Genes & genetic systems最新文献

The role played by error catastrophe is explicitly taken into account in a mathematical formulation to analyze COVID-19 data. The idea is to combine the mathematical genetics formalism of the error catastrophe of mutations in virus gene loci with the standard model of epidemics, which lacks the explicit incorporation of the effect of mutation on the spreading of viruses. We apply this formalism to the case of SARS-CoV-2 virus. We assume the universality of the error catastrophe in the process of analyzing the data. This means that some basic parameter to describe the error catastrophe is independent of which group (country or city) we deal with. Concretely, we analyze Omicron variant data from South Africa and then analyze cases from Japan using the same value of the basic parameter derived in the South Africa analysis. The excellent fit between the two sets of data, one from South Africa and the other from Japan, using the common values of genetic parameters, justifies our assumption of the universality of these parameters.

Obtaining high-quality nucleic acid extracted from seaweeds is notoriously difficult due to contamination with polysaccharides and polyphenolic compounds after cell disruption. Specific methods need to be employed for RNA isolation in different seaweed species, and therefore studies of the thiamine biosynthesis pathway have been limited. Two selected Malaysian species which are highly abundant and underutilized, namely Gracilaria sp. and Padina sp., representing the red and brown seaweeds, respectively, were collected to develop optimized total RNA extraction methods. Prior to that, DNA was extracted, and amplification of the 18S rRNA gene and the THIC gene (encoding the first enzyme in the pyrimidine branch of the thiamine biosynthesis pathway) from the DNA template was successful in Gracilaria sp. only. RNA was then extracted from both seaweeds using three different existing methods, with some modifications, using cetyltrimethylammonium bromide, guanidine thiocyanate and sodium dodecyl sulphate. Methods I and III proved to be efficient for Padina sp. and Gracilaria sp., respectively, for the extraction of highly purified RNA, with A₂₆₀/A₂₈₀ values of 2.0 and 1.8. However, amplification of the housekeeping gene glyceraldehyde-3-phosphate dehydrogenase and the THIC gene was successful in only Gracilaria sp. cDNA derived from extracted RNA. Further modifications are required to improve the exploitation of nucleic acids from brown seaweeds, which has been proven to be difficult. This work should pave the way for molecular studies of seaweeds generally and for the elucidation, specifically, of the thiamine biosynthesis pathway.

The transposon Tam3 of Antirrhinum (snapdragon) has acquired properties that distinguish it from other transposons. Mobile DNA, commonly referred to as a transposable element or transposon, is considered to be synonymous with a selfish factor. That is, a transposable element increases in copy number and moves copies of itself independently of the survival of the host organism. Therefore, the host collectively regulates the transposition activities of most transposable elements in its genome by epigenetic means. However, our analyses of the structure and behavior of Tam3, as shown by the following five results, provide evidence that it does not behave in a selfish manner in relation to the host. 1) Active transposable elements normally increase the abundance of their non-autonomous elements, whereas Tam3 is known to have no non-autonomous elements, and a limited number of around 10 copies of autonomous elements present in the genome have been isolated as active copies. 2) Tam3 does not transpose at 25 ℃, which is the optimal growth temperature for Antirrhinum. Transposition of Tam3 occurs only at low temperatures of about 15 ℃, which is stressful for Antirrhinum. 3) Few strains of Antirrhinum have been found to contain genes that specifically suppress Tam3 transposition. 4) Most of the Tam3 insertions found in Antirrhinum genes do not affect the host genome, and the expression of these host genes is not completely suppressed. 5) Transcription and translation of the Tam3 transposase gene are not epigenetically regulated by the host. These five experimental results constitute evidence that Tam3 retains features that are dissimilar to those of many other transposons and that it does not behave in a selfish manner that is detrimental to the survival of the host. In this review, we consider what kinds of behavior are required if transposons are to establish a mutually beneficial relationship with their hosts, with reference to Tam3.

Conifers are important in many forest ecosystems. They have a long generation time and are immobile; therefore, they require considerable plasticity to adapt to environmental stresses. Moreover, conifers have a large genome, a high proportion of which is occupied by repetitive elements. Retrotransposons are the most highly represented repetitive elements in conifers whose whole-genome sequences have been examined. These retrotransposons are usually silenced, to maintain genome integrity; however, some are activated by environmental stress. The insertion of retrotransposons into genic regions is associated with phenotypic and genetic diversity. The large number and high diversity of retrotransposons in conifer genomes suggest that they play a role in adaptation to the environment. In this review, progress in research on the roles of retrotransposons in the stress responses of conifers is reviewed, and potential future work is discussed.

To investigate the gene expression pattern and related biological changes during osteogenic differentiation of human mesenchymal stem cells (hMSCs), we downloaded expression data for four uninduced hMSC samples, and 12 osteogenic induction samples at day 2, 8, 12 or 25, in the GSE37558 dataset. Differentially expressed genes (DEGs) between groups were screened, followed by short time-series expression miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA). Osteogenic differentiation-related genes were extracted from the GeneCards database. Next, functional enrichment was performed, and protein-protein interaction (PPI) and lncRNA-miRNA-mRNA networks were constructed. Compared to uninduced hMSC samples, 163, 341, 447 and 537 DEGs were found in osteogenic induction samples at day 2, 8, 12 and 25, respectively, showing a sustainably increased trend. From STEM, WGCNA and the GeneCards database, a total of 107 key genes associated with osteogenic differentiation were screened; these genes were enriched in biological processes, such as ossification, ECM-receptor interaction, vasculature development, cartilage development and bone mineralization, as well as the Wnt signaling pathway and the chemokine signaling pathway. The PPI network identified four hub genes, STAT5A, TWIST1, FOXO1 and LEP. The lncRNA-miRNA-mRNA network revealed regulatory axes for STAT5A, FOXO1 and LEP. Three and two regulatory axes were found for STAT5A and LEP, respectively. Multiple regulatory axes for FOXO1 were found, such as MIR155HG-miR-223-FOXO1. This study identifies candidate key targets that may play important roles in regulating osteogenic differentiation of hMSCs, and provides novel information to further investigate the molecular regulation mechanism. More experiments are required to evaluate the effects of these genes on osteogenic differentiation of hMSCs.

In Madagascar, the house mouse (Mus musculus) is widely believed to have colonized with human activities and is now one of the most abundant rodents on the island. However, its genetic background at the genomic level remains unclear, and clarifying this would help us to infer the timing of introduction and route of migration. In this study, we determined the whole-genome sequences of five Madagascar house mice captured from an inland location in Madagascar. We examined the genetic background of samples by analyzing the mitochondrial and autosomal genomes. We confirmed that the mitochondrial genome lineages of collected samples formed a single clade placed at one of the most basal positions in the Mus musculus species. Autosomal genomic sequences revealed that these samples are most closely related to the subspecies M. m. castaneus (CAS), but also contain a genetic component of the subspecies M. m. domesticus (DOM). The signature of a strong population bottleneck 1,000-3,000 years ago was observed in both mitochondrial and autosomal genomic data. In a comparison with global samples of M. musculus, the Madagascar samples showed strong genetic affinity to many CAS samples across a wide range of Indian Ocean coastal and insular regions, with divergence time estimated as around 4,000 years ago. These findings support the proposition that the ancestors of these animals started to colonize the island with human agricultural activity and experienced a complex history during their establishment.