Cytochrome c oxidase

We report an unusual case of encephalo-entero-myopathy associated with the A8344G mutation in the tRNA(Lys) gene of mitochondrial DNA (mtDNA). This patient had mitochondrial myopathy, multiple lipomatosis, mild hearing loss, stroke-like episodes, and paralytic ileus, but she lacked the canonical clinical features of MERRF, myoclonus, epilepsy, or ataxia. We conducted genetic, biochemical, histochemical, and immunohistochemical studies in skeletal muscle, brain, intestine, and lipoma tissue. The mutation was abundant in all tissues, and cytochrome c oxidase (COX) activity was selectively decreased in brain and small intestine. COX deficiency was also documented histochemically and immunohistochemically in the small intestine, suggesting that mitochondrial dysfunction played a role in the pathogenesis of paralytic ileus. This case illustrates an unusual and dramatic clinical phenotype of the A8344G mutation, characterized by stroke-like episodes and acute ileus.

The fern genus Dryopteris (Dryopteridaceae) is represented in the Hawaiian Islands by 18 endemic taxa and one non-endemic, native species. The goals of this study were to determine whether Dryopteris in Hawai’i is monophyletic and to infer the biogeographical origins of Hawaiian Dryopteris by determining the geographical distributions of their closest living relatives. We sequenced two chloroplast DNA fragments, rbcL and the trnL-F intergenic spacer (IGS), for 18 Hawaiian taxa, 45 non-Hawaiian taxa, and two outgroup species. For individual fragments, we estimated phylogenetic relationships using Bayesian inference and maximum parsimony. We performed a combined analysis of both cpDNA fragments employing Bayesian inference, maximum parsimony, and maximum likelihood. These analyses indicate that Hawaiian Dryopteris is not monophyletic, and that there were at least five separate colonizations of the Hawaiian Islands by different species of dryopteroid ferns, with most of the five groups having closest relatives in SE Asia. The results suggest that one colonizing ancestor, perhaps from SE Asia, gave rise to eight endemic taxa (the glabra group). Another colonizing ancestor, also possibly from SE Asia, gave rise to a group of five endemic taxa (the exindusiate group). Dryopteris fusco-atra and its two varieties, which are endemic to Hawai’i, most likely diversified from a SE Asian ancestor. The Hawaiian endemic Nothoperanema rubiginosum has its closest relatives in SE Asia, and while the remaining two species, D. wallichiana and D. subbipinnata, are sister species, their biogeographical origins could not be determined from these analyses due to the widespread distributions of D. wallichiana and its closest non-Hawaiian relative.

Hemileia vastatrix is a biotrophic fungus, causing coffee leaf rust in all coffee growing countries, leading to serious social and economic problems. Gene expression studies may have a key role unravelling the transcriptomics of this pathogen during interaction with the plant host. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is currently the golden standard for gene expression analysis, although an accurate normalisation is essential for adequate conclusions. Reference genes are often used for this purpose, but the stability of their expression levels requires validation under experimental conditions. Moreover, pathogenic fungi undergo important biomass variations along their infection process in planta, which raises the need for an adequate method to further normalise the proportion of fungal cDNA in the total plant and fungus cDNA pool. In this work, the expression profiles of seven reference genes [glyceraldehyde-3-phosphate dehydrogenase (GADPH), elongation factor (EF-1), Beta tubulin (β-tubulin), cytochrome c oxidase subunit III (Cyt III), cytochrome b (Cyt b), Hv00099, and 40S ribosomal protein (40S_Rib)] were analysed across 28 samples, obtained in vitro (germinated uredospores and appressoria) and in planta (post-penetration fungal growth phases). Gene stability was assessed using the statistical algorithms incorporated in geNorm and NormFinder tools. Cyt b, 40S_Rib, and Hv00099 were the most stable genes for the in vitro dataset, while 40S_Rib, GADPH, and Cyt III were the most stable in planta. For the combined datasets (in vitro and in planta), 40S_Rib, GADPH, and Hv00099 were selected as the most stable. Subsequent expression analysis for a gene encoding an alpha subunit of a heterotrimeric G-protein showed that the reference genes selected for the combined dataset do not differ significantly from those selected specifically for the in vitro and in planta datasets. Our study provides tools for correct validation of reference genes in obligate biotrophic plant pathogens, as well as the basis for RT-qPCR studies in H. vastatrix.► Reference genes were selected for Hemileia vastatrix in planta RT-qPCR studies. ► Gene stability was assessed using geNorm and NormFinder programmes. ► 40S_Rib, GADPH, and Hv00099 were the most stable reference genes. ► An extra correction step enabled normalisation of fungal biomass in planta.

A total of 300 dragonflies (Odonata) were collected from six different localities of China and Pakistan. Sixty seven representative samples were selected to sequence their mitochondrial cytochrome oxidase subunit I (COI). An examination of the resultant sequences identified 21 different dragonfly species, belonging to 15 distinct genera, two families, Libellulidae and Gomphidae. Sequence alignment was executed using Clustal-W in BioEdit v6. The phylogenetic tree was constructed through Neighbor-joining method by using Jukes-Cantor model, and genetic divergence was calculated via Kimura 2-parameter using MEGA7, while Genetic diversity was calculated by DnaSP v5. The maximum genetic divergence was observed for Crocothemis servilia, at 20.49%, followed by Libellulidae sp. with 22.30% while minimum divergence (0.82%) was observed for Melligomphus ardens. Likewise, a significant genetic diversity was observed for all species. However, Crocothemis servilia species presented maximum value (176 mutations) followed by Libellulidae spp. (150 mutations), whereas minimum value (3 mutations) was observed by Orthetrum testaceum. Interestingly, the diversity of C. servilia, all of which are collected from a single location of China, is much higher than those from Pakistan, which were collected from 5 different places with a spatial distance exceeding 500 Kms. Our results are useful in gaining a full appreciation of the global diversity of dragonflies and the development of conservation measures of this insect.

Hydrobiologia 471: 149–155, 2002. L. Watling & M. Risk (eds), Biology of Cold Water Corals. © 2002 Kluwer Academic Publishers. Printed in the Netherlands. ... DNA sequences of the mitochondrial COI gene have low levels of divergence among deep-sea octocorals ( ...

After a brief review of the hybrid QM/MM molecular dynamics scheme and its coupling to the metadynamics method, I will show how such a combination of computational tools can be used to study chemical reactions of general biological interest. Specifically, by using such a reactive hybrid paradigm, where the QMdriver is a Car–Parrinello Lagrangian dynamics, we have inspected the ATP hydrolysis reaction in the anti-freezing protein known as heat shock cognate protein (Hsc70) and the unconventional propagation of protons across peptide groups in the H-path of the bovine cytochrome c oxidase. While the former represents a fundamental reaction operated by all living beings in a wealth of processes and functions, the second one is involved in cell respiration. For both systems accurate X-ray data are available, yet the actual reaction mechanism escapes experimental probes. The simulations presented here provide the complementary information missing in experiments, offer a direct insight into the reaction mechanisms at a molecular level, and allow to understand which pathways nature can follow to realize these processes fundamental to living organisms.