Study of the relationship between the cultivars of Vitis vinifera and the white-fruited and hermaphrodite Chinese wild grapes

Chinese wild grapes are almost exclusively dioecious and black-fruited, with rare reports of white and hermaphrodite types in V. davidii. To reveal the molecular mechanisms of these phenotypic variations, specific primers were designed to detect the genotypes of mybA-related genes in Vitis species, including the Chinese wild Vitis species, V. riparia, V. rupestris, cultivars of Vitis vinifera and its hybrids. We report here that three mybA-related genes, VvmybA1a, VvmybA2 and VvmybA3, were only detected in cultivars of V. vinifera and its hybrids, but not in V. riparia, V. rupestris or Chinese wild Vitis species, indicating that these genes could be used to test the genetic relationship to V. vinifera. On the other hand, the genes were not detected in the dioecious varieties of V. davidii, but were in the hermaphrodites. In particular, the white-fruited varieties were homozygous for VvmybA1a and showed a low expression of mybA-related genes and UFGT during the entire maturation period. Simple sequence repeat analysis showed that the hermaphrodite varieties of V. davidii, including the white-fruited varieties, were more closely related to V. vinifera cv. Pinot Noir and V. labruscana cv. Kyoho. These results suggested that the white-fruited and hermaphrodite varieties of V. davidii could be the result of its crossing with V. vinifera. It provides a new approach to identify truly Chinese wild varieties and to search for possible hybridization events.     

Phylogenetic analysis of the genus Pseudoroegneria and the Triticeae tribe using the rbcL gene

The Pseudoroegneria species are perennial grasses in the Triticeae tribe, whose St genome has been linked to several important polyploid species. Due to frequent hybridization and complex genetic mechanism, the relationships within Pseudoroegneria, and within the Triticeae have been heavily disputed. Using the chloroplast rbcL gene we estimated the nucleotide diversity of 8 Pseudoroegneria species. We also examined the phylogenetic relationships within Pseudoroegneria and of Pseudoroegneria within the Triticeae. The estimates of nucleotide diversity indicated that Pseudoroegneria tauri and Pseudoroegneria spicata species had the highest diversity, while Pseudoroegneria gracillima had the lowest diversity. The phylogenetic analysis of Pseudoroegneria placed all P. spicata species into a clade separate from the other Pseudoroegneria species, while the relationship of the other Pseudoroegneria species could not be determined. Due to the groupings of Pseudoroegneria with the polyploid Elymus, our results strongly supported Pseudoroegneria as the maternal genome donor to Elymus. There was also weak support that P. spicata may be the maternal donor to the StH Elymus species.     

Isolation and characterization of the Erwinia herbicola bio operon and the sequences of the bioA and bioB genes

The biotin operon of Erwinia herbicola was cloned and characterized. The operon consists of five genes arranged in the order, bioABFCD. The operon is negatively regulated via the interaction of a proposed biotin repressor with an operator sequence that lies between the bioA and bioB genes. The nucleotide sequences of bioA (7,8-diaminopelargonic acid transferase), bioB (biotin synthetase) and the regulatory region were determined and analyzed. The deduced amino acid sequences of bioA and bioB are also aligned with currently available homologs to obtain the UPGMA (unweighted pair group method with arithmetic mean) evolutionary tree.     

Fossil and Genetic Evidence for the Polyphyletic Nature of the Planktonic Foraminifera "Globigerinoides", and Description of the New Genus Trilobatus

Planktonic foraminifera are one of the most abundant and diverse protists in the oceans. Their utility as paleo proxies requires rigorous taxonomy and comparison with living and genetically related counterparts. We merge genetic and fossil evidence of “Globigerinoides”, characterized by supplementary apertures on spiral side, in a new approach to trace their “total evidence phylogeny” since their first appearance in the latest Paleogene. Combined fossil and molecular genetic data indicate that this genus, as traditionally understood, is polyphyletic. Both datasets indicate the existence of two distinct lineages that evolved independently. One group includes “Globigerinoides” trilobus and its descendants, the extant “Globigerinoides” sacculifer, Orbulina universa and Sphaeroidinella dehiscens. The second group includes the Globigerinoides ruber clade with the extant G. conglobatus and G. elongatus and ancestors. In molecular phylogenies, the trilobus group is not the sister taxon of the ruber group. The ruber group clusters consistently together with the modern Globoturborotalita rubescens as a sister taxon. The re-analysis of the fossil record indicates that the first “Globigerinoides” in the late Oligocene are ancestral to the trilobus group, whereas the ruber group first appeared at the base of the Miocene with representatives distinct from the trilobus group. Therefore, polyphyly of the genus "Globigerinoides" as currently defined can only be avoided either by broadening the genus concept to include G. rubescens and a large number of fossil species without supplementary apertures, or if the trilobus group is assigned to a separate genus. Since the former is not feasible due to the lack of a clear diagnosis for such a broad genus, we erect a new genus Trilobatus for the trilobus group (type species Globigerina triloba Reuss) and amend Globoturborotalita and Globigerinoides to clarify morphology and wall textures of these genera. In the new concept, Trilobatus n. gen. is paraphyletic and gave rise to the Praeorbulina / Orbulina and Sphaeroidinellopsis / Sphaeroidinella lineages.     

X-Y Exchange and the Coevolution of the X and Y Rdna Arrays in Drosophila melanogaster

The nucleolus organizers on the X and Y chromosomes of Drosophila melanogaster are the sites of 200-250 tandemly repeated genes for ribosomal RNA. As there is no meiotic crossing over in male Drosophila, the X and Y chromosomal rDNA arrays should be evolutionarily independent, and therefore divergent. The rRNAs produced by X and Y are, however, very similar, if not identical. Molecular, genetic and cytological analyses of a series of X chromosome rDNA deletions (bb alleles) showed that they arose by unequal exchange through the nucleolus organizers of the X and Y chromosomes. Three separate exchange events generated compound X·Y ^L chromosomes carrying mainly Y-specific rDNA. This led to the hypothesis that X-Y exchange is responsible for the coevolution of X and Y chromosomal rDNA. We have tested and confirmed several of the predictions of this hypothesis: First, X· Y^L chromosomes must be found in wild populations. We have found such a chromosome. Second, the X·Y^L chromosome must lose the Y^L arm, and/or be at a selective disadvantage to normal X⁺ chromosomes, to retain the normal morphology of the X chromosome. Six of seventeen sublines founded from homozygous X·Y^Lbb stocks have become fixed for chromosomes with spontaneous loss of part or all of the appended Y^L. Third, rDNA variants on the X chromosome are expected to be clustered within the X⁺ nucleolus organizer, recently donated (" Y") forms being proximal, and X-specific forms distal. We present evidence for clustering of rRNA genes containing Type 1 insertions. Consequently, X-Y exchange is probably responsible for the coevolution of X and Y rDNA arrays.     

Electroretinogram Characteristics and the Spectral Mechanisms of the Median Ocellus and the Lateral Eye in Limulus polyphemus

Electrical responses (ERG) to light flashes of various wavelengths and energies were obtained from the dorsal median ocellus and lateral compound eye of Limulus under dark and chromatic light adaptation. Spectral mechanisms were studied by analyzing (a) response waveforms, e.g. response area, rise, and fall times as functions of amplitude, (b) slopes of amplitude-energy functions, and (c) spectral sensitivity functions obtained by the criterion amplitude method. The data for a single spectral mechanism in the lateral eye are (a) response waveforms independent of wavelength, (b) same slope for response-energy functions at all wavelengths, (c) a spectral sensitivity function with a single maximum near 520 mµ, and (d) spectral sensitivity invariance in chromatic adaptation experiments. The data for two spectral mechanisms in the median ocellus are (a) two waveform characteristics depending on wavelength, (b) slopes of response-energy functions steeper for short than for long wavelengths, (c) two spectral sensitivity peaks (360 and 530–535 mµ) when dark-adapted, and (d) selective depression of either spectral sensitivity peak by appropriate chromatic adaptation. The ocellus is 200–320 times more sensitive to UV than to visible light. Both UV and green spectral sensitivity curves agree with Dartnall's nomogram. The hypothesis is favored that the ocellus contains two visual pigments each in a different type of receptor, rather than (a) various absorption bands of a single visual pigment, (b) single visual pigment and a chromatic mask, or (c) fluorescence. With long duration light stimuli a steady-state level followed the transient peak in the ERG from both types of eyes.     

A ten-year comparative study of the population dynamics and parasitoidism in the native paper wasp Polistes fuscatus and the invasive P. dominulus

The invasive success of Polistes dominulus in North America has been attributed to its greater productivity relative to native Polistes. Liberation from parasites and parasitoids are thought to be major factors contributing to the high productivity of P. dominulus. We analyzed historical records of colony relative abundance and productivity of P. dominulus and the sympatric, native Polistes fuscatus from 1995 to 2010 using historical data from our Michigan Polistes study site. We also analyzed evidence of parasitoids from 294 P. fuscatus and 507 P. dominulus archived combs from 2001 to 2010. Additionally, we examined field and laboratory colonies from outside of our study site for parasites and parasitoids in 2009 and 2010. We documented one parasite and three parasitoids exploiting Polistes in our Michigan study sites. Our historical records document that P. dominulus initially displaced P. fuscatus rapidly, then slowed, and finally the two populations stabilized. Furthermore, the historical pattern of decreasing displacement of P. fuscatus by P. dominulus corresponded temporally with a significant decline in the productivity and a significant increase in Dibrachys cavus infestation of P. dominulus. Our evidence indicates that the parasitoid, D. cavus, is a major factor in stabilizing the populations of the sympatric P. dominulus and P. fuscatus.     

Transformation of Brassica napus and Brassica oleracea Using Agrobacterium tumefaciens and the Expression of the bar and neo Genes in the Transgenic Plants

An efficient and largely genotype-independent transformation method for Brassica napus and Brassica oleracea was established based on neo or bar as selectable marker genes. Hypocotyl explants of Brassica napus and Brassica oleracea cultivars were infected with Agrobacterium strains containing chimeric neo and bar genes. The use of AgNO₃ was a prerequisite for efficient shoot regeneration under selective conditions. Vitrification was avoided by decreasing the water potential of the medium, by decreasing the relative humidity in the tissue culture vessel, and by lowering the cytokinin concentration. In this way, rooted transformed shoots were obtained with a 30% efficiency in 9 to 12 weeks. Southern blottings and genetic analysis of S1-progeny showed that the transformants contained on average between one and three copies of the chimeric genes. A wide range of expression levels of the chimeric genes was observed among independent transformants. Up to 25% of the transformants showed no detectable phosphinotricin acetyltransferase or neomycin phosphotransferase II enzyme activities although Southern blottings demonstrated that these plants were indeed transformed.     

A conserved and species-specific functional interaction between the Werner syndrome-like exonuclease atWEX and the Ku heterodimer in Arabidopsis

Werner syndrome is associated with mutations in the DNA helicase RecQ3 [a.k.a. Homo sapiens (hs)WRN]. The function of hsWRN is unknown although biochemical studies suggest a role in DNA ends stability and repair. Unlike other RecQ family members, hsWRN possesses an N-terminal domain with exonuclease activity, which is stimulated by interaction with the Ku heterodimer. While this interaction is intriguing, we do not know whether it is important for hsWRN function. Although flies, worms, fungi and plants do not have RecQ-like (RQL) helicases with an intrinsic exonuclease activity, they possess proteins having domains homologous to the hsWRN exonuclease. The genome of Arabidopsis thaliana (at) encodes multiple RQL and a single protein with homology to the WRN exonuclease domain, atWEX (Werner-like Exonuclease). Here we show that atWEX has properties that are similar to hsWRN. atWEX binds to and is stimulated by atKu. Interestingly, stimulation by Ku is species-specific, as hsKu does not stimulate atWEX exonuclease activity. Likewise, atKu fails to enhance the exonuclease activity of hsWRN. Thus, in spite of the differences in structural organization, the functional interaction between WRN-like exonucleases and Ku has been preserved through evolutionary radiation of species, emphasizing the importance of this interaction in cell function.     

Artificial and factitious foods support the development and reproduction of the predatory mite Amblyseius swirskii

The generalist predatory mite Amblyseius swirskii Athias-Henriot (Acari: Phytoseiidae) was reared on Ephestia kuehniella Zeller eggs (Lepidoptera: Pyralidae), decapsulated dry cysts of the brine shrimp Artemia franciscana Kellogg (Anostraca: Artemiidae), and on meridic artificial diets (composed of honey, sucrose, tryptone, yeast extract, and egg yolk) supplemented with pupal hemolymph of the Chinese oak silkworm Antheraea pernyi (Guérin-Méneville) (Lepidoptera: Saturniidae) (AD1), with E. kuehniella eggs (AD2) or with A. franciscana cysts (AD3). Development, reproduction and predation capacity of the predatory mites were assessed in the first (G1) and sixth generation (G6) of rearing on the different diets. Immature survival rates in G1 were similar on all diets (96.8–100 %). After six generations, however, survival of A. swirskii was significantly reduced on all diets except on A. franciscana cysts. Oviposition rates did not differ between generations when females were fed on E. kuehniella, AD2 or AD3. The total number of deposited eggs was similar among diets except in G6 where the females fed on A. franciscana cysts produced more eggs than those maintained on E. kuehniella eggs. On most diets the intrinsic rates of increase in G1 were superior to those in G6, except for predators supplied with A. franciscana cysts where no differences were observed among generations. Female mites did not lose their capacity to kill first instar Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) after six generations on the different diets, but predation rates in G6 on E. kuehniella were lower than in G1. In conclusion, the different factitious and artificial diets tested in the present study supported the development and reproduction of A. swirskii for a single generation but fitness losses occurred to a varying degree after several generations on E. kuehniella eggs or the artificial diets. Artificial diet enriched with A. franciscana cysts yielded better results than the other artificial diets. Amblyseius swirskii performed best on decapsulated Artemia cysts indicating their potential for use in the mass production of the predator or to sustain its populations in the crop after release.     

Insulator and Ovo proteins determine the frequency and specificity of insertion of the gypsy retrotransposon in Drosophila melanogaster

The gypsy retrovirus of Drosophila is quite unique among retroviruses in that it shows a strong preference for integration into specific sites in the genome. In particular, gypsy integrates with a frequency of >10% into the regulatory region of the ovo gene. We have used in vivo transgenic assays to dissect the role of Ovo proteins and the gypsy insulator during the process of gypsy site-specific integration. Here we show that DNA containing binding sites for the Ovo protein is required to promote site-specific gypsy integration into the regulatory region of the ovo gene. Using a synthetic sequence, we find that Ovo binding sites alone are also sufficient to promote gypsy site-specific integration into transgenes. These results indicate that Ovo proteins can determine the specificity of gypsy insertion. In addition, we find that interactions between a gypsy provirus and the gypsy preintegration complex may also participate in the process leading to the selection of gypsy integration sites. Finally, the results suggest that the relative orientation of two integrated gypsy sequences has an important role in the enhancer-blocking activity of the gypsy insulator.     

Physiological and biochemical contributions to the taxonomy of the genus Chlorella

1. Rabbit antisera to soluble cytochrome c-553 and to ferredoxin were characterized by double immunodiffusion, the antiserum to cytochrome c-553 also by immuno-electrophoresis and by the quantitative precipitation reaction.
2. Soluble cytochromes c-553 were isolated from 11 strains of Chlorella belonging to 8 species and from one strain of Scenedesmus. Their reactivity with antiserum to soluble cytochrome c-553 from Chlorella fusca var. vacuolata 211-8b was studied.
3. With the double immunodiffusion method, the soluble cytochromes c-553 from C. fusca var. vacuolata 211-8b, C. fusca var. rubescens 232/1, C. fusca var. fusca 343, and Scenedesmus obliquus 276-3b appear immunologically identical.
4. The soluble cytochromes c-553 from C. zofingiensis 211-14a, 211-14b, and 211-14c show in the cross reaction a partial immunological relationship with that from C. fusca var. vacuolata 211-8b.
5. The soluble cytochromes c-553 from C. sorokiniana 211-8k, C. vulgaris 211-11c and 211-19, C. saccharophila 211-1 a, and C. homosphaera 211-8e (Ca.) do not show a cross reaction with that from C. fusca var. vacuolata 211-8b.
6. These results indicate that not only C. fusca var. fusca, but also C. fusca var. vacuolata, C. fusca var. rubescens, and possibly C. zofingiensis might be more closely related to the genus Scenedesmus than to the Chlorella species of the “C. vulgaris group” (i.e., C. sorokiniana, C. vulgaris, and C. saccharophila).
7. An application of the double immunodiffusion method with an antiserum to ferredoxin from C. vulgaris 211-8m revealed that the ferredoxins from 20 strains of 9 Chlorella species and from one strain of Scenedesmus do not exhibit any immunological differences as compared to the homologous antigen.

     

Biophysics and Structure of the Patch and the Gigaseal

Interpreting channel behavior in patches requires an understanding of patch structure and dynamics, especially in studies of mechanosensitive channels. High resolution optical studies show that patch formation occurs via blebbing that disrupts normal membrane structure and redistributes in situ components including ion channels. There is a 1-2 μm region of the seal below the patch where proteins are excluded and this may consist of extracted lipids that form the gigaseal. Patch domes often have complex geometries with inhomogeneous stresses due to the membrane-glass adhesion energy (E_a), cytoskeletal forces, and possible lipid subdomains. The resting tension in the patch dome ranges from 1-4 mN/m, a significant fraction of the lytic tension of a bilayer (∼10 mN/m). Thus, all patch experiments are conducted under substantial, and uneven, resting tension that may alter the kinetics of many channels. E_a seems dominated by van der Waals attraction overlaid with a normally repulsive Coulombic force. High ionic strength pipette saline increased E_a and, surprisingly, increased cytoskeletal rigidity in cell-attached patches. Low pH pipette saline also increased E_a and reduced the seal selectivity for cations, presumably by neutralizing the membrane surface charge. The seal is a negatively charged, cation selective, space with a resistance of ∼7 gigohm/μm in 100 mM KCl, and the high resistivity of the space may result from the presence of high viscosity glycoproteins. Patches creep up the pipette over time with voltage independent and voltage dependent components. Voltage-independent creep is expected from the capillary attraction of E_a and the flow of fresh lipids from the cell. Voltage-dependent creep seems to arise from electroosmosis in the seal. Neutralization of negative charges on the seal membrane with low pH decreased the creep rate and reversed the direction of creep at positive pipette potentials.     

Rooting Around the Eutherian Family Tree: the Origin and Relations of the Taeniodonta

Placing early groups into the overall phylogeny of eutherian mammals can be challenging, particularly when the group does not have extant members. We investigated the relationships of the Taeniodonta, an extinct group from the Late Cretaceous through Paleogene of North America. This group has a few purported close relatives, including Cimolestes, Procerberus, and Alveugena, that may form a sequence of ancestors and descendants. The leading hypothesis is that Procerberus gave rise to taeniodonts through Alveugena. We test this hypothesis and analyze relations to known stem and crown Eutheria to determine the place of taeniodonts in eutherian phylogeny. Cladistic analyses were performed using previously published characters and datasets, namely a taeniodont/cimolestid specific dataset and a reanalysis of Wible and colleagues (2009), with added taxa for both. Our studies suggest that taeniodonts arose from Cimolestes through Alveugena, that Procerberus is more distantly related to taeniodonts, and that taeniodonts and their relatives are stem eutherians. We diagnose the Taeniodonta based on these analyses. Other Paleogene groups, especially those allied with Cimolestes such as tillodonts and pantolestans, merit further study. Our findings indicate that stem eutherians such as the Taeniodonta, in addition to crown eutherians, continued to diversify during the Paleogene.     

Old and new hypotheses about the homology of the compound bones from the cheek and otico-occipital regions of the anuran skull

We studied the larval development of compound bones from the otico-occipital and cheek regions in species of the neobatrachian genera Batrachyla, Hylorina, Leptodactylus, Odontophrynus and Pleurodema. Comparisons were made using a set of Ambystoma spp. (Caudata) and Ceratophrys ornata (Anura; Ceratophryidae) larvae. As suggested by previous studies, we verified the compound nature of the exoccipital (two centers, anurans only), frontoparietal (one center, most anurans and Ambystoma; three centers, some anurans), and squamosal (two centers, all anurans and Ambystoma) bones. We discuss old and new homology hypotheses for each of the compound bone centers in the context of the most widely accepted scenario of lissamphibian origins and relationships, i.e., monophyletic Lissamphibia that includes the clade Batrachia (Caudata + Anura) and the most divergent Gymnophiona. Our findings have a direct impact on our understanding of the composition of the skull in Lissamphibia. We recognized the presence of the following bones: (i) opisthotic (fused to the exoccipital) and tabular (fused to the squamosal) in Batrachia (Anura + Caudata) and (ii) supratemporal (fused to the parietal portion of the frontoparietal) in Anura. Separate centers of the parietal were found only in Pleurodema.     

Genetic Interactions Between Shox2 and Hox Genes During the Regional Growth and Development of the Mouse Limb

The growth and development of the vertebrate limb relies on homeobox genes of the Hox and Shox families, with their independent mutation often giving dose-dependent effects. Here we investigate whether Shox2 and Hox genes function together during mouse limb development by modulating their relative dosage and examining the limb for nonadditive effects on growth. Using double mRNA fluorescence in situ hybridization (FISH) in single embryos, we first show that Shox2 and Hox genes have associated spatial expression dynamics, with Shox2 expression restricted to the proximal limb along with Hoxd9 and Hoxa11 expression, juxtaposing the distal expression of Hoxa13 and Hoxd13. By generating mice with all possible dosage combinations of mutant Shox2 alleles and HoxA/D cluster deletions, we then show that their coordinated proximal limb expression is critical to generate normally proportioned limb segments. These epistatic interactions tune limb length, where Shox2 underexpression enhances, and Shox2 overexpression suppresses, Hox-mutant phenotypes. Disruption of either Shox2 or Hox genes leads to a similar reduction in Runx2 expression in the developing humerus, suggesting their concerted action drives cartilage maturation during normal development. While we furthermore provide evidence that Hox gene function influences Shox2 expression, this regulation is limited in extent and is unlikely on its own to be a major explanation for their genetic interaction. Given the similar effect of human SHOX mutations on regional limb growth, Shox and Hox genes may generally function as genetic interaction partners during the growth and development of the proximal vertebrate limb.