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Current Issues in Molecular Biology May 2024A single nucleotide variant in mitochondrial DNA (mtDNA) 1555A>G is associated with drug-induced hearing loss. For the 1555A>G mutation site, 1555A wild-type and 1555G...
A single nucleotide variant in mitochondrial DNA (mtDNA) 1555A>G is associated with drug-induced hearing loss. For the 1555A>G mutation site, 1555A wild-type and 1555G mutant-type plasmids were constructed, respectively. In this study, a PCR method based on the TaqMan amplification refractory mutation system was proposed to detect mtDNA 1555A>G. A common upstream primer, a common TaqMan probe, and two downstream allele-specific primers with mismatched bases were designed. One-step amplification and detection of the wild-type and mutant type at the 1555 site were realized for the deafness-related gene through two reactions. Based on this detection method, the minimum detection limit of the wild-type and mutant type detection systems for plasmids was 50 copies/μL. The minimum sensitivity for the detection of nucleic acids in real dried blood spot (DBS) samples was 0.1 ng/μL. In the normal DBS DNA sample, the detection limit of the mutation abundance reached 0.78%. The specificity of the detection method was 100%, and the coefficient of variation was less than 3.36%. This approach was validated using clinical DNA extracted from 113 DBS samples of newborns. Additionally, it showed 100% agreement with bi-directional Sanger sequencing. It can be used as an optional method for the clinical detection of deafness-related genes.
PubMed: 38920998
DOI: 10.3390/cimb46060326 -
Current Issues in Molecular Biology May 2024The mitochondrial genome of Pumpo (), a prominent breed contributing to livestock farming, was sequenced using the Illumina HiSeq 2500 platform. Assembly and annotation...
The mitochondrial genome of Pumpo (), a prominent breed contributing to livestock farming, was sequenced using the Illumina HiSeq 2500 platform. Assembly and annotation of the mitochondrial genome were achieved through a multifaceted approach employing bioinformatics tools such as Trim Galore, SPAdes, and Geseq, followed by meticulous manual inspection. Additionally, analyses covering tRNA secondary structure and codon usage bias were conducted for comprehensive characterization. The 16,341 base pair mitochondrial genome comprises 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Phylogenetic analysis places Pumpo within a clade predominantly composed of European cattle, reflecting its prevalence in Europe. This comprehensive study underscores the importance of mitochondrial genome analysis in understanding cattle evolution and highlights the potential of genetic improvement programs in livestock farming, thus contributing to enhanced livestock practices.
PubMed: 38920992
DOI: 10.3390/cimb46060320 -
Cells Jun 2024Neurodegenerative disorders are affecting millions of people worldwide, impacting the healthcare system of our society. Among them, Alzheimer's disease (AD) is the most...
Neurodegenerative disorders are affecting millions of people worldwide, impacting the healthcare system of our society. Among them, Alzheimer's disease (AD) is the most common form of dementia, characterized by severe cognitive impairments. Neuropathological hallmarks of AD are β-amyloid (Aβ) plaques and neurofibrillary tangles, as well as endoplasmic reticulum and mitochondria dysfunctions, which finally lead to apoptosis and neuronal loss. Since, to date, there is no definitive cure, new therapeutic and prevention strategies are of crucial importance. In this scenario, cannabinoids are deeply investigated as promising neuroprotective compounds for AD. In this study, we evaluated the potential neuroprotective role of cannabinerol (CBNR) in an in vitro cellular model of AD via next-generation sequencing. We observed that CBNR pretreatment counteracts the Aβ-induced loss of cell viability of differentiated SH-SY5Y cells. Moreover, a network-based transcriptomic analysis revealed that CBNR restores normal mitochondrial and endoplasmic reticulum functions in the AD model. Specifically, the most important genes regulated by CBNR are related mainly to oxidative phosphorylation (, , , ), protein folding () and degradation (, , ), and glucose () and lipid (, , ) metabolism. Therefore, these results suggest that CBNR could be a new neuroprotective agent helpful in the prevention of AD dysfunctions.
Topics: Humans; Alzheimer Disease; Mitochondria; Endoplasmic Reticulum; Cannabinoids; Amyloid beta-Peptides; Endoplasmic Reticulum Chaperone BiP; Cell Line, Tumor; Gene Expression Profiling; Transcriptome; Cell Survival; Neuroprotective Agents; Models, Biological; Gene Regulatory Networks
PubMed: 38920643
DOI: 10.3390/cells13121012 -
Mitochondrial DNA. Part B, Resources 2024The first registered Itoh hybrid cv. Hexie in China is a naturally occurring intersectional hybrid of Sect. and Sect. . In this study, we sequenced, assembled, and...
The first registered Itoh hybrid cv. Hexie in China is a naturally occurring intersectional hybrid of Sect. and Sect. . In this study, we sequenced, assembled, and analyzed the complete chloroplast genome of Itoh hybrid cv. Hexie. The result showed that the chloroplast genome of Hexie, with a typical circular tetrad structure, is 152,958 bp in length, comprising a large single copy (LSC) region of 84,613 bp, a small single copy (SSC) region of 17,051 bp, and two reverse complementary sequences (IRs) of 25,647 bp. The chloroplast genome encoded 116 genes, including 80 protein-coding genes, 32 tRNA genes, and 4 rRNA genes. Phylogenetic analysis inferred from the shared protein-coding genes showed that the Itoh hybrid cv. Hexie had the closest phylogenetic relationship with , followed by , indicating that was its maternal parent. This study provides a molecular resource for phylogenetic and maternal parent studies of Itoh hybrid, contributing to a basis for Itoh hybrid breeding strategies in the future.
PubMed: 38919813
DOI: 10.1080/23802359.2024.2368214 -
Mitochondrial DNA. Part B, Resources 2024belongs to the Homoneurinae subfamily of Lauxaniidae, and it is widely distributed and common in China. This study reports the newly sequenced mitochondrial genome of ....
belongs to the Homoneurinae subfamily of Lauxaniidae, and it is widely distributed and common in China. This study reports the newly sequenced mitochondrial genome of . The sequence is 15,469 bp long and contains 37 genes (13 protein-coding, 22 tRNA, and 2 rRNA genes) and a control region. The overall base composition is 38.4% for A, 37.7% for T, 14.1% for C, and 9.8% for G, with a bias toward A + T (76.1%). Phylogenetic analysis show that is a sister genus of . We have successfully sequenced the mitochondrial genome of , which can be useful in investigating the phylogenetic status of Homoneurinae. Our results provide data for further studies of phylogeny in Diptera.
PubMed: 38919812
DOI: 10.1080/23802359.2024.2333560 -
Mitochondrial DNA. Part B, Resources 2024Chu, 1979 (Lepidoptera: Geometridae) is a major insect pest in jujube plantation. In this study, we have sequenced the complete mitochondrial genome of . The circular...
Chu, 1979 (Lepidoptera: Geometridae) is a major insect pest in jujube plantation. In this study, we have sequenced the complete mitochondrial genome of . The circular genome was 15,557 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one AT-rich region (GenBank accession no. MZ507574). The nucleotide composition was significantly biased (A, T, C, and G were 41.85%, 39.65%, 10.97%, and 7.53%, respectively) with A + T contents of 81.50%. The Bayesian phylogenetic analysis of the concatenated nucleotide sequences of 13 PCGs from 30 species in the subfamily Ennominae and two outgroup species was performed. The results indicated that was closely related to in the subfamily Ennominae.
PubMed: 38919810
DOI: 10.1080/23802359.2024.2368219 -
Mitochondrial DNA. Part B, Resources 2024(Wang, 1979) is an endemic fish in China that is sparsely distributed in the Hainan provinces and Guangxi Zhuang Autonomous Region (GZAR). In this study, the complete...
(Wang, 1979) is an endemic fish in China that is sparsely distributed in the Hainan provinces and Guangxi Zhuang Autonomous Region (GZAR). In this study, the complete mitochondrial genome of from the Hainan population from the Wanquan River was sequenced, and its phylogenetic relationship was analyzed. The circular mtDNA was 16,581 bp in length, and the overall base composition was A (32.0%), C (27.5%), T (24.8%), and G (15.70%), with a slight bias toward A + T. The complete mitogenome encoded 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis indicated that the most closely related fish to from the Hainan population was from the Guangxi population. These findings offer basic molecular data and a better understanding of the phylogenetic relationships among the species.
PubMed: 38919809
DOI: 10.1080/23802359.2024.2323004 -
Mitochondrial DNA. Part B, Resources 2024We determined the complete mitochondrial DNA sequence of a Biwa goby, (Tanaka, 1916) using next-generation sequencing methods. The composition of its mitogenome is the...
We determined the complete mitochondrial DNA sequence of a Biwa goby, (Tanaka, 1916) using next-generation sequencing methods. The composition of its mitogenome is the same as that observed in most other vertebrates, comprising of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions. Our molecular phylogenetic analysis confirmed the close phylogenetic relationship between and . This mitogenome information will be useful for distribution surveys using environmental DNA and the development of conservation strategies for this species.
PubMed: 38919808
DOI: 10.1080/23802359.2024.2368732 -
Journal of Nanobiotechnology Jun 2024Parkinson's disease (PD) is the second largest group of neurodegenerative diseases, and its existing drug treatments are not satisfactory. Natural cell membrane drugs...
Parkinson's disease (PD) is the second largest group of neurodegenerative diseases, and its existing drug treatments are not satisfactory. Natural cell membrane drugs are used for homologous targeting to enhance efficacy. In this study, microfluidic electroporation chip prepared mesenchymal stem cell-derived neuron-like cell membrane-coated curcumin PLGA nanoparticles (MM-Cur-NPs) was synthesized and explored therapeutic effect and mechanism in PD. MM-Cur-NPs can protect neuron from damage, restore mitochondrial membrane potential and reduce oxidative stress in vitro. In PD mice, it also can improve movement disorders and restore damaged TH neurons. MM-Cur-NPs was found to be distributed in the brain and metabolized with a delay within 24 h. After 1 h administration, MM-Cur-NPs were distributed in brain with a variety of neurotransmitters were significantly upregulated, such as dopamine. Differentially expressed genes of RNA-seq were enriched in the inflammation regulation, and it was found the up-expression of anti-inflammatory factors and inhibited pro-inflammatory factors in PD. Mechanically, MM-Cur-NPs can not only reduce neuronal apoptosis, inhibit the microglial marker IBA-1 and inflammation, but also upregulate expression of neuronal mitochondrial protein VDAC1 and restore mitochondrial membrane potential. This study proposes a therapeutic strategy provide neuroprotective effects through MM-Cur-NPs therapy for PD.
Topics: Animals; Mesenchymal Stem Cells; Mice; Apoptosis; Nanoparticles; Neurons; Parkinson Disease; Inflammation; Cell Membrane; Membrane Potential, Mitochondrial; Curcumin; Mice, Inbred C57BL; Microfluidics; Male; Oxidative Stress
PubMed: 38918856
DOI: 10.1186/s12951-024-02587-1 -
BMC Genomics Jun 2024Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder featured by abnormal movements, arising from the extensive neuronal loss and glial...
Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder featured by abnormal movements, arising from the extensive neuronal loss and glial dysfunction in the striatum. Although the causes and pathogenetic mechanisms of HD are well established, the development of disease-modifying pharmacological therapies for HD remains a formidable challenge. Laduviglusib has demonstrated neuroprotective effects through the enhancement of mitochondrial function in the striatum of HD animal models. Ferroptosis is a nonapoptotic form of cell death that occurs as a consequence of lethal iron-dependent lipid peroxidation and mitochondrial dysfunction. However, the ferroptosis-related mechanisms underlying the neuroprotective effects of laduviglusib in the striatum of HD patients remain largely uncharted. In this study, we leveraged single-nucleus RNA sequencing data obtained from the striatum of HD patients in stages 2-4 to identify differentially expressed genes within distinct cell-type. We subsequently integrated these differentially expressed genes of HD, laduviglusib target genes and ferroptosis-related genes to predict the ferroptosis-related mechanisms underpinning the neuroprotective effects of laduviglusib in HD patients. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses unveiled that the effects of laduviglusib on direct pathway striatal projection neurons (dSPNs) is mainly associated with Th17 cell differentiation pathways. Conversely, its impact on indirect pathway striatal projection neurons (iSPNs) extends to the Neurotrophin signaling pathway, FoxO signaling pathway, and reactive oxygen species pathway. In microglia, laduviglusib appears to contribute to HD pathology via mechanisms related to Th17 cell differentiation and the FoxO signaling pathway. Further, molecular docking results indicated favorable binding of laduviglusib with PARP1 (associated with dSPNs and iSPNs), SCD (associated with astrocytes), ALOX5 (associated with microglia), and HIF1A (associated with dSPNs, iSPNs, and microglia). In addition, the KEGG results suggest that laduviglusib may enhance mitochondrial function and protect against neuronal loss by targeting ferroptosis-related signaling pathways, particularly mediated by ALOX5 in microglia. These findings provide valuable insights into the potential mechanisms through which laduviglusib exerts its effects on distinct cell-types within the HD striatum.
Topics: Ferroptosis; Huntington Disease; Humans; Corpus Striatum; Neuroprotective Agents
PubMed: 38918688
DOI: 10.1186/s12864-024-10534-5