Conservation of upstream regulators of scute on the notum of cyclorraphous Diptera

Bristles on the notum of many cyclorraphous flies are arranged into species-specific stereotyped patterns. Differences in the spatial expression of the proneural gene scute correlate with the positions of bristles in those species looked at so far. However, the examination of a number of genes encoding trans-regulatory factors, such as pannier, stripe, u-shaped, caupolican and wingless, indicates that they are expressed in conserved domains on the prospective notum. This suggests that the function of a trans-regulatory network of genes is relatively unchanged in derived Diptera, and that many differences are likely to be due to changes in cis-regulatory sequences of scute. In contrast, in Anopheles gambiae, a basal species with no stereotyped bristle pattern, the expression patterns of pannier and wingless are not conserved, and expression of AgASH, the Anopheles proneural gene, does not correlate in a similar manner with the bristle pattern. We discuss the possibility that independently acting cis-regulatory sequences at the scute locus may have arisen in the lineage giving rise to cyclorraphous flies.     

Identification of the site of inhibition of mitogenic signaling by oncogenic ras-p21 by a ras effector peptide

We have previously found that a ras switch 1 domain peptide (PNC-7, residues 35–47) selectively blocks oocyte maturation induced by oncogenic (Val 12–containing) ras-p21 protein and also blocks c-raf–induced oocyte maturation. We now find that oncogenic ras-p21 does not inhibit oocyte maturation of a constitutively activated raf protein (raf BXB) that is lacking most of the first 301 amino terminal amino acids, including the major ras binding domain and accessory ras-binding regions. We also find that a dominant negative raf that completely blocks c-raf–induced maturation likewise does not block raf-BXB–induced maturation. We conclude that PNC-7 blocks ras by binding to the amino-terminal domain of raf and that raf BXB must initiate signal transduction in the cytosol.     

Latitudinal differentiation in the effects of the toxic dinoflagellate Alexandrium spp. on the feeding and reproduction of populations of the copepod Acartia hudsonica

Blooms of the dinoflagellate Alexandrium spp. increase in their frequency, toxicity and historical presence with increasing latitude from New Jersey (USA) to the Gaspé peninsula (Canada). Biogeographic variation in these blooms results in differential exposure of geographically separate copepod populations to toxic Alexandrium. We hypothesize that the ability of copepods to feed and reproduce on toxic Alexandrium should be higher in copepods from regions that are frequently exposed to toxic Alexandrium blooms. We tested this hypothesis with factorial common environment experiments in which female adults of the copepod Acartia hudsonica from five separate populations ranging from New Jersey to New Brunswick were fed toxic and non-toxic strains of Alexandrium, and the non-toxic flagellate Tetraselmis sp. Consistent with the hypothesis, when fed toxic Alexandrium we observed significantly higher ingestion and egg production rates in the copepods historically exposed to toxic Alexandrium blooms relative to copepods from regions in which Alexandrium is rare or absent. Such differences among copepod populations were not observed when copepods were fed non-toxic Alexandrium or Tetraselmis sp. These results were also supported by assays in which copepods from populations both historically exposed and naïve to toxic Alexandrium blooms were fed mixtures of toxic Alexandrium and Tetraselmis sp. Two-week long experiments demonstrated that when copepods from populations naïve to toxic Alexandrium were fed a toxic strain of Alexandrium they failed to acclimate, such that their ingestion rates remained low throughout the entire two-week period. The differences observed among populations suggest that local adaptation of populations of A. hudsonica from Massachusetts (USA) to New Brunswick (Canada) has occurred, such that some populations are resistant to toxic Alexandrium.     

Studies on the mechanism of reduction of W-inducible sulAp expression by recF overexpression in Escherichia coli K-12

UV-inducible sulAp expression, an indicator of the SOS response, is reduced by recF ⁺ overexpression in vivo. Different DNA-damaging agents and amounts of RecO and RecR were tested for their effects on this phenotype. It was found that recF ⁺ overexpression reduced sulAp expression after DNA damage by mitomycin C or nalidixic acid. recO ⁺ and recR ⁺ overexpression partially suppressed the reduction of UV-induced sulAp expression caused by recF ⁺ overexpression. The requirement for ATP binding to RecF to produce the phenotype was tested by genetically altering the putative phosphate binding cleft of recF in a way that should prevent the mutant recF protein from binding ATP that should prevent the mutant recF protein from binding ATP. It was found that a change of lysine to glutamine at codon 36 results in a mutant recF protein (RecF4115) that is unable to reduce UV-inducible sulAp expression when overproduced. It is inferred from these results that recF overexpression may reduce UV-inducible sulAp expression by a mechanism that is sensitive to the ability of RecF to bind ATP and to the levels of RecO and RecR (RecOR) in the cell, but not to the type of DNA damage per se. Models are explored that can explain how recF ⁺ overexpression reduces UV induction of sulAp and how RecOR overproduction might suppress this phenotype.     

Identification of the site of inhibition of oncogenic ras-p21-induced signal transduction by a peptide from a ras effector domain

We have previously found that a peptide corresponding to residues 35–47 of the ras-p21 protein, from its switch 1 effector domain region, strongly inhibits oocyte maturation induced by oncogenic p21, but not by insulin-activated cellular wild-type p21. Another ras–p21 peptide corresponding to residues 96–110 that blocks ras–jun and jun kinase (JNK) interactions exhibits a similar pattern of inhibition. We have also found that c-raf strongly induces oocyte maturation and that dominant negative c-raf strongly blocks oncogenic p21-induced oocyte maturation. We now find that the p21 35–47, but not the 96–110, peptide completely blocks c-raf-induced maturation. This finding suggests that the 35–47 peptide blocks oncogenic ras at the level of raf; that activated normal and oncogenic ras–p21 have differing requirements for raf-dependent signaling; and that the two oncogenic-ras-selective inhibitory peptides, 35–47 and 96–110, act at two different critical downstream sites, the former at raf, the latter at JNK/jun, both of which are required for oncogenic ras-p21 signaling.     

Comparative analysis of genetic relationship and diagnostic markers of several taxa of Guizotia Cass. (Asteraceae) as revealed by AFLPs and RAPDs

Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) were employed to examine the genetic relationship between Guizotia taxa, to suggest the taxonomic status of some of these taxa, and to identify their diagnostic markers. Results from AFLPs and RAPDs share some features in common, both revealing G. scabra ssp. schimperi as the most closely related taxon to G. abyssinica, and indicating that G. arborescens and G. zavattarii are the most divergent taxa. Most of the diagnostic markers revealed in this study were specific to G. arborescens and G. zavattarii. Our analysis suggests that G. scabra ssp. scabra, G. scabra ssp. schimperi, Chelelu and Ketcha are separate species. In this study, AFLP was found to be superior to RAPD in detecting genetic variation, in internal consistency of the data and in the fitness of its clusters to genetic similarity data. AFLPs revealed genetic relationship between Guizotia taxa that is more inline with the cytogenetic and hybridization studies than that revealed by RAPDs.     

The Evolution of RecD Outside of the RecBCD Complex

The common understanding of the function of RecD, as derived predominantly from studies in Escherichia coli, is that RecD is one of three enzymes in the RecBCD double-stranded break repair DNA recombination complex. However, comparative genomics has revealed that many organisms possess a recD gene even though the other members of the complex, recB and recC, are not present. Further, bioinformatic analyses have shown that there is substantial sequence dissimilarity between recD genes associated with recB and recC (recD1), and those that are not associated with recBC (recD2). Deinococcus radiodurans, known for its extraordinary DNA repair capability, is one such organism that does not possess either recB or recC, and yet does possess a recD gene. The recD of D. radiodurans was deleted and this mutant was shown to have a capacity to repair double-stranded DNA breaks equivalent to wild-type. The phylogenetic history of recD was studied using a dataset of 120 recD genes from 91 fully sequenced species. The analysis focused upon the role of gene duplication and functional genomic context in the evolution of recD2, which appears to have undergone numerous independent events resulting in duplicate recD2 genes. The role of RecD as part of the RecBCD complex appears to have a divergence from an earlier ancestral RecD function still preserved in many species including D. radiodurans.     

Losses of seeds of temperate trees to soil fungi: effects of habitat and host ecology

Evidence suggests that impacts of fungal pathogens on tree recruitment tend to be greater in the forest understory than in openings, and that shade-tolerant trees are less vulnerable than shade-intolerant species. To investigate the role that harmful soil fungi may have in reducing regeneration of temperate trees, we applied fungicide to buried seeds of matched pairs of species differing in their relative shade tolerance and/or successional status (Acer negundo versus Acer saccharum, Prunus virginiana versus Prunus serotina, and Pinus strobus versus Tsuga canadensis), in three habitats that differed in their degree of openness (old field, forest gap, and forest understory). Our results indicated that soil fungi reduced germination of A. negundo, P. virginiana, P. serotina. and T. canadensis, and reduced viability of ungerminated seeds of P. strobus; no significant effects of fungi on seeds of A. saccharum were detected. However, we found seeds were not less likely to survive following burial in forest understory than in gaps. As well, results for only one species pair (A. negundo versus A. saccharum) were consistent with the prediction that shade-intolerant or successional species should be more susceptible to fungal attack than mature forest species. These results contrast with other studies of temperate and especially tropical forest trees.     

Potentially active copies of the gypsy retroelement are confined to the y chromosome of some strains of drosophila melanogaster possibly as the result of the female-specific effect of the flamenco gene

Gypsy is an endogenous retrovirus present in the genome of Drosophila melanogaster. This element is mobilized only in the progeny of females which contain active gypsy elements and which are homozygous for permissive alleles of a host gene called flamenco (flam). Some data strongly suggest that gypsy elements bearing a diagnostic HindIII site in the central region of the retrovirus body represent a subfamily that appears to be much more active than elements devoid of this site. We have taken advantage of this structural difference to assess by the Southern blotting technique the genomic distribution of active gypsy elements. In some of the laboratory Drosophila stocks tested, active gypsy elements were found to be restricted to the Y chromosome. Further analyses of 14 strains tested for the permissive vs. restrictive status of their flamenco alleles suggest that the presence of permissive alleles of flam in a stock tends to be associated with the confinement of active gypsy elements to the Y chromosome. This might be the result of the female-specific effect of flamenco on gypsy activity. Received: 13 June 1997 / Accepted: 27 August 1997     

Identification and physical characterization of yeast glucoamylase structural genes

Summary Each one of at least three unlinked STA loci (STA1, STA2 and STA3), in the genome of Saccharomyces diastaticus controls starch hydrolysis by coding for an extracellular glucoamylase. Cloned STA2 sequences were used as hybridization probes to investigate the physical structure of the family of STA genes in the genomes of different Saccharomyces strains. Sta⁺ strains, each carrying a single genetically defined STA locus, were crossed with a Sta^– strain and the segregation behavior of the functional locus (i.e. Sta⁺) and sequences homologous to a cloned STA2 glucoamylase structural gene at that locus were analyzed. The results indicate that in all strains examined there is a multiplicity of sequences that are homologous to STA2 DNA but that only the functional STA loci contain extensive 5 and 3 homology to each other and can be identified as residing on unique fragments of DNA; that all laboratory yeast strains examined contain extensive regions of the glucoamylase gene sequences at or closely linked to the STA1 chromosomal position; that the STA1 locus contains two distinct glucoamylase gene sequences that are closely linked to each other; and that all laboratory strains examined also contain another ubiquitous sequence that is not allelic to STA1 and is nonfunctional (Sta^–), but has retained extensive sequence homology to the 5 end of the cloned STA2 gene. It was also determined that the DEX genes (which control dextrin hydrolysis in S. diastaticus), MAL5 (a gene once thought to control maltose metabolism in yeast) and the STA genes are allelic to each other in the following manner: STA1 and DEX2, STA1 and MAL5, and STA2 and DEX1 and STA3 and DEX3.     

Ecological biogeography of species of Gelonus,Acantholybas and Amorbus in Australia

Geographic ranges and host plants of 10 species of Australian coreid, Gelonus tasmanicus, Acantholybas brunneus, Amorbus alternatus, Am. atomarius, Am. biguttatus, Am. bispinus, Am. obscuricornis, Am. rhombifer, Am. robustus and Am. rubiginosus, were summarized using data from specimen collection labels and sampling. One process (CLIMEX ) and two correlative range‐modelling programs (BIOCLIM and DOMAIN ) were used to infer the bioclimatic profiles of each species. By inference from the maximum range predictions made by CLIMEX , the suggestion that G. tasmanicus, Am. atomarius and Am. obscuricornis are temperate species was supported. Similarly, the suggestions that Ac. brunneus was a subtropical species and Am. biguttatus and Am. rhombifer are predominantly tropical species were supported. That Am. alternatus, Am. robustus and Am. rubiginosus are apparently ubiquitous species was supported. Comparison of the bioclimatic profiles of the habitats of G. tasmanicus and Am. obscuricornis within Tasmania using BIOCLIM supported information available in the published literature, that is, that G. tasmanicus is better suited to sites at higher elevations than Am. obscuricornis. In addition, the suggestion that the regions of high Amorbus species endemism should overlap with regions of high eucalypt species endemism was also supported. This finding is taken as evidence that the evolutionary radiation of Amorbus has followed that of the eucalypts. Using these models we have obtained preliminary insights into the biology of each species and the environmental characteristics of their preferred climatic envelope. This is an achievement that might never have been attained through concentrated study given that these insects can vary from being rare to, at best, locally common in occurrence.     

Identification of a novel gene family,paralogs of inhibitor of apoptosis proteins present in plants,fungi, and animals

Only few orthologs of animal apoptosis regulators have been found in plants. Recently, the ectopic expression of mammalian inhibitor of apoptosis proteins (IAPs) has been shown to affect plant programmed cell death. Here, we identified two novel proteins homologous to Arabidopsis thaliana IAP-like protein (AtILP) 1 and 2 by applying an improved motif searching method. Furthermore, homologs of AtILP1 were found to occur as a novel gene family in other organisms such as fungi and animals including Homo sapiens (HsILP1). Like baculovirus IAP repeats (BIRs) in IAPs, ILPs contain two highly conserved BIR-like domains (BLDs) with a putative C2HC-type zinc finger. Phylogenetic analyses indicated that ILPs are putative paralogs of IAPs. Homology modeling revealed that the three-dimensional structure of BLD in HsILP1 is similar to that of BIR. Transient expression of HsILP1 resulted in inhibition of etoposide-induced apoptosis in HEK293 and HeLaS3 cells. These findings suggest that ILPs are conserved in a wide range of eukaryotes including plants, and that their functions are closely related to those of IAPs.     

两种梧桐叶绿体基因组密码子使用偏性分析

为了分析美丽梧桐、云南梧桐叶绿体基因组密码子的使用偏性,该研究通过筛选美丽梧桐、云南梧桐叶绿体基因组中各52条蛋白编码序列,并利用CodonW、CUSP和SPSS软件对其密码子使用模式及偏性进行了分析。结果表明:(1)美丽梧桐、云南梧桐的GC含量分别为38.12%、38.05%,表明叶绿体基因组内富含A/T碱基。(2)有效密码子数(ENC)范围为36.91～56.46、36.55～58.04,表明多数密码子偏性较弱。(3)相对同义密码子(RSCU)分析显示,RSCU1的密码子各有29个,其中28个以A、U结尾。(4)中性绘图显示,GC_3与GC_(12)的相关性不显著,回归曲线斜率分别为0.195和0.304,说明密码子偏好性主要受到自然选择的影响。(5) ENC-plot分析中大部分基因分布于曲线的周围和下方,ENC比值多分布于-0.04～0.10之间,表明突变会影响密码子偏性的形成。此外,17、18个密码子分别被鉴定为美丽梧桐、云南梧桐的最优密码子。以上结果说明美丽梧桐、云南梧桐叶绿体基因组的密码子使用偏性可能受选择和突变共同作用,且使用模式较为相似,但具有一定的差异,可能与适应环境的进化机制有关。     

Overexpression of fIbA, an early regulator of Aspergillus asexual sporulation, leads to activation of brIA and premature initiation of development

Aspergillus nidulans reproduces asexually by forming thousands of mitotically derived spores atop highly specialized multicellular organs termed conidiophores. We have identified a gene called flbA (for fluffy low brlA expression) that is required for initiation of A. nidulans conidiophore development. flbA mutants form abnormal colonies that have a distinct fluffy phenotype characterized by tightly interwoven aerial hyphae that autolyse as the colony matures. The requirement for fIbA in conidiophore development precedes activation of brlA, a primary regulator of conidiophore development. The wild-type flbA gene was isolated and found to encode a 3.0 kb mRNA that is expressed throughout the A. nidulans asexual life cycle. Overexpression of fIbA using an Inducible promoter resulted in misscheduled expression of brlA in vegetative ceils and caused hyphal tips to differentiate into spore-producing structures. Sequence analysis of a nearly full-length fIbA cDNA clone showed that fibA is predicted to encode a 717-amino-acid polypeptide with 30% identity to the Saccharomyces cerevisiae SST2 protein. SST2 is required by yeast cells for resuming growth following prolonged exposure to yeast mating pheromone and for mating partner discrimination. We propose that fIbA plays a related role in a signalling pathway for Aspergillus conidiophore development.     

Extracellular Production of Yeast Protease

The groEL gene of the alkaliphilic Bacillus sp. strain C-125 was cloned in Escherichia coli and sequenced. The groEL gene encoded a polypeptide of 544 amino acids and was preceded by the incomplete groES gene, lacking its 5′-end. The sequence of the derived amino acids was 87.5% identical to that of B. subtilis, 85.4% identical to that of B. stearothemophilus, and 60.9% identical to that of E. coli. The GroEL protein was expressed in E. coli. Purified GroEL protected yeast a-glucosidase from irreversible aggregation at a high temperature and the addition of Mg-ATP was essential for reactivation of the a-glucosidase. The addition of E. coli GroES increased recovery of the enzyme activity, indicating that C-125 GroEL could function in coordination with E. coli GroES.     

The Thermostable Direct Hemolysin Gene (tdh) of Vibrio hollisae Is Dissimilar in Prevalence to and Phylogenetically Distant from the tdh Genes of Other Vibrios: Implications in the Horizontal Transfer of the tdh Gene

Vibrio hollisae strains isolated recently from patients in various locations were examined for the presence of the thermostable direct hemolysin gene (tdh) using nucleic acid hybridization and polymerase chain reaction assays. The results were consistent with the previous finding that all strains of V. hollisae carry the tdh gene. In contrast, the tdh gene has been detected in a minority of strains for other Vibrio species (V. parahaemolyticus, V. cholerae non-O1, and V. mimicus). Detailed phylogenetic analysis showed that the tdh genes of the non-V. hollisae species were very closely related to each other and that the tdh gene of V. hollisae was distantly related to the tdh genes of the non-V. hollisae species. These results and the proposed insertion sequence-mediated tdh transfer mechanism suggest that the tdh gene may have been maintained stably in V. hollisae and that the tdh genes of the non-V. hollisae species may have been involved in recent horizontal transfer.     

Invasions of equilibria: tests of resource competition using two species of algae

Summary Single-species, steady-state chemostat cultures of two freshwater diatoms showed that Fragilaria crotonensis had a lower equilibrial requirement for silicate than did Tabellaria fenestratra. Using this information, resource competition theory predicts that Fragilaria should be able to invade silicate-limited equilibrium populations of Tabellaria, but Tabellaria should not be able to invade silicatelimited Fragilaria. This prediction was supported by a series of invasion experiments. The two species did not have detectable differences in their phosphate requirements. Invasion experiments showed that Fragilaria could invade Tabellaria cultures, but that Tabellaria could not invade Fragilaria cultures under phosphate-limited conditions. These results are consistent with predictions based on previous studies of the phosphate physiology of these genera.