Showing 101 - 110 of 257 Items
A genomewide survey argues that every zygotic gene product is dispensable for the initiation of somatic homolog pairing in Drosophila
Date: 2008-11-01
Creator: Jack R. Bateman, C. Ting Wu
Access: Open access
- Studies from diverse organisms show that distinct interchromosomal interactions are associated with many developmental events. Despite recent advances in uncovering such phenomena, our understanding of how interchromosomal interactions are initiated and regulated is incomplete. During the maternal-to-zygotic transition (MZT) of Drosophila embryogenesis, stable interchromosomal contacts form between maternal and paternal homologous chromosomes, a phenomenon known as somatic homolog pairing. To better understand the events that initiate pairing, we performed a genomewide assessment of the zygotic contribution to this process. Specifically, we took advantage of the segregational properties of compound chromosomes to generate embryos lacking entire chromosome arms and, thus, all zygotic gene products derived from those arms. Using DNA fluorescence in situ hybridization (FISH) to assess the initiation of pairing at five separate loci, this approach allowed us to survey the entire zygotic genome using just a handful of crosses. Remarkably, we found no defect in pairing in embryos lacking any chromosome arm, indicating that no zygotic gene product is essential for pairing to initiate. From these data, we conclude that the initiation of pairing can occur independently of zygotic control and may therefore be part of the developmental program encoded by the maternal genome. Copyright © 2008 by the Genetics Society of America.
Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme
Date: 1998-01-01
Creator: Leigh Ann Lipscomb, Nadine C. Gassner, Sheila D. Snow, Aimee M. Eldridge, Walter A., Baase, Devin L. Drew, Brian W. Matthews
Access: Open access
- The substitution of methionines with leucines within the interior of a protein is expected to increase stability both because of a more favorable solvent transfer team as well as the reduced entropic cost of holding a leucine side chain in a defined position. Together, these two terms are expected to contribute about 1.4 kcal/mol to protein stability for each Met → Leu substitution when fully buried. At the same time, this expected beneficial effect may be offset by steric factors due to differences in the shape of leucine and methionine. To investigate the interplay between these factors, all methionines in T4 lysozyme except at the amino-terminus were individually replaced with leucine. Of these mutants, M106L and M120L have stabilities 0.5 kcal/mol higher than wild-type T4 lysozyme, while M6L is significantly destabilized (-2.8 kcal/mol). M102L, described previously, is also destabilized (-0.9 kcal/mol). Based on this limited sample it appears that methionine-to-leucine substitutions can increase protein stability but only in a situation where the methionine side chain is fully or partially buried, yet allows the introduction of the leucine without concomitant steric interference. The variants, together with methionine-to-lysine substitutions at the same sites, follow the general pattern that substitutions at rigid, internal sites tend to be most destabilizing, whereas replacements at more solvent-exposed sites are better tolerated.
Site-specific transformation of Drosophila via φC31 integrase-mediated cassette exchange
Date: 2006-06-30
Creator: Jack R. Bateman, Anne M. Lee, C. Ting Wu
Access: Open access
- Position effects can complicate transgene analyses. This is especially true when comparing transgenes that have inserted randomly into different genomic positions and are therefore subject to varying position effects. Here, we introduce a method for the precise targeting of transgenic constructs to predetermined genomic sites in Drosophila using the φC31 integrase system in conjunction with recombinase-mediated cassette exchange (RMCE). We demonstrate the feasibility of this system using two donor cassettes, one carrying the yellow gene and the other carrying GFP. At all four genomic sites tested, we observed exchange of donor cassettes with an integrated target cassette carrying the mini-white gene. Furthermore, because RMCE-mediated integration of the donor cassette is necessarily accompanied by loss of the target cassette, we were able to identify integrants simply by the loss of mini-white eye color. Importantly, this feature of the technology will permit integration of unmarked constructs into Drosophila, even those lacking functional genes. Thus, φC31 integrase-mediated RMCE should greatly facilitate transgene analysis as well as permit new experimental designs. Copyright © 2006 by the Genetics Society of America.
Accurate transcription of truncated ribosomal DNA templates in a Drosophila cell-free system
Date: 1982-01-01
Creator: B. D. Kohorn, P. M.M. Rae
Access: Open access
- An extract of Drosophila melanogaster Kc cells is shown to give specific and accurate transcription of truncated segments of cloned D. melanogaster ribosomal DNA (rDNA). When clones are digested with restriction enzymes so that the initiation site is flanked by 0.3 kilobase (kb) of nontranscribed spacer and >0.4 kb of external transcribed spacer, RNA polymerase I activity in the extract parallels in vivo rRNA synthesis in selection of the coding strand of template and the site of transcription initiation. When >0.3 kb of the nontranscribed spacer is contiguous with transcribed spacer, in vitro initiations evidently also occur in repeated sequences adjacent to the site of in vivo initiation; when ≤0.4 kb of the external transcribed spacer is present in a segment, expected transcripts are heterogeneous in length or not detectable. Transcription in the cell-free system requires the specific addition of D. melanogaster rDNA: neither D. virilis rDNA, vector plasmid, nor clones of D. melanogaster genes that are transcribed in vivo by RNA polymerases II and III serve as templates in the system. Drosophila rDNA units that have an interruption in the 28S rRNA coding region are not transcribed in vivo, but restriction digests of a recombinant phage DNA that contains such a unit are active as template for in vitro rDNA transcription.
Environmental issues in russia
Date: 2008-12-01
Creator: Laura A. Henry, Vladimir Douhovnikoff
Access: Open access
- This review examines the literature available on the state of the environment and environmental protection in the Russian Federation. As the largest country on Earth, rich in natural resources and biodiversity, Russia's problems and policies have global consequences. Environmental quality and management are influenced by the legacy of Soviet economic planning and authoritarian governance, as well as by Russia's post-Soviet economic recession and current strategies of economic development. Russia achieved a reduction in some pollutants owing to the collapse of industrial production in the 1990s, but many environmental indicators suggest growing degradation. Russia has signed on to a number of international environmental agreements, but its record on implementation is mixed, and it discourages environmental activism. Scholarship on the Russian environment is a limited, but growing, field, constrained by challenges of data availability, yet it offers great potential for testing scientific and social scientific hypotheses. ©2008 by Annual Reviews.
Is variation in susceptibility to Phytophthora ramorum correlated with population genetic structure in coast live oak (Quercus agrifolia)?
Date: 2005-01-01
Creator: Richard S. Dodd, Daniel Hüberli, Vlad Douhovnikoff, Tamar Y. Harnik, Zara, Afzal-Rafii, Matteo Garbelotto
Access: Open access
- California coastal woodlands are suffering severe disease and mortality as a result of infection from Phytophthora ramorum. Quercus agrifolia is one of the major woodland species at risk. This study investigated within- and among-population variation in host susceptibility to inoculation with P. ramorum and compared this with population genetic structure using molecular markers. Susceptibility was assessed using a branch-cutting inoculation test. Trees were selected from seven natural populations in California. Amplified fragment length polymorphism molecular markers were analysed for all trees used in the trials. Lesion sizes varied quantitatively among individuals within populations, with up to an eightfold difference. There was little support for population differences in susceptibility. Molecular structure also showed a strong within-population, and weaker among-population, pattern of variation. Our data suggest that susceptibility of Q. agrifolia to P. ramorum is variable and is under the control of several gene loci. This variation exists within populations, so that less susceptible local genotypes may provide the gene pool for regeneration of woodlands where mortality is high. © New Phytologist (2004).
Sexual reproduction is more prevalent in continental landscapes in the expanding arctic shrub, Salix glauca
Date: 2019-12-01
Creator: David A. Watts, Vladimir Douhovnikoff, Eric Post
Access: Open access
- The recent expansion of arctic deciduous shrubs has been well documented across a range of habitats, but the phenomenon is not universal. Their spread is often associated with increases in temperature and other abiotic factors, while variation in habitat moisture and herbivory can mediate the location and rate of this rise in abundance. Much less is known about the mode of increase of arctic shrubs. For one such shrub, Salix glauca, we used microsatellite markers to assess the prevalence of clonal growth (i.e. vegetative spread) and sexual reproduction (i.e. recruitment from seed) at sites with maritime and continental climates and differing in the density of large herbivores. We sampled individuals in plots reflecting the spatial scale of expansion in locations where S. glauca recently increased in abundance. The 400 samples collected across the four sites comprised 310 genotypes. Though evidence of sexual recruitment was common across all sites, coastal sites contained both more and larger clonal genotypes. While we expected soil conditions would be influential, the factors that best predicted the likelihood of clonality, genet size and vascular plant cover, suggest the light environment is of primary importance. Furthermore, in spite of the large distances between sites, there was no suggestion of genetic differentiation into distinct populations. These results indicate that differences in climate and herbivory can influence not only where and how extensively deciduous shrubs spread, but how they are likely to do so. We suggest future research integrating how mode of increase is associated with the rate of spread will advance projections of change in arctic ecosystems.
The Role of the Golgi ELMO Proteins in Cell Adhesion in Arabidopsis thaliana
Date: 2021-01-01
Creator: Wesley James Hudson
Access: Open access
- Proper growth and development of plant cells is dependent upon successful cell adhesion between cells, and this is mostly mediated by pectin in the plant cell wall. Previously, the Kohorn Laboratory identified a non-enzymatic Golgi protein named ELMO1 as it is required for cell adhesion, likely acting as a scaffold for cell wall polymer synthesis. Plants with mutant ELMO1 demonstrate a weak defective cellular adhesion phenotype as well as reduced mannose content in the cell wall. ELMO1 has homologous proteins in at least 29 different vascular plants. These homologues have 2 possible deletions in their amino acid sequence, but protein modeling determined that these variations will not affect protein structure. There are 5 homologous ELMO1 proteins in Arabidopsis thaliana that have been aptly named ELMO2, ELMO3, ELMO4, ELMO5. elmo2-/-mutants revealed no mutant adhesion phenotypes, while elmo1-/-elmo2-/-double mutants revealed strong defects in adhesion. Confocal microscopy of propidium iodide-stained seedlings confirmed the lack of a phenotype for elmo2-/-mutants and showed disorganized gapping cells for the elmo1-/-elmo2-/-mutant. Additionally, while elmo2-/-did not have any change to root or hypocotyl length, elmo1-/-elmo2-/- mutants were significantly shorter in both regards. Taken together, these data support that ELMO2 and ELMO1 are partially redundant.
Molecular characterization of putative neuropeptide, amine, diffusible gas and small molecule transmitter biosynthetic enzymes in the eyestalk ganglia of the American lobster, Homarus americanus
Date: 2018-12-01
Creator: Andrew E. Christie, Meredith E. Stanhope, Helen I. Gandler, Tess J. Lameyer, Micah G., Pascual, Devlin N. Shea, Andy Yu, Patsy S. Dickinson, J. Joe Hull
Access: Open access
- The American lobster, Homarus americanus, is a model for investigating the neuromodulatory control of physiology and behavior. Prior studies have shown that multiple classes of chemicals serve as locally released/circulating neuromodulators/neurotransmitters in this species. Interestingly, while many neuroactive compounds are known from Homarus, little work has focused on identifying/characterizing the enzymes responsible for their biosynthesis, despite the fact that these enzymes are key components for regulating neuromodulation/neurotransmission. Here, an eyestalk ganglia-specific transcriptome was mined for transcripts encoding enzymes involved in neuropeptide, amine, diffusible gas and small molecule transmitter biosynthesis. Using known Drosophila melanogaster proteins as templates, transcripts encoding putative Homarus homologs of peptide precursor processing (signal peptide peptidase, prohormone processing protease and carboxypeptidase) and immature peptide modifying (glutaminyl cyclase, tyrosylprotein sulfotransferase, protein disulfide isomerase, peptidylglycine-α-hydroxylating monooxygenase and peptidyl-α-hydroxyglycine-α-amidating lyase) enzymes were identified in the eyestalk assembly. Similarly, transcripts encoding full complements of the enzymes responsible for dopamine [tryptophan-phenylalanine hydroxylase (TPH), tyrosine hydroxylase and DOPA decarboxylase (DDC)], octopamine (TPH, tyrosine decarboxylase and tyramine β-hydroxylase), serotonin (TPH or tryptophan hydroxylase and DDC) and histamine (histidine decarboxylase) biosynthesis were identified from the eyestalk ganglia, as were those responsible for the generation of the gases nitric oxide (nitric oxide synthase) and carbon monoxide (heme oxygenase), and the small molecule transmitters acetylcholine (choline acetyltransferase), glutamate (glutaminase) and GABA (glutamic acid decarboxylase). The presence and identity of the transcriptome-derived transcripts were confirmed using RT-PCR. The data presented here provide a foundation for future gene-based studies of neuromodulatory control at the level of neurotransmitter/modulator biosynthesis in Homarus.
The pyloric neural circuit of the herbivorous crab Pugettia producta shows limited sensitivity to several neuromodulators that elicit robust effects in more opportunistically feeding decapods
Date: 2008-05-01
Creator: Patsy S. Dickinson, Elizabeth A. Stemmler, Andrew E. Christie
Access: Open access
- Modulation of neural circuits in the crustacean stomatogastric nervous system (STNS) allows flexibility in the movements of the foregut musculature. The extensive repertoire of such resulting motor patterns in dietary generalists is hypothesized to permit these animals to process varied foods. The foregut and STNS of Pugettia producta are similar to those of other decapods, but its diet is more uniform, consisting primarily of kelp. We investigated the distribution of highly conserved neuromodulators in the stomatogastric ganglion (STG) and neuroendocrine organs of Pugettia, and documented their effects on its pyloric rhythm. Using immunohistochemistry, we found that the distributions of Cancer borealis tachykinin-related peptide I (CabTRP I), crustacean cardioactive peptide (CCAP), proctolin, red pigment concentrating hormone (RPCH) and tyrosine hydroxylase (dopamine) were similar to those of other decapods. For all peptides except proctolin, the isoforms responsible for the immunoreactivity were confirmed by mass spectrometry to be the authentic peptides. Only two modulators had physiological effects on the pyloric circuit similar to those seen in other species. In non-rhythmic preparations, proctolin and the muscarinic acetylcholine agonist oxotremorine consistently initiated a full pyloric rhythm. Dopamine usually activated a pyloric rhythm, but this pattern was highly variable. In only about 25% of preparations, RPCH activated a pyloric rhythm similar to that seen in other species. CCAP and CabTRP I had no effect on the pyloric rhythm. Thus, whereas Pugettia possesses all the neuromodulators investigated, its pyloric rhythm, when compared with other decapods, appears less sensitive to many of them, perhaps because of its limited diet.