AVMf: An Open-Source Framework and Implementation of the Alternating Variable Method

The Alternating Variable Method (AVM) has been shown to be a fast and effective local search technique for search-based software engineering. Recent improvements to the AVM have generalized the representations it can optimize and have provably reduced its running time. However, until now, there has been no general, publicly-available implementation of the AVM incorporating all of these developments. We introduce AVMf, an object-oriented Java framework that provides such an implementation. AVMf is available from http://avmframework.org for configuration and use in a wide variety of projects

Tissue- and development-specific induction and turnover of hsp70 transcripts from loci 87A and 87C after heat shock and during recovery in Drosophila melanogaster

The haploid genome of Drosophila melanogaster normally carries at least five nearly identical copies of heat-shock-inducible hsp70 genes, two copies at the 87A7 and three copies at the 87C1 chromosome sites. We used in situ hybridization of the cDNA, which hybridizes with transcripts of all five hsp70 genes, and of two 3' untranslated region (3'UTR; specific for the 87A7- and 87C1-type hsp70 transcripts) riboprobes to cellular RNA to examine whether all these copies were similarly induced by heat shock in different cell types of D. melanogaster. Our results revealed remarkable differences not only in the heat-shock-inducibility of the hsp70 genes at the 87A7 and 87C1 loci, but also in their post-transcriptional metabolism, such as the stability of the transcripts and of their 3'UTRs in different cell types in developing embryos and in larval and adult tissues. Our results also revealed the constitutive presence of the heat-shock-inducible form of Hsp70 in a subset of late spermatogonial cells from the second-instar larval stage onwards. We suggest that the multiple copies of the stress-inducible hsp70 genes do not exist in the genome of D. melanogaster only to produce large amounts of the Hsp70 rapidly and at short notice, but that they are specifically regulated in a developmental-stage-specific manner. It is likely that the cost/benefit ratio of not producing or of producing a defined amount of Hsp70 under stress conditions varies for different cell types and under different physiological conditions and, accordingly, specific regulatory mechanisms operating at the transcriptional and post-transcriptional levels have evolved

Restriction enzyme digestion of heterochromatin in Drosophila nasuta

In situ digestion of metaphase and polytene chromosomes and of interphase nuclei in different cell types of Drosophila nasuta with restriction enzymes revealed that enzymes like AluI, EcoRI, HaeIII, Sau3a and SinI did not affect Giemsa-stainability of heterochromatin while that of euchromatin was significantly reduced; TaqI and SalI digested both heterochromatin and euchromatin in mitotic chromosomes. Digestion of genomic DNA with AluI, EcoRI, HaeIII, Sau3a and KpnI left a 23 kb DNA band undigested in agarose gels while with TaqI, no such undigested band was seen. The AluI resistant 23 kb DNA hybridized insitu specifically with the heterochromatic chromocentre. It appears that the digestibility of heterochromatin region in genome ofDrosophila nasuta with the tested restriction enzymes is dependent on the availability of their recognition sites

The hnRNP A1 homolog Hrp36 is essential for normal development, female fecundity, omega speckle formation and stress tolerance in Drosophila melanogaster

Hrp36/Hrb87F is one of the most abundant and well-characterized hnRNP A homolog in Drosophila and is shown to have roles in regulation of alternative splicing, heterochromatin formation, neurodegeneration, etc. Yet, hrp36 null individuals were reported to be viable and without any apparent phenotype, presumably because of overlapping functions provided by Hrp38 and related proteins. Here we show that loss of both copies of hrp36 gene slows down development with significant reduction in adult life span, decreased female fecundity and high sensitivity to starvation and thermal stresses. In the absence of Hrp36, the nucleoplasmic omega speckles are nearly completely disrupted. The levels of nuclear matrix protein Megator and the chromatin remodeller ISWI are significantly elevated in principal cells of larval Malpighian tubules, which also display additional endoreplication cycles and good polytene chromosomes. We suggest that besides the non-coding hsr omega-n transcripts, the Hrp36 protein is also a core constituent of omega speckles. The heat-shock-induced association of other hnRNPs at the hsr omega locus is affected in hrp36 null cells, which may be one of the reasons for their high sensitivity to cell stress. Therefore, in spite of the functional redundancy provided by Hrp38, Hrp36 is essential for normal development and for survival under conditions of stress

Developmental regulation and complex organization of the promoter of the non-coding hsrω gene of Drosophila melanogaster

The nucleus-limited large non-coding hsrω-n RNA product of the93D or the hsrω gene of Drosophila melanogaster binds to a variety of RNA-binding proteins involved in nuclear RNA processing. We examined the developmental and heat shock induced expression of this gene by in situ hybridization of nonradioactively labelled riboprobe to cellular transcripts in intact embryos, larval and adult somatic tissues of wild type and an enhancer-trap line carrying the hsrω05241 allele due to insertion of aP-LacZ-rosy + transposon at - 130 bp position of the hsrω promoter. We also examined LacZ expression in the enhancer-trap line and in two transgenic lines carrying different lengths of the hsrω promoter upstream of the LacZ reporter. The hsrΩ gene is expressed widely at all developmental stages; in later embryonic stages, its expression in the developing central nervous system was prominent. In spite of insertion of a big transposon in the promoter, expression of the hsrω05241 allele in the enhancer-trap line, as revealed byin situ hybridization to hsrω transcripts in cells, was similar to that of the wild type allele in all the embryonic, larval and adult somatic tissues examined. Expression of the LacZ gene in this enhancer-trap line was similar to that of the hsrω RNA in all diploid cell types in embryos and larvae but in the polytene cells, the LacZ gene did not express at all, neither during normal development nor after heat shock. Comparison of the expression patterns of hsrω gene and those of the LacZ reporter gene under its various promoter regions in the enhancer-trap and transgenic lines revealed a complex pattern of regulation, which seems to be essential for its dynamically varying expression in diverse cell types

Male sterility associated with overexpression of the noncoding hsrω gene in cyst cells of testis of Drosophila melanogaster

Of the several noncoding transcripts produced by the hsrΩ gene of Drosophila melanogaster, the nucleus-limited > 10-kb hsrΩ-n transcript colocalizes with heterogeneous nuclear RNA binding proteins (hnRNPs) to form fine nucleoplasmic omega speckles. Our earlier studies suggested that the noncoding hsrΩ-n transcripts dynamically regulate the distribution of hnRNPs in active (chromatin bound) and inactive (in omega speckles) compartments. Here we show that a P transposon insertion in this gene's promoter (at -130 bp) in the hsrΩ05241 enhancer-trap line had no effect on viability or phenotype of males or females, but the insertion-homozygous males were sterile. Testes of hsrΩ05241 homozygous flies contained nonmotile sperms while their seminal vesicles were empty. RNA:RNA in situ hybridization showed that the somatic cyst cells in testes of the mutant male flies contained significantly higher amounts of hsrΩ-n transcripts, and unlike the characteristic fine omega speckles in other cell types they displayed large clusters of omega speckles as typically seen after heat shock. Two of the hnRNPs, viz. HRB87F and Hrp57A, which are expressed in cyst cells, also formed large clusters in these cells in parallel with the hsrΩ-n transcripts. A complete excision of the P transposon insertion restored male fertility as well as the fine-speckled pattern of omega speckles in the cyst cells. The in situ distribution patterns of these two hnRNPs and several other RNA-binding proteins (Hrp40, Hrb57A, S5, Sxl, SRp55 and Rb97D) were not affected by hsrΩ mutation in any of the meiotic stages in adult testes. The present studies, however, revealed an unexpected presence (in wild-type as well as mutant) of the functional form of Sxl in primary spermatocytes and an unusual distribution of HRB87F along the retracting spindle during anaphasetelophase of the first meiotic division. It appears that the P transposon insertion in the promoter region causes a misregulated overexpression of hsrΩ in cyst cells, which in turn results in excessive sequestration of hnRNPs and formation of large clusters of omega speckles in these cell nuclei. The consequent limiting availability of hnRNPs is likely totrans-dominantly affect processing of other pre-mRNAs in cyst cells. We suggest that a compromise in the activity of cyst cells due to the aberrant hnRNP distribution is responsible for the failure of individualization of sperms in hsrΩ05241 mutant testes. These results further support a significant role of the noncoding hsrΩ-n transcripts in basic cellular activities, namely regulation of the availability of hnRNPs in active (chromatin bound) and inactive (in omega speckles) compartments

Ayurvedic Amalaki Rasayana and Rasa-Sindoor suppress neurodegeneration in fly models of Huntington’s and Alzheimer’s diseases

We examined two Ayurvedic Rasayana formulations, claimed to facilitate ‘healthy ageing’, for their role in neuroprotection in fly models of polyQ (127Q and Huntington’s) and Alzheimer’s disorders. Our earlier findings showed that dietary supplement of Amalaki Rasayana, a preparation derived from Indian gooseberry fruits, and Rasa-Sindoor, an organo-metallic Bhasma prepared from mercury and sulphur, improves general well-being of fruit flies. Here we show that dietary supplement of either of these formulations during larval period substantially suppressed neurodegeneration in fly models of polyQ and Alzheimer’s disorders without any side-effects. Dietary Amalaki Rasayana or Rasa-Sindoor prevented accumulation of inclusion bodies and heat shock proteins, suppressed apoptosis, elevated the levels of heterogeneous nuclear ribonucleoproteins and cAMP response element binding protein and at the same time improved the ubiquitin–proteasomal system for better protein clearance in affected cells. Our studies suggest, the potential of these Ayurvedic formulations in providing a holistic relief from the increasingly common neurodegenerative disorders

Cell cycle and DNA content of mitotic cells in brain ganglia of drosophila larvae

The programmes of replication of hetero- and euchromatin regions, mitotic cell cycle and the DNA content in metaphases in brain ganglia from late third instar larvae of Drosophila melanogaster (wild type and a tumour bearing mutant, 1(2)gl, strain) and of Drosophila nasuta were examined by autoradiography of [3H]thymidine labelled (continuous or pulse) cells and by cytophotometry, respectively. Brain ganglia labelled continuously with [3H]thymidine for 24 h in vitro showed a significantly high proportion of cells with incorporation of radioactivity restricted to heterochromatin only. Pulse labelling of brain ganglia from larvae of Drosophila melanogaster and Drosophila nasuta followed by chase for different time intervals showed that (i) the frequency of labelled metaphases was more than 50% within 15 to 30 min of chase and remained higher than 50% in nearly all the chase samples till 24 h, (ii) euchromatin labelled metaphases appeared with a low frequency within 1 to 4 h chase period but the heterochromatin labelled metaphases continued to be more common in the later chase samples also, (iii) single chromatid labelled second cycle metaphases were seen within 1 to 4 h after the pulse, but their frequency did not increase in the later samples. Cytophotometry of feulgen-DNA and Hoechst 33258 stained metaphases in late third instar larval brain ganglia revealed a greater variation in the DNA content of individual metaphases, although the means were close to the expected 4 C content. It appears that in relation to the known asymmetric cell divisions of neuroblast and other neural cells, the mitotically active cells in brain ganglia comprise a heterogenous population with widely varying lengths of the different phases of cell cycle; some of them may not cycle regularly and may possibly have a discontinuous S-phase

A-T specific DNA ligands and hypotonic induced supercondensation of chromocentre in brain cells of Drosophila nasuta larvae in relation to their synthetic activities

When A-T base specific DNA ligands like Hoechst 33258 (H) or Distamycin A (DA) treated brain ganglia of D. nasura larvae are exposed 10 a pre-fixation hypotonic (hy) solution, the heterochromatic chromocentre (cc) becomes supercondensed in 40-60% interphase nuclei. In the present study, the effects of these DNA ligands on DNA and RNA synthesis in larval brain ganglia and the relationship of cc supercondensation with these synthetic activities of a cell has been examined by autoradiography. It is seen that both the frequency of replicating cells and the rate of 3H-thymidine uptake are inhibited by the treatment, more so in the population of cells in which the cc is supercondensed. H treatment has no effect on the rate of 3H-uridine uptake in transcribing nuclei although, compared to the control ganglia, the frequency of labelled nuclei is reduced after treatment. The cc supercondensation is shown to occur preferentially in nuclei which are active in DNA and/or RNA synthesis

The hyperactive X-chromosome is not early replicating in mitotically active somatic cells of Drosophila nasuta males

The temporal order of repluication of the X chromosome(s) in mitotically dividing male und female cells in early embryos and in brain ganglia of Drosophila nasuta larvae was examined uSing [3H] thymidine pulse labelling and autoradiography. Both the X chromosomes in female cells and the single X chromosome in male cells replicated in complete synchrony with the autosume set in the nucleus. Thus, unlike the well-known early completion or replication by the hemizygous X chromosome in polytene nuclei in the salivary glands of male Drosophila larvae, the single X chromosome in mitotically dividing cells does not replicate earlier than the autosomes. We conclude transcriptional hyperactivity of the single X chromosome required for dosage compensation in somatic cells of male Drosophila is not dependent upon its early replication