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Biology subjects

Ratiu, A. C.

Publications and source records attributed to Ratiu, A. C..

8 recordsLinked to original sources

dScaff - an automatic bioinformatics framework for scaffolding draft de novo assemblies based on reference genome data

Rapid evolution of long-read sequencing technologies requires accurate, fast and user-friendly genome assembly and scaffolding tools. In this article we present Digital Scaffolding (dScaff), a bioinformatics tool that performs scaffolding of de novo genome assemblies based on reference scaffolds or chromosomes. dScaff makes use of a series of bash and R scripts in order to create a minimal complete scaffold from a genome assembly, with future features to be implemented. Herein, we demonstrate the functionality of dScaff on a novel genome assembly pertaining to a recently sequenced local strain of Drosophila suzukii.

bioinformatics↗

Novel insights into the economic relevant phenotypes of Bombyx mori strains from Romanian breeding centres

The silkworm, Bombyx mori, has an inestimable economic and pharmaceutical value, but it is also a very effective model organism for biological and biotechnological sciences. Herein, we characterize several phenotypic parameters particular for B[a]neasa 1 (B1) and Galben de B[a]neasa (GB) Romanian silkworm breeds, as well as of Auriu Chinez (ACH) and JH3 breeds originating from China and, respectively, Japan. Our analysis revealed concrete differences and similarities between the phenotypic properties of the four breeds, allowing their grouping consecutive to PCA and KODAMA analyses. Our study is the first to characterize the four breeds regarding their biological competencies and offers a glimpse at various ventures aiming at the employment and amelioration of these silkworm breeds.

evolutionary biology↗

qDATA - an R application implementing a practical framework for analyzing quantitative Real-Time PCR data

Gene expression assays that are based on quantitative real-time PCR (qRT-PCR) method are still very popular, therefore, we developed qDATA, a modern open-source R based bioinformatics application that offers a quick and intuitive analysis of raw cycle threshold (Ct) values. The application relies on a straightforward specific data input consisting in Ct values and a few other mandatory fields specifying the experimental and control groups, as well as the target and house-keeping genes. Afterwards, it automatically performs descriptive statistics, normality and statistical testing on 2-{Delta}Ct (or {Delta}Ct) and 2-{Delta}{Delta}Ct terms calculated with Livaks method. Each computation is indicated in dedicated tabs that display their output consisting in dynamic data tables and publishing quality graphs. We also detail a qRT-PCR data analysis framework that depends on performing exhaustive {Delta}Ct calculations within discrete biological replicates (BRs). The Livak formula is used for the complete sets of available data. These prerequisites arguably lead to an improved data analysis and statistical relevance. In order to maximize the relevance of the results we recommend using at least three BRs and three technical replicates. The efficiency of our computing approach was tested with qDATA using input Ct values corresponding to immune related gene expression evaluated in experimental infection of Drosophila melanogaster and summer versus winter Apis mellifera workers, respectively. Our results reveal that our working strategy is very reliable and highlight the efficacy and performance of qDATA application.

genetics↗

A novel P{lacW} insertion in the CG18135 gene of Drosophila melanogaster is linked to pupal lethality and gene overexpression in adult males

Drosophila melanogaster has been at the forefront of genetic studies and biochemical modelling for over a century. Yet, the functions of many genes are still unknown mainly because no phenotypic data are available. Herein, we present first evidence data regarding the particular molecular and other quantifiable phenotypes, such as viability and anatomical anomalies, induced by a novel P{lacW} insertional mutant allele of CG18135 gene. So far, the CG18135 functions have only been theorized based on electronic annotation and presumptive associations inferred upon high-throughput proteomics or RNA sequencing experiments. The descendants of individuals harboring the CG18135P{lacW}CG18135 allele were scored in order to assess mutant embryos, larvae and pupae viability versus Canton Special. Our results revealed that the homozygous CG18135P{lacW}CG18135/CG18135P{lacW}CG18135 genotype determines significant lethality both at the inception of larval stage and during pupal development. Few imago escapers that breach the puparium and even more rarely fully exit from it exhibit specific eye depigmentation, wing abnormal unfolding and strong locomotor impairment with apparent spasmodic legs movements. Their maximum lifespan is shorter than two days. When using the quantitative Real-Time PCR (qRT-PCR) method to confirm that CG18135 is indeed upregulated in males compared to females an unexpected gene upregulation was also detected in heterozygous mutants comparative to wild-type flies, probably because of regulatory perturbations induced by P{lacW} transposon. Our work provides the first phenotypic evidence for the essential role of CG18135, a scenario in accordance with the putative role of this gene in the carbohydrate binding processes.

genetics↗

A bioinformatics pipeline for the assessment of the evolutionary relationship of some Drosophila species based on class II transposons mapping

Transposons are mobile DNA sequences, known for their ability to insert into other locations in the genome. Genome sequencing allowed the identification of the high content of transposons in various model organisms. Here, we present a bioinformatics pipeline developed to estimate the evolutionary relationship between Drosophila melanogaster and other Drosophilidae based on the comparative analysis of the presence and distribution of class II transposons. Our study reveals that the presence and distribution of transposons hobo, HB, Tc1, Tc1-2, hopper and Bari1 points to close evolutionary relationship among D. melanogaster, D. simulans, D. sechellia and D. yakuba, which is in accordance with other data available in literature.

bioinformatics↗

Genome ARTIST_v2 software - a support for annotation of class II natural transposons in new sequenced genomes

Transposon annotation is a very dynamic field of genomics and various tools assigned to support this bioinformatics endeavor were reported. Genome ARTIST (GA) software was initially developed for mapping artificial transposons mobilized during insertional mutagenesis projects. Now, the new functions of GA_v2 qualify it as an effective companion for mapping and annotation of class II natural transposons in assembled genomes, contigs or sequencing reads. Tabular export of mapping and annotation data for subsequent high-throughput data analysis, the export of a list of flanking sequences around either the coordinates of insertion or around the target site duplications (TSDs) and generation of a consensus sequence for the respective flanking sequences are all key assets of GA_v2. Additionally, we developed two accompanying short scripts that enable the user to annotate transposons existent in assembled genomes and to use various annotation offered by FlyBase for Drosophila melanogaster genome. Herein, we present the applicability of GA_v2 for a preliminary annotation of the class II transposon P-element in the genome of D. melanogaster strain Horezu, Romania, which was sequenced with Nanopore technology in our laboratory. Our results point that GA_v2 is a reliable tool to be integrated in pipelines designed to perform transposon annotation in new sequenced genomes. GA_v2 is open source software compatible with Ubuntu, Mac OS and Windows and is available at https://github.com/genomeartist/genomeartist and at www.genomeartist.ro.

bioinformatics↗

Insertions of P{lacW} and P{EP} artificial transposons on the chromosomal divisions of Drosophila melanogaster are not randomly distributed

Herein we describe the distribution of P{lacW} and P{EP} artificial transposons in the genome of Drosophila melanogaster. A total number of 5,560 P{lacW} and 3,786 P{EP} insertions available on FlyBase were extracted from this database and ordered according to the chromosomal regions they hit. Comparative bioinformatics analysis revealed that the insertions patterns are similar for P{lacW} and P{EP}. The two patterns are significantly correlated for chromosomes X, 2L, 2R and 3L, but not for 3R.\n\nFourier analysis revealed a periodic behaviour in the distribution of insertions, which approximates insertional hotspots. Our results raise questions concerning if and how the local chromosomal landscape affects the insertion patterns of different but related transposons.

genomics↗

Relative quantification of Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia and Aggregatibacter actinomycetemcomitans high-risk bacterial species in Romanian patients evaluated for periodontal disease

Three bacterial species pertaining to the red complex (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) and Aggregatibacter actinomycetemcomitans were investigated in relation to the incidence and severity of periodontal disease. A total of 259 patients were included in this study, 179 being diagnosed with periodontal disease. The gingival crevicular fluid samples were obtained from periodontal pockets and the presence and levels of target bacteria were assessed following DNA extraction and real-time quantitative PCR. Our results account for significant positive associations between the number of bacterial species from the red complex coexisting within a patient and several clinical signs (gingival bleeding, inflammation and bone deterioration). A similar positive association was found between bacterial load of the red complex species and the clinical Case Type diagnostic of the periodontal disease, as well as the probing depth with the most evident results for T. denticola. In conclusion, our study, a first for the Romanian population, confirms previous results found elsewhere and finds a possible regional pathogenic specificity for T. denticola as a major factor for periodontitis severity.

epidemiology↗