CanVaS: Documenting the genetic variation spectrum of Greek cancer patients

National genetic variation registries vastly increase the level of detail for the relevant population, while directly affecting patient management. Herein, we report CanVaS, a Cancer Variation reSource aiming to document the genetic variation of cancer patients in Greece. CanVaS comprises germline genetic data from 7,363 Greek individuals with a personal and/or family history of malignancy. The data set incorporates approximately 24,000 functionally annotated rare variants in 97 established or suspected cancer susceptibility genes. For each variant, allele frequency for the Greek population, interpretation for clinical significance, anonymized family and segregation information, as well as phenotypic traits of the carriers, are included. Moreover, information on the geographic distribution of the variants across the country is provided, enabling the study of Greek population isolates. Direct comparisons between Greek (sub)populations with relevant genetic resources are supported, allowing fine-grain localized adjustment of guidelines and clinical decision-making. Most importantly, anonymized data are available for download, while the Leiden Open Variation Database schema is adopted, enabling integration/interconnection with central resources. CanVaS could become a stepping-stone for a countrywide effort to characterize the cancer genetic variation landscape, concurrently supporting national and international cancer research. The database can be accessed at: http://ithaka.rrp.demokritos.gr/CanVaS.

The Coming of Age for Big Data in Systems Radiobiology, an Engineering Perspective

As high-throughput approaches in biological and biomedical research are transforming the life sciences into information-driven disciplines, modern analytics platforms for big data have started to address the needs for efficient and systematic data analysis and interpretation. We observe that radiobiology is following this general trend, with -omics information providing unparalleled depth into the biomolecular mechanisms of radiation response-defined as systems radiobiology. We outline the design of computational frameworks and discuss the analysis of big data in low-dose ionizing radiation (LDIR) responses of the mammalian brain. Following successful examples and best practices of approaches for the analysis of big data in life sciences and health care, we present the needs and requirements for radiation research. Our goal is to raise awareness for the radiobiology community about the new technological possibilities that can capture complex information and execute data analytics on a large scale. The production of large data sets from genome-wide experiments (quantity) and the complexity of radiation research with multidimensional experimental designs (quality) will necessitate the adoption of latest information technologies. The main objective was to translate research results into applied clinical and epidemiological practice and understand the responses of biological tissues to LDIR to define new radiation protection policies. We envisage a future where multidisciplinary teams include data scientists, artificial intelligence experts, DevOps engineers, and of course radiation experts to fulfill the augmented needs of the radiobiology community, accelerate research, and devise new strategies.

A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes)

A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data. We constructed an ingroup matrix of 62 full-length mitogenome sequences from 20 catfish families together with four cypriniform outgroups, spanning 15,557 positions in total. Partitioned maximum likelihood analyses and Bayesian relaxed clock dating using fossil age constraints provide some useful and novel insights into the evolutionary history of this group. Loricarioidei are recovered as the first siluriform group to diversify, rendering Neotropics the cradle of the order. The next deepest clade is the South American Diplomystoidei placed as a sister group to all the remaining Siluroidei. The two multifamilial clades of "Big Asia" and "Big Africa" are also recovered, albeit nodal support for the latter is poor. Within "Big Asia", Bagridae are clearly polyphyletic. Other interfamilial relationships, including Clariidae + Heteropneustidae, Doradidae + Auchenipteridae and Ictaluridae + Cranoglanididae are robustly resolved. Our chronogram shows that siluriforms have a Pangaean origin, at least as far back as the Early Cretaceous. The inferred timeline of the basal splits corroborates the "Out-of-South America" hypothesis and accords well with the fossil record. The divergence of Siluroidei most likely postdated the final separation of Africa and South America. An appealing case of phylogenetic affinity elaborated by biogeographic dispersal is exemplified by the Early Paleogene split between the Southeast Asian Cranoglanididae and Ictaluridae, with the latter radiating into North America's freshwater realm by Eocene. The end of Cretaceous probably concludes the major bout of diversification at the family level while with the dawn of the Cenozoic a prolific radiation is evident at the generic level.

Brain Radiation Information Data Exchange (BRIDE): integration of experimental data from low-dose ionising radiation research for pathway discovery

BACKGROUND

The underlying molecular processes representing stress responses to low-dose ionising radiation (LDIR) in mammals are just beginning to be understood. In particular, LDIR effects on the brain and their possible association with neurodegenerative disease are currently being explored using omics technologies.

RESULTS

We describe a light-weight approach for the storage, analysis and distribution of relevant LDIR omics datasets. The data integration platform, called BRIDE, contains information from the literature as well as experimental information from transcriptomics and proteomics studies. It deploys a hybrid, distributed solution using both local storage and cloud technology.

CONCLUSIONS

BRIDE can act as a knowledge broker for LDIR researchers, to facilitate molecular research on the systems biology of LDIR response in mammals. Its flexible design can capture a range of experimental information for genomics, epigenomics, transcriptomics, and proteomics. The data collection is available at: .

Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins

There is growing evidence for the involvement of Y-complex nucleoporins (Y-Nups) in cellular processes beyond the inner core of nuclear pores of eukaryotes. To comprehensively assess the range of possible functions of Y-Nups, we delimit their structural and functional properties by high-specificity sequence profiles and tissue-specific expression patterns. Our analysis establishes the presence of Y-Nups across eukaryotes with novel composite domain architectures, supporting new moonlighting functions in DNA repair, RNA processing, signaling and mitotic control. Y-Nups associated with a select subset of the discovered domains are found to be under tight coordinated regulation across diverse human and mouse cell types and tissues, strongly implying that they function in conjunction with the nuclear pore. Collectively, our results unearth an expanded network of Y-Nup interactions, thus supporting the emerging view of the Y-complex as a dynamic protein assembly with diverse functional roles in the cell.

Assessment and reconstruction of novel HSP90 genes: duplications, gains and losses in fungal and animal lineages

Hsp90s, members of the Heat Shock Protein class, protect the structure and function of proteins and play a significant task in cellular homeostasis and signal transduction. In order to determine the number of hsp90 gene copies and encoded proteins in fungal and animal lineages and through that key duplication events that this family has undergone, we collected and evaluated Hsp90 protein sequences and corresponding Expressed Sequence Tags and analyzed available genomes from various taxa. We provide evidence for duplication events affecting either single species or wider taxonomic groups. With regard to Fungi, duplicated genes have been detected in several lineages. In invertebrates, we demonstrate key duplication events in certain clades of Arthropoda and Mollusca, and a possible gene loss event in a hymenopteran family. Finally, we infer that the duplication event responsible for the two (a and b) isoforms in vertebrates occurred probably shortly after the split of Hyperoartia and Gnathostomata.

The complete mitochondrial genome of the loggerhead turtle Caretta caretta (Testudines: Cheloniidae): genome description and phylogenetic considerations

The marine turtle Caretta caretta is a widely distributed species that is facing critical population decline, especially in the Mediterranean rookeries. Molecular markers, such as mitochondrial DNA (mtDNA) sequences, are of great importance for the description and monitoring of turtle migratory populations. The complete sequence of the C. caretta mitochondrial genome is presented here. The genome comprises 16,440 base pairs, containing 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes), and a control region, all organized similar to the majority of vertebrate mitogenomes. MtDNA length polymorphism and heteroplasmy were observed among, and within, individuals due to the variable size of a microsatellite repeat residing at the 3' end of the control region. The use of the above repeat as a marker for individual fingerprinting is discussed. Furthermore, phylogenetic analyses among Testudines based on complete mitogenomes, as well as among marine turtles based on partial mtDNA sequences, are considered.

Genotype and allele frequencies of heme oxygenase-1 promoter region in a Greek cohort

BACKGROUND

Heme oxygenase-1 (HO-1) is an enzyme, which catabolizes heme into carbon monoxide, biliverdin and free iron. The induction of this enzyme is an important cytoprotective mechanism, which occurs as an adaptive and beneficial response to a wide variety of oxidant stimuli. HO-1 inducibility is mainly modulated by a (GT)(n) polymorphism in the promoter region, and has been shown that short (S) repeats are associated with greater up-regulation of HO-1, compared with long (L) repeats.

METHODS

In the present study, 250 healthy Greek individuals have been screened in order to estimate the frequencies of (GT)(n) alleles in the HO-1 gene.

RESULTS

Nineteen different alleles, ranging from 17 to 39 repeats, with (GT)(23) and (GT)(30) being the most common ones, were identified.

CONCLUSION

The possible role of this polymorphism in disease states is discussed.

Promoter complexity and tissue-specific expression of stress response components in Mytilus galloprovincialis, a sessile marine invertebrate species

The mechanisms of stress tolerance in sessile animals, such as molluscs, can offer fundamental insights into the adaptation of organisms for a wide range of environmental challenges. One of the best studied processes at the molecular level relevant to stress tolerance is the heat shock response in the genus Mytilus. We focus on the upstream region of Mytilus galloprovincialis Hsp90 genes and their structural and functional associations, using comparative genomics and network inference. Sequence comparison of this region provides novel evidence that the transcription of Hsp90 is regulated via a dense region of transcription factor binding sites, also containing a region with similarity to the Gamera family of LINE-like repetitive sequences and a genus-specific element of unknown function. Furthermore, we infer a set of gene networks from tissue-specific expression data, and specifically extract an Hsp class-associated network, with 174 genes and 2,226 associations, exhibiting a complex pattern of expression across multiple tissue types. Our results (i) suggest that the heat shock response in the genus Mytilus is regulated by an unexpectedly complex upstream region, and (ii) provide new directions for the use of the heat shock process as a biosensor system for environmental monitoring.

Analysis and characterization of the transcriptional unit of a newMytilus galloprovincialis(Mollusca: Bivalvia)hsp70gene

We isolated, analysed and characterized the transcriptional unit of an hsp70 gene of Mytilus galloprovincialis (Mollusca: Bivalvia). Sequence analysis of a total of 3653 bp, revealed a 1914 bp ORF encoding for a 637-amino acid polypeptide that exhibits all the characteristic signatures of the cytoplasmic members of the HSP70 family. The ORF is not interrupted by introns and its 5'-flanking region contains five putative heat shock elements (HSEs), both indicating for an inducible hsp70 gene. Furthermore, nucleotide and amino acid sequence alignments with HSP70 genes from several molluscan and non-molluscan species confirmed that the newly isolated gene, the first complete in the genus Mytilus and in the Mollusca phylum, is a cytoplasmic and inducible hsp70 gene.

Three new satellite sequences and a mobile element found inside HSP70 introns of the Mediterranean mussel (Mytilus galloprovincialis)

We report the characterization of 3 new repetitive sequences from the bivalve mollusc Mytilus galloprovincialis, designated Mg1, Mg2, and Mg3, with monomer lengths of 169, 260, and 70 bp, respectively. The 3 repeats together constitute approximately 7.8% of the M. galloprovincialis genome and were found, together with ApaI-type 2 repeats, inside the introns of 2 genes of the HSP70 family, hsc70 and hsc71. Both the monomer length and the genomic content of the repeats indicate satellite sequences. The Mg1 repetitive region and its flanking sequences exhibit significant homology to CvE, a member of the Pearl family of mobile elements found in the eastern oyster (Crassostrea virginica). Thus, the whole homologous region is designated MgE, the first putative transposable element characterized in M. galloprovincialis. The ApaI, Mg2, and Mg3 repeats are continuously arranged inside the introns of both the hsc70 and hsc71 genes. The presence of perfect inverted repeats flanking the ApaI-Mg2-Mg3 repetitive region, as well as a sequence analysis of the repeats, indicates a transposition-like insertion of this region. The genes of the HSP70 family are highly conserved, and the presence of repetitive DNA or of mobile elements inside their introns is reported here for the first time.

Identification of Several Cytoplasmic HSP70 Genes from the Mediterranean Mussel (Mytilus galloprovincialis) and Their Long-Term Evolution in Mollusca and Metazoa

The HSP70 protein family consists one of the most conserved and important systems for cellular homeostasis under both stress and physiological conditions. The genes of this family are poorly studied in Mollusca, which is the second largest metazoan phylum. To study these genes in Mollusca, we have isolated and identified five HSP70 genes from Mytilus galloprovincialis (Mediterranean mussel) and investigated their short-term evolution within Mollusca and their long-term evolution within Metazoa. Both sequence and phylogenetic analyses suggested that the isolated genes belong to the cytoplasmic (CYT) group of the HSP70 genes. Two of these genes probably represent cognates, whereas the remaining probably represent heat-inducible genes. Phylogenetic analysis including several molluscan CYT HSP70s reveals that the cognate genes in two species have very similar sequences and form intraspecies phylogenetic clades, differently from most metazoan cognate genes studied thus far, implying either recent gene duplications or concerted evolution. The M. galloprovincialis heat-inducible genes show intraspecies phylogenetic clustering, which in combination with the higher amino acid than nucleotide identity suggests that both gene conversion and purifying selection should be responsible for their sequence homogenization. Phylogenetic analysis including several metazoan HSP70s suggests that at least two types of CYT genes were present in the common ancestor of vertebrates and invertebrates, the first giving birth to the heat-inducible genes of invertebrates, whereas the other to both the heat-inducible genes of vertebrates and the cognate genes of all metazoans. These analyses also suggest that inducible and cognate genes seem to undergo divergent evolution.

Isolation, characterization, and localization of beta-tubulin genomic clones of three Drosophila montium subgroup species

Genomic libraries were constructed from three Drosophila species, namely Drosophila auraria, Drosophila serrata, and Drosophila kikkawai, belonging to the Drosophila montium subgroup of the Drosophila melanogaster species group. Clones containing beta-tubulin specific sequences were isolated, characterized by restriction endonuclease digestions and Southern hybridizations, and mapped by in situ hybridization on the polytene chromosomes of the species studied. The distribution of the beta-tubulin loci was found to be similar in D. montium species and D. melanogaster.

The genome of the olive fruit fly Bactrocera oleae: localization of molecular markers by in situ hybridization to the salivary gland polytene chromosomes

Nine specific DNA probes (genomic or cDNA) from Ceratitis capitata have been mapped by in situ hybridization to the salivary gland polytene chromosomes of the olive fruit fly Bactrocera oleae, a major agricultural pest, thus establishing molecular markers for the 5 autosomal chromosomes. Taking into account the present results, as well as previous data obtained mainly by in situ hybridizations, chromosomal homologies among B. oleae, C. capitata and B. tryoni are established. Data show extensive linkage group conservation among the 3 taxa of the economically important and globally distributed family, the Tephritidae.Key words: Bactrocera oleae, Tephritidae, salivary gland, polytene chromosomes, in situ hybridization, mapping.

The hsp70 locus of Drosophila auraria (montium subgroup) is single and contains copies in a conserved arrangement

The restriction endonuclease pattern of a number of hsp70-homologous clones isolated from a library of heat shock cDNA from Drosophila auraria, a species belonging to the montium subgroup of the melanogaster species group, reveals two types of clones, A and B, differing in a single restriction site. Both types, as well as hsp70-specific probes derived from both hsp70 loci of Drosophila melanogaster, hybridize in situ with a single band at region 32 A of the 2L polytene arm, indicating a clustered organization of the hsp70 gene copies in D. auraria. The longest type B clone was sequenced and it was found that one strand contains an open reading frame (ORF) exhibiting great identity with a previously described hsp70 gene of D. auraria (now denoted as type A) and with its counterparts of D. melanogaster, while its second strand, unlike the type A clone, does not contain a long antiparallel coupled ORF (LAC ORF) because of a base substitution resulting in a premature stop codon. After additional data had been derived from isolation and characterization of hsp70-homologous genomic clones, together with Southern analysis of genomic DNA, we found that two hsp70 gene copies are present at the above locus of D. auraria with an inverted tandem repeat organization, while the presence of a third hsp70 gene is not clearly evident. The above results are compared with those observed at the homologous loci of some melanogaster subgroup species (D. melanogaster and its sibling species), in which, however, the hsp70 locus is duplicated, and with the more distantly related Dipteran Anopheles albimanus.

Heat shock gene expression during recovery after transient cold shock in Drosophila auraria (Diptera: Drosophilidae)

Newly synthesized polypeptides during recovery from prolonged cold treatment (0 degree to -1 degree C) of Drosophila auraria, a montium subgroup species, of the melanogaster species group, were analysed in denaturing polyacrylamide gels. In addition, during the cold shock recovery period, Northern analysis of the hsp83 mRNA was performed. A significant induction of two polypeptides, which exhibited electrophoretic mobilities, with the heat inducible 83 and 70 kD hsp83 and hsp70 was detected, but no such induction was evident in the so-called 'small' hsp genes. These results are compared and discussed with those observed in D. melanogaster.

The organization of the alpha-tubulin gene family in the Drosophila montium subgroup of the melanogaster species group

The alpha 1-, alpha 2-, alpha 3-, and alpha 4-tubulin genes have been mapped by in situ hybridization to the polytene chromosomes of five species representative of the Drosophila montium subgroup geographical distribution. A lambda phage clone containing alpha 1-tubulin specific sequences was isolated from a genomic DNA library of Drosophila auraria and its restriction endonuclease pattern is presented. Both well-characterized heterologous and homologous probes were used to assess orthogonality of gene members between species groups. The in situ hybridization pattern observed in all species studied is consistent with that of Drosophila melanogaster, since alpha 1-, alpha 2-, and alpha 3-tubulin genes are located on the same polytene arm, and the alpha 4-tubulin gene is found on a different arm. Cross-hybridization was observed among alpha 1-, alpha 2-, and alpha 3-tubulin specific sequences in all species studied, using either heterologous or homologous probes. However, unlike D. melanogaster, in all montium species studied, both alpha 1- and alpha 3-tubulin specific probes hybridize to the same polytene band, indicating a clustered organization of the above genes. The chromosomal organization of this gene family would suggest that taxa within the montium subgroup are closer to their common ancestors than are the taxa in the melanogaster species group. A mode of evolution for this gene family in Drosophila is proposed.

The heat-shock gene hsp83 of Drosophila auraria: genomic organization, nucleotide sequence, and long antiparallel coupled ORFs (LAC ORFs)

The genomic organization of the hsp83 gene of Drosophila auraria, a far-eastern endemic species belonging to the montium subgroup of the melanogaster species group, is presented here. Based on in situ hybridization on polytene chromosomes, cDNA and genomic clone mapping, nucleotide sequencing, and genomic Southern analysis, hsp83 is shown to be present as a single-copy gene at locus 64B on the 3L chromosome arm in D. auraria. This gene is organized into two exons separated by a 929-bp intron. The first exon represents the mRNA leader sequence and is not translated, while the coding region, having a length of 2,151 bp, is solely included in the second exon. Nucleotide sequence comparisons of D. auraria hsp83 with homologous sequences from other organisms show high conservation of the coding region (88-92% identity) in the genus Drosophila, in addition to the conserved genomic organization of two-exons-one-intron, of comparable size and arrangement. A phylogenetic tree based on the protein sequences of homologous genes from representative organisms is in accord with the accredited phylogenetic position of D. auraria. In the hsp83 gene region, a second case of long antiparallel coupled open reading frames (LAC ORFs) for this species was found. The antiparallel to the hsp83 gene ORF is 1,554 bases long, while the two ORFs overlap has a size of 1,548 bp. The anti-hsp83 ORF does not show significant homology to any known gene sequences. In addition, no similar LAC ORF structures were found in homologous gene regions of other organisms.

The glutamate dehydrogenase, E74 and putative actin gene loci in the Drosophila montium subgroup. Chromosomal homologies among the montium species and D. melanogaster

DNA-specific sequences from an enzyme-coding gene (glutamate dehydrogenase, gdh), a regulatory protein-coding gene (E74) and genes of the actin family were mapped by in situ hybridization on the polytene chromosomes of six species representative of the geographical distribution of the Drosophila montium subgroup of the melanogaster species group. In all species studied, one hybridization signal was detected for the gdh and E74 genes, and seven signals for the actin genes. The distribution of the actin-related loci in five montium species is similar to that of the other Drosophila species studied so far, although they present an extra signal. This distribution differs in the sixth montium species studied, D. kikkawai. Taking into account the present results, as well as previous data obtained mainly by in situ hybridizations, homologies among the polytene chromosomes of the montium subgroup species, as well as between these species and D. melanogaster, were also established.

Variations in the heat-induced protein pattern of several Drosophila montium subgroup species (Diptera:Drosophilidae)

After temperature elevation, the newly synthesized polypeptides from several Drosophila montium subgroup species, of the melanogaster species group, were analyzed in denaturing acrylamide gels. The pattern obtained is characteristic of the heat shock response already documented for many other Drosophila species, although the relative electrophoretic mobility of the "small" heat shock proteins exhibits a species-specific pattern. Based on the above pattern, the montium species are placed in three distinct groups. The present data is consistent with that previously used to propose a northeast to southwest evolutionary mode of expansion for the montium subgroup species.

The Drosophila montium subgroup species. Phylogenetic relationships based on mitochondrial DNA analysis

Mitochondrial DNA (mtDNA) restriction site maps for three Drosophila montium subgroup species of the melanogaster species group, inhabiting Indian and Afrotropical montium subgroup territories, were established. Taking into account previous mtDNA data concerning six oriental montium species, a phylogeny was established using distance-matrix and parsimony methods. Both genetic diversity and mtDNA size variations were found to be very narrow, suggesting close phylogenetic relationships among all montium species studied. The phylogenetic trees that were constructed revealed three main lineages for the montium subgroup species studied: one consisting of the Afrotropical species Drosophila seguyi, which is placed distantly from the other species, one comprising the north-oriental (Palearctic) species, and one comprising the southwestern (south-oriental, Australasian, Indian, and Afrotropical) species. The combination of the mtDNA data presented here with data from other species belonging to the melanogaster and obscura subgroups revealed two major clusters: melanogaster and obscura. The melanogaster cluster is further divided into two compact lineages, comprising the montium subgroup species and the melanogaster complex species; the species of the other complex of the melanogaster subgroup, yakuba, disperse among the obscura species. The above grouping is in agreement with the mtDNA size variations of the species. Overall, among all subgroups studied, the species of the montium subgroup seem to be the most closely related.

The heat shock genes in the Drosophila montium subgroup: chromosomal localization and evolutionary implications

The hsp70, hsp83, hsromega, and the small heat shock protein genes were mapped on the polytene chromosomes of six species, representative of the geographical distribution of the Drosophila montium subgroup of the melanogaster species group. In addition, based on hybridization conditions, the putative locus of the hsp68 gene is given. In contrast to the situation in the melanogaster subgroup species, the hsp70 locus is single in the montium species. The hsp83, hsromega and the small hsp loci are also single in the montium genomes studied here, a common feature of all Drosophila species. Among the hsp genes studied, the small hsp genes and the hsromega-homologous sequences exhibit a higher degree of divergence between the melanogaster and the montium subgroups. Our results support the idea that the montium subgroup species has a genome organization closer to that of the common ancestor compared with the melanogaster subgroup species.

The Afrotropical Drosophila montium subgroup: Balbiani ring 1, polytene chromosomes, and heat shock response of Drosophila vulcana

A detailed photographic map of the salivary gland polytene chromosomes of Drosophila vulcana, an Afrotropical species of the montium subgroup of the melanogaster group, is presented, along with chromosomal rearrangements, such as reverse tandem duplications and inversions, the well-formed Balbiani ring 1, and the most prominent puffs during normal larval and white prepupal development and after ecdysone treatment. In addition, the heat inducible protein and puffing pattern and the loci of the major heat shock genes, namely, hsp70, hsp83, the "small" hsps, and a putative hsp68, of this species were studied. In the light of the data revealed by the above studies, phylogenetic relationship among the montium subgroup species are attempted.

A Drosophila hsp70 gene contains long, antiparallel, coupled open reading frames (LAC ORFs) conserved in homologous loci

A clone isolated from a Drosophila auraria heat-shock cDNA library presents two long, antiparallel, coupled (LAC) open reading frames (ORFs). One strand ORF is 1,929 nucleotides long and exhibits great identity (87.5% at the nucleotide level and 94% at the amino acid level) with the hsp70 gene copies of D. melanogaster, while the second strand ORF, in antiparallel in-frame register arrangement, is 1,839 nucleotides long and exhibits 32% identity with a putative, recently identified, NAD(+)-dependent glutamate dehydrogenase (NAD(+)-GDH). The overlap of the two ORFs is 1,824 nucleotides long. Computational analysis shows that this LAC ORF arrangement is conserved in other hsp70 loci in a wide range of organisms, raising questions about possible evolutionary benefits of such a peculiar genomic organization.

The beta-tubulin gene family evolution in the Drosophila montium subgroup of the melanogaster species group

The beta 1-, beta 2-, and beta 3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to the Drosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The beta-tubulin genes in the montium subgroup seem to be organized in a cluster, or in a semicluster or are completely dispersed. The clustered arrangements is found in the North-Oriental sibling species D. auraria, D. triauraria, and D. quadraria. The semiclustered arrangement, wherein the beta 1 and beta 2 genes are located at the same locus while beta 3 is at a different one, appears in the South-Oriental species D. bicornuta, D. serrata, and D. birchii, as well as in the Afrotropical species D. diplacantha and D. seguyi. The complete separation of the genes is observed in the Indian species D. kikkawai and D. jambulina and in the Afrotropical species D. vulcana. Based on the above results, a possible mode of evolution of the beta-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among the montium species are discussed.

Cytotaxonomic differentiation of the afrotropical Drosophila montium subgroup: D. diplacantha and D. seguyi. The major role of reverse tandem duplications

Aiming to establish phylogenetic relationships among species of the montium subgroup, detailed polytene chromosome maps are given showing intraspecific polymorphism and ecdysone induced larval puffing pattern profiles of two Afrotropical members of this subgroup, Drosophila diplacantha and D. seguyi. Both species exhibit two unique characteristics that define the montium subgroup, namely, a large number of reverse tandem duplications and a progressive darkening of anterior spiracles of the late third instar larvae, which is accompanied by a definite temporal and spatial puffing pattern of the salivary gland chromosomes. In contrast with the well-formed Balbiani ring 1 (BR1) observed in Oriental and Indian montium species, BR1 exhibits a different developmental profile in D. diplacantha, while it is obscured in D. seguyi. Although phyletic comparisons of five species from five different complexes within the subgroup show some conservation in banding and puffing pattern homologies, an analysis to assign map sections by sequential rearrangements remains unresolved at this time. The evolution of the subgroup is discussed in relation with the sharing of reverse tandem duplications, especially those including the montium BRs.

The beta-tubulin genes of Drosophila auraria are arranged in a cluster

When the beta 1-, beta 2- and beta 3-tubulin-specific DNAs from Drosophila melanogaster were used as probes to recognize tubulin-specific sequences in the chromosomes of Drosophila auraria, they were found to hybridize to the same polytene band in region 32C of the 2L polytene chromosome. Three overlapping clones were isolated from a lambda EMBL3 genomic library of D. auraria, and they all contain beta-tubulin-specific sequences based on hybridization and partial-sequencing experiments of subcloned fragments. These clones hybridize in situ to the same polytene chromosome band in region 32C and they represent an approximately 35-kb fragment of genomic DNA.

Mitochondrial DNA evolution in the Montium-species subgroup of Drosophila

Mitochondrial DNA (mtDNA) restriction-site maps for six species (10 strains) of the Drosophila montium subgroup were established. A total of 50 restriction sites were mapped, corresponding to 1.67% of the mtDNA genome. On the basis of differences in the restriction sites, nucleotide divergence (delta) was calculated for each pair of species (strains), and phylogenetic trees were constructed by using distance-matrix and parsimony methods. Comparison of the resultant phylogenetic trees shows that the sibling species D. auraria and D. quadraria are closely related. At the other extreme, considerable divergence was observed between the two strains of D. serrata and between D. serrata and D. birchii, a finding that contrasts with their grouping within the same species complex. Nevertheless, our data indicate that these six oriental montium species are rather closely related.

Rapid isolation of mitochondrial DNA. Mitochondrial DNA from Drosophila serrata

A simple and rapid method for isolation of high quality mitochondrial DNA (mtDNA) is presented in this report. Using this method, isolation and restriction site maps for 10 enzymes of the mtDNA of Drosophila serrata were established.

Insecticidal effects of essential oils. A study of the effects of essential oils extracted from eleven Greek aromatic plants on Drosophila auraria

Effects of the essential oils (EOs) extracted from eleven aromatic plants belonging to the Lamiaceae family (common in the Greek flora) were examined upon three different developmental stages of Drosophila auraria. All of the EOs examined exhibited insecticidal effects, either by preventing egg hatching, or by causing the death of larvae and adult flies. In several cases, malformation and/or prohibition of puparium formation was also observed.

The polytene chromosomes of Drosophila triauraria and D. quadraria, sibling species of D. auraria

The polytene chromosomes of Drosophila triauraria and D. quadraria, two of the sibling species of D. auraria, were examined. The polytene chromosomes of all three species exhibit very clear homology. Unlike the stock of D. auraria that we studied, D. triauraria and D. quadraria carry heterozygous paracentric inversions. In both species, 2R and 3R are the arms where these inversions are concentrated. In addition, in D. quadraria, the 3L chromosome arm is very complicated because of heterozygous inversions. The mode of inheritance of these rearrangements was studied. A homozygous strain for all chromosome arms of D. triauraria was isolated, while a homozygous strain was obtained only for the arms X, 2L, 3L, and 4 of D. quadraria. Like D. auraria, both species show a large number of inverted tandem duplications in the paired condition, even in the chromosomes of their hybrids. Small deletions were also detected, one of which, in D. triauraria, is homozygous terminal. Hypotheses are discussed concerning the relationships of the species and the existence of inverted tandem duplications.

The Balbiani ring and the polytene chromosomes of Drosophila bicornuta

A study of the BR1 and of the most prominent puffs during larval development and after in vitro ecdysterone treatment, as well as of the banding pattern and inverted tandem chromosomal duplications of the salivary gland chromosomes of Drosophila bicornuta, is presented in this report. These data are compared and discussed with those of D. auraria and D. serrata, two other montium species.

Developmental changes in fat body and midgut chromosomes of Drosophila auraria

Changes in puffing activity of fat body (FB) and midgut (MG) chromosomes of Drosophila auraria during late larval and white prepupal development as well as after in vitro culture with or without ecdysterone were studied and compared with those of the salivary gland (SG). The Balbiani Rings characteristic of the SG chromosomes of D. auraria, are not formed in FB and MG. Most of the inverted tandem chromosomal duplications that have been found to be common to all three tissues showed differentiation of puffing activity of the bands considered to be homologous. The major early ecdysone puffs 73A and 73B (considered to be homologues of D. melanogaster puffs 74EF and 75B, respectively), together with other early ecdysone puffs were present in all three tissues. Clear intermoult and postintermoult puffs were not evident in FB and MG chromosomes. However, a small set of late ecdysone puffs could be scored in FB, while no late ecdysone puffs were abserved in MG. Other tissue-specific puffs were identified, but a very small number of them were limited to MG.

Comparison of the polytene chromosomes of the salivary gland, the fat body and the midgut nuclei of Drosophila auraria

Photo-maps of the fat body and midgut polytene chromosomes of Drosophila auraria were constructed. These photo-maps are compared with a new, more detailed photo-map of the salivary gland chromosomes of the same species. Seven, not previously described inverted tandem-duplications were detected, raising the number of such structures found in this species to 31. The constancy of the banding pattern based on the analysis of the above chromosomes is discussed.

Evolutionary implications of duplications and Balbiani rings in Drosophila. A study of Drosophila serrata

Drosophila serrata, a species of subgroup montium, exhibits in its salivary-gland chromosomes a high number of inverted tandem duplications and a well-formed Balbiani ring. A photographic map, the duplications, and the Balbiani ring of this species are presented. Also presented are the most prominent puffs during normal larval development and after ecdysone treatment, as well as intercalary heterochromatin regions of the above chromosomes. These data are discussed and compared with those of Drosophila auraria, another species of subgroup montium. All the inverted tandem duplications found in both species are homozygous and are not accompanied by other types of chromosomal rearrangements. These results argue in favor of the relatively old origin of these structures. The similarity of the structure and the developmental profile of the Balbiani ring 1 in both species may indicate a necessary role served by the Balbiani ring 1 and hence its selection during evolution.