Evolution of patterns of gene expression in Hawaiian picture-wingedDrosophila

Summary The tissue and stage specificity of expression of five enzymes was examined by electrophoretic analysis of relative enzyme levels in extracts of 13 larval and adult tissues in 27 species of Hawaiian picture-wingedDrosophila. The developmentally regulated patterns of enzyme expression thus characterized were compared to a modal standard phenotype. About 30% of the pattern features analyzed differed significantly from the standard in one or more species. Many of these regulatory differences are essentially qualitative, with tissue specific differences in enzyme activity in excess of 100 fold for some species pairs. The adaptive significance of these pattern differences is unknown, but the results provide strong direct evidence for rapid evolution of new patterns of gene regulation in this group of organisms.     

Fluctuating Mutation Bias and the Evolution of Base Composition in Drosophila

The idea that the pattern of point mutation in Drosophila has remained constant during the evolution of the genus has recently been challenged. A study of the nucleotide composition focused on the Drosophila saltans group has evidenced unsuspected nucleotide composition differences among lineages. Compositional differences are associated with an accelerated rate of amino acid replacement in functionally less constrained regions. Here we reassess this issue from a different perspective. Adopting a maximum-likelihood estimation approach, we focus on the different predictions that mutation and selection make about the nonsynonymous-to-synonymous rate ratio. We investigate two gene regions, alcohol dehydrogenase (Adh) and xanthine dehydrogenase (Xdh), using a balanced data set that comprises representatives from the melangaster, obscura, saltans, and willistoni groups. We also consider representatives of the Hawaiian picture-winged group. These Hawaiian species are known to have experienced repeated bottlenecks and are included as a reference for comparison. Our results confirm patterns previously detected. The branch ancestral to the fast-evolving willistoni/saltans lineage, where most of the change in GC content has occurred, exhibits an excess of synonymous substitutions. The shift in mutation bias has affected the extent of the rate variation among sites in Xdh. Received: 4 May 1999 / Accepted: 26 July 1999     

Vitellogenin protein diversity in the HawaiianDrosophila

Egg and female hemolymph proteins were resolved via SDS-polyacrylamide gel electrophoresis in a diverse array of 33 endemic Hawaiian drosophilids, encompassing 17 picture-winged species, 3 of theantopocerus species group, 9 fungus feeders, 1 species from each of the modified mouthparts,crassifemur and ciliated tarsus groups, and 1Scaptomyza species. Molecular weights of the two (10 species) or three vitellogenin bands (22 species) were highly variable, spanning a 7-kD range. The largest vitellogenin, V₁, was the most variable, showing a change of some 10% in its mean size of 47.6 kD. The smallest V₃ vitellogenin, mean size 44.1 kD, was evolutionarily the most conservative in size. The speciesDrosophila hawaiiensis was found to be polymorphic for two/three vitellogenin bands and, also, polymorphic with respect to the size of the V₁ protein. No inter- or intrapopulation variability in vitellogenin size was detected in 10 other species examined. The major features of vitellogenin protein evolution in the HawaiianDrosophila are change in molecular weight and regulatory differences that result in quantitative differences between species in patterns of vitellogenin protein production. This research was supported by NSF Grants DEB-7619872 and PCM-7913074. This paper is No. III in the series “Studies of Oogenesis in Natural Populations of Drosophilidae.”     

Relation of Intergroup Variation in Allogrooming to Group Social Structure and Ectoparasite Loads in Red Howlers (Alouatta seniculus)

We compare the allogrooming behavior of 5 troops (average size = 8.2) of red howlers (Alouatta seniculus) from the Venezuelan Llanos with that of other A. seniculus and Alouatta spp. of the genus. In 126.9 observation hr, we recorded 118 allogrooming events, with an average bout length of 109 sec. Females groomed more frequently than males did, but as groomees there is no significant differences between sexes. Adult males groomed adult females mostly in a sexual context (before copulation). Allogrooming rates differ significantly among groups. There are also significant differences among members of the same troop both as groomers and groomees, which we explain in the context of the social behavior and history of each troop. There is no significant correlation between weight of the groomee and duration of the grooming bout. However, the examination of grooming rates and ectoparasite load suggests that allogrooming may have hygienic consequences. Differences in allogrooming rates among species of Alouatta are related to differences in group kin structure and patterns of female competition, in particular, coalition formation. We conclude that the social structure and the degree of relatedness among individuals within a group (or among individuals in a population in interpopulation comparisons) is a more important determinant of allogrooming rate than body size or group size. Our results emphasize the importance of considering intergroup and interpopulational variation in behavior.     

Effects of organic acids on lipid synthesis and ecdysis in Triatoma infestans eggs

Scarce bibliographical data exists on the enzymes in Lepidosiren paradoxa and analysis of several enzymes was considered worthy of investigation. Distribution of ADH, ALP, FBALD, GAPDH, G3PDH, G6PDH, GPI, LDH, MDH, and PGM was identified in ten tissues (retina, heart, muscle, liver, kidney, lung, gut, gills, brain, and ovary) of the South American lungfish and compared with patterns previously described in other vertebrates. Compared with earlier results differences in the number of loci expressed were observed for ADH, G3PDH, GPI, and MDH. The number of loci expressed and/or in tissue specificity of several enzymes (ADH, FBALD, GAPDH, G3PDH, G6PDH and PGM) were found to be similar to those of other vertebrates. Differences were detected in ALP due to the absence of an intestinal-specific form typical of fish, amphibians, reptiles and birds; further differences were observed in GPI and MDH due to their tissue expression. The differences in LDH involve the LDH-A₄ isozyme which was most common in tissues. Overall, comparison with other vertebrates reveals that in L. paradoxa the tissue-restricted expressions of some enzymes are similar, while others have retained an ancestral pattern and exhibit a more widespread tissue expression of genes.     

Complex cis-acting regulatory genes demonstrated in Drosophila hybrids

Drosophila heteroneura and D differens are closely related, interfertile species of the Hawaiian picture-winged group. They display marked qualitative and quantitative differences in the pattern of expression of alcohol dehydrogenase (ADH) and an aldehyde oxidase (AO-1). These presumptive regulatory differences are revealed by comparisons of the relative levels of these enzymes in various tissues in larvae and adults. In hybrids produced between parents carrying different electrophoretic alleles at the structural loci for these two enzymes, each allele is expressed according to the developmental program characteristic of the parent from which it was derived. This result indicates control of the differences in pattern of expression by one or more cis-acting sites associated with each structural locus. The distribution of activity among all the three forms of these dimeric enzymes produced in hybrids indicates that the pattern differences reflect differential accumulation of enzyme molecules, not altered catalytic properties. As expected, the regulatory differences segregate with the electrophoretic markers in backcrosses.     

Biogeographic analysis of the Uhu and LOA elements in the Hawaiian Drosophila

Two transposable elements have been isolated from the Hawaiian Drosophila, the Uhu and LOA elements. The Uhu element has been shown to be present in a group of closely related species, the planitibia subgroup of the picture-winged Drosophila. This study examines the distribution of the Uhu element in several other subgroups of the picture-winged Drosophila, as well as the modified-mouthparts and antopocerus groups of the Hawaiian Drosophila. The LOA element has a much more limited distribution, having only been found in representatives of the planitibia and grimshawi subgroups of the picture-winged Drosophila. For both the Uhu and LOA elements there is an inverse correlation between the copy number of the element and the age of the island on which the species is endemic, i.e., species endemic to the Island of Hawaii, the youngest island, have the highest copy number, while species endemic to Kauai, the oldest island, have the lowest copy number of the element. The correlation suggests there is a relationship between speciation and the activity of transposable elements. Received: 6 January 1997; in revised form: 6 August 1997 / Accepted: 21 August 1997     

Intra-specific rDNA-ITS restriction site variation and an improved protocol to distinguish species and hybrids in the Daphnia longispina complex

A collaborative research effort was undertaken to evaluate the robustness of a recently developed genetic tool for species identification of members in the morphologically variable Daphnia longispina species complex. This genetic method, based on restriction fragment length polymorphism (RFLP) of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA (rDNA) with restriction enzymes Mwo I and Sau96 I [Billiones et al., 2004. Hydrobiologia 526: 43–53], was applied to many different European populations. Results were compared with two or more independently obtained characters (morphology, allozymes, mitochondrial DNA (mtDNA), or cloned rDNA-ITS sequences). Individuals of most taxa were readily identified, but unexpected ITS-RFLP patterns were found in many individuals indicated by other markers to be D. galeata or one of its hybrids. Among 43 investigated D. galeata populations (902 specimen analysed by ITS-RFLP), deviant RFLP fragment patterns occurred in 26 (i.e., more than half) of the populations. The deviant patterns could be attributed to the loss of one single restriction site in the ITS2 region. This loss made the distinction of D. galeata from other species unreliable, and F1 hybrids could not be identified. Future users should be aware of this shortcoming of the Billions et al. [2004. Hydrobiologia 526: 43–53] protocol. As a solution to this problem, we present an improved genetic identification protocol based on a simple double digestion of the rDNA-ITS region with the restriction enzymes BsrB I and EagI. Sequence analyses of rDNA-ITS clones and preliminary testing indicate that the new protocol is unaffected by the rDNA variation which troubled the Mwo I/Sau96 I protocol. Further, the new protocol identifies all European species of the D. longispina complex, as well as their F1 hybrids. However, a wider screening is required to verify its general utility for all species, since yet unknown variation may occur. Guest editor: Piet Spaak Cladocera: Proceedings of the 7th International Symposium on Cladocera     

Members of two gene families encoding ubiquitin-conjugating enzymes, AtUBC1-3 and AtUBC4-6, fromArabidopsis thaliana are differentially expressed

Covalent attachment of ubiquitin to other intracellular proteins is essential for many physiological processes in eukaryotes, including selective protein degradation. Selection of proteins for ubiquitin conjugation is accomplished, in part, by a group of enzymes designated E2s or ubiquitin-conjugating enzymes (UBCs). At least six types of E2s have been identified in the plantArabidopsis thaliana; each type is encoded by a small gene family. Previously, we described the isolation and characterization of two three-member gene families, designatedAtUBC1-3 andAtUBC4-6, encoding two of these E2 types. Here, we investigated the expression patterns, of theAtUBC1-3 andAtUBC4-6 genes by the histochemical analysis of transgenicArabidopsis containing the corresponding promoters fused to the -glucuronidase-coding region. Staining patterns showed that these genes are active in many stages of development and some aspects of cell death, but are not induced by heat stress. Within the two gene families, individual members exhibited both overlapping and complementary expression patterns, indicating that at least one member of each gene family is expressed in most cell types and at most developmental stages. Different composite patterns of expression were observed between theAtUBC1-3 andAtUBC4-6 families, suggesting distinct biochemical and/or physiological functions for the encoded E2s inArabidopsis.     

Evolution of Novel O-methyltransferases from the Vanilla planifolia Caffeic Acid O-methyltransferase

The biosynthesis of many plant secondary compounds involves the methylation of one or more hydroxyl groups, catalyzed by O-methyltransferases (OMTs). Here, we report the characterization of two OMTs, Van OMT-2 and Van OMT-3, from the orchid Vanilla planifolia Andrews. These enzymes catalyze the methylation of a single outer hydroxyl group in substrates possessing a 1,2,3-trihydroxybenzene moiety, such as methyl gallate and myricetin. This is a substrate requirement not previously reported for any OMTs. Based on sequence analysis these enzymes are most similar to caffeic acid O-methyltransferases (COMTs), but they have negligible activity with typical COMT substrates. Seven of 12 conserved substrate-binding residues in COMTs are altered in Van OMT-2 and Van OMT-3. Phylogenetic analysis of the sequences suggests that Van OMT-2 and Van OMT-3 evolved from the V. planifolia COMT. These V. planifolia OMTs are new instances of COMT-like enzymes with novel substrate preferences.     

Drosophila acetylcholinesterase: Characterization of different mutants resistant to insecticides

Selection of field populations originating from several countries allowed us to isolate 13 strains ofDrosophila melanogaster resistant to parathion.In vitro studies of acetylcholinesterase inhibition by paraoxon have been carried out on purified enzymes: most of the resistant strains harbor an altered acetylcholinesterase. Enzymes with higher resistance levels have been characterized with respect to their cross-resistance toward several insecticides. The patterns obtained have permitted us to group them and to delineate four categories. The existence of four distinct types of protein suggests that several mutations of acetylcholinesterase are responsible for insecticide resistance inDrosophila.     

Tooth Wear Difference Between the Yuanmou Hominoid and <Emphasis Type="Italic">Lufengpithecus</Emphasis>

The Late Miocene hominoids recovered from Lufeng (Lufengpithecus) and Yuanmou of Yunnan Province, China, are among the most numerous hominoid fossils in Eurasia. They have yielded critical evidence for the evolutionary history, biogeography and paleobiology of Miocene hominoids. We examined and compared the wear pattern and differences of 804 molars of the Yuanmou hominoid and Lufengpithecus. Our results indicate that both the upper and lower molars of the Yuanmou hominoids were more heavily worn than those of Lufengpithecus. The wear patterns of the individual molars between the Yuanmou hominoid and Lufengpithecus also are different. The heaviest wear of lower molars of the Yuanmou hominoid occur in M₂, followed by M₁ and M₃. In Lufengpithecus, M₁ and M₃ were more heavily worn than M₂. There are differences in wear between the upper and lower molars for the two hominoids. Among the various factors related to tooth wear, we suggest that the main reason for the tooth wear differences between the Yuanmou hominoid and Lufengpithecus may be that they had different diets. More soft dietary items like leaves and berries were probably consumed by Lufengpithecus, and the Yuanmou hominoid may mainly have feed on harder or frugivorous diets. This result complements findings from previous studies of tooth size proportion, and the development of lower molar shearing crests in the 2 samples. Enamel thickness, living environment, behavior patterns, and population structure also might account for dental wear differences between the Yuanmou hominoid and Lufengpithecus.     

Lipiniella arenicola (Chironomidae) compared withChironomus muratensis andCh. nudiventris: Distribution patterns related to depth and sediment characteristics,diet, and behavioural response to reduced oxygen concentrations

Density patterns ofLipiniella arenicola andChironomus muratensis were studied in Lake Wolderwijd (The Netherlands) using geostatistics, and compared with patterns of depth and silt contents of the sediment.L. arenicola was restricted to shallow (depth <1 m), sandy silt (silt content <5%), wind-exposed sediments.Ch. muratensis occurred all over the lake, but the highest densities were found in the sheltered silty North-West corner. Gut analyses of IV-instar larvae from the Ventjagers flats (Haringvliet, Lower Rhine-Meuse) showed thatL. arenicola fed by selectively grazing on benthic algae,Ch. muratensis by filtering and non-selective grazing, andCh. nudiventris by non-selective grazing. In the laboratory, behavioural responses to reduced oxygen concentrations were tested with the impedance conversion technique.L. arenicola was more sensitive to low oxygen concentrations (<3 mg l^–1) than bothChironomus species. It is argued that the differences in resistance to hypoxia and feeding behaviour are in accordance with the differences in distribution patterns. The restriction ofL. arenicola to the pure sand habitats is not attributable to an especially high sensitivity to low dissolved oxygen concentrations alone. Several behavioural adaptations enableL. arenicola larvae to live in the shallow, wind-exposed pure-sand habitats: the ability to select food items, tube strength, and site selection of ovipositing females or planktonic larvae.     

Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus <Emphasis Type="Italic">Sordaria macrospora</Emphasis>

The filamentous fungus Sordaria macrospora forms complex three-dimensional fruiting bodies that protect the developing ascospores and ensure their proper discharge. Several regulatory genes essential for fruiting body development were previously isolated by complementation of the sterile mutants pro1, pro11 and pro22. To establish the genetic relationships between these genes and to identify downstream targets, we have conducted cross-species microarray hybridizations using cDNA arrays derived from the closely related fungus Neurospora crassa and RNA probes prepared from wild-type S. macrospora and the three developmental mutants. Of the 1,420 genes which gave a signal with the probes from all the strains used, 172 (12%) were regulated differently in at least one of the three mutants compared to the wild type, and 17 (1.2%) were regulated differently in all three mutant strains. Microarray data were verified by Northern analysis or quantitative real time PCR. Among the genes that are up- or down-regulated in the mutant strains are genes encoding the pheromone precursors, enzymes involved in melanin biosynthesis and a lectin-like protein. Analysis of gene expression in double mutants revealed a complex network of interaction between the pro gene products.     

An asparaginase of Aspergillus nidulans is subject to oxygen repression in addition to nitrogen metabolite repression

Summary Of five amidohydrolase activities subject to nitrogen metabolite repression in Aspergillus nidulans, l-asparaginase shows clearest evidence of also being subject to repression by atmospheric oxygen. Such oxygen repressibility is only evident under nitrogen metabolite derepressed conditions. Asparaginase levels are also considerably elevated by areA300, an altered function allele of the positive acting wide domain regulatory gene areA mediating nitrogen metabolite repression and are drastically reduced by loss of function mutations in areA. A. nidulans has two l-asparaginase enzymes and it has been shown by the use of appropriate mutants that these regulatory effects are exerted on the expression of that specified by the ahrA gene but probably not that specified by the apnA gene. Present address: (until 25 August, 1988) Department of Genetics, University of Georgia, Athens, GA 30602, USA     

A comparison of the fate and effects of prochloraz in artifical and natural sediments

The current draft EC regulatory guidance document for the authorisation of plant protection products, directive EEC 91/414, contains provision for testing the potential toxicity of pesticides to sediment dwelling organisms. Development of an appropriate method is currently in progress, by a German regulatory and industry working group. The compounds which are expected to trigger sediment toxicity data are likely to be those which are relatively persistent, with a high K _ow, with the potential for significant adsorption to sediments, and may have previously demonstrated toxicity to aquatic organisms. The current proposal from this working group involves an artificial sediment, prepared in accordance with OECD guideline 207, as used for earthworm toxicity tests. The implications of using this sediment on the distribution, fate and availability of the compound under test are considered. This paper presents toxicity data for Chironomus riparius generated using radiolabelled Prochloraz^® in systems using this artificial sediment and two natural sediments. The fate of prochloraz was also investigated in the same systems and compared with data generated from sediment/water studies carried out in accordance with regulatory guidelines. At the maximum Predicted Environmental Concentration (PEC) of 195 g^-1 nominal, prochloraz had no effects on the survival and development of Chironomus riparius. The fate of the compound in the systems used was enhanced possibly as a result of photodegradation.     

Physiological analysis of Methylobacterium extorquens AM1 grown in continuous and batch cultures

Chemostat cultures of Methylobacterium extorquens AM1 grown on methanol or succinate at a range of dilution rates were compared to batch cultures in terms of enzyme levels, poly-β-hydroxybutyrate content, and intracellular concentrations of adenine and pyridine nucleotides. In both chemostat and batch cultures, enzymes specific to C₁ metabolism were up-regulated during growth on methanol and down-regulated during growth on succinate, polyhydroxybutyrate levels were higher on succinate, intracellular ATP levels and the energy charge were higher during growth on methanol, while the pools of reducing equivalents were higher during growth on succinate. For most of the tested parameters, little alteration occurred in response to growth rate. Overall, we conclude that the chemostat cultivation conditions developed in this study roughly mimic the growth in batch cultures, but provide a better control over the culturing conditions and a better data reproducibility, which are important for integrative functional studies. This study provides baseline data for future work using chemostat cultures, defining key similarities and differences in the physiology compared to existing batch culture data.     

Expression profiling analysis for genes related to meat quality and carcass traits during postnatal development of backfat in two pig breeds

The competitive equilibrium of fatty acid biosynthesis and oxidation in vivo determines porcine subcutaneous fat thickness (SFT) and intramuscular fat (IMF) content. Obese and lean-type pig breeds show obvious differences in adipose deposition; however, the molecular mechanism underlying this phenotypic variation remains unclear. We used pathway-focused oligo microarray studies to examine the expression changes of 140 genes associated with meat quality and carcass traits in backfat at five growth stages (1–5 months) of Landrace (a leaner, Western breed) and Taihu pigs (a fatty, indigenous, Chinese breed). Variance analysis (ANOVA) revealed that differences in the expression of 25 genes in Landrace pigs were significant (FDR adjusted permutation, P<0.05) among 5 growth stages. Gene class test (GCT) indicated that a gene-group was very significant between 2 pig breeds across 5 growth stages (P _ErmineJ<0.01), which consisted of 23 genes encoding enzymes and regulatory proteins associated with lipid and steroid metabolism. These findings suggest that the distinct differences in fat deposition ability between Landrace and Taihu pigs may closely correlate with the expression changes of these genes. Clustering analysis revealed a very high level of significance (FDR adjusted, P<0.01) for 2 gene expression patterns in Landrace pigs and a high level of significance (FDR adjusted, P<0.05) for 2 gene expression patterns in Taihu pigs. Also, expression patterns of genes were more diversified in Taihu pigs than those in Landrace pigs, which suggests that the regulatory mechanism of micro-effect polygenes in adipocytes may be more complex in Taihu pigs than in Landrace pigs. Based on a dynamic Bayesian network (DBN) model, gene regulatory networks (GRNs) were reconstructed from time-series data for each pig breed. These two GRNs initially revealed the distinct differences in physiological and biochemical aspects of adipose metabolism between the two pig breeds; from these results, some potential key genes could be identified. Quantitative, real-time RT-PCR (QRT-PCR) was used to verify the microarray data for five modulated genes, and a good correlation between the two measures of expression was observed for both 2 pig breeds at different growth stages (R=0.874±0.071). These results highlight some possible candidate genes for porcine fat characteristics and provide some data on which to base further study of the molecular basis of adipose metabolism.