altered by recurrent copy-neutral loss of heterozygosity.

Conclusions

The present study has uncovered new aberrations containing cancer genes. The oncogene FUS is a candidate gene in the 16p region that is frequently gained in never smokers. Multiple genetic pathways defined by gains of MYC, deletions of RB1 and WRN or gains on 7p and 7q are involved in lung adenocarcinoma in never smokers.     

Larvae and Juveniles of the Genus Liparis (Pisces: Liparidae) from the Northwestern Sea of Japan

Larvae and juveniles of Liparis ochotensis, L. latifrons, L. tartaricus, L.brashnikovi, and L. kusnetzovi (Liparidae) are described for the first time based on ichthyoplankton catches carried out in the northwestern Sea of Japan in the decade 1992–2002. Our earlier published data on the larval development of L. agassizii and juveniles of L. punctulatus are supplemented. It is shown that larval development in the Liparis includes a planktonic stage. The larvae of different species turn into juveniles at a different lengths: under 15 mm in the case of littoral species and at about or over 20 mm in the case of sublittoral species. The major morphological characteristics of larvae of different Liparis species—body height and shape, pelvic disk length, preanal length, presence of a notch in the dorsal fin, pigmentation pattern, and others—have been distinguished. Original illustrations of larvae and juveniles are provided.     

Peculiarities of early ontogenesis of the tubenose poacher, <Emphasis Type="Italic">Pallasina barbata</Emphasis> steindachner, 1876 (Pisces,Agonidae) from Peter the Great Bay (Sea of Japan)

Based on the analysis of original material (52 specimens of Pallasina barbata larvae and juveniles), sampled in the Peter the Great Bay (Sea of Japan) from 1992 to 2006, the ontogenetic stages of this species were described for the first time. It is shown that P. barbata has a planktonic larval stage in its development. The major morphologic features that are typical for larvae and juveniles during their development were revealed. It was shown that snout length, head length and pectoral fin size are increased with growth; at the same time body height and eye diameter are decreased, and the nature of larval pigmentation is changed. The main differences between P. barbata and close species are shown. Original illustrations of larvae and juvenile are provided.