Linkage of early-onset osteoarthritis and chondrocalcinosis to human chromosome 8q.

Calcium pyrophosphate-deposition disease (CPDD), also called "chondrocalcinosis" or "pseudogout," is a disorder characterized by the deposition of calcium-containing crystals in joint tissue, which leads to arthritis-like symptoms. The presence of these crystals in joint tissue is a common finding in the elderly, and, in this population, there is a poor correlation with joint pain. In contrast, early-onset CPDD has been described in several large families in which the disease progresses to severe degenerative osteoarthritis (OA). In these families, an autosomal dominant mode of inheritance is observed, with an age at onset between the 2d and 5th decades of life. In this report, we describe a large New England family with early-onset CPDD and severe degenerative OA. We found genetic linkage between the disease in this family and chromosome 8q, with a multipoint lod score of 4.06. These results suggest that a defective gene at this location causes the disease in this family.     

The promastigote surface protease of Leishmania

The infective forms o f several protozoan parasites are covered with a limited number o f major surface proteins. In this respect, Leishmania is no exception, and recent investigations have demonstrated on promostigotes the presence o f a single surface glycoprotein. In contrast to the major surface proteins o f other protozoans which have no known enzymatic activities, the surface protein of Leishmania. is a protease which is active on living cells. In this review, Clement Bordier presents the current structural, functional and immunological information concerning this intriguing and potentially important enzyme.     

Phytochromes A and B mediate red-light-induced positive phototropism in roots

The interaction of tropisms is important in determining the final growth form of the plant body. In roots, gravitropism is the predominant tropistic response, but phototropism also plays a role in the oriented growth of roots in flowering plants. In blue or white light, roots exhibit negative phototropism that is mediated by the phototropin family of photoreceptors. In contrast, red light induces a positive phototropism in Arabidopsis roots. Because this red-light-induced response is weak relative to both gravitropism and negative phototropism, we used a novel device to study phototropism without the complications of a counteracting gravitational stimulus. This device is based on a computer-controlled system using real-time image analysis of root growth and a feedback-regulated rotatable stage. Our data show that this system is useful to study root phototropism in response to red light, because in wild-type roots, the maximal curvature detected with this apparatus is 30 degrees to 40 degrees, compared with 5 degrees to 10 degrees without the feedback system. In positive root phototropism, sensing of red light occurs in the root itself and is not dependent on shoot-derived signals resulting from light perception. Phytochrome (Phy)A and phyB were severely impaired in red-light-induced phototropism, whereas the phyD and phyE mutants were normal in this response. Thus, PHYA and PHYB play a key role in mediating red-light-dependent positive phototropism in roots. Although phytochrome has been shown to mediate phototropism in some lower plant groups, this is one of the few reports indicating a phytochrome-dependent phototropism in flowering plants.     

MATCHING THE SHAPE OF TIME-INTENSITY CURVES1

Time-Intensity Curves are often summarized by average curves. From these curves TI-parameters are inferred. In this paper a different method is proposed in which the shape of the curves is the central concept. Isotropic scaling factors are computed for each curve. These factors can be tabled and inspected. Often a large number of scaling factors will be computed, which makes it hard to study them in a table. In such cases they can be represented in a plot, for which in this paper PCA is suggested. In this plot a structure in the scaling factors for the different TI-curves may become visible. It is also possible to make a plot in which the homogeneity of the panel of subjects can be studied.     

``Two' Many Optimalities

In evolutionary biology, a trait is said to be optimal if it maximizes the fitness of the organism, that is, if the trait allows the organism to survive and reproduce better than any other competing trait would. In engineering, a design is said to be optimal if it complies with its functional requirements as well as possible. Cognitive science is both a biological and engineering discipline and hence it uses both notions of optimality. Unfortunately, the lack of a clear methodological stance on this tissue has made it common for researchers to conflate these two kinds of optimality. In this paper, I argue that a strict distinction must kept in order to avoid inaccurate assumptions.     

'Bioethics' is subordinate to morality in Japan

Disputes over brain death and euthanasia are used to illuminate the question whether there really is a Japanese way of thinking in bioethics. In Japanese thought, a person does not exist as an individual but as a member of the family, community or society. I describe these features of Japanese society as 'mutual dependency'. In this society, an act is 'good' and 'right' when it is commonly done, and it is 'bad' and 'wrong' when nobody else does it. Thus, outsiders to this ring of mutual dependency encounter ostracism. One feature of this society is a lack of open discussion which leads to the existence of multiple standards. This Japanese morality even prevails over written laws. In Japan, there is a public stance that euthanasia does not exist. On the other hand, there are certain decisions which have permitted euthanasia. Similarly, organ transplants were performed from brain dead donors, while that procedure was not accepted officially by the medical profession. In this situation, there is a danger that human rights will be neglected. So far bioethical approaches have not helped to work out these problems. This may be because Japanese think that bioethics is subordinate to morality. The current dispute over brain death involves a struggle for the establishment of a rational society in Japan. Overcoming mutual dependency and ostracism is essential to resolve this struggle and to lead Japan into a society of mutual respect where all individuals, families and communities are esteemed.     

Is a genome a codeword of an error-correcting code?

Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction.     

Use and abuse of variance models in regression

In (nonlinear) regression with heteroscedastic errors, introduction of a variance model can be useful to obtain good estimators of the regression parameter. For example, the variance model can be used to obtain the optimal weights in weighted least squares. Methodology of this kind is often used in the analysis of assay data in clinical chemistry, pharmacokinetics, and toxicology. In a series of papers in the pharmacological literature, Sheiner and Beal and others advocate the extended least squares (ELS) methodology that combines regression and variance model into a single objective function based on normal-theory maximum likelihood. The inadequacy of this method is folklore in the (mathematical) statistical literature. In this article it is pointed out that this methodology may lead to inconsistent estimators in practically relevant situations. A review is given of other methods that may be preferable to ELS.     

A weighted principal component analysis and its application to gene expression data

In this work, we introduce in the first part new developments in Principal Component Analysis (PCA) and in the second part a new method to select variables (genes in our application). Our focus is on problems where the values taken by each variable do not all have the same importance and where the data may be contaminated with noise and contain outliers, as is the case with microarray data. The usual PCA is not appropriate to deal with this kind of problems. In this context, we propose the use of a new correlation coefficient as an alternative to Pearson's. This leads to a so-called weighted PCA (WPCA). In order to illustrate the features of our WPCA and compare it with the usual PCA, we consider the problem of analyzing gene expression data sets. In the second part of this work, we propose a new PCA-based algorithm to iteratively select the most important genes in a microarray data set. We show that this algorithm produces better results when our WPCA is used instead of the usual PCA. Furthermore, by using Support Vector Machines, we show that it can compete with the Significance Analysis of Microarrays algorithm.     

Breast reduction with short L scar

I didactically compared the breast as a glandular cone with an envelope of skin and subcutaneous tissue. The aesthetic alterations of the breast are classified in four groups related to form, to volume, to grams, and to ptosis in centimeters. An imaginary plane that passes by the mammary sulcus (plane A) will determine the area of the breast that is ptotic. The projection of this plane in the anterior part of the breast is called point A. The distance between point A and the nipple will give in centimeters the amount of ptosis. I use this distance to draw geometrically in the breast the amount of excess of skin to be removed to correct the ptosis. In group I, the volume is normal and part of the mammary gland is under plane A. In this type of breast, the skin is resected, and since there is no excess of breast tissue, the breast that is under plane A is used as an inferior pedicle flap to give a better volume to the new breast. In group II, the base of the breast is large, the height is normal, and the volume is increased by the enlargement of the base. In this type of breast, the excess of breast under plane A and a wedge under the nipple are resected to reach the normal volume at the end of the surgery. In group III, the base is normal and the volume of the breast is increased by the height. For treatment, I resect the excess of breast under plane A as well as a segment at the base to reduce its height. In group IV, the volume of the breast is increased by the size of the base and the height of the cone, and I treat by resection of the excess of tissue under the ptotic area, a wedge under the areola, and a transversal segment in the base to reduce all the dimensions. In the final result of this technique in the majority of patients I will obtain a short scar. This technique was used in 1083 patients from January of 1979 to May of 1988.     

Ganglion ultrastructure in phylactolaemate Bryozoa: evidence for a neuroepithelium

In contrast to other Bryozoa, members of the subtaxon Phylactolaemata bear a subepithelial cerebral ganglion that resembles a hollow vesicle rather than being compact. In older studies this ganglion was said to originate by an invagination of the pharyngeal epithelium. Unfortunately, documentation for this is fragmentary. In chordates the central nervous system also arises by an invagination-like process, but this mode is uncommon among invertebrate phyla. As a first attempt to gather more data about this phenomenon, cerebral ganglia in two phylactolaemate species, Fredericella sultana and Plumatella emarginata, were examined at the ultrastructural level. In both species the ganglion bears a small central lumen. The ganglionic cells are organized in the form of a neuroepithelium. They are polarized and interconnected by adherens junctions on their apical sides and reside on a basal lamina. The nerve cell somata are directed towards the central lumen, whereas the majority of nervous processes are distributed basally. Orientation of the neuroepithelial cells can be best explained by the possibility that they develop by invagination. A comparison with potential outgroups reveals that a neuroepithelial ganglion is at least derived. Since, however, a reliable phylogenetic system of the Bryozoa is missing, a decision on whether such a ganglion is apomorphic for Bryozoa or evolved within this taxon can hardly be made.     

Cpn20: Siamese twins of the chaperonin world

The chloroplast cpn20 protein is a functional homolog of the cpn10 co-chaperonin, but its gene consists of two cpn10-like units joined head-to-tail by a short chain of amino acids. This double protein is unique to plastids and was shown to exist in plants as well plastid-containing parasites. In vitro assays showed that this cpn20 co-chaperonin is a functional homolog of cpn10. In terms of structure, existing data indicate that the oligomer is tetrameric, yet it interacts with a heptameric cpn60 partner. Thus, the functional oligomeric structure remains a mystery. In this review, we summarize what is known about this distinctive chaperonin and use a bioinformatics approach to examine the expression of cpn20 in Arabidopsis thaliana relative to other chaperonin genes in this species. In addition, we examine the primary structure of the two homologous domains for similarities and differences, in comparison with cpn10 from other species. Lastly, we hypothesize as to the oligomeric structure and raison d’être of this unusual co-chaperonin homolog. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Glycogen synthesis in the absence of glycogenin in the yeast Saccharomyces cerevisiae

In eukaryotic cells, glycogenin is a self-glucosylating protein that primes glycogen synthesis. In yeast, the loss of function of GLG1 and GLG2, which encode glycogenin, normally leads to the inability of cells to synthesize glycogen. In this report, we show that a small fraction of colonies from glg1glg2 mutants can switch on glycogen synthesis to levels comparable to wild-type strain. The occurrence of glycogen positive glg1glg2 colonies is strongly enhanced by the presence of a hyperactive glycogen synthase and increased even more upon deletion of TPS1. In all cases, this phenotype is reversible, indicating the stochastic nature of this synthesis, which is furthermore illustrated by colour-sectoring of colonies upon iodine-staining. Altogether, these data suggest that glycogen synthesis in the absence of glycogenin relies on a combination of several factors, including an activated glycogen synthase and as yet unknown alternative primers whose synthesis and/or distribution may be controlled by TPS1 or under epigenetic silencing.     

Multi-slice ultrasound image calibration of an intelligent skin-marker for soft tissue artefact compensation

In this paper, a novel multi-slice ultrasound (US) image calibration of an intelligent skin-marker used for soft tissue artefact compensation is proposed to align and orient image slices in an exact H-shaped pattern. Multi-slice calibration is complex, however, in the proposed method, a phantom based visual alignment followed by transform parameters estimation greatly reduces the complexity and provides sufficient accuracy. In this approach, the Hough Transform (HT) is used to further enhance the image features which originate from the image feature enhancing elements integrated into the physical phantom model, thus reducing feature detection uncertainty. In this framework, slice by slice image alignment and calibration are carried out and this provides manual ease and convenience.     

Autophagy contributes to lysosomal storage disorders

Degradation in the lysosome/vacuole is not the final step of autophagy. In particular, for starvation-induced autophagy it is necessary to release the breakdown products back into the cytosol. However, some researchers ignore this last step and simply refer to the endpoint of autophagy as degradation, or perhaps even cargo delivery. In many cases this is not a serious issue; however, the analysis of autophagy’s role in certain diseases makes clear that this can be a significant error.     

Allele and locus classification in electrophoretic population studies

The electrophoretic separation of protein variants having slightly different mobilities is a basic tool of biochemical population genetics. In certain situations it is difficult to determine how to classify the variants as alleles of a number of genetic loci, that is, as variant subsets within each of which the Mendelian laws hold. In this article, we develop and analyze a series of algorithms for solving various versions and generalizations of this problem of optimal classification.     

Autophagy contributes to lysosomal storage disorders

Degradation in the lysosome/vacuole is not the final step of autophagy. In particular, for starvation-induced autophagy it is necessary to release the breakdown products back into the cytosol. However, some researchers ignore this last step and simply refer to the endpoint of autophagy as degradation, or perhaps even cargo delivery. In many cases this is not a serious issue; however, the analysis of autophagy's role in certain diseases makes clear that this can be a significant error.     

Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking

In single-particle analysis, a three-dimensional (3-D) structure of a protein is constructed using electron microscopy (EM). As these images are very noisy in general, the primary process of this 3-D reconstruction is the classification of images according to their Euler angles, the images in each classified group then being averaged to reduce the noise level. In our newly developed strategy of classification, we introduce a topology representing network (TRN) method. It is a modified method of a growing neural gas network (GNG). In this system, a network structure is automatically determined in response to the images input through a growing process. After learning without a masking procedure, the GNG creates clear averages of the inputs as unit coordinates in multi-dimensional space, which are then utilized for classification. In the process, connections are automatically created between highly related units and their positions are shifted where the inputs are distributed in multi-dimensional space. Consequently, several separated groups of connected units are formed. Although the interrelationship of units in this space are not easily understood, we succeeded in solving this problem by converting the unit positions into two-dimensional (2-D) space, and by further optimizing the unit positions with the simulated annealing (SA) method. In the optimized 2-D map, visualization of the connections of units provided rich information about clustering. As demonstrated here, this method is clearly superior to both the multi-variate statistical analysis (MSA) and the self-organizing map (SOM) as a classification method and provides a first reliable classification method which can be used without masking for very noisy images.