D-loop mutations in mitochondrial DNA: link with mitochondrial DNA depletion?

Clinical presentation of the patients with mitochondrial DNA depletion is quite diverse and is suggestive of genetic heterogeneity. Autosomal recessive inheritance of the disease appears likely, thus implying the nuclear origin of the disease. This has been demonstrated recently in large families with neonatal presentation of the disease. Here, we report upon a family with one child having a late-onset disease associated with severe mitochondrial DNA depletion. The presence of mitochondrial alterations in the muscle of the patient's mother prompted us to extensively analyse the mitochondrial DNA in the family. We found mitochondrial DNA multiple deletions, but also three heteroplasmic point mutations of the D-loop region, two of which (T119C and T408A) affect conserved regions involved in the mtDNA replication process. These mutations were non-randomly distributed in the maternal lineage and, for one of them, among single muscle fibres. Involvement of the mitochondrial DNA in its own depletion appears therefore possible. It may act in close relationship with a hypothetical modified nuclear factor.     

Recombination in human mitochondrial DNA?

The possibility of recombination in human mitochondrial DNA (mtDNA) has been hotly debated over the last few years. In this study, a general model of recombination in circular molecules is developed and applied to a recently published African sample (n = 21) of complete mtDNA sequences. It is shown that the power of correlation measures to detect recombination in circular molecules can be vanishingly small and that the data are consistent with the given model and no recombination only if the overall heterogeneity in mutation rate is <0.09.     

Are traits that experience reinforcement also under sexual selection?

Where closely related species occur in sympatry, reinforcement may result in the evolution of traits involved in species recognition that are at the same time used for within-species mate choice. Drosophila serrata lives in forested habitat on the east coast of Australia, and over the northern half of its distribution it coexists with a closely related species, Drosophila birchii. Here we show that the strength of reinforcing selection in natural populations is sufficient to generate reproductive character displacement along a 36-km transect across the contact between sympatric and allopatric populations of D. serrata. The sympatric and allopatric populations display genetically based differences in male cuticular hydrocarbons (CHCs), while female CHCs changed with latitude across the contact. The directional changes observed in male CHCs between sympatric and allopatric regions were the same changes that were generated by experimental sympatry in the laboratory, providing direct evidence that the changes across the contact zone are due to the presence of D. birchii. We show that sympatric and allopatric females differ in preference for male CHCs and that females from allopatric populations prefer allopatric-like male CHCs over sympatric-like CHCs. Male attractiveness within D. serrata may therefore be compromised by reinforcing selection, preventing the spread of sympatric-like blends to the area of allopatry.     

Is mitochondrial DNA content a potential biomarker of mitochondrial dysfunction?

Mitochondrial dysfunction is central to numerous diseases of oxidative stress. Changes in mitochondrial DNA (MtDNA) content, often measured as mitochondrial genome to nuclear genome ratio (Mt/N) using real time quantitative PCR, have been reported in a broad range of human diseases, such as diabetes and its complications, obesity, cancer, HIV complications, and ageing. We propose the hypothesis that MtDNA content in body fluids and tissues could be a biomarker of mitochondrial dysfunction and review the evidence supporting this theory. Increased reactive oxygen species resulting from an external trigger such as hyperglycaemia or increased fat in conditions of oxidative stress could lead to enhanced mitochondrial biogenesis, and increased Mt/N. Altered MtDNA levels may contribute to enhanced oxidative stress and inflammation and could play a pathogenic role in mitochondrial dysfunction and disease. Changes in Mt/N are detectable in circulating cells such as peripheral blood mononuclear cells and these could be used as surrogate to predict global changes in tissues and organs. We review a large number of studies reporting changes in MtDNA levels in body fluids such as circulating blood cells, cell free serum, saliva, sperm, and cerebrospinal fluid as well as in tumour and normal tissue samples. However, the data are often conflicting as the current methodology used to measure Mt/N can give false results because of one or more of the following reasons (1) use of mitochondrial primers which co-amplify nuclear pseudogenes (2) use of nuclear genes which are variable and/or duplicated in numerous locations (3) a dilution bias caused by the differing genome sizes of the mitochondrial and nuclear genome and (4) template preparation protocols which affect the yields of nuclear and mitochondrial genomes. Development of robust and reproducible methodology is needed to test the hypothesis that MtDNA content in body fluids is biomarker of mitochondrial dysfunction.     

Is mitochondrial DNA a strictly neutral marker?

Variation and change in mitochondrial DNA (mtDNA) is often assumed to conform to a constant mutation rate equilibrium neutral model of molecular evolution. Recent evidence, however, indicates that the assumptions underlying this model are frequently violated. The mitochondria) genome may be subject to the same suite of forces known to be acting in the nuclear genome, including hitchhiking and selection, as well as forces that do not affect nuclear variation. Wherever possible, evolutionary studies involving mtDNA should incorporate statistical tests to investigate the forces shaping sequence variation and evolution.     

Does spatial variation in predation pressure modulate selection for aposematism?

It is widely believed that aposematic signals should be conspicuous, but in nature, they vary from highly conspicuous to near cryptic. Current theory, including the honest signal or trade‐off hypotheses of the toxicity–conspicuousness relationship, cannot explain why adequately toxic species vary substantially in their conspicuousness. Through a study of similarly toxic Danainae (Nymphalidae) butterflies and their mimics that vary remarkably in their conspicuousness, we show that the benefits of conspicuousness vary along a gradient of predation pressure. Highly conspicuous butterflies experienced lower avian attack rates when background predation pressure was low, but attack rates increased rapidly as background predation pressure increased. Conversely, the least conspicuous butterflies experienced higher attack rates at low predation pressures, but at high predation pressures, they appeared to benefit from crypsis. Attack rates of intermediately conspicuous butterflies remained moderate and constant along the predation pressure gradient. Mimics had a similar pattern but higher attack rates than their models and mimics tended to imitate the signal of less attacked model species along the predation pressure gradient. Predation pressure modulated signal fitness provides a possible mechanism for the maintenance of variation in conspicuousness of aposematic signals, as well as the initial survival of conspicuous signals in cryptic populations in the process of aposematic signal evolution, and an alternative explanation for the evolutionary gain and loss of mimicry.     

The inheritance of mitochondrial DNA heteroplasmy: random drift, selection or both?

The mammalian mitochondrial genome (mtDNA) is a small double-stranded DNA molecule that is exclusively transmitted down the maternal line. Pathogenic mtDNA mutations are usually heteroplasmic, with a mixture of mutant and wild-type mtDNA within the same organism. A woman harbouring one of these mutations transmits a variable amount of mutant mtDNA to each offspring. This can result in a healthy child or an infant with a devastating and fatal neurological disorder. Understanding the biological basis of this uncertainty is one of the principal challenges facing scientists and clinicians in the field of mitochondrial genetics.     

Are lichens active under snow in continental Antarctica?

Photosynthetic activity, detected as chlorophyll a fluorescence, was measured for lichens under undisturbed snow in continental Antarctica using fibre optics. The fibre optics had been buried by winter snowfall after being put in place the previous year under snow-free conditions. The fibre optics were fixed in place using specially designed holding devices so that the fibre ends were in close proximity to selected lichens. Several temperature and PPFD (photosynthetic photon flux density) sensors were also installed in or close to the lichens. By attaching a chlorophyll a fluorometer to the previously placed fibre optics it proved possible to measure in vivo potential photosynthetic activity of continental Antarctic lichens under undisturbed snow. The snow cover proved to be a very good insulator for the mosses and lichens but, in contrast to the situation reported for the maritime Antarctic, it retained the severe cold of the winter and prevented early warming. Therefore, the lichens and mosses under snow were kept inactive at subzero temperatures for a prolonged time, even though the external ambient air temperatures would have allowed metabolic activity. The results suggest that the major activity period of the lichens was at the time of final disappearance of the snow and lasted about 10-14 days. The activation of lichens under snow by high air humidity appeared to be very variable and species specific. Xanthoria mawsonii was activated at temperatures below -10 degrees C through absorption of water from high air humidity. Physcia dubia showed some activation at temperatures around -5 degrees C but only became fully activated at thallus temperatures of 0 degrees C through liquid water. Candelariella flava stayed inactive until thallus temperatures close to zero indicated that liquid water had become available. Although the snow cover represented the major water supply for the lichens, lichens only became active for a brief time at or close to the time the snow disappeared. The snow did not provide a protected environment, as reported for alpine habitats, but appeared to limit lichen activity. This provides at least one explanation for the observed negative effect of extended snow cover on lichen growth.     

What regulates mitochondrial DNA copy number in animal cells?

The study of the control of mitochondrial DNA copy number spans several decades and has identified many factors involved in the replication of the mitochondrial genome. However, the mechanisms involved in the regulation of this process are still obscure, particularly in animal cells. During the past decade, however, the identification of human diseases associated with drastically reduced levels of mtDNA caused renewed interest in this topic. Here, I will discuss recent work that sheds some light on how animal cells might maintain and control mtDNA levels.     

Finding specific RNA motifs: function in a zeptomole world?

We have developed a new method for estimating the abundance of any modular (piecewise) RNA motif within a longer random region. We have used this method to estimate the size of the active motifs available to modern SELEX experiments (picomoles of unique sequences) and to a plausible RNA World (zeptomoles of unique sequences: 1 zmole = 602 sequences). Unexpectedly, activities such as specific isoleucine binding are almost certainly present in zeptomoles of molecules, and even ribozymes such as self-cleavage motifs may appear (depending on assumptions about the minimal structures). The number of specified nucleotides is not the only important determinant of a motif's rarity: The number of modules into which it is divided, and the details of this division, are also crucial. We propose three maxims for easily isolated motifs: the Maxim of Minimization, the Maxim of Multiplicity, and the Maxim of the Median. These maxims together state that selected motifs should be small and composed of as many separate, equally sized modules as possible. For evenly divided motifs with four modules, the largest accessible activity in picomole scale (1-1000 pmole) pools of length 100 is about 34 nucleotides; while for zeptomole scale (1-1000 zmole) pools it is about 20 specific nucleotides (50% probability of occurrence). This latter figure includes some ribozymes and aptamers. Consequently, an RNA metabolism apparently could have begun with only zeptomoles of RNA molecules.     

Are long corolla tubes in Pedicularis driven by pollinator selection?

The evolution of long corolla tubes has been hypothesized to be driven by long-tongued pollinators.Corolla tubes in Pedicularis species can be longer than 10 cm which may function as flower stalks to increase visual attractiveness to pollinators because these species provide no nectar and are pollinated by bumblebees. The corolla tube length was manipulated(shorter or longer) in two Pedicularis species in field to examine whether longer tubes are more attractive to pollinators and produce more seeds than short tubes. Our results did not support the pollinator attraction hypothesis, leaving the evolution of long tubes in Pedicularis remains mysterious.     

Is there a direct ontogenetic criterion in systematics?

Much recent literature focuses on whether ontogenetic information can be used as a direct criterion for determining the polarity of character trasformations in systematic analysis. This paper reviews the relevant literature and concludes that the ontogenetic criterion is dependent on parsimony rather than the sequence observed during ontogeny. It is not, therefore, based on the discredited arguments of recapitulation. From the perspective of phyologenetic systematics the ontogenetic criterion is a valid means of polarizing character transformations that represents a special case of a broader methodology involving parsimony. The alternative perspective perspective of patttern cladistics holds that polarity should be contained within the data and not imposed upon it. Thus, ontogeny is not required to polarize characters, but ontogenetic information can generate unequivocal character interpretations in terms of the relative generality of related attributes, and in the sense that absence precedes presence. Furthermore, ontogeny is central to systematics, providing empirical evidence of character transformation, information on the whole life cycle and an escape from systematics being teleologically related to phylogenetic inference and the theory of evolution.     

Induction of direct repeat recombination by psoralen–DNA adducts in Saccharomyces cerevisiae: Defects in DNA repair increase gene copy number variation

Psoralen photoreaction produces covalent monoadducts and interstrand crosslinks in DNA. The interstrand DNA crosslinks are complex double strand lesions that require the involvement of multiple pathways for repair. Homologous recombination, which can carry out error-free repair, is a major pathway for crosslink repair; however, some recombination pathways can also produce DNA rearrangements. Psoralen photoreaction-induced recombination in yeast was measured using direct repeat substrates that can detect gene conversions, a form of conservative recombination, as well as deletions and triplications, which generate gene copy number changes. In repair-proficient cells the major products of recombination were gene conversions, along with substantial fractions of deletions. Deficiencies in DNA repair pathways increased non-conservative recombination products. Homologous recombination-deficient rad51, rad54, and rad57 strains had low levels of crosslink-induced recombination, and most products were deletions produced by single strand annealing. Nucleotide excision repair-deficient rad1 and rad2 yeast had increased levels of triplications, and rad1 cells had lower crosslink-induced recombination. Deficiencies in post-replication repair increased crosslink-induced recombination and gene copy number changes. Loss of REV3 function, in the error-prone branch, and of RAD5 and UBC13, in the error-free branch, produced moderate increases in deletions and triplications; rad18 cells, deficient in both post-replication repair sub-pathways, exhibited hyperrecombination, with primarily non-conservative products. Proper functioning of all the DNA repair pathways tested was required to maintain genomic stability and avoid gene copy number variation in response to interstrand crosslinks.     

Are there lessons from negative results in studies using video playback?

The use of video playback is a growing practice in animal behaviour. Studies that lead to unpredicted negative results are often considered failures and remain unpublished. In this article I review some of the published and unpublished studies that have led to negative results. Analysis of these studies suggests that no particular problem is responsible for more than a small number of negative results. I suggest further investigation of the potential causes of these negative results to assess their importance to the outcome of video playback experiments. Received: 31 January 2000 / Received in revised form: 27 March 2000 / Accepted: 28 March 2000     

How choosy should I be? The relative searching time predicts evolution of choosiness under direct sexual selection

Most theoretical research in sexual selection has focused on indirect selection. However, empirical studies have not strongly supported indirect selection. A well-established finding is that direct benefits and costs exert a strong influence on the evolution of mate choice. We present an analytical model in which unilateral mate choice evolves solely by direct sexual selection on choosiness. We show this is sufficient to generate the evolution of all possible levels of choosiness, because of the fundamental trade-off between mating rate and mating benefits. We further identify the relative searching time (RST, i.e. the proportion of lifetime devoted to searching for mates) as a predictor of the effect of any variable affecting the mating rate on the evolution of choosiness. We show that the RST: (i) allows one to make predictions about the evolution of choosiness across a wide variety of mating systems; (ii) encompasses all alternative variables proposed thus far to explain the evolution of choosiness by direct sexual selection; and (iii) can be empirically used to infer qualitative differences in choosiness.     

Are single-stranded circles intermediates in plasmid DNA replication?

Plasmid pC194 exists as circular double-stranded and single-stranded DNA in Bacillus subtilis and Staphylococcus aureus. We report here that the plasmid pHV33, composed of pBR322 and pC194, exists as double- and single-stranded DNA in Escherichia coli, provided that the replication functions of pC194 are intact. Single-stranded pHV33 DNA is converted to double-stranded DNA by complementary strand synthesis probably initiated at rriB, a primosome assembly site present on pBR322. The efficiency of complementary strand synthesis affects the double-stranded copy number, which suggests that single-stranded DNA is a plasmid replication intermediate.