Duplication and divergence: the evolution of nematode globins

In common with many other groups, nematodes express globins with unknown functions. Nematode globin-like genes can be divided into class 1 globins, similar to vertebrate myoglobins, and a wide range of additional classes. Here we show that class 1 nematode globins possess a huge amount of diversity in gene sequence and structure. There is evidence for multiple events of gene duplication, intron insertion and loss between species, and for allelic variation effecting both synonymous and non-synonymous sites within species. We have also examined gene expression patterns in class I globins from a variety of species. The results show variation in the degree of gene expression, but the tissue specificity and temporal specificity of expression may be more conserved in the phylum. Because the structure-function relationships for the binding and transport of oxygen by globins are well understood, the consequences of genetic variation causing amino acid changes are explored. The gene family shows great promise for discovering unique insights into both structure-function relationships of globins and their physiologial roles.     

Presence and partial characterisation of a major proteolytic enzyme in the larval gut of Callosobruchus maculatus

Protease activity in the gut of larvae of the bruchid beetle, Callosobruchus maculatus (a storage pest of cowpea seeds), has been investigated to help clarify nutritional mechanisms in view of reports that these insects carry out little or no proteolysis (Applebaum, 1964). Larval gut homogenates showed protease activity against a variety of different protein substrates, but did not hydrolyse a synthetic trypsin substrate. The proteolytic activity had a pH optimum of 5.4. It was not inhibited by serine protease inhibitors, but was inhibited by reagents reactive against-SH groups. Protein trypsin inhibitors from legume seeds which are not hosts to C. maculatus (soybean, limabean) were not effective inhibitors of the larval proteolytic activity but a cowpea protease inhibitor preparation and aprotinin partially inhibited proteolysis. The latter two inhibitors also inhibited the plant thiol protease papain. It is suggested that C. maculatus has replaced the normal insect proteases with an enzyme similar to plant proteases to evade the antimetabolic effects of trypsin/chymotrypsin inhibitors in seeds. Besides trypsin/chymotrypsin inhibitors, cowpea seeds also contain proteins which inhibit papain; these inhibitors were purified and were shown to be effective inhibitors of C. maculatus larval protease.

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Mise en évidence et caractérisation partielle d'une enzyme protéolytique importante du tube digestif des larves de Callosobruchus maculatus

Résumé Callosobruchus maculatus attaque les graines stockées particulièrement de Vigna unguiculata. L'activité protéolytique du tube digestif des larves a été examinée. Aucune hydrolyse n'a été observée contre la N-benzoyl arginine p-nitroanilide (substrat de la trypsine synthétique), mais la protéolyse a été mise en évidence en utilisant la viciline de V. unguiculata comme substrat naturel ou la myoglobine comme substrat artificiel, le p.H optimum est de 5,4. Les inhibiteurs chimiques des protéases de la sérine n'ont pas altéré l'activité enzymatique, mais les réactifs du groupe SH l'ont inhibée. Nous suggérons que cette protéase est une thiol protéase, c'est à dire avec un groupe actif semblable à celui de la papaïne, protéase végétale. En accord avec cette hypothèse, les inhibiteurs de protéine efficaces seulement contre la trypsine, c'est à dire les inhibiteurs de la trypsine de Glycine max et de la trypsine de Phaseolus lunatus n'affectent pas cette protéase larvaire, tandis que les protéines avec une faible action inhibitrice contre la papaïne (préparation inhibitrice de la protéase de V. unguiculata, aprotinine) inhibent partiellement la protéolyse par des extraits de tube digestif larvaire.Des inhibiteurs protéiques de papaïne extraits de graines de V. unguiculata sont des inhibiteurs très efficaces de la protéase larvaire. On peut penser que C. maculatus contient une protéase semblable aux protéases végétales, plutôt qu'aux protéases classiques, d'insectes, ce qui permet d'éviter les effets antimétaboliques directs des inhibiteurs de protéase (inhibiteurs de trypsine et de chymotrypsine) trouvés en quantité relativement importantes dans les graines de légumineuses.

     

A Novel Neutral Protease from <Emphasis Type=Italic>Thermoactinomyces</Emphasis> Species 27a: Sequencing of the Gene,Purification, and Characterization of the Enzyme

The nucleotide sequence of the previously cloned (Zabolotskaya, M. V., Nosovskaya, E. A., Kaplun, M. A., and Akimkina, T. V. (2001). Mol. Gen. Mikrobiol. Virusol. No 1, 32–34) DNA fragment from Thermoactinomyces sp. 27a (GenBank Accession No. AY280367) containing the metalloproteinase gene was determined. A continuous open reading frame encoding a polypeptide of 673 aa was revealed. Analysis of this sequence demonstrated that the metalloproteinase from Thermoactinomyces sp. 27a is synthesized as a preproprotein and includes a leader peptide (26 aa), N-terminal propeptide (215 aa), mature region (317 aa), and additional C-terminal domain (115 aa). The recombinant enzyme from Thermoactinomyces sp. 27a was expressed in Bacillus subtilis AJ73 cells and purified by anion exchange chromatography to an electrophoretically homogeneous state. The determined N-terminal amino acid sequence of the mature protein was identical to that deduced from the gene. The obtained data suggest that the mature protein should include 432 aa and have a calculated molecular weight of 46,262 Da. However, the molecular weight of the mature protein determined by mass spectrometry was 34,190 ± 70 Da indicating a C-terminal processing. Theproteinase was not inhibited by phenylmethyl sulfonyl fluoride but was inhibited by o-phenanthroline and ethylenediaminetetraacetic acid. The enzyme had maximum activity by azocasein hydrolysis at 55°C and pH 6.5–7.5; it was stable at pH 7.5–8.5 and remained stable at 50°C for several hours. The k_cat/K_m for 3-(2-furyl)acryloyl-glycyl-L-leucine amide hydrolysis was (2.8 ± 0.1) ×10³ M^–1×s^–1.     

Spatial, seasonal and species variations of harmful algal blooms in the South Yellow Sea and East China Sea

The occurrences of harmful algal blooms (HABs), in terms of frequency and area in the Chinese coastal waters, have been increasing since 1980s and caused considerable economic losses. In the present study, we have analyzed spatial and seasonal characteristics of HAB events in the southern Yellow Sea and East China Sea along Chinese coast from 1933 to 2004. With a total 435 HAB records, the most frequent HAB occurrence area (FHA) is off the Yangtze River mouth and another two FHA areas are located south of the Yangtze River estuary along about isobaths of 30–60 m coastal water in the East China Sea. The time of HAB occurrence shifted during our study period: from autumn (August–October) before 1980s to July–August in 1980s, during May–July in 1990s, and May–June for the period of 2000–2004. Causative species were found to be different: Noctiluca scintillans and Skeletonema costatum were dominant causative species prior to 2000; and Prorocentrum donghaiense Lu was dominant from 2000 to 2004 and also caused large blooms in May. Trichodesmium sp. caused many HABs in autumn (August–October) prior to 1980s with only one HAB between 1980 and 2004. The changes of the dominant HAB species may have affected the timings of HAB occurrence, as well as the increasing HAB-affected areas in recent years.     

The monosaccharide transporter gene family in Arabidopsis and rice: a history of duplications, adaptive evolution, and functional divergence

Current hypotheses of gene duplicate divergence propose that surviving members of a gene duplicate pair may evolve, under conditions of purifying or nearly neutral selection, in one of two ways: with new function arising in one duplicate while the other retains original function (neofunctionalization [NF]) or partitioning of the original function between the 2 paralogs (subfunctionalization [SF]). More recent studies propose that SF followed by NF (subneofunctionalization [SNF]) explains the divergence of many duplicate genes. In this analysis, we evaluate these hypotheses in the context of the large monosaccharide transporter (MST) gene families in Arabidopsis and rice. MSTs have an ancient origin, predating plants, and have evolved in the seed plant lineage to comprise 7 subfamilies. In Arabidopsis, 53 putative MST genes have been identified, with one subfamily greatly expanded by tandem gene duplications. We searched the rice genome for members of the MST gene family and compared them with the MST gene family in Arabidopsis to determine subfamily expansion patterns and estimate gene duplicate divergence times. We tested hypotheses of gene duplicate divergence in 24 paralog pairs by comparing protein sequence divergence rates, estimating positive selection on codon sites, and analyzing tissue expression patterns. Results reveal the MST gene family to be significantly larger (65) in rice with 2 subfamilies greatly expanded by tandem duplications. Gene duplicate divergence time estimates indicate that early diversification of most subfamilies occurred in the Proterozoic (2500-540 Myr) and that expansion of large subfamilies continued through the Cenozoic (65-0 Myr). Two-thirds of paralog pairs show statistically symmetric rates of sequence evolution, most consistent with the SF model, with half of those showing evidence for positive selection in one or both genes. Among 8 paralog pairs showing asymmetric divergence rates, most consistent with the NF model, nearly half show evidence of positive selection. Positive selection does not appear in any duplicate pairs younger than approximately 34 Myr. Our data suggest that the NF, SF, and SNF models describe different outcomes along a continuum of divergence resulting from initial conditions of relaxed constraint after duplication.     

Variation in life-history characteristics among populations of North American wood turtles: a view from the north

Life-history traits such as age at maturity, body size and clutch size tend to vary across a species' distribution. The purpose of our study was to describe the demography of a newly discovered population of North American wood turtles Glyptemys insculpta at the species' northern range limit, and to compare our findings to those of other studies to test hypotheses about adaptive life-history variation. Turtles were hand-captured from May to October 2005 and 2006 along a 4.5 km stretch of river located in the Sudbury District, ON, Canada (46°N). Fifty-five captured individuals provided a population density estimate of 1.3 turtles/100 m of river. Juveniles comprised 35% of wood turtles captured, and growth ring counts (i.e. age estimates) indicated recruitment in each of the past 11 years. Among populations, we found a nonlinear pattern in body size variation with the largest turtles in the north, smallest turtles in the centre of the range, and intermediate-sized turtles in the south. This nonlinear pattern in body size was reflected in clutch size variation. Selective pressures to overcome years of low recruitment may have resulted in larger body sizes and hence large clutch sizes at northern latitudes while conspecifics at southern latitudes can achieve larger body sizes because they live in a more productive environment. Population density decreased with latitude, likely as a result of a gradient in habitat productivity.     

Primary cultures and the levels of cytochromeP450 in hepatocytes from mouse,rat, hamster,and rabbit liver

Summary Hepatocyte primary cultures (HPC) derived from rat, mouse, hamster, and rabbit liver were characterized for a variety of parameters. The conditions that maximized recovery, attachment, and survival varied between species. Hepatocytes from all four species were capable of attaching in serum-free Williams’ medium E (WME), but optimal attachment as monolayer cultures was achieved for mouse and hamster HPC in medium receiving 1% calf serum supplementation. Hamster hepatocytes required additional cations, whereas rabbit and rat hepatocytes displayed maximal attachment in medium supplemented with 10% calf serum. Survival of mouse and rabbit hepatocytes after 24 h in serum supplemented media was in the order of 90%. Rat and hamster hepatocyte 24 h survival was approximately 70 and 60%, respectively, and was not significantly affected by serum supplementation. Hepatocytes from each species varied in their content of cytochromeP450 at the time of isolation and in the rate of reduction during culture. Mouse and rat hepatocytes demonstrated the most rapid decline in content during the initial 24 h in culture, whereas concentrations in rabbit hepatocytes were virtually unchanged. The rate of decline inP450 concentrations in hamster hepatocytes was intermediate between those displayed by rat and rabbit hepatocytes. These studies have delineated conditions useful for the culture of hepatocytes from four species and have documented the status of an important parameter of their functional capability. This study was supported by EPA contract 68-01-6179. C. J. Maslansky was a recipient of a Monsanto Fund Fellowship in Toxicology.     

Genetic variation in the Italian crested newt, Triturus carnifex, and the origin of a non-native population north of the Alps

Genetic variation over 40 protein loci and 46 populations representing three taxa of crested newts revealed moderate genetic distances between Triturus carnifex carnifex, T. c. macedonicus and T. cristatus. Two populations from the Geneva Basin (presumed to be introduced) were genetically similar to T. c. carnifex and dissimilar to T. c. macedonicus and T. cristatus, showing that they belong to T. c. carnifex and not to native T. cristatus. A significant pattern of spatial genetic variation was found within T. c. carnifex along a north to south axis, from Croatia to Calabria. The Genevan populations showed highest genetic similarity with T. carnifex from Tuscany, suggesting that the propagule originated from that area. Effects of a population genetic bottleneck associated with the introduction could not be documented. The observed high allelic variation in Genevan T. c. carnifex could not be directly explained by introgression from T. cristatus. Comparisons across the range, including zones of hybridization within the T. cristatus superspecies, indicated that some alleles typical for the Genevan population may represent the so-called `hybrizymes'.     

南沙群岛珊瑚礁浮游动物多样性与群落结构

珊瑚礁是地球上已知的海洋生物多样性最高的生态系统,为了深入分析珊瑚礁的浮游动物多样性和群落结构,2004年5月5-15日在南沙群岛渚碧礁布设10个大面站(漏湖、礁坪各5个)和1个连续站(位于礁坪),使用网目孔径分别为169 μm和505 μm的两种浮游生物网进行垂直拖网采样.结果表明:共鉴定浮游动物种类96种和幼虫17个类群(或类型),其中桡足类最多,达65种,其次是幼虫;浮游动物数量丰富-根据169 μm网具样品的数据,平均丰度高达926.0±1,155.8 inds./m3,优势类群依次是桡足类、被囊类和幼虫,优势种为奥氏胸刺水蚤(Centropages orsinii)、珍妮纺锤水蚤(Acartia shuzheni)、长尾住囊虫(Oikopleura longicauda)、梭形住囊虫(O.fusifornis)和腹足类面盘幼虫(Gastropoda veliger);渚碧礁浮游动物空间分布差异相当显著,漏湖区形成与礁坪区不同的群落,前者种类多、丰度高、优势种突出、均匀度低,而后者则完全相反,浮游动物群落的空间变化是由珊瑚礁礁盘的空间异质性所造成.浮游动物昼夜变化明显,夜间出现的种数和平均丰度分别是日间的4.6和46.2倍.浮游动物群落以终生浮游生物的种类和数量占多数,它们来源于礁外海水,有的也属于礁栖类型.在珊瑚礁中,中小型浮游动物无论在种类还是丰度方面都占有非常重要的位置.     

Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions

Invasive species are predicted to suffer from reductions in genetic diversity during founding events, reducing adaptive potential. Integrating evidence from two literature reviews and two case studies, we address the following questions: How much genetic diversity is lost in invasions? Do multiple introductions ameliorate this loss? Is there evidence for loss of diversity in quantitative traits? Do invaders that have experienced strong bottlenecks show adaptive evolution? How do multiple introductions influence adaptation on a landscape scale? We reviewed studies of 80 species of animals, plants, and fungi that quantified nuclear molecular diversity within introduced and source populations. Overall, there were significant losses of both allelic richness and heterozygosity in introduced populations, and large gains in diversity were rare. Evidence for multiple introductions was associated with increased diversity, and allelic variation appeared to increase over long timescales (~100 years), suggesting a role for gene flow in augmenting diversity over the long‐term. We then reviewed the literature on quantitative trait diversity and found that broad‐sense variation rarely declines in introductions, but direct comparisons of additive variance were lacking. Our studies of Hypericum canariense invasions illustrate how populations with diminished diversity may still evolve rapidly. Given the prevalence of genetic bottlenecks in successful invading populations and the potential for adaptive evolution in quantitative traits, we suggest that the disadvantages associated with founding events may have been overstated. However, our work on the successful invader Verbascum thapsus illustrates how multiple introductions may take time to commingle, instead persisting as a ‘mosaic of maladaptation’ where traits are not distributed in a pattern consistent with adaptation. We conclude that management limiting gene flow among introduced populations may reduce adaptive potential but is unlikely to prevent expansion or the evolution of novel invasive behaviour.     

The mouse pubic symphysis as a remodeling system: morphometrical analysis of proliferation and cell death during pregnancy, partus and postpartum

Marked changes in mice pubic symphysis occur by the end of pregnancy. Tissue remodeling involves a dynamic balance between cell proliferation and programmed cell death as well as changes in the extracellular matrix components. Therefore, it is important to consider both of these cellular behaviors when investigating the mechanism that regulates interpubic tissue remodeling, growth during late pregnancy and partus ensuring involution during the postpartum period. Proliferating and programmed death cells were identified by immunohistochemistry (proliferating cell nuclear antigen and TUNEL detection, respectively) and the rates at which these processes occurred were determined by morphometric analysis. The results demonstrated that cellular proliferation was intense during the period of ligament formation, from D15 to D18, thereafter abruptly declining on D19. From parturition (D19) onwards, an ever-increasing decline in the cellular proliferation levels could be observed. The quantitative analyses of cellular death showed opposite results when compared to cellular proliferation. During early pregnancy the cycle of cellular renovation was clearly proliferative and during late mouse pregnancy the cycle was directed by programmed cellular death. Although the high levels of cellular death during postpartum involution could be shown by the TUNEL-positive cells, we were unable to observed picnotic nucleus at the light microscopy.     

Drosophila subpulchrella, a new species of the Drosophila suzukii species subgroup from Japan and China (Diptera: Drosophilidae)

Drosophila (Sophophora) subpulchrella Takamori and Watabe, sp. nov., of the D. suzukii subgroup in the D. melanogaster species group, is described from Japan and southern China, and compared with its sibling species, D. pulchrella Tan et al. distributed in the Yun‐Gui Highland, south‐western China. The results of cross‐experiments show a complete pre‐mating isolation between D. subpulchrella and D. pulchrella.     

Automata networks as preprocessing technique of artificial neural network in estimating primary production and dominating phytoplankton levels in a reservoir: An experimental work

Artificial Neural Networks (ANN) is computational architectures that can be used for estimating primary production levels and dominating phytoplankton species in reservoirs. Automata Networks (AN) were applied as a pre-processing method with subsequent ANN model development for Demirdöven Dam Reservoir. The primary purpose of using pre-processing technique was to distinguish the suitable and appropriate constituents of the input parameters' matrix, to eliminate redundancy, to enhance prediction power and calculation efficiency. The data were collected monthly over two years. The applications have yielded following results: The correlation coefficients (r values) between predicted and observed counts were as high as 0.83, 0.87, 0.83 and 0.88 for Cyclotella ocellata, Sphaerocystis schroeteri, Staurastrum longiradiatum counts, and Chlorophyll-a (Chl-a) concentrations respectively with AN. The performance of AN based pre-processing technique was compared with the performance of a well-known pre-processing technique, namely Principle Component Analysis(PCA), experimentally. r values between the predicted and observed C. ocellata, S. schroeteri and S. longiradiatum counts, and (Chl-a) were as high as 0.80, 0.86, 0.81 and 0.86 respectively with PCA.     

Variation in female mate choice within guppy populations: population divergence,multiple ornaments and the maintenance of polymorphism

The evolutionary significance of variation in mate choice behaviour is currently a subject of some debate and considerable empirical study. Here, I review recent work on variation within and among guppy (Poecilia reticulata) populations in female mate choice and mating preferences. Empirical results demonstrate that there is substantial variation within and among populations in female responsiveness and choosiness, and much of this variation is genetic. Evidence for variation in preference functions also exists, but this appears to be more equivocal and the relative importance of genetic variation is less clear cut. In the second half of this review I discuss the potential significance of this variation to three important evolutionary issues: the presence of multiple male ornaments, the maintenance of polymorphism and divergence in mate recognition among populations. Studies of genetic variation in mate choice within populations indicate that females have complex, multivariate preferences that are able to evolve independently to some extent. These findings suggest that the presence of multiple male ornaments may be due to multiple female mating preferences. The extreme polymorphism in male guppy colour patterns demands explanation, yet no single satisfactory explanation has yet emerged. I review several old ideas and a few new ones in order to identify the most promising potential explanations for future empirical testing. Among these are negative frequency dependent selection, environmental heterogeneity coupled with gene flow, and genetic constraints. Last, I review the relative extent of within and among-population variation in mate choice and mating preferences in order to assess why guppies have not speciated despite a history of isolation and divergence. I argue that variation within guppy populations in mate choice and enhanced mating success of new immigrants to a pool are major impediments to population divergence of the magnitude that would be required for speciation to occur.     

Review of the biology and ecology of a ragweed leaf beetle,Ophraella communa (Coleoptera: Chrysomelidae), which is a biological control agent of an invasive common ragweed,Ambrosia artemisiifolia (Asterales: Asteraceae)

A ragweed leaf beetle, Ophraella communa (Coleoptera: Chrysomelidae), has been highlighted as a potential biological control agent of Ambrosia artemisiifolia. O. communa and A. artemisiifolia are native in North America and alien species in East Asia and Europe. As an invasive weed, A. artemisiifolia causes severe economic losses as reducing agricultural production as well as producing severe allergenic pollen. As an herbivore insect, O. communa has strong host preference on A. artemisiifolia. All the developmental stages of O. communa can be found on A. artemisiifolia and it attacks a single plant in repeated and extended manners. With few individuals on A. artemisiifolia, O. communa can completely defoliate before pollen production. Therefore, O. communa had been focused as a biological control of this invasive weed, but its introduction was denied because of possible damage on an important crop, Helianthus annuus. O. communa was accidentally introduced in East Asia and Europe in 1990s and 2010s, respectively. Fortunately, O. communa population was well established to suppress A. artemisiifolia in the introduced areas. Following detailed field surveys and host specificity tests of O. communa were conducted and proved a strong potential of O. communa as a biological control agent of A. artemisiifolia. Moreover, O. communa has been investigated in physiological and evolutionary studies. In this study, the potential of O. communa as a biological control agent and a study organism are reviewed.     

Evolutionary acceleration in the most endangered mammal of Canada: speciation and divergence in the Vancouver Island marmot (Rodentia, Sciuridae)

The Vancouver Island marmot is the most endangered mammal of Canada. Factors which have brought this population to the verge of extinction have not yet been fully elucidated, but the effects of deforestation and habitat fragmentation on survival rates, as well as those of variation in rainfall, temperature, snowpack depth and snowmelt strongly suggest that marmots on the island are struggling to keep pace with environmental changes. Genetic analyses, however, seem to indicate that the Vancouver Island marmot may merely represent a melanistic population of its parental species on the mainland. Were it not for its black pelage colour, it is unlikely that it would have attracted much attention as a conservation priority. Our study uses three-dimensional coordinates of cranial landmarks to further assess phenotypic differentiation of the Vancouver Island marmot. A pattern of strong interspecific divergence and low intraspecific variation was found which is consistent with aspects of drift-driven models of speciation. However, the magnitude of shape differences relative to the putatively neutral substitutions in synonymous sites of cytochrome b is too large for being compatible with a simple neutral model. A combination of bottlenecks and selective pressures due to natural and human-induced changes in the environment may offer a parsimonious explanation for the large phenotypic differentiation observed in the species. Our study exemplifies the usefulness of a multidisciplinary approach to the study of biological diversity for a better understanding of evolutionary models and to discover aspects of diversity that may be undetected by using only a few genetic markers to characterize population divergence and uniqueness.     

DNA barcoding as a tool for early warning and monitoring alien duckweeds (Lemna sp.pl.): the case of Central Italy

Aquatic habitats are vulnerable to the invasion of alien species, so early warning protocols are necessary for eradication. The presence in Italy of two alien duckweeds in freshwaters has been documented: Lemna minuta, that showed high invasivity, and L. valdiviana, still confined to south Lazio. These two species may be mistaken for each other and for the domestic L. minor and L. gibba due to morphological variation. Here, we assess the applicability of DNA barcoding as a complement to morphological analysis for monitoring the spread of alien Lemna. We chose two chloroplast genome sequences for their ability to discriminate all Lemna species: the 5’ intron of the trnK gene and the matK gene. Among 48 samples of Lemna collected at 20 sites in Central Italy, 20 were identified as L. minor, 19 as L. minuta, five as L. trisulca and four as L. gibba. L. minuta was present at most sampling sites; in particular, at six locations of Lake Trasimeno, eight L. minuta samples were found. We demonstrate that DNA sequence analyses with cost-effective barcoding techniques can effectively support expert efforts in species determination for an early alert system of invasive Lemna species.