The role of mitochondrial DNA mutation on neurodegenerative diseases

Many researchers have reported that oxidative damage to mitochondrial DNA (mtDNA) is increased in several age-related disorders. Damage to mitochondrial constituents and mtDNA can generate additional mitochondrial dysfunction that may result in greater reactive oxygen species production, triggering a circular chain of events. However, the mechanisms underlying this vicious cycle have yet to be fully investigated. In this review, we summarize the relationship of oxidative stress-induced mitochondrial dysfunction with mtDNA mutation in neurodegenerative disorders.     

Nuclear integrations of mitochondrial DNA in primates: inference of associated mutational events

To infer the possible mutational events taking place along the interorganellar transfer of genetic material from mitochondria to the nucleus, four integrations of mitochondrial DNA (mtDNA) in the human genome were characterized together with their flanking nuclear sequences. By determining their presence/absence status in different primate species, these integrations were inferred to have occurred on the lineages leading to catarrhines (Old World monkeys and hominoids), to hominoids and to humans, respectively. In case of a polymorphic state, with respect to its presence in a certain species, each preintegration sequence was either cloned in the same species or in a primate taxon that branched off before the transfer of the mtDNA to the nucleus took place. For the four mtDNA integrations presented here, random mobilization of the mtDNA and differing mechanisms for generating free ends in the nuclear target sequences can be inferred. Additionally, no common sequence features at the preintegration sites could be observed for these integrations. Moreover, the comparisons of the sites before and after integration suggest different ways of integration. Thus, mtDNA integrations represent unique molecular recombinations in the evolutionary history and can, according to their presence/absence status in different species, help to determine the branching order in phylogenetic trees.     

Differential mitochondrial protein expression profiling in neurodegenerative diseases

Alterations in mitochondrial structure or function have been described in a variety of human diseases for nearly half a century. The complete sequence of the human mitochondrial genome has been published in 1981. The mitochondrial proteome database however, is still incomplete. Here I give a short review on recent advances to determine the complete set of mitochondrial proteins. The main emphasis is put on gel-based proteomic approaches to identify differentially expressed mitochondrial proteins in neurodegenerative diseases.     

Phantom mutation hotspots in human mitochondrial DNA

Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30 000 published hypervariable segment I sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.     

Automated amplification and sequencing of human mitochondrial DNA

Part of the human mitochondrial D-loop region was amplified by two successive rounds of polymerase chain reaction (PCR) amplification. In the second PCR reaction, nested primers were used, of which one contained the M13-21 universal primer sequence. By using nonequal concentrations of primers in the second amplification, single-stranded DNA was generated. This was then sequenced directly by the diodeoxy chain termination method using dye-labelled universal sequencing primers in conjunction with a fluorescence-based DNA sequencer. This enabled a 403-base-pair hypervariable segment of the D-loop region to be readily sequenced in a single reaction. This paper describes a protocol which enables mitochondrial sequence information to be generated rapidly and automatically. It is likely to be of importance in forensic analysis where the DNA is too degraded or of insufficient quantity to be analysed by other techniques.     

Mutational analysis of whole mitochondrial DNA in patients with MELAS and MERRF diseases

Mitochondrial diseases are clinically and genetically heterogeneous disorders, which make the exact diagnosis and classification difficult. The purpose of this study was to identify pathogenic mtDNA mutations in 61 Korean unrelated families (or isolated patients) with MELAS or MERRF. In particular, the mtDNA sequences were completely determined for 49 patients. From the mutational analysis of mtDNA obtained from blood, 5 confirmed pathogenic mutations were identified in 17 families, and 4 unreported pathogenically suspected mutations were identified in 4 families. The m.3243A>G in the tRNA^Leu(UUR) was predominantly observed in 10 MELAS families, and followed by m.8344A>G in the tRNA^Lys of 4 MERRF families. Most pathogenic mutations showed heteroplasmy, and the rates were considerably different within the familial members. Patients with a higher rate of mutations showed a tendency of having more severe clinical phenotypes, but not in all cases. This study will be helpful for the molecular diagnosis of mitochondrial diseases, as well as establishment of mtDNA database in Koreans.     

Microchip electrophoresis of Alu elements for gender determination and inference of human ethnic origin

We performed a series of multi‐locus PCRs followed by the rapid and efficient microchip electrophoretic sorting of Alu products with LIF detection. Five polymorphic human‐specific Alu insertions (RC5, A1, PV92, TPA and ACE) were used for inference of human ethnicity and two monomorphic Alu insertions for sex typing, one fixed on the X chromosome (AluSTXa) and the other on the Y chromosome (AluSTYa). These markers were used to generate unique DNA profiles for five different DNA samples. The PCR‐based assays used primers that flank the insertion point to determine genotypes based on the presence or absence of the Alu element. A1, RC5, PV92, TPA and ACE were used for ethnicity determinations and have two alleles, each indicating the presence (+) or absence (?) of the Alu element on the paired chromosomes, which results in three genotypes (+/+, +/? or ?/?). RC5 and A1 did not show ethnic heterogeneity resulting in a homozygous (?/?) genotype, which correctly inferred that DNA samples originating from a Caucasian male and an Asian male were not of African ancestry. The results from the five Alu markers indicated that these Alu loci could assist in identifying the individual's ethnicity using microchip electrophoresis in under 15 min of separation time. Using microchip electrophoresis and mixed genotype ratios, male DNA‐to‐female DNA of 1:9, corresponding to a ratio of Y‐to‐X chromosomes of 1:19, was also detected for both AluSTXa and AluSTYa to provide gender identification without requiring separation of female from male cells prior to the assay.     

Spectroscopic inference on the structure of liquid ammonia

IR and Raman spectral data of liquid NH₃ and ND₂H are analysed. Spectroscopic evidence is in favour of extensive hydrogen bonding in the liquid. The number, frequencies and intensities of the transitions in the 3200–3500 cm^?1 region can be explained if cyclic dimers are the major species present in liquid NH₃. This hypothesis is compatible with the low viscosity and low boiling point of liquid NH₃.     

Molecular mechanisms of polypeptide aggregation in human diseases

Protein aggregation is implicated in a plethora of neurodegenerative diseases. The proteins found to aggregate in these diseases are unrelated in their native structures and amino acid sequences, but form similar insoluble fibrils with characteristic cross-beta sheet morphologies called amyloid in the aggregated state. While both the mechanism of aggregation and the structure of the aggregates are not fully understood at the molecular level, recent studies provide strong support for the idea that protein aggregation into highly stable, insoluble amyloid structures is a general property of the polypeptide chain. For proteins with a unique native state, it is known that aggregation occurs under conditions that promote native-state destabilization in vitro and in vivo. Taken together, the results of several important recent investigations suggest three broad molecular frameworks that may underlie the conversion of normally soluble peptides and proteins into insoluble amyloid fibrils: (1) edge-strand hydrogen bonding, (2) domain-swapping, and (3) self-association of amyloidogenic fragments. We argue that these underlying scenarios are not mutually exclusive and may be protein-dependent - i.e., a protein with a high content of hinge-regions may aggregate via a runaway domain-swap, whereas a protein with a high content of amyloidogenic fragments may aggregate primarily by the self-association of these fragments. These different scenarios provide frameworks to understand the molecular mechanism of polypeptide aggregation.     

The application of thermoanalytical methods in studies on the pathomechanism of human diseases

This mini-review attempts to give a short summary of the application of temperature-dependent techniques in bio-medical research. Results obtained by thermal analysis provide valuable support to scientific theories on various human pathophysiological processes as well as to several therapeutic approaches. Special attention is focussed on cardiovascular disease, since of approx. 11 million deaths occurring per annum in developed countries more than 3.9 million were due to this disease, as recorded by WHO. Recent research on the pathogenesis of atherosclerosis has concentrated on the physico-chemical nature of the arteries and on the roles of serum lipoproteins and defects in cellular metabolism of cholesterol. An understanding of the physical and chemical nature of lipids accumulated in the arterial wall may help explain how it gets into the artery and how it can be removed. Smectic cholesteryl-ester phases had been observed in a number of fatty streaks and advanced atherosclerotic lesions within the arteries. These phases have physical characteristics that can be identified with the polarizing or electron microscope, by calorimetry, by NMR spectrometry or by X-ray diffraction.

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Zusammenfassung Es wird versucht, einen kurzen überblick über die Anwendung temperaturabhängiger Techniken in der biomedizinischen Forschung zu geben. Thermoanalyti-sche Ergebnisse bieten eine wertvollen Beitrag für wissenschaftliche Theorien zu verschiedenen pathophysiologischen Vorgängen beim Menschen als auch für verschiedene therapeutische Methoden. Besondere Aufmerksamkeit wird Herzkreislaufkrankheiten geschenkt, da laut WHO-Berichten von den jährlich etwa 11 Millionen Todesfällen in den hochentwickelten Ländern mehr als 3,9 Millionen auf diese Krankheiten zurückzuführen sind. Die jüngste Forschung auf dem Gebiete der Pathogenese von Atherosklerose konzentrierte sich auf die physikalisch-chemische Natur der Arterien sowie auf die Rolle von Serumlipoproteinen und Defekte im Zellmetabolismus von Cholesterol. Eine eingehende Untersuchung der physikalischen und chemischen Natur von den in der Arterienwand angehäuften Lipiden kann helfen zu erklären, wie diese in die Arterie gelangen und wie sie von dort entfernt werden können. In einer Anzahl von fettigen Bändern und krankhaften atherosklerotischen Veränderungen im fortgeschrittenen Stadium in den Arterien wurden smektische Cholesterylesterphasen beobachtet. Diese Phasen besitzen physikalische Eigenschaften, die mittels Polarisations- oder Elektronenmikroskop, Kalorimetrie, NMR-Spektroskopie und Röntgendiffraktion identifiziert werden können.

     

Baicalin induces apoptosis in human osteosarcoma cell through ROS-mediated mitochondrial pathway

Baicalin is extracted from a traditional Chinese herb, Scutellaria baicalensis. In this study, the anticancer activity and underlying mechanisms of baicalin towards human osteosarcoma cell (HOS) were investigated. Baicalin could inhibit HOS cell proliferation in a concentration-dependent manner. Mitochondrial membrane potential decreased obviously after treated with different concentration of baicalin by flow cytometry assay and revealed that baicalin triggered a significant generation of reactive oxygen species (ROS). Western blotting assay further revealed that baicalin-induced cell apoptosis by suppressing Bcl-2 level, then activating caspase-9 and caspase-3. In vivo experiment, baicalin significantly suppressed tumour growth in female BALB/C nude mice bearing HOS tumours. In addition, baicalin did show toxicity to treated animal by comparing the body weight increase and mortality. In general, the present results demonstrated that baicalin-induced apoptosis in human osteosarcoma cell via a ROS-mediated mitochondrial pathway. The paper indicated that baicalin is a promising candidate for the treatment of HOS.     

Chelating agents for human diseases related to aluminium overload

The aim of this review is to give a general view on the current status of the role of aluminium in human health and disease. The main aspects of aluminium metabolism in humans are covered, summarizing the state of knowledge on the absorption, distribution, retention and excretion of aluminium, giving particular emphasis to the main metabolic pathways of this metal ion in different organs. Then the pathological consequences of aluminium overload in man, its role in neurodegenerative diseases and the emerging implication of this metal ions in different pathologies are treated. Finally, the function of different chelators utilized in clinical practice in the therapy of aluminium depending diseases is discussed and the latest studies on aluminium chelators are presented. Some emphasis is given to the parallelism between iron and aluminium chelators, and in particular interesting correlations between structural parameters of these two trivalent metal ions are presented.     

Extremely high levels of human mitochondrial DNA heteroplasmy in single hair roots

For many years it has been assumed that the vast majority of mitochondrial genomes of a single individual are identical, both in the same tissue and within different tissues. Incidences of heteroplasmy (i.e., the occurrence of two or more codominating types of molecules within the mitochondrial DNA population of the same individual) were thought to be extremely rare. This study strongly supports the thesis that heteroplasmy is a principle, rather than an exception, in mitochondrial DNA genetics. During direct sequencing of the first hypervariable segment of the human mitochondrial control region (HV1) in 100 single hair roots obtained from 35 individuals, 24 different heteroplasmic positions were identified. Unusually high levels of heteroplasmy (up to six positions in the HV1 region) were encountered in two individuals. Two individuals related in maternal lineage shared the same heteroplasmic positions. Moreover, highly variable levels of heteroplasmy were observed even among roots from the same individual. The most probable mechanisms involved in generating so many mismatches are mutations occurring presumably in the female germline, followed by differential segregation of mitotypes during the development of individual hairs. Generally, heteroplasmy complicates sequence comparisons in mitochondrial DNA testing performed for forensic purposes, but in some cases it can substantially increase the discriminating power of the analysis.     

Tomatidine-stimulated maturation of human embryonic stem cell-derived cardiomyocytes for modeling mitochondrial dysfunction

Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) have been reported to exhibit immature embryonic or fetal cardiomyocyte-like phenotypes. To enhance the maturation of hESC-CMs, we identified a natural steroidal alkaloid, tomatidine, as a new substance that stimulates the maturation of hESC-CMs. Treatment of human embryonic stem cells with tomatidine during cardiomyocyte differentiation stimulated the expression of several cardiomyocyte-specific markers and increased the density of T-tubules. Furthermore, tomatidine treatment augmented the number and size of mitochondria and enhanced the formation of mitochondrial lamellar cristae. Tomatidine treatment stimulated mitochondrial functions, including mitochondrial membrane potential, oxidative phosphorylation, and ATP production, in hESC-CMs. Tomatidine-treated hESC-CMs were more sensitive to doxorubicin-induced cardiotoxicity than the control cells. In conclusion, the present study suggests that tomatidine promotes the differentiation of stem cells to adult cardiomyocytes by accelerating mitochondrial biogenesis and maturation and that tomatidine-treated mature hESC-CMs can be used for cardiotoxicity screening and cardiac disease modeling.Subject terms: Heart failure, Embryonic stem cells, Stem-cell differentiation     

Multiphoton imaging of actin filament formation and mitochondrial energetics of human ACBT gliomas

We studied the three-dimensional (3D) distribution of actin filaments and mitochondria in relation to ACBT glioblastoma cells migration. We embedded the cells in the spheroid form within collagen hydrogels and imaged them by in situ multiphoton microscopy (MPM). The static 3D overlay of the distribution of actin filaments and mitochondria provided a greater understanding of cell-to-cell and cell-to-substrate interactions and morphology. While imaging mitochondria to obtain ratiometric redox index based on cellular fluorescence from reduced nicotinamide adenine dinucleotide and oxidized flavin adenine dinucleotide we observed differential sensitivity of the migrating ACBT glioblastoma cells to femtosecond laser irradiation employed in MPM. We imaged actin-green fluorescent protein fluorescence in live ACBT glioma cells and for the first time observed dynamic modulation of the pools of actin during migration in 3D. The MPM imaging, which probes cells directly within the 3D cancer models, could potentially aid in working out a link between the functional performance of mitochondria, actin distribution and cancer invasiveness.     

Gas chromatography — mass spectrometry in diagnosis of human metabolic diseases

Many human diseases result in characteristic changes in the biochemical composition of the cells and body fluids. Gas chromatography-mass spectrometry (GC-MS) and computer handling of the data are suitable for detecting such changes, e.g. the production of abnormal metabolites in a patient. The methods can be used to diagnose and study about 100 different metabolic disorders and have resulted in the discovery of 30 new inborn errors of metabolism.     

Signals in asbestos related diseases in human breath - preliminary results

Several diseases occur due to asbestos exposure. Until today, asbestos predicted mortality and morbidity will increase because of the long latency period. Actually, the methods to investigate asbestos related disease are mostly invasive. Therefore, the aim of the present paper was to investigate, whether signals in human breath could be correlated to Asbestos related lung diseases using a multi-capillary column (MCC) connected to an ion mobility spectrometer (IMS) as non-invasive method. Here, the breath samples of 10 mL of 25 patients suffering from asbestos related diseases. This group includes patients with asbestos related pleural thickening with and without pulmonary fibrosis. Twelve healthy persons constitute the control group and the breath samples are compared with those of the BK4103 patients. In total 83 peaks are found in the IMS-Chromatogram. A discrimination was possible with p-values <0.001 for two peaks (99.9 %), <0.01 (99 %) for 5 peaks and <0.05 (95 %) for 17 peaks. The most discrimination peaks alpha pinene and 4-ethyltoluol were identified among some others with lower p-values. The corresponding Box-and-Whisker-Plots comparing both groups are presented. In addition, a decision tree including all peaks was created that shows a differentiation with alpha pinene between BK4103 (pleural plaques group) and the control group. In addition, the sensitivity was calculated to 96 %, specificity was 50 %, positive and negative predictive values were 80 % and 86 %. Ion mobility spectrometry was introduced as non-invasive method to separate both groups Asbestos related and healthy. Naturally, the findings need further confirmation on larger population groups, but encourage further investigations, too.     

BagReg: Protein inference through machine learning

Protein inference from the identified peptides is of primary importance in the shotgun proteomics. The target of protein inference is to identify whether each candidate protein is truly present in the sample. To date, many computational methods have been proposed to solve this problem. However, there is still no method that can fully utilize the information hidden in the input data.In this article, we propose a learning-based method named BagReg for protein inference. The method firstly artificially extracts five features from the input data, and then chooses each feature as the class feature to separately build models to predict the presence probabilities of proteins. Finally, the weak results from five prediction models are aggregated to obtain the final result. We test our method on six public available data sets. The experimental results show that our method is superior to the state-of-the-art protein inference algorithms.