iPReditor-CMG: Improving Predictive RNA Editor for Crop Mitochondrial Genomes Using Genomic Sequence Features and Optimal Support Vector Machine

Cytosine (C) to uracil (U) RNA editing is one of the most important post-transcriptional processes, however exploring C-to-U editing events efficiently within the crop mitochondrial genome remains a challenge. An improving predictive RNA editor for crop mitochondrial genomes, iPReditor-CMG, was proposed, which was based on SVM, three common crop mitochondrial genomes and self-sequenced tobacco mitochondrial ATPase. After multi-combination feature extracting, high-dimension feature screening and multi-test independent predicting, the results showed that the average accuracy of intraspecific prediction was 0.85, and the highest value even up to 0.91, which outperformed the previous reference models. While the prediction accuracies were 0.78 between dicotyledons and no more than 0.56 between dicotyledons and monocotyledons, implying a possible similarity in C-to-U editing mechanisms among close relatives. The best model was finally identified with an independent test accuracy of 0.91 and an area under the curve of 0.88, and further suggested that five unreported feature sequences TGACA, ACAAC, GTAGA, CCGTT and TAACA were closely associated with the editing phenomenon. Multiple evaluation findings supported that the iPReditor-CMG could be effectively applied to predict crop mitochondrial editing sites, which may contribute to insight into their recognition mechanisms and even other post-transcriptional events in crop mitochondria.

Terpene-rich Fractions of Ficus Mucoso (Welw) Modulate Lipopolysaccharide-induced Inflammatory Mediators and Aberrant Permeability of the Inner Mitochondrial Membrane in Murine Animal Model

Ficus mucoso is traditionally used to treat various infections. This study compared the efficacy of terpene-rich fractions of F. mucoso root bark on LPS-induced inflammation, liver mitochondrial permeability transition (mPT) pore, an index of mitochondrial health, and associated pathological alterations. Terpene-Rich fractions of Dichloromethane (TRDF) and Ethylacetate fractions of F. mucoso (TREF) were obtained according to the method described by Ferguson (1956). A single intraperitoneal injection of 1 mg/kg lipopolysaccharide (LPS) were given to mice to induce systemic inflammation for 72hrs. Evaluation of the effects of the TRDF and TREF on levels of pro-inflammatory mediators (TNF-α, IL-1β, IL-6) and antioxidant indices against LPS-induced hepatic damage were carried out. Mitochondrial swelling was monitored spectrophotometrically as well as mitochondrial ATPase activity and lipid peroxidation. This study reveals that TRDF and TREF possess anti-inflammatory potentials which is related to reduction in levels of pro-inflammatory cytokines, restoration of antioxidant status, reduction in levels of liver marker enzymes as well as associated pathological injury. Furthermore, LPS caused induction of opening of the liver mPT pore which was significantly inhibited by TRDF at 100 and 200 mg/kg bw by 71% and 88% respectively, but only at 100 mg/kg TREF. Furthermore, mitochondrial ATPase activity was inhibited largely by TRDF. The UPLC-ESI-MS analysis revealed the presence of terpenoid derivatives and a few aromatic metabolites in TRDF. The terpene dominance of TRDF metabolites was further justified on the 1H NMR fingerprint.Overall, TRDF is more effective as a cocktail of anti-inflammatory compounds than TREF against LPS-induced acute systemic inflammation.

Identification of the cell-type-specific ER membrane protein Tanmp expressed in hypothalamic tanycytes and subsets of neurons

Genomes of higher eukaryotes encode many uncharacterized proteins, and the functions of these proteins cannot be predicted from the primary sequences due to a lack of conserved functional domains. During a screening of novel noncoding RNAs abundantly expressed in mouse brains, we incidentally identified a gene termed Tanmp, which encoded an endoplasmic reticulum (ER) protein without known functional domains. Tanmp is specifically expressed in the nervous system, and the highest expression was observed in a specialized cell type called tanycyte that aligns the ventral wall of the third ventricle in the hypothalamus. Immunostaining of Tanmp revealed the fine morphology of tanycytes with highly branched apical ER membranes. Immunoprecipitation revealed that Tanmp associates with mitochondrial ATPase at least in vitro, and ER and mitochondrial signals occasionally overlapped in tanycytes. Mutant mice lacking Tanmp did not exhibit overt phenotypes, suggesting that Tanmp is not essential in mice reared under normal laboratory conditions. We also found that RNA probes that are predicted to uniquely detect Tanmp mRNA cross-reacted with uncharacterized RNAs, highlighting the importance of experimental validation of the specificity of probes during the hybridization-based study of RNA localization.

David Herman Maclennan. 3 July 1937—24 June 2020

David Herman MacLennan, one of Canada's foremost biomedical scientists, was known internationally for his research on the molecular mechanism of muscle contraction in human health and disease. David was born on 3 July 1937 in Swan River, Manitoba, and grew up in farm country. After obtaining a BS (Agriculture) in plant science from the University of Manitoba in 1959, David completed his MSc (1961) and PhD (1963) in biology at Purdue. A post-doctoral fellowship at the Enzyme Institute at the University of Wisconsin followed, where he was appointed as an assistant professor (1964–1968). At Wisconsin David published a series of elegant papers on the isolation and characterization of the mitochondrial ATPase and protein components of the electron transfer system. In 1969 he was recruited back to Canada as an associate professor in the Banting and Best Department of Medical Research at the University of Toronto, where he spent the rest of his illustrious career. Here, David shifted his focus to determine how calcium regulates muscle contraction, with a focus on the role of the sarcoplasmic reticulum (SR). David was a scientist who knew where a field was going and he often got there first, incorporating new technologies along the way. His early discovery of the Ca 2+ ATPase pump that controls calcium uptake into the SR was the key to muscle relaxation. His lab systematically characterized the components of the SR, including the ryanodine receptor which acts as a calcium release channel to allow muscle contraction. David's discoveries of these molecular mechanisms and their application to debilitating muscle disease are an inspiring scientific legacy. Although David published hundreds of papers, many cited hundreds of times, gave hundreds of invited seminars and won many prestigious awards, including Fellow of the Royal Society of London in 1994, his greatest legacy is the people he trained, many of whom went on to leadership positions in research and at universities around the world.

Crystal and solution structures of a novel antimicrobial peptide from Chrysomya megacephala

Antimicrobial peptides (AMPs) are small amphipathic peptides that exhibit bactericidal activity against a wide range of pathogenic microorganisms and are considered to be potential substitutes for antibiotics effective against microbial infection. PSK, an 84-amino-acid AMP recently isolated from Chrysomya megacephala larvae, probably belongs to the mitochondrial ATPase inhibitor family according to its sequence. No member of this family from an insect has been structurally characterized to date. In this study, the crystal structure of full-length PSK determined by molecular replacement using an ab initio modeled ensemble as a search model and a solution structure obtained from small-angle X-ray scattering (SAXS) measurements are reported. The crystal structure reveals a distinct fold compared with those of homologous peptides, in that PSK comprises two antiparallel α-helices rather than a single long helix, which is in good agreement with the SAXS-based ab initio model. However, the peptide exists as a monomer in solution, even though a stable dimer was observed in the crystal structure. This apparent contradiction may reflect different oligomerization states that may be implicated in its bioactivity. The data presented here have established a solid basis for further mechanistic studies of this novel insect AMP.

Metformin induces apoptosis via uterus mitochondrial permeability transition pore opening and protects against estradiol benzoate-induced uterine defect and associated pathophysiological disorder in female Wistar rats

Background Some antitumor or anticancer agents have been shown to execute cell death by induction of mitochondrial permeability transition (mPT) pore opening in order to elicit their chemotherapeutic effect. Therefore, this study investigated the effect of metformin on cell death via rat uterus mPT pore and estradiol benzoate-induced uterine defect and associated pathophysiological disorder in female rat. Mitochondria were isolated using differential centrifugation. The mPT pore opening, cytochrome c release and mitochondrial ATPase activity were determined spectrophotometrically. Caspases 9 and 3 activities, MDA and estradiol levels and SOD, GSH activities, were determined using ELISA technique. Histological and histochemical assessments of the uterine section were carried out using standard methods. Results Metformin at concentrations 10–90 μg/mL, showed no significant effect on mPT pore opening, mATPase activity and release of cytochrome c. However, oral administration of metformin caused mPT pore opening, enhancement of mATPase activity and activation of caspases 9 and 3 significantly at 300 and 400 mg/kg. Metformin protected against estradiol benzoate (EB)-induced uterine defect and other associated pathophysiological disorder. It also improved the antioxidant defense system. The histological evaluation revealed the protective effect of metformin on the cellular architecture of the uterus while the histochemical examination showed severe hyperplasia in the uterine section of EB-treated rats, remarkably reversed by metformin co-treatment. Conclusion This study suggests that metformin at high doses induces apoptosis via rat uterus mPT pore opening and protects against EB-induced uterine defect (hyperplasia) and associated pathophysiological disorder.

Stigmasterol isolated from the chloroform fraction of Adenopus breviflorus Benth fruit induces mitochondrial-dependent apoptosis in rat liver

Objectives Decoction of Adenopus breviflorus fruit is used in folkloric medicine for treating dysmenorrhea and gonorrhea. Phytochemicals from A. breviflorus may be potent in inducing mitochondrial-dependent apoptosis via the opening of the mitochondrial permeability transition (MPT) pore. Therefore, this study investigated the in vitro effects of stigmasterol isolated from the chloroform fraction of A. breviflorus (CFAB) and also the increasing concentration of CFAB on the opening of rat liver mitochondrial permeability transition (MPT) pore. Methods Fractionation of CFAB on column chromatography yielded a needle-like crystal which structure was elucidated by standard spectroscopic techniques. The effects of stigmasterol and CFAB on MPT pore opening were assayed spectrophotometrically. Also, the effect of CFAB on mitochondrial ATPase (mATPase) activity and cytochrome c (Cyt c) release were determined. Results Stigmasterol isolated from CFAB induced MPT pore opening significantly (p<0.05) when compared with the control. Similarly, CFAB significantly (p<0.05) induced MPT pore opening in rat liver mitochondria in a concentration-dependent manner in the presence and absence of the triggering agent – calcium ion. Furthermore, the increasing concentration of CFAB significantly (p<0.05) stimulated mitochondrial ATPase (mATPase) activity and Cyt c release in a concentration-dependent manner. Conclusions The study showed that stigmasterol isolated from the chloroform fraction of A. breviflorus is a potent inducer of mitochondrial-dependent apoptosis. Also, the study further revealed that CFAB possesses potent bioactive compounds which can induce the mitochondrial-dependent apoptosis through the opening of the mitochondrial permeability transition pore, activation of mitochondrial ATPase (mATPase) activity and cytochrome c release.

Modulatory effect of methanol extract of Annona muricata stem bark on mitochondrial membrane permeability transition pore in normal rat liver and monosodium glutamate-induced uterine hyperplasia

Objectives Uterine fibroids are benign tumors that develop in many women of reproductive age. Surgery is the main approach to treatment while other options are also associated with adverse effects. Studies have shown that certain bioactive agents present in medicinal plants elicit their anti-tumor activity by induction of mitochondrial permeability transition (mPT) opening. This research therefore aimed at investigating the effect of methanol extract of Annona muricata (MEAM) on mPT pore opening in normal and monosodium glutamate-induced uterine hyperplasia using female Wistar rats. Methods Mitochondria, isolated from rat liver were exposed to different concentrations (20, 60, 100, 140 and 180 μg/mL) of MEAM. The mPT pore opening, cytochrome c release, mitochondrial ATPase (mATPase) activity and the percentage lipid peroxidation were assessed spectrophotometrically. Histological effects of MEAM on the liver, brain and uterus of normal and MSG-treated rats were investigated. Results The in vitro results showed a significant induction of mPT pore opening by 2.4, 4.2 and 6.4 folds, release of cytochrome c and enhancement of mATPase activity at 100,140 and 180 μg/mL, respectively. However, oral administration of MEAM did not induce mPT pore opening, neither any significant release of cytochrome c nor enhancement of mATPase activity at all the dosages used. However, histological assay revealed the presence of MSG-induced cellular damage and uterine hyperplasia which was ameliorated by MEAM co-administration. Conclusions These findings suggest that MEAM contains phytochemicals that can ameliorate MSG-induced damage and uterine hyperplasia in rats; however, the mechanism might not be via upregulation of mitochondrial-mediated apoptosis.

Sulforaphane Attenuates Isoproterenol-Induced Myocardial Injury in Mice

The development of isoproterenol- (ISO-) induced oxidative stress in the myocardium results in myocardial necrosis. Sulforaphane (SFN-0.4% of sulforaphane from standardized broccoli sprout extract) possesses chemoprotective, antidiabetic, and antibacterial activities and is also active against cardiovascular-related problems due to its antioxidant properties. This study was designed to investigate the cardioprotective effect of SFN against isoproterenol-induced myocardial injury in mice. Healthy male Swiss albino mice weighing 20–30 g were used in this study. These mice were randomly divided into five groups ( n = 6 ). All the mice in the experimental groups received isoproterenol (5 mg/kg bw, via i.p.) consecutively for 2 days. The mice were treated with SFN (4 mg/kg bw) and α-tocopherol (TCF) (10 mg/kg bw) by oral gavage for 1-7 days as pre- and posttreatment for the prophylactic and treatment groups, respectively. On day 10, the following parameters were studied: heart weight to body weight ratio, antioxidant parameters, and cardiac markers; and mitochondrial enzymes were estimated for cardioprotection. Administration of isoproterenol in mice showed an increased level of serum cardiac markers and heart mitochondrial ATPase enzymes. An increased level of myocardial thiobarbituric acid-reactive substance and decreased levels of endogenous antioxidant enzymes indicated that oxidative stress is induced by isoproterenol in the myocardium. The administration of SFN in mice restored the levels of all biochemical parameters to near-normal levels. Histopathological studies further confirmed the protective effect of sulforaphane. This study concluded that treatment with SFN boosts the endogenous antioxidant activity and prevents isoproterenol-induced myocardial injury.