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Veterinary Sciences May 2024Cattle ticks are a significant health concern in tropical livestock production due to their hematophagous behavior and potential as vectors for human and animal...
Cattle ticks are a significant health concern in tropical livestock production due to their hematophagous behavior and potential as vectors for human and animal pathogens. In this study, we investigated the tick population present in dairy cattle production, calves, and grazing areas of livestock systems in the northwestern Colombian Amazon. Identification was based on taxonomic keys and molecular markers. Phylogenetic relationships were established using mitochondrial and 16S genes. Population structure analysis was performed considering age, racial type ( vs. ), and the influence of environmental factors and the geomorphological landscape on tick population dynamics. Our findings revealed the presence of a single tick species, with a unique haplotype identified for each mitochondrial gene assessed. Phylogenetic analysis classified the found species within Clade A of the complex. Ticks were more prevalent during periods of low rainfall and high temperature, and cows exhibited the highest tick abundance. Thus, these results provide insights into the population characteristics and distribution of the tick species present in dairy cattle production systems in the northwestern part of the Colombian Amazon. This information is fundamental for developing targeted strategies based on seasonal variation and host characteristics to mitigate tick infestation severity in the region.
PubMed: 38921991
DOI: 10.3390/vetsci11060244 -
Insects Jun 2024Currently, the subfamily Meconematinae encompasses 1029 species, but whole-mitochondrial-genome assemblies have only been made available for 13. In this study, the whole...
Currently, the subfamily Meconematinae encompasses 1029 species, but whole-mitochondrial-genome assemblies have only been made available for 13. In this study, the whole mitochondrial genomes (mitogenomes) of nine additional species in the subfamily Meconematinae were sequenced. The size ranged from 15,627 bp to 17,461 bp, indicating double-stranded circular structures. The length of the control region was the main cause of the difference in mitochondrial genome length among the nine species. All the mitogenomes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (CR). The majority strand encoded 23 genes, and the minority strand encoded 14 genes. A phylogenetic analysis reaffirmed the monophyletic status of each subfamily, but the monophysitism of , and was not supported.
PubMed: 38921128
DOI: 10.3390/insects15060413 -
Insects May 2024Using Illumina sequencing technology, we generated complete mitochondrial genomes (mitogenomes) of three constituent species of the aphid genus Koch, (Blanchard),...
Using Illumina sequencing technology, we generated complete mitochondrial genomes (mitogenomes) of three constituent species of the aphid genus Koch, (Blanchard), Ghulamullah, and (Geoffroy). The sizes of the mitogenomes range from 15,306 to 15,410 bp, primarily due to variations in the length of non-coding regions. The mitogenomes consist of 37 coding genes arranged in the order of the ancestral insect mitogenome, a control region, and a repeat region between and According to the COI-based analysis, one previously reported mitogenome of should be assigned to . The gene order, nucleotide composition, and codon usage in the mitogenomes are highly conserved and similar to those of other species of Aphidinae. The tandem repeat units differ in nucleotide composition, length, and copy number across three species. Within the widespread Eurasian species , variation in repeat units among different geographic populations is observed, indicating that the repeat region may provide valuable insights for studying the intraspecific diversification of aphids. Phylogenetic analyses based on 28 complete mitogenomes of Aphidinae supported the monophyly of Aphidinae, Aphidini, Macrosiphini, and two subtribes of Aphidini. was monophyletic. and formed a sister group, while was placed basally. Characterization of the mitogenomes of provides valuable resources for further comparative studies and for advancing our understanding of the aphid mitogenome architecture.
PubMed: 38921104
DOI: 10.3390/insects15060389 -
Current Issues in Molecular Biology Jun 2024The family Scolopacidae presents a valuable subject for evolutionary research; however, molecular studies of Scolopacidae are still relatively understudied, and the...
The family Scolopacidae presents a valuable subject for evolutionary research; however, molecular studies of Scolopacidae are still relatively understudied, and the phylogenetic relationships of certain species remain unclear. In this study, we sequenced and obtained complete mitochondrial DNA (mtDNA) from and partial mtDNA from , and . The complete mtDNA contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 tRNA genes, and a control region. Scolopacidae contained three types of start codons and five types of stop codons (including one incomplete stop codon, T--). In 13 protein-coding genes, average uncorrected pairwise distances (Aupd) revealed that was the least conserved while had the lowest evolutionary rate. The ratio of Ka/Ks suggested that all PCGs were under purifying selection. Using two methods (maximum likelihood and Bayesian inference) to analyze the phylogenetic relationships of the family Scolopacidae, it was found that the genera and were clustered into another sister group, while the genus is more closely related to the genus . The genera , and form a monophyletic group. This study improves our understanding of the evolutionary patterns and phylogenetic relationships of the family Scolopacidae.
PubMed: 38921040
DOI: 10.3390/cimb46060369 -
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 -
Wellcome Open Research 2023We present a genome assembly from an individual female (a tachinid fly; Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence is 670.7 megabases in span. Most...
We present a genome assembly from an individual female (a tachinid fly; Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence is 670.7 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 27,893 protein coding genes.
PubMed: 38919871
DOI: 10.12688/wellcomeopenres.19575.1 -
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