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Chromosome Pairing and Fertility in Polyploids
Published in Christopher B. Gillies, Fertility and Chromosome Pairing: Recent Studies in Plants and Animals, 2020
Polyploidy can be subdivided into at least two types. In autopolyploids, only one basic genome is present as multiple copies, while in allopolyploids, genomes from two or more species origins are present, presumably following a hybridization event. Since the generation of viable hybrids and allopolyploids requires some phylogenetic relationship between the parental species, it is expected that some homology will exist between chromosomes of the genomes in an allopolyploid. This has resulted in the introduction of the term segmental allopolyploid to describe a polyploid containing partially homologous (homoeologous) genomes.19 The existence of partially homologous chromosomes in allopolyploids allows for variability in pairing behavior so that in such cases pairing may be between identical homologues from one genome type — autosyndesis, or it may be between partially homologous chromosomes from different genomes — allosyndesis.20 While in practice it is often difficult to classify many polyploids as strict autopolyploids or allopolyploids, for convenience I deal separately with issues peculiar to each type.
Analysis of Small RNA Species: Phylogenetic Trends
Published in S. K. Dutta, DNA Systematics, 2019
Mirko Beljanski, Liliane Le Goff
As shown here, many small RNAs have been characterized by excellent analytical methods. However, their respective biological roles in the cells of different species need to be demonstrated accurately in order to elucidate their possible phylogenetic relationship and their part in the life of the cell.
Homology of Nonrepeated DNA Sequences in Phylogeny of Fungal Species
Published in S. K. Dutta, DNA Systematics, 2019
Attempts have been made to evaluate various parameters used for the study of phylogenetic relationships in fungi, but the discussion entered mainly on the properties of genomes in relation to evolution. From the data available on the dG and dC ratios obtained from diverse fungi as reviewed earlier, it can be concluded that these organisms do not follow the monophyletic pathway of evolution. Compared to higher organisms, fungi have smaller amounts of repetitive sequences and are mostly organized according to the long period interspersion mode, the two exceptions being the Myxomycetes and Acrasiales, where the repetitive sequences are organized according to the short period interspersion mode. The general mechanism of gene evolution such as by duplication, transposition and insertion, fusion, and recombination during sexual exchange is also applicable to fungi. Methods to study the phylogenetic relationship such as direct comparison of sequences by hybridization and restriction analysis or the sequencing of individual genes were also discussed.
Stress-mediated hyperactivity and anhedonia resistant to diazepam and fluoxetine in drosophila
Published in Stress, 2021
Ana Belén Ramos-Hryb, Mauro Federico Ramirez, Cilene Lino-de-Oliveira, Mario Rafael Pagani
Drosophila is a suitable organism for modeling human diseases due to their phylogenetic relationship with vertebrates and powerful genetic tools (Bellen et al., 2010). Moreover, monoamines are required to control fly behaviors (Hidalgo et al., 2017; Mohammad et al., 2016a; Neckameyer & Matsuo, 2008; Ries et al., 2017). The evolutionary conserved role of 5-HT in stress-dependent behaviors, reinforces the idea of using Drosophila in neurobiology research (Kasture et al., 2018; Ries et al., 2017). Few attempts to develop a model for depression in Drosophila have been made since Brown et al. (1996) reported learned helplessness in flies (Brown et al., 1996). Noteworthy flies chronically exposed to vibrations reduced walking or climbing as compared to controls. This depressive-like state correlated with reduced 5-HT release at the mushroom body which was reverted by the serotonin precursor 5-hydroxy-L-tryptophan (Ries et al., 2017). In addition, Drosophila exposed for ten days to random sequences of variable stresses exhibited high immobility, aggressiveness, and anhedonia-like behavior, all reverted by fluoxetine (Araujo et al., 2018). Thus far, no study reported a short, random and variable protocol that induces stress phenotypes for rapid screening of psychopharmacological agents. The aim of this study was to develop a novel and time-efficient stress protocol for the study of psychopharmacological agents in Drosophila.
Integrated metabolomics and 16S rRNA sequencing to investigate the regulation of Chinese yam on antibiotic-induced intestinal dysbiosis in rats
Published in Artificial Cells, Nanomedicine, and Biotechnology, 2019
Yaping Sun, Tong Liu, Yanpo Si, Bing Cao, Yanli Zhang, Xiaoke Zheng, Weisheng Feng
Samples were sequenced on an Illumina MiSeq platform, according to the manufacturer's recommendations, provided by LC-Bio. Paired-end reads was assigned to samples based on their unique barcode and truncated by cutting off the barcode and primer sequence. Paired-end reads were merged using FLASH. Quality filtering on the raw tags were performed under specific filtering conditions to obtain the high-quality, clean tags according to the FastQC (V 0.10.1). Chimeric sequences were filtered using Verseach software (v2.3.4). Sequences with ≥97% similarity were assigned to the same operational taxonomic units (OTUs) by Verseach (v2.3.4) [20]. Representative sequences were chosen for each OTU, and taxonomic data were then assigned to each representative sequence using the RDP (Ribosomal Database Project) classifier. The differences of the dominant species in different groups, multiple sequence alignment were conducted using the PyNAST software to study phylogenetic relationship of different OTUs. OTUs abundance information was normalized using a standard of sequence number corresponding to the sample with the least sequences. Alpha diversity is applied in analyzing the complexity of species diversity for a sample through 4 indices, including Chao1, Shannon, Simpson, and Observed species (Supplementary material). All these indices in our samples were calculated with QIIME (Version 1.8.0). Beta diversity analysis was used to evaluate the differences in species complexity of samples. Beta diversity was calculated by principle co-ordinates analysis (PCoA) and cluster analysis by QIIME software (Version 1.8.0)
Pre-colonization with the commensal fungus Candida albicans reduces murine susceptibility to Clostridium difficile infection
Published in Gut Microbes, 2018
Laura Markey, Lamyaa Shaban, Erin R. Green, Katherine P. Lemon, Joan Mecsas, Carol A. Kumamoto
Libraries were prepared from each sample and sequenced as described.57 Briefly, PCR amplification of the V4 region of the 16S rRNA gene was performed with primers that included adapters for Illumina sequencing and twelve base barcodes. Two hundred fifty bp paired-end sequencing was performed using an Illumina MiSeq. Base calling was performed using CASAVA 1.8 and the resulting fastq files were used as input for downstream analysis using QIIME (1.8.0).22 Briefly, the paired-end reads from the fastq files were joined, barcodes extracted and then demultiplexed. The operational taxonomic units (OTUs) were determined using a closed reference approach by aligning reads to the Greengenes Database (version 13_8) at 99% identity. The Greengenes phylogenetic tree was used to define the phylogenetic relationship between OTUs. The resultant OTU tables contained the relative abundance of bacterial taxa in each sample. These tables were used to calculate overall diversity within each sample. To compare the composition and diversity of samples to each other taking into account phylogenetic relatedness, the OTU tables were used to calculate the weighted UniFrac distance matrix, which was summarized with Principal Coordinate Analysis. Permanova analysis was performed using Qiime.