Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation.

Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies of mtDNA per cell, and their integrity, are maintained by nuclear-encoded mtDNA replication and repair machineries. Aberrant mtDNA replication and mtDNA breakage are believed to cause deletions within mtDNA. The genomic location and breakpoint sequences of these deletions show similar patterns across various inherited and acquired diseases, and are also observed during normal ageing, suggesting a common mechanism of deletion formation. However, an ongoing debate over the mechanism by which mtDNA replicates has made it difficult to develop clear and testable models for how mtDNA rearrangements arise and propagate at a molecular and cellular level. These deletions may impair energy metabolism if present in a high proportion of the mtDNA copies within the cell, and can be seen in primary mitochondrial diseases, either in sporadic cases or caused by autosomal variants in nuclear-encoded mtDNA maintenance genes. These mitochondrial diseases have diverse genetic causes and multiple modes of inheritance, and show notoriously broad clinical heterogeneity with complex tissue specificities, which further makes establishing genotype-phenotype relationships challenging. In this review, we aim to cover our current understanding of how the human mitochondrial genome is replicated, the mechanisms by which mtDNA replication and repair can lead to mtDNA instability in the form of large-scale rearrangements, how rearranged mtDNAs subsequently accumulate within cells, and the pathological consequences when this occurs.

The good, the bad and the ugly of transposable elements annotation tools.

Transposable elements are repetitive and mobile DNA segments that can be found in virtually all organisms investigated to date. Their complex structure and variable nature are particularly challenging from the genomic annotation point of view. Many softwares have been developed to automate and facilitate TEs annotation at the genomic level, but they are highly heterogeneous regarding documentation, usability and methods. In this review, we revisited the existing software for TE genomic annotation, concentrating on the most often used ones, the methodologies they apply, and usability. Building on the state of the art of TE annotation software we propose best practices and highlight the strengths and weaknesses from the available solutions.

Interactions of mitochondrial and skeletal muscle biology in mitochondrial myopathy.

Mitochondrial dysfunction in skeletal muscle fibres occurs with both healthy aging and a range of neuromuscular diseases. The impact of mitochondrial dysfunction in skeletal muscle and the way muscle fibres adapt to this dysfunction is important to understand disease mechanisms and to develop therapeutic interventions. Furthermore, interactions between mitochondrial dysfunction and skeletal muscle biology, in mitochondrial myopathy, likely have important implications for normal muscle function and physiology. In this review, we will try to give an overview of what is known to date about these interactions including metabolic remodelling, mitochondrial morphology, mitochondrial turnover, cellular processes and muscle cell structure and function. Each of these topics is at a different stage of understanding, with some being well researched and understood, and others in their infancy. Furthermore, some of what we know comes from disease models. Whilst some findings are confirmed in humans, where this is not yet the case, we must be cautious in interpreting findings in the context of human muscle and disease. Here, our goal is to discuss what is known, highlight what is unknown and give a perspective on the future direction of research in this area.

Complications after total ankle arthroplasty- A systematic review.

BACKGROUND: Total ankle arthroplasty was developed as an alternative option to ankle arthrodesis in patients with end-stage ankle osteoarthritis. Multiple trials have assessed the outcomes of ankle arthroplasty, but complication risk or relative effectiveness is not systematized in literature. AIM: Review complications of new designs of total ankle arthroplasty and the relationship between their severity and failure rates. METHODS: We reviewed complications and revision rates of prospective studies of primary total ankle arthroplasty that included more than 50 patients and with minimum 2 years follow-up. RESULTS: We included 22 studies (4412 ankles, median age of 61.9 years) with an adjusted mean follow-up time of 66.6 ± 40.9 months. The adjusted mean complication rate was 23.7 % (2.4-52 %), mostly high-grade complications (35.6 %). We found a statistically significant positive correlation between high- and medium-grade complications and revision rates. CONCLUSION: Patient selection is crucial to successfully treat end-stage ankle osteoarthritis. Further multicenter clinical trials with consistent reporting of complications are warranted.

Refractory esophagitis caused by Candida nivariensis: second description of this yeast in Brazil and a literature review.

Candida nivariensis caused refractory esophagitis in a 36-year-old Brazilian man coinfected with HIV and Leishmania. A literature review on this rare fungal pathogen is also presented. The diagnosis was made, and pathogen identification was performed using matrix-assisted laser desorption ionization-time of flight mass spectrometry and sequencing of the LSU/26S region. An antifungigram was performed using broth microdilution. A literature search of PubMed was performed. The causative agent, C. nivariensis, was resistant to fluconazole and voriconazole. The patient's condition worsened considerably, and he passed away. This is the second report of this Candida species in Brazil and the first case reported worldwide of refractory esophagitis in a patient coinfected with HIV and Leishmania. The case illustrates the importance of precise identification and antifungal susceptibility testing when isolating this emerging pathogen.

Multiple long-range host shifts of major Wolbachia supergroups infecting arthropods.

Wolbachia is a genus of intracellular bacterial endosymbionts found in 20-66% of all insect species and a range of other invertebrates. It is classified as a single species, Wolbachia pipientis, divided into supergroups A to U, with supergroups A and B infecting arthropods exclusively. Wolbachia is transmitted mainly via vertical transmission through female oocytes, but can also be transmitted across different taxa by host shift (HS): the direct transmission of Wolbachia cells between organisms without involving vertically transmitted gametic cells. To assess the HS contribution, we recovered 50 orthologous genes from over 1000 Wolbachia genomes, reconstructed their phylogeny and calculated gene similarity. Of 15 supergroup A Wolbachia lineages, 10 have similarities ranging from 95 to 99.9%, while their hosts' similarities are around 60 to 80%. For supergroup B, four out of eight lineages, which infect diverse and distantly-related organisms such as Acari, Hemiptera and Diptera, showed similarities from 93 to 97%. These results show that Wolbachia genomes have a much higher similarity when compared to their hosts' genes, which is a major indicator of HS. Our comparative genomic analysis suggests that, at least for supergroups A and B, HS is more frequent than expected, occurring even between distantly-related species.

Osteosynthesis or primary arthrodesis for displaced intra-articular calcaneus fractures Sanders type IV - A systematic review.

BACKGROUND: Displaced intra-articular calcaneus fractures (DIACF) Sanders type IV represent a challenge in its management and questions remain about the best treatment option available. This study aimed to compare the outcomes of primary subtalar arthrodesis (PSTA) and osteosynthesis in these fractures. METHODS: Studies concerning DIACF Sanders type IV, from 2005 to 2020 were systematically reviewed. Only studies evaluating functional outcomes with American Orthopaedic Foot & Ankle Society ankle-hindfoot (AOFAS) score were admitted allowing for results comparison. RESULTS: In total, 9 studies met the inclusion criteria. These reported on the results of 142 patients, from which 41 submitted to PSTA and 101 to osteosynthesis, with an average follow-up period over 2 years. We found a significant moderate negative correlation between the reported AOFAS score and the Coleman Methodology Score obtained. Late subtalar arthrodesis was 13.63% of the total osteosynthesis performed. CONCLUSIONS: Clinical outcomes after PSTA and osteosynthesis, for the treatment of Sanders type IV fractures, do not seem very different, yet careful data interpretation is crucial. Additional powered randomized controlled trials are necessary to assess which surgical strategy is better.

Mitochondrial DNA disorders: from pathogenic variants to preventing transmission.

Mitochondrial DNA (mtDNA) disorders are recognized as one of the most common causes of inherited metabolic disorders. The mitochondrial genome occurs in multiple copies resulting in both homoplasmic and heteroplasmic pathogenic mtDNA variants. A biochemical defect arises when the pathogenic variant level reaches a threshold, which differs between variants. Moreover, variants can segregate, clonally expand, or be lost from cellular populations resulting in a dynamic and tissue-specific mosaic pattern of oxidative deficiency. MtDNA is maternally inherited but transmission patterns of heteroplasmic pathogenic variants are complex. During oogenesis, a mitochondrial bottleneck results in offspring with widely differing variant levels to their mother, whilst highly deleterious variants, such as deletions, are not transmitted. Complemented by a complex interplay between mitochondrial and nuclear genomes, these peculiar genetics produce marked phenotypic variation, posing challenges to the diagnosis and clinical management of patients. Novel therapeutic compounds and several genetic therapies are currently under investigation, but proven disease-modifying therapies remain elusive. Women who carry pathogenic mtDNA variants require bespoke genetic counselling to determine their reproductive options. Recent advances in in vitro fertilization techniques, have greatly improved reproductive choices, but are not without their challenges. Since the first pathogenic mtDNA variants were identified over 30 years ago, there has been remarkable progress in our understanding of these diseases. However, many questions remain unanswered and future studies are required to investigate the mechanisms of disease progression and to identify new disease-specific therapeutic targets.

The rearranged mitochondrial genome of Leptopilina boulardi (Hymenoptera: Figitidae), a parasitoid wasp of Drosophila.

The partial mitochondrial genome sequence of Leptopilina boulardi (Hymenoptera: Figitidae) was characterized. Illumina sequencing was used yielding 35,999,679 reads, from which 102,482 were utilized in the assembly. The length of the sequenced region of this partial mitochondrial genome is 15,417 bp, consisting of 13 protein-coding, two rRNA, and 21tRNA genes (the trnaM failed to be sequenced) and a partial A+T-rich region. All protein-coding genes start with ATN codons. Eleven protein-coding genes presented TAA stop codons, whereas ND6 and COII that presented TA, and T nucleotides, respectively. The gene pattern revealed extensive rearrangements compared to the typical pattern generally observed in insects. These rearrangements involve two protein-coding and two ribosomal genes, along with the 16 tRNA genes. This gene order is different from the pattern described for Ibalia leucospoides (Ibaliidae, Cynipoidea), suggesting that this particular gene order can be variable among Cynipoidea superfamily members. A maximum likelihood phylogenetic analysis of the main groups of Apocrita was performed using amino acid sequence of 13 protein-coding genes, showing monophyly for the Cynipoidea superfamily within the Hymenoptera phylogeny.