Is the most frequent allele the oldest?

Exact and approximate expressions are obtained for the probability that the most frequent allele is oldest, in neutral allele models in which all mutations produce new alleles. The higher the mutation rate, the less likely is it that the most frequent allele would be oldest. The results are in agreement with simulation studies by Ewens and Gillespie (1974) (Theor. Popul. Biol.6, 35–57), and limit the range of validity of a suggestion made by Crow (1972) (J. Hered.63, 306–316) with respect to the statistical testing of the neutral allele hypothesis.     

When should we save the most endangered species?

At the heart of our efforts to protect threatened species, there is a controversial debate about whether to give priority to cost-effective actions or whether focusing solely on the most endangered species will ultimately lead to preservation of the greatest number of species. By framing this debate within a decision-analytic framework, we show that allocating resources solely to the most endangered species will typically not minimise the number of extinctions in the long-term, as this does not account for the risk of less endangered species going extinct in the future. It is only favoured when our planning timeframe is short or we have a long-term view and we are optimistic about future conditions. Conservation funding tends to be short-term in nature, which biases allocations to more endangered species. Our work highlights the need to consider resource allocation for biodiversity over the long-term; 'preventive conservation', rather than just short-term fire-fighting.     

Puncture versus capture: which stresses animals the most?

Journal of Comparative Physiology B - The prerogative of animal welfare science includes wild species and ecological studies. Yet, guidance enshrined in legislation is narrowly derived from studies...     

When and where was the most recent common ancestor?

 The structured coalescent is investigated for single-locus, digenic samples in the diffusion limit of the unidimensional stepping-stone model for homogeneous, isotropic migration and random genetic drift. Let T denote the scaled time to the most recent common ancestor (MRCA) of the two genes, and let Z designate the scaled deviation of the position of the MRCA from the average position of the two genes. The joint probability density of T and Z is evaluated explicitly. Both the marginal and conditional distributions of T have infinite expectation, as does the marginal distribution of Z. Conditioned on T = τ, the distribution of Z is Gaussian with mean zero and variance 2τ. The main results are extended to anisotropic migration. The results establish the existence of and define in the diffusion limit a retrospective stochastic process for digenic samples in one spatial dimension. Received: 1 May 2001 / Revised version: 2 September 2001 / Published online: 8 February 2002     

Identifying and characterizing the most significant β-glucosidase of the novel species Aspergillus saccharolyticus

The newly discovered fungal species Aspergillus saccharolyticus was found to produce a culture broth rich in β-glucosidase activity. In this present work, the main β-glucosidase of A.?saccharolyticus responsible for the efficient hydrolytic activity was identified, isolated, and characterized. Ion exchange chromatography was used to fractionate the culture broth, yielding fractions with high β-glucosidase activity and only 1 visible band on an SDS-PAGE gel. Mass spectrometry analysis of this band gave peptide matches to β-glucosidases from aspergilli. Through a polymerase chain reaction approach using degenerate primers and genome walking, a 2919 bp sequence encoding the 860 amino acid BGL1 polypeptide was determined. BGL1 of A.?saccharolyticus has 91% and 82% identity with BGL1 from Aspergillus aculeatus and BGL1 from Aspergillus niger , respectively, both belonging to Glycoside Hydrolase family 3. Homology modeling studies suggested β-glucosidase activity with preserved retaining mechanism and a wider catalytic pocket compared with other β-glucosidases. The bgl1 gene was heterologously expressed in Trichoderma reesei QM6a, purified, and characterized by enzyme kinetics studies. The enzyme can hydrolyze cellobiose, p-nitrophenyl-β-d-glucoside, and cellodextrins. The enzyme showed good thermostability, was stable at 50?°C, and at 60?°C it had a half-life of approximately 6?h.     

Are splicing mutations the most frequent cause of hereditary disease?

Disease-causing point mutations are assumed to act predominantly through subsequent individual changes in the amino acid sequence that impair the normal function of proteins. However, point mutations can have a more dramatic effect by altering the splicing pattern of the gene. Here, we describe an approach to estimate the overall importance of splicing mutations. This approach takes into account the complete set of genes known to be involved in disease and suggest that, contrary to current assumptions, many mutations causing disease may actually be affecting the splicing pattern of the genes.     

Are most of the domoic acid-producing species of the diatom genus Pseudo-nitzschia cosmopolites?

Records from all oceans, most of them published during 1990–2000, and personal unpublished observations of nine Pseudo-nitzschia taxa known as potential domoic acid (DA) producers have been used to outline their geographical distribution. Pseudo-nitzschia seriata f. seriata as the only taxon was found in the North Atlantic Ocean exclusively. The records of P. multistriata were too few and the identification of P. turgidula from the North Atlantic too unreliable to provide an idea about their distribution. Pseudo-nitzschia pungens and the less frequently recorded P. fraudulenta, P. multiseries and P. australis appeared to be cosmopolites. The wide distribution of the apparently most efficient DA producers, P. australis and P. multiseries, is especially noteworthy. The records of P. delicatissima and P. pseudodelicatissima also indicate a cosmopolitan distribution although with the qualification of certain taxonomic and identification ambiguities. Hence, the question of whether most DA-producing Pseudo-nitzschia species are cosmopolites may be answered with a tentative “yes”.     

What are the most relevant parameters for malnutrition in nursing homes?

Prevention of malnutrition is an important issue among older nursing homes residents. From this perspective it is crucial that malnutrition is detected in an early stage. Hence, parameters and tools are required that are suitable for these institutions. Based on recent publications an assessment has been made to identify which parameters are most relevant in nursing homes. The literature study indicates that a wide scope of parameters exists for screening of malnutrition. Only a limited number has been studied in the elderly. In addition, more complicated parameters and tools have not revealed substantial added value to relatively simple parameters, such as foodrecords, weight loss and Body Mass Index.     

De-ubiquitylation is the most critical step in the ubiquitin-mediated homeostatic control of the NF-κB/IKK basal activity

The role of ubiquitylation in signal-induced activation of nuclear factor -κB (NF-κB) has been well established, while its involvement in maintaining NF-κB basal activity is less certain. Recent evidences demonstrate that in unstimulated cells, NF-κB homeostasis is actually the result of opposing forces: pro-activating activity of the IκB Kinase (IKK) and inhibitory activity of the Inhibitor of -κB (IκB) proteins. It is well known that endogenous de-ubiquitylating mechanisms are less effective on Ub motifs containing UbG76A. Here, we show that overexpression of a ubiquitin (Ub) G76A mutant leads to persistent activation of the IKK/NF-κB pathway in the absence of extra-cellular stimuli. In contrast, no effects on NF-κB activation were observed upon expression of UbK48R and UbK63R mutants, which are known to impair elongation of Lys⁴⁸- and Lys⁶³-linked poly-ubiquitin chains, respectively. Overall, these findings indicate that under basal conditions, the rate of de-ubiquitylation, rather than that of substrate ubiquitylation, is critical for the maintenance of appropriate levels of IKK/NF-κB activity.     

First webspace deepening: comparing the four-flap and five-flap Z-plasty. Which gives the most gain?

A two-part investigation was undertaken to determine whether a four- or a five-flap Z-plasty gives the greatest increase in length (deepening) over the same radius of a web. In part A, flaps were designed on a model of a webspace made from a plastic frame and Speedo fabric; four types of flaps, three different central limb lengths, and three trials for each length gave a total of 36 observations. In part B, flaps were designed on the natural axillary webs of the pig; three Yorkshire pigs with one type of flap per axillary web gave a total of 12 observations. In part A, the stereometric elongation (percent deepening) produced by the five-flap Z-plasty was similar to that of a single 60-degree Z-plasty (4-cm central limb; five-flap versus a single Z procedure, 72.5+/-4.3 versus 75.0+/-2.5 percent). The 90-degree four-flap procedure gave a 1.59 times greater deepening than the five-flap procedure (4-cm central limb; 90-degree four flap technique, 114.2+/-1.4 percent). The 120-degree four-flap technique gave 2.0 and 1.26 times greater deepening than the five-flap and 90-degree four-flap procedures, respectively (4-cm central limb; 120-degree four-flap technique, 144.2+/-1.4 percent). In part B, the 90-degree four-flap Z-plasty again produced a significantly greater lengthening (1.57 times) than the five-flap procedure (132.7+/-6.4 versus 84.0+/-4.0 percent; p<0.05), and the percentage of elongation of the 120-degree four-flap procedure was 1.27 times greater than that of the 90-degree four-flap technique (167.3+/-7.0 versus 131.3+/-2.3 percent; p < 0.05). In conclusion, the four-flap Z-plasty produced greater webspace deepening than that of the five-flap Z-plasty. The 120-degree four-flap procedure gave the greatest percentage of elongation, but it was more difficult to design and close than the 90-degree four-flap Z-plasty.     

Sensitivity to stress in the bivalve Macoma balthica from the most northern (Arctic) to the most southern (French) populations: low sensitivity in Arctic populations because of genetic adaptations?

The stress sensitivity, determined in copper exposureexperiments and in survival in air tests, and thegenetic structure, measured by means of isoenzymeelectrophoresis, were assessed in populations of theBaltic clam Macoma balthica (L.) from itssouthern to its northern distribution limit, in orderto test the hypotheses that near the distributionlimit the clams would be more stress sensitive andwould have a lower genetic variability. Thepopulations in west and north Europe show a stronggenetic resemblance. The populations in the sub-ArcticWhite Sea are genetically slightly different, and showa low stress sensitivity. The populations in theArctic Pechora Sea are genetically very distant fromthe other populations, and show the lowest stresssensitivity. Near the southern distribution limit, inagreement with the hypotheses, genetic variability islow and stress sensitivity high. On the other hand, incontrast to expectation, near the northerndistribution limit, in the populations of the PechoraSea, the genetic variability was higher, thus notreduced, and the stress sensitivity was low comparedto all other populations. Yet, it remains a questionif such is due to gradual physiologicalacclimatization (and ongoing differential selection)or to genetic adaptation.     

Is halogen content the most important factor in the removal of halogenated trace organics by MBR treatment?

This study investigated the relationship between physicochemical properties (namely halogen content and hydrophobicity) of halogenated trace organics and their removal efficiencies by a laboratory scale membrane bioreactor (MBR) under stable operating conditions. The reported results demonstrated a combined effect of halogen content and hydrophobicity on the removal. Compounds with high halogen content (>0.3) were well removed (>85%) when they possessed high hydrophobicity (Log D>3.2), while those with lower Log D values were also well removed if they had low halogen content (<0.1). General indices such as the BIOWIN index (which is based on only biodegradation) or a more specific index such as the halogen content (which captures a chemical aspect) appeared insufficient to predict the removal efficiency of halogenated compounds in MBR. Experimental data confirmed that the ratio of halogen content and Log D, which incorporates two important physico-chemical properties, is comparatively more suitable.     

Sympatric,parapatric or allopatric: the most important way to classify speciation?

The most common classification of modes of speciation begins with the spatial context in which divergence occurs: sympatric, parapatric or allopatric. This classification is unsatisfactory because it divides a continuum into discrete categories, concentrating attention on the extremes, and it subordinates other dimensions on which speciation processes vary, such as the forces driving differentiation and the genetic basis of reproductive isolation. It also ignores the fact that speciation is a prolonged process that commonly has phases in different spatial contexts. We use the example of local adaptation and partial reproductive isolation in the intertidal gastropod Littorina saxatilis to illustrate the inadequacy of the spatial classification of speciation modes. Parallel divergence in shell form in response to similar environmental gradients in England, Spain and Sweden makes this an excellent model system. However, attempts to demonstrate 'incipient' and 'sympatric' speciation involve speculation about the future and the past. We suggest that it is more productive to study the current balance between local adaptation and gene flow, the interaction between components of reproductive isolation and the genetic basis of differentiation.     

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.