Analysis of disease-associated ND4 mutations: How do we know which mutation is pathogenic?

It is not uncommon to identify more than one mtDNA replacement mutations in the specimens from patients. However, we usually do not know if the identified mtDNA mutation is pathogenic or not. Even functional assays are available to use, we would not know which mutation(s) is to be tested. To provide a rapid method for initial evaluation for the pathogenicity of the replacement mutation, we compared three evolutional analyses: primate conservation index (PCI), mammalian conservation index (MCI), and conservation index across a wide spectrum of species (CI). After analyzing 35 so-called diseases-associated replacement mutations of ND4, we found 8 pathogenic mutations, 15 nonpathogenic mutations, and 12 mutations of undetermined significance. The MCI classification appears to be the best one among the three systems. This study demonstrates that evolutional analysis can serve as a rapid evaluation for the pathogenicity of mtDNA replacement mutations.     

Origin of anterior patterning. How old is our head?

Most animals that display a bilateral symmetry (bilaterians) share homologous regulatory genes involved in head development. Recently, homologues of several of these genes have been cloned from animals that are radially organized, such as coral, sea anemones, jellyfish or hydra (cnidarians). Surprisingly, some of these are expressed apically and/or during apical patterning in hydrozoans, suggesting that head patterning is much older than previously thought.     

How random is the toss of a coin?

Background

The toss of a coin has been a method used to determine random outcomes for centuries. It is still used in some research studies as a method of randomization, although it has largely been discredited as a valid randomization method. We sought to provide evidence that the toss of a coin can be manipulated.

Methods

We performed a prospective experiment involving otolaryngology residents in Vancouver, Canada. The main outcome was the proportion of “heads” coin tosses achieved (out of 300 attempts) by each participant. Each of the participants attempted to flip the coin so as to achieve a heads result.

Results

All participants achieved more heads than tails results, with 7 of the 13 participants having significantly more heads results (p ≤ 0.05). The highest proportion of heads achieved was 0.68 (95% confidence interval 0.62–0.73, p < 0.001).

Interpretation

Certain people are able to successfully manipulate the toss of a coin. This throws into doubt the validity of using a coin toss to determine a chance result.The toss or flip of a coin to randomly assign a decision traditionally involves throwing a coin into the air and seeing which side lands facing up. This method may be used to resolve a dispute, see who goes first in a game or determine which type of treatment a patient receives in a clinical trial. There are only 2 possible outcomes, “heads” or “tails,” although, in theory, landing on an edge is possible. (Research suggests that when the coin is allowed to fall onto a hard surface, the chance of this happening is in the order of 1 in 6000 tosses.¹)When a coin is flipped into the air, it is supposedly made to rotate about an axis parallel to its flat surfaces. The coin is initially placed on a bent forefinger, and the thumb is released from under the coin surface, where it has been held under tension. The thumbnail strikes the part of the coin unsupported by the index finger, sending it rotating upward. All this is done with an upward movement of the hand and forearm. The coin may be allowed to fall to the floor or other surface or it may be caught by the “tosser” and sometimes turned onto the back of the opposite hand and then revealed. The catching method should not matter, provided it is consistent for each toss. The opponent often calls the toss when the coin is airborne, although in the case of randomization for clinical trials, this is unnecessary because one is simply looking for an outcome.Open in a separate windowThe appeal of the coin toss that it is a simple, seemingly unbiased, method of deciding between 2 options. Although the outcome of a coin toss should be at even odds, the outcome may well not be. Historically, the toss of a coin before a duel reputedly decided which person had his back to the sun — an obvious advantage when taking aim! In medical trials, a simple statistical manipulation can have a dramatic effect on the treatment a patient receives. Our hypothesis is that with minimal training, the outcome of the toss can be weighted heavily to the call of the tosser, thus abolishing the 50:50 chance result that is expected and allowing for manipulation of an apparently random event.     

How old is the most recent ancestor of two copies of an allele?

An important clue to the evolutionary history of an allele is the structure of the neighboring region of the genome, which we term the genomic background of the allele. Consider two copies of the allele. How similar we expect their genomic background to be is strongly influenced by the age of their most recent common ancestor (MRCA). We apply diffusion theory, first used by Motoo Kimura as a tool for predicting the changes in allele frequencies over time and developed by him in many articles in this journal, to prove a variety of new results on the age of the MRCA under the simplest demographic assumptions. In particular, we show that the expected age of the MRCA of two copies of an allele with population frequency f is just 2Nf generations, where N is the effective population size. Our results are a first step in running exact coalescent simulations, where we also simulate the history of the population frequency of an allele.     

How is the individuality of a face recognized?

A familiar face is instantly recognized in a crowd. This cannot be achieved through a feature by feature comparison of the observed face with either an average face (norm-based model of face recognition) or with a set of similarly constructed faces stored in memory (exemplar-based model of face recognition). A modified norm-based model is thus proposed. Instead of memorizing an average face, the normal variations for each facial feature are used to construct a multidimensional volume of face-space devoid of unusual features, here defined as features whose metrics lie below the 5th or above the 95th percentiles for that feature. A face consisting of 100 independently variable features will thus have, on average, 10 unusual features. Face identification then becomes exception-reporting. It requires only 10 such rare features to render a given face a one in 10¹³ faces (P=0.05¹⁰=9.8×10⁻¹⁴). In a world containing 6.7×10⁹ people, such a face would be unique. Faces remembered in this way can have their unusual features exaggerated or attenuated without loss of identity. This is the basis of caricatures and anti-caricatures. It also means that individuals belonging to a foreign race, possessing several features with modes beyond the “usual range” of the own-race population, will all look alike. Features that render a face unique in the own-race population are now shared by everyone in the foreign race.Average faces are more beautiful than the faces used in the averaging process. This makes evolutionary sense. Natural selection increases the frequency of fit features at the expense of maladaptive features. “Usual features” are therefore fitter than “unusual features”, and play an important role in mate selection. Such an existing fundamental sexual attribute could easily have been harnessed for the fast and efficient recognition of individuals in the community.     

How much structuring is beneficial with regard to examination scores? A prospective study of three forms of active learning

Many studies have demonstrated a superiority of active learning forms compared with traditional lecture. However, there is still debate as to what degree structuring is necessary with regard to high exam outcomes. Seventy-five students from a premedical school were randomly attributed to an active lecture group, a cooperative group, or a collaborative learning group. The active lecture group received lectures with questions to resolve at the end of the lecture. At the same time, the cooperative group and the collaborative group had to work on a problem and prepare presentations for their answers. The collaborative group worked in a mostly self-directed manner; the cooperative group had to follow a time schedule. For the additional work of preparing the poster presentation, the collaborative and cooperative groups were allowed 50% more working time. In part 1, all groups worked on the citric acid cycle, and in part 2, all groups worked on molecular genetics. Collaborative groups had to work on tasks and prepare presentations for their answers. At the end of each part, all three groups were subjected to the same exam. Additionally, in the collaborative and cooperative groups, the presentations were marked. All evaluations were performed by two independent examiners. Exam results of the active lecture groups were highest. Results of the cooperative group were nonsignificantly lower than the active lecture group and significantly higher than the collaborative group. The presentation quality was nonsignificantly higher in the collaborative group compared with the cooperative group. This study shows that active lecturing produced the highest exam results, which significantly differed from collaborative learning results. The additional elaboration in the cooperative and collaborative learning setting yielded the high presentation quality but apparently could not contribute further to exam scores. Cooperative learning seems to be a good compromise if high exam and presentation scores are expected.     

How is a tissue built?

Tissues change in many ways in the period that they are part of a living organism. They are created in fairly repeatable structural patterns, and we know that the patterns are due to both the genes and the (mechanical) environment, but we do not know exactly what part or percentage of a particular pattern to consider the genes, or the environment, responsible for. We do not know much about the beginning of tissue construction (morphogenesis) and we do not know the methods of tissue construction. When the tissue structure is altered to accommodate a new loading, we do not know how the decision is made for the structural reconstruction. We do know that tissues grow or reconstruct themselves without ceasing to continue with their structural function, but we do not understand the processes that permit them to accomplish this. Tissues change their structures to altered mechanical environments, but we are not sure how. Tissues heal themselves and we understand little of the structural mechanics of the process. With the objective of describing the interesting unsolved mechanics problems associated with these biological processes, some aspects of the formation, growth, and adaptation of living tissues are reviewed. The emphasis is on ideas and models. Beyond the objective is the hope that the work will stimulate new ideas and new observations in the mechanical and chemical aspects of developmental biology.     

Congenital sucrase–isomaltase deficiency: identification of a common Inuit founder mutation

Background:

Congenital sucrase–isomaltase deficiency is a rare hereditary cause of chronic diarrhea in children. People with this condition lack the intestinal brush-border enzyme required for digestion of di- and oligosaccharides, including sucrose and isomaltose, leading to malabsorption. Although the condition is known to be highly prevalent (about 5%–10%) in several Inuit populations, the genetic basis for this has not been described. We sought to identify a common mutation for congenital sucrase–isomaltase deficiency in the Inuit population.

Methods:

We sequenced the sucrase–isomaltase gene, SI, in a single Inuit proband with congenital sucrase–isomaltase deficiency who had severe fermentative diarrhea and failure to thrive. We then genotyped a further 128 anonymized Inuit controls from a variety of locales in the Canadian Arctic to assess for a possible founder effect.

Results:

In the proband, we identified a novel, homozygous frameshift mutation, c.273_274delAG (p.Gly92Leufs*8), predicted to result in complete absence of a functional protein product. This change was very common among the Inuit controls, with an observed allele frequency of 17.2% (95% confidence interval [CI] 12.6%–21.8%). The predicted Hardy–Weinberg prevalence of congenital sucrase–isomaltase deficiency in Inuit people, based on this single founder allele, is 3.0% (95% CI 1.4%–4.5%), which is comparable with previous estimates.

Interpretation:

We found a common mutation, SI c.273_274delAG, to be responsible for the high prevalence of congenital sucrase–isomaltase deficiency among Inuit people. Targeted mutation testing for this allele should afford a simple and minimally invasive means of diagnosing this condition in Inuit patients with chronic diarrhea.Congenital sucrase–isomaltase deficiency (Online Mendelian Inheritance in Man database no. #222900; www.omim.org/entry/222900) is a rare autosomal recessive form of carbohydrate malabsorption caused by reduced or absent activity of sucrase–isomaltase, a heterodimeric intestinal brush-border enzyme required for digestion of di- and oligosaccharides, including sucrose and isomaltose (Figure 1). In infants and children with this condition, exposure to specific carbohydrates, such as sucrose, results in profound fermentative diarrhea, gaseous abdominal distention, malabsorption, malnutrition and failure to thrive.^1,2 Presentation is generally after weaning, due to the introduction of sucrose-containing foods such as fruits; affected people may “self-treat” by developing a dislike of sweet foods. Because symptoms tend to improve with age, adolescents and adults with undiagnosed congenital sucrase–isomaltase deficiency may be misdiagnosed with irritable bowel syndrome.^3–5 If the condition is recognized, relief can be obtained by limiting the offending sugars, for instance, by giving a carbohydrate-free infant formula, and/or by oral digestive enzyme replacement (e.g., sacrosidase).^6,7Open in a separate windowFigure 1:Sucrase–isomaltase catalyzes the hydrolysis of the α-1,2 glycosidic bond in sucrose (A), α-1,4 glycosidic bond in maltose (B) and α-1,6 glycosidic bond in isomaltose (C), as well as α-1,4 and α-1,6 limit dextrins generated from dietary starch by α-amylase (not depicted). Blue circles depict sites of hydrolysis.Although congenital sucrase–isomaltase deficiency is rare (about 0.2%) in North Americans of European ancestry,⁸ it is relatively common in northern regions. The prevalence in Inuit people in Greenland has been estimated to be as high as 5%–10% in studies from 1972 and 1987.^9,10 In the region now known as Nunavut, the combined prevalence of congenital sucrase–isomaltase deficiency at 2 sites (Repulse Bay and Chesterfield Inlet) has been estimated at 7% in a study from 1978.¹¹ Small case series further support a high prevalence of sucrose malabsorption in locales as geographically dispersed as northern Alaska, the northwest coast of Hudson Bay and southern Manitoba.^12,13The current diagnostic gold standard for congenital sucrase–isomaltase deficiency is demonstration of complete or near-complete absence of sucrase and/or isomaltase activity in biopsy tissue of the small bowel.¹⁴ This method is direct, but it is also invasive and poses technical challenges in young patients. Also commonly used are the oral sucrose tolerance test and hydrogen breath test, in which blood glucose and breath hydrogen, respectively, are measured after an oral sucrose load.¹⁵ Of note, oral sucrose loading inevitably provokes acute abdominal discomfort and diarrhea in patients with this condition. A third option, a therapeutic trial of carbohydrate-free foods, provides a clinically meaningful demonstration of disordered carbohydrate digestion, but is not sufficiently specific to be diagnostic of congenital sucrase–isomaltase deficiency. Lastly, genetic testing of SI, the gene for this condition, is now clinically available. To date, the Human Gene Mutation Database contains a total of 16 SI mutations.¹⁶ In people of European descent, 4 mutations account for most disease alleles.¹⁷ We sought to identify a common mutation for congenital sucrase–isomaltase deficiency in the Inuit population.     

How natural is a nature reserve?: an ideological study of British nature conservation landscapes

Areas set apart for nature conservation in Britain are broadly categorised according to their cultural purpose, and names are assigned to these in this paper. Nature reserves may be similar to zoos and botanic gardens in aiming to maintain the diversity of species and if so are termed biodiversity reserves. This tradition understands nature as a static collection of entities apart from humans. Maintaining traditional management at a site is arguably a good way to sustain species, it also retains old ways in which humans and nature were integrated in the life of the nation and so are called historic countryside parks. There is growing interest in wilderness areas, where nature is seen as primarily processes protected from human interference. Despite the strength of each of these, they suffer from attempting to restrict nature to a ghetto, a process that is economically and environmentally costly. Companion places are places which set sustainable examples of integrating human life and economic activity with maintaining biodiversity and offering an opportunity to encounter wild processes at the heart of life. The language of these four types, or vectors, of nature reserves is offered to help the discussion of our place in nature.     

How blind is double-blind? A study of fish oil versus placebo

The distinctive aftertaste associated with fish oil preparations used in clinical trials of omega-3 fatty acids may weaken the double-blind. This double-blind pilot study was designed to examine whether normal subjects could correctly 'guess' if they were receiving capsules containing concentrated fish oil or capsules of pure olive oil. The informed consent was designed to give subjects ambiguous expectations about what oil they might be receiving to examine whether this would influence their guess. Despite a marked difference in taste experience, there was no significant difference in correct guesses between the two groups. The results suggest that altering subjects' expectations could further improve the validity of the double-blind.     

How selfish is a cowbird nestling?

Brood-parasitic young are reared in the nests of different species and can derive no genetic benefit from the survival of host offspring. However, although the nestlings of many parasitic cuckoo and honeyguide species routinely kill host young soon after hatching, nestling brown-headed cowbirds, Molothrus ater, tolerate host offspring and are commonly reared alongside them for at least part of the nestling period. I used comparative analyses of data from the literature to investigate whether brown-headed cowbird nestlings gain direct benefits by allowing host young to live. The brown-headed cowbird (44 g) parasitizes many passerines (adult mass range about 5-90 g) and the likelihood that host young survive to fledge from parasitized nests varies between species. In common with previous work, I found that host offspring mortality was highest in species whose offspring were relatively small compared with the cowbird nestling. Furthermore, cowbird nestlings were most likely to fledge when reared alongside host young of intermediate size. In these nests, one or two host young typically fledged as well. I suggest that cowbirds, and other host-tolerant brood parasites, could benefit from the presence of host nestlings through the assistance that host chicks offer in soliciting a higher provisioning rate, and that such benefits might outweigh the costs of having competition for food at each nest visit. Variation in this cost-benefit ratio could explain differences between brood parasite species in their tolerance of host young.