XVII.—Utilization of Dietary Purines and Pyrimidines by Drosophila melanogaster

1957 ◽  
Vol 66 (4) ◽  
pp. 339-359 ◽  
Author(s):  
James H. Sang
Keyword(s):  
Drosophila Melanogaster ◽  
Orotic Acid ◽  
De Novo ◽  
Normal Growth ◽  
Energy Utilization ◽  
Good Growth ◽  
Response Curves ◽  
Adenylic Acid ◽  
Multicellular Organisms

SynopsisDrosophila melanogaster larvæ when cultured aseptically on a synthetic diet require exogenous ribose nucleic acid (RNA) for normal growth even though they can synthesize their own endogenous RNA from simple precursors. The optimum dietary supply lies between 0.4 and 0.7 per cent RNA. Individual bases, nucleosides and nucleotides which make up RNA cannot substitute for the whole polynucleotide, but adenine, adenosine, adenylic acid, guanosine and guanylic acid are used and stimulate growth to varying degrees. The pyrimidines and their nucleosides and nucleotides are not used when fed singly.It is shown that the de novo synthesis of purines may be more difficult than that of pyrimidines, and that if a source of purines is supplied (as adenylic acid), then the nucleosides and nucleotides of both cytosine and uracil are utilized by the larvæ, whereas the free bases are not. Cytidylic and uridylic acids seem to be interchangeable, and together with an adequate supply of adenylic acid give as good growth as RNA. Orotic acid and 2—6-diaminopurine are not used by the larvæ under the conditions described, but hypoxanthine and inosine are: xanthine and xanthosine can also be shown to have an effect on growth.Dose-response curves were determined for adenylic, guanylic, cytidylic and uridylic acids under conditions which allow the determination of the optimal supplies of each. These are found to be about 0.110, 0.080, 0.025 and 0.025 per cent, respectively. The requirement of RNA is therefore primarily a requirement of adenylic acid, since more than enough of the other nucleotides should be available when the supply of RNA is optimal. The optimal supply of adenine corresponds almost exactly with the optimal supply of adenylic acid, though a somewhat delayed larval development may be a result of energy utilization in the base-nucleoside-nucleotide conversion.These results are discussed in the light of our knowledge of purine and pyrimidine utilization in other multicellular organisms, particularly the rat, and possible applications of the findings are considered.

Apoptosis and development

2003 ◽  
Vol 39 ◽  
pp. 11-24 ◽  
Author(s):  
Justin V McCarthy
Keyword(s):  
Drosophila Melanogaster ◽  
Mammalian Cells ◽  
Cell Number ◽  
Model Organisms ◽  
Biological Processes ◽  
Nematode Caenorhabditis Elegans ◽  
Apoptotic Pathway ◽  
Genetic Pathways ◽  
Evolutionarily Conserved ◽  
Multicellular Organisms

Apoptosis is an evolutionarily conserved process used by multicellular organisms to developmentally regulate cell number or to eliminate cells that are potentially detrimental to the organism. The large diversity of regulators of apoptosis in mammalian cells and their numerous interactions complicate the analysis of their individual functions, particularly in development. The remarkable conservation of apoptotic mechanisms across species has allowed the genetic pathways of apoptosis determined in lower species, such as the nematode Caenorhabditis elegans and the fruitfly Drosophila melanogaster, to act as models for understanding the biology of apoptosis in mammalian cells. Though many components of the apoptotic pathway are conserved between species, the use of additional model organisms has revealed several important differences and supports the use of model organisms in deciphering complex biological processes such as apoptosis.

Preparation, spectral properties and biological activities of 5-bromo-6-methyl-2'-deoxyuridine and 5-iodo-6-methyl-2'-deoxyuridine

1980 ◽  
Vol 45 (8) ◽  
pp. 2364-2370 ◽  
Author(s):  
Antonín Holý ◽  
Erik De Clercq
Keyword(s):  
Antiviral Activity ◽  
Spectral Properties ◽  
De Novo ◽  
Biological Activities ◽  
Rabbit Kidney ◽  
Kidney Cells ◽  
Cd Spectra ◽  
Methyl Derivatives ◽  
Primary Rabbit

Reaction of 3',5'-di-O-benzoyl-6-methyl-2'-deoxyuridine (IIa) with elementary bromine or iodine afforded 5-halogeno derivatives IIc and IId which on methanolysis gave 5-bromo-6-methyl-2'-deoxyurine (Ic) and 5-iodo-6-methyl-2'-deoxyurine (Id), respectively. The CD spectra of Ic, Id and 6-methyl-2'-deoxyuridine (Ia) are compared and discussed with regard to determination of the nucleoside conformation. Unlike 5-bromo- and 5-iodo-2'-deoxyuridine, the 6-methyl derivatives Ic and Id exhibit neither antibacterial nor antiviral activity. Nor do they exert any antimetabolic effect on the de novo DNA synthesis in primary rabbit kidney cells.

In vivo study of the biosynthesis of long-chain fatty acids using deuterated water

1995 ◽  
Vol 269 (2) ◽  
pp. E247-E252 ◽  
Author(s):  
H. O. Ajie ◽  
M. J. Connor ◽  
W. N. Lee ◽  
S. Bassilian ◽  
E. A. Bergner ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
De Novo ◽  
Chain Elongation ◽  
Deuterated Water ◽  
De Novo Synthesis ◽  
Isotopomer Distribution ◽  
Long Chain ◽  
Mass Isotopomer

To determine the contributions of preexisting fatty acid, de novo synthesis, and chain elongation in long-chain fatty acid (LCFA) synthesis, the synthesis of LCFAs, palmitate (16:0), stearate (18:0), arachidate (20:0), behenate (22:0), and lignocerate (24:0), in the epidermis, liver, and spinal cord was determined using deuterated water and mass isotopomer distribution analysis in hairless mice and Sprague-Dawley rats. Animals were given 4% deuterated water for 5 days or 8 wk in their drinking water. Blood was withdrawn at the end of these times for the determination of deuterium enrichment, and the animals were killed to isolate the various tissues for lipid extraction for the determination of the mass isotopomer distributions. The mass isotopomer distributions in LCFA were incompatible with synthesis from a single pool of primer. The synthesis of palmitate, stearate, arachidate, behenate, and lignocerate followed the expected biochemical pathways for the synthesis of LCFAs. On average, three deuterium atoms were incorporated for every addition of an acetyl unit. The isotopomer distribution resulting from chain elongation and de novo synthesis can be described by the linear combination of two binomial distributions. The proportions of preexisting, chain elongation, and de novo-synthesized fatty acids as a percentage of the total fatty acids were determined using multiple linear regression analysis. Fractional synthesis was found to vary, depending on the tissue type and the fatty acid, from 47 to 87%. A substantial fraction (24-40%) of the newly synthesized molecules was derived from chain elongation of unlabeled (recycled) palmitate.

scholarly journals nanotatoR: a tool for enhanced annotation of genomic structural variants

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Surajit Bhattacharya ◽  
Hayk Barseghyan ◽  
Emmanuèle C. Délot ◽  
Eric Vilain
Keyword(s):  
De Novo ◽  
Genome Mapping ◽  
Gene List ◽  
Sufficient Information ◽  
Rna Seq ◽  
Structural Variants ◽  
De Novo Genome Assembly ◽  
Pathogenic Variants ◽  
Increased Sensitivity

Abstract Background Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity. Results We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient’s phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.). nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR’s annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM. Conclusions The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.

scholarly journals Transcriptomic and Proteomic Analyses Reveal the Diversity of Venom Components from the Vaejovid Scorpion Serradigitus gertschi

Toxins ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 359 ◽  
Author(s):  
Maria Romero-Gutiérrez ◽  
Carlos Santibáñez-López ◽  
Juana Jiménez-Vargas ◽  
Cesar Batista ◽  
Ernesto Ortiz ◽  
...  
Keyword(s):  
Serine Proteases ◽  
De Novo ◽  
Sequence Similarity ◽  
Scorpion Venom ◽  
Secretory Proteins ◽  
Host Defense Peptides ◽  
The Family ◽  
Pathogenesis Related ◽  
Molecular Masses

To understand the diversity of scorpion venom, RNA from venomous glands from a sawfinger scorpion, Serradigitus gertschi, of the family Vaejovidae, was extracted and used for transcriptomic analysis. A total of 84,835 transcripts were assembled after Illumina sequencing. From those, 119 transcripts were annotated and found to putatively code for peptides or proteins that share sequence similarities with the previously reported venom components of other species. In accordance with sequence similarity, the transcripts were classified as potentially coding for 37 ion channel toxins; 17 host defense peptides; 28 enzymes, including phospholipases, hyaluronidases, metalloproteases, and serine proteases; nine protease inhibitor-like peptides; 10 peptides of the cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 protein superfamily; seven La1-like peptides; and 11 sequences classified as “other venom components”. A mass fingerprint performed by mass spectrometry identified 204 components with molecular masses varying from 444.26 Da to 12,432.80 Da, plus several higher molecular weight proteins whose precise masses were not determined. The LC-MS/MS analysis of a tryptic digestion of the soluble venom resulted in the de novo determination of 16,840 peptide sequences, 24 of which matched sequences predicted from the translated transcriptome. The database presented here increases our general knowledge of the biodiversity of venom components from neglected non-buthid scorpions.

scholarly journals Drosophila Ana2 is a conserved centriole duplication factor

2010 ◽  
Vol 188 (3) ◽  
pp. 313-323 ◽  
Author(s):  
Naomi R. Stevens ◽  
Jeroen Dobbelaere ◽  
Kathrin Brunk ◽  
Anna Franz ◽  
Jordan W. Raff
Keyword(s):  
Drosophila Melanogaster ◽  
Caenorhabditis Elegans ◽  
De Novo ◽  
Protein Family ◽  
Centriole Duplication

In Caenorhabditis elegans, five proteins are required for centriole duplication: SPD-2, ZYG-1, SAS-5, SAS-6, and SAS-4. Functional orthologues of all but SAS-5 have been found in other species. In Drosophila melanogaster and humans, Sak/Plk4, DSas-6/hSas-6, and DSas-4/CPAP—orthologues of ZYG-1, SAS-6, and SAS-4, respectively—are required for centriole duplication. Strikingly, all three fly proteins can induce the de novo formation of centriole-like structures when overexpressed in unfertilized eggs. Here, we find that of eight candidate duplication factors identified in cultured fly cells, only two, Ana2 and Asterless (Asl), share this ability. Asl is now known to be essential for centriole duplication in flies, but no equivalent protein has been found in worms. We show that Ana2 is the likely functional orthologue of SAS-5 and that it is also related to the vertebrate STIL/SIL protein family that has been linked to microcephaly in humans. We propose that members of the SAS-5/Ana2/STIL family of proteins are key conserved components of the centriole duplication machinery.

Group fractionation and determination of the number of ribosomal subunit proteins from Drosophila melanogaster embryos

Biochemistry ◽  
1980 ◽  
Vol 19 (7) ◽  
pp. 1425-1433 ◽  
Author(s):  
W. Yean Chooi ◽  
Linda M. Sabatini ◽  
Elizabeth Dolliver ◽  
Michael Macklin ◽  
Dean Fraser
Keyword(s):  
Drosophila Melanogaster ◽  
Ribosomal Subunit

scholarly journals Lasy wybranych dużych obszarów leśnych = The forests in selected examples of Poland’s Large Forest Areas

2021 ◽  
Vol 93 (3) ◽  
pp. 463-483
Author(s):  
Roman Zielony
Keyword(s):  
Forest Management ◽  
Spatial Planning ◽  
Forest Cover ◽  
De Novo ◽  
Proper Noun ◽  
Nature Protection ◽  
Key Issues ◽  
1960S And 1970S ◽  
The 1960S

Key issues for spatial planning and development, nature protection and forestry in Poland relate to the problems encountered in determining the area of forests included within – and the boundaries of – what are known as the Large Forest Areas (LFAs) in Poland. Even as overall forest cover in the country has increased steadily – by about 2.5 million ha overall – since 1945, the data available for the LFAs relate to measurements made as long ago as in the 1960s and 1970s. Even then, it is often unclear whether it is total areas or areas of forest that are being referred to in relation to the LFAs. There is thus an urgent need for meas-urements to be updated, with a view to the present-day boundaries of the Areas being delim-ited. Some 80‑100 LFAs are in fact distinguished in Poland, in line with definitions relating to total area exceeding 10,000 ha (100 km2) and forest cover exceeding 35%. While many of the LFAs received Proper-Noun names at one point or another in their histories, as used locally in a given region, and in guides and publications, there are also less culturall-defined areas that still await naming. Efforts to determine the boundaries of the LFAs at this point allow, not only for renewed or de novo determination of their overall areas and areas of forest, but also for an advancement of our knowledge regarding any items of cultural heritage that may be present within LFAs. Such data will be useful or essential as new physiographic, economic and tourist guide-studies are developed; and they will encourage and facilitate the more-detailed analysis and assess-ment of forest management taking place within the limits of the LFAs. In line with the effort made to achieve the above goals, this article details selected problems encountered with the delimitation of forest boundaries and areas, as these are exemplified by the Polish LFAs of the Białowieża, Bolimów, Borki, Knyszyn, Kampinos, Noteć, Romincka, Tuchola, Łuków and Chojnów Forests. Figures for overall area and area of forest were indeed obtained and are presented here for the selected examples of LFAs, which are also augmented by the so-called Dobrzejewice and Lubniewice Forests not distinguished in this way before now.

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