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Wellcome Open Research 2023We present a genome assembly from an individual female (the Orange-tailed Mining Bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence is 330.7...
We present a genome assembly from an individual female (the Orange-tailed Mining Bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence is 330.7 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,908 protein coding genes.
PubMed: 38813552
DOI: 10.12688/wellcomeopenres.19982.1 -
Wellcome Open Research 2023We present a genome assembly from an individual male (the Six-belted Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 511.4 megabases in...
We present a genome assembly from an individual male (the Six-belted Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 511.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,114 protein coding genes.
PubMed: 38813550
DOI: 10.12688/wellcomeopenres.20279.1 -
Wellcome Open Research 2023We present a genome assembly from an individual (the fish leech; Annelida; Clitellata; Hirudinida; Piscicolidae). The genome sequence is 171.1 megabases in span. Most...
We present a genome assembly from an individual (the fish leech; Annelida; Clitellata; Hirudinida; Piscicolidae). The genome sequence is 171.1 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.1 kilobases in length.
PubMed: 38813549
DOI: 10.12688/wellcomeopenres.19488.1 -
Wellcome Open Research 2023We present a genome assembly from an individual male (the July Highflyer; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 423.3 megabases in...
We present a genome assembly from an individual male (the July Highflyer; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 423.3 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.89 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,324 protein coding genes.
PubMed: 38813548
DOI: 10.12688/wellcomeopenres.20182.1 -
Frontiers in Veterinary Science 2024The purpose of this study was to improve the quality of frozen-thawed Piedmontese bull semen by incorporating MitoTEMPO (MT) in extended semen before cryopreservation....
The purpose of this study was to improve the quality of frozen-thawed Piedmontese bull semen by incorporating MitoTEMPO (MT) in extended semen before cryopreservation. Semen was collected from 4 fertile bulls, using an artificial vagina, once weekly for 6 consecutive weeks. Semen samples were pooled, diluted with Bullxcell extender, and supplemented with different concentrations of MT (0 as control, 5, 10, 20, 40, and 80 μM) before cooling, equilibration, and freezing procedures. The frozen-thawed semen was assessed for motility, vitality, acrosome intactness, plasma membrane integrity, DNA integrity, apoptosis, mitochondrial membrane potential, intracellular ROS level and fertilizing capability. The results showed that MT at concentrations of 10, 20, and 40 μM improved the total, progressive, and rapid motility directly after thawing while, at the highest tested concentration (80 μM), it decreased the progressive and rapid motility after 1, 2, and 3 h of incubation. The sperm kinetics including STR and LIN were noticeably increased at concentrations of 10, 20, and 40 μM directly after thawing (0 h), whereas the MT effect was variable on the other sperm kinetics during the different incubation periods. MitoTEMPO improved the sperm vitality at all tested concentrations, while the acrosomal and DNA integrity were improved at 20 μM and the mitochondrial membrane potentials was increased at 80 μM. The cleavage and blastocyst formation rates were significantly increased by using semen treated with 20 μM MT compared with controls. These findings suggest a potential use of MT mainly at a concentration of 20 μM as an additive in the cryopreservation media of bull semen to improve sperm quality.
PubMed: 38812559
DOI: 10.3389/fvets.2024.1376057 -
Scientific Reports May 2024Cryopreservation of sperm can cause oxidative stress and damage, leading to decreased different functional parameters and fertilization potential. In this study, we...
Cryopreservation of sperm can cause oxidative stress and damage, leading to decreased different functional parameters and fertilization potential. In this study, we evaluated two types of HS donors: NaHS, a fast-releasing donor, and GYY4137, a slow-releasing donor during cryopreservation of goat sperm. Initially, we determined that 1.5 and 3 μM NaHS, and 15 and 30 μM GYY4137 are optimal concentrations that improved different sperm functional parameters including motility, viability, membrane integrity, lipid peroxidation, and ROS production during incubation at 38.5 °C for 90 min. We subsequently evaluated the impact of the optimal concentration of NaHS and GYY4137 supplementation on various functional parameters following thawing during cryopreservation. Our data revealed that supplementation of extender improved different parameters including post-thaw sperm motility, viability, membrane integrity, and reduced DNA damage compared to the frozen-thawed control group. The supplementation also restored the redox state, decreased lipid peroxidation, and improved mitochondrial membrane potential in the thawed sperm. Finally, we found that supplementation of the extender with NaHS and GYY4137 enhanced IVF outcomes in terms of blastocyst rate and quality of blastocysts. Our results suggest that both donors can be applied for cryopreservation as antioxidants to improve sperm quality and IVF outcomes of frozen-thawed goat sperm.
Topics: Male; Cryopreservation; Animals; Oxidative Stress; Fertilization in Vitro; Spermatozoa; Goats; Sperm Motility; Semen Preservation; Organothiophosphorus Compounds; Lipid Peroxidation; Hydrogen Sulfide; Cryoprotective Agents; Cell Survival; Female; Reactive Oxygen Species; Membrane Potential, Mitochondrial; Semen Analysis; Morpholines; Sulfides
PubMed: 38811647
DOI: 10.1038/s41598-024-62485-2 -
Wellcome Open Research 2023We present a genome assembly from cultured (a marine green alga; Chlorophyta; None; Pseudoscourfieldiales; Pycnococcaceae). The genome sequence is 32.2 megabases in...
We present a genome assembly from cultured (a marine green alga; Chlorophyta; None; Pseudoscourfieldiales; Pycnococcaceae). The genome sequence is 32.2 megabases in span. Most of the assembly is scaffolded into 44 chromosomal pseudomolecules (99.67%). The mitochondrial and plastid genomes have also been assembled, and the length of the mitochondrial scaffold is 24.3 kilobases and of the plastid genome has been assembled and is 80.2 kilobases in length.
PubMed: 38808318
DOI: 10.12688/wellcomeopenres.20345.1 -
Frontiers in Cell and Developmental... 2024Mitochondrial health has gained attention in a number of diseases, both as an indicator of disease state and as a potential therapeutic target. The quality and amount of...
BACKGROUND
Mitochondrial health has gained attention in a number of diseases, both as an indicator of disease state and as a potential therapeutic target. The quality and amount of mitochondrial DNA (mtDNA) and RNA (mtRNA) can be important indicators of mitochondrial and cell health, but are difficult to measure in complex tissues.
METHODS
mtDNA and mtRNA in zebrafish retina samples were fluorescently labeled using RNAscope™ hybridization, then mitochondria were stained using immunohistochemistry. Pretreatment with RNase was used for validation. Confocal images were collected and analyzed, and relative amounts of mtDNA and mtRNA were reported. Findings regarding mtDNA were confirmed using qPCR.
RESULTS
Signals from probes detecting mtDNA and mtRNA were localized to mitochondria, and were differentially sensitive to RNase. This labeling strategy allows for quantification of relative mtDNA and mtRNA levels in individual cells. As a demonstration of the method in a complex tissue, single photoreceptors in zebrafish retina were analyzed for mtDNA and mtRNA content. An increase in mtRNA but not mtDNA coincides with proliferation of mitochondria at night in cones. A similar trend was measured in rods.
DISCUSSION
Mitochondrial gene expression is an important component of cell adaptations to disease, stress, or aging. This method enables the study of mtDNA and mtRNA in single cells of an intact, complex tissue. The protocol presented here uses commercially-available tools, and is adaptable to a range of species and tissue types.
PubMed: 38808224
DOI: 10.3389/fcell.2024.1346778 -
Frontiers in Cell and Developmental... 2024Sporadic inclusion body myositis (sIBM) is a distinct subcategory of Idiopathic Inflammatory Myopathies (IIM), characterized by unique pathological features such as... (Review)
Review
Sporadic inclusion body myositis (sIBM) is a distinct subcategory of Idiopathic Inflammatory Myopathies (IIM), characterized by unique pathological features such as muscle inflammation, rimmed vacuoles, and protein aggregation within the myofibers. Although hyperactivation of the immune system is widely believed as the primary cause of IIM, it is debated whether non-immune tissue dysfunction might contribute to the disease's onset as patients with sIBM are refractory to conventional immunosuppressant treatment. Moreover, the findings that mitochondrial dysfunction can elicit non-apoptotic programmed cell death and the subsequent immune response further support this hypothesis. Notably, abnormal mitochondrial structure and activities are more prominent in the muscle of sIBM than in other types of IIM, suggesting the presence of defective mitochondria might represent an overlooked contributor to the disease onset. The large-scale mitochondrial DNA deletion, aberrant protein aggregation, and slowed organelle turnover have provided mechanistic insights into the genesis of impaired mitochondria in sIBM. This article reviews the disease hallmarks of sIBM, the plausible contributors of mitochondrial damage in the sIBM muscle, and the immunological responses associated with mitochondrial perturbations. Additionally, the potential application of mitochondrial-targeted chemicals as a new treatment strategy to sIBM is explored and discussed.
PubMed: 38808223
DOI: 10.3389/fcell.2024.1403463 -
Frontiers in Molecular Neuroscience 2024The mammalian central nervous system coordinates a network of signaling pathways and cellular interactions, which enable a myriad of complex cognitive and physiological...
The mammalian central nervous system coordinates a network of signaling pathways and cellular interactions, which enable a myriad of complex cognitive and physiological functions. While traditional efforts to understand the molecular basis of brain function have focused on well-characterized proteins, recent advances in high-throughput translatome profiling have revealed a staggering number of proteins translated from non-canonical open reading frames (ncORFs) such as 5' and 3' untranslated regions of annotated proteins, out-of-frame internal ORFs, and previously annotated non-coding RNAs. Of note, microproteins < 100 amino acids (AA) that are translated from such ncORFs have often been neglected due to computational and biochemical challenges. Thousands of putative microproteins have been identified in cell lines and tissues including the brain, with some serving critical biological functions. In this perspective, we highlight the recent discovery of microproteins in the brain and describe several hypotheses that have emerged concerning microprotein function in the developing and mature nervous system.
PubMed: 38807924
DOI: 10.3389/fnmol.2024.1386219