Intention Understanding in Autism

When we observe a motor act (e.g. grasping a cup) done by another individual, we extract, according to how the motor act is performed and its context, two types of information: the goal (grasping) and the intention underlying it (e.g. grasping for drinking). Here we examined whether children with autistic spectrum disorder (ASD) are able to understand these two aspects of motor acts. Two experiments were carried out. In the first, one group of high-functioning children with ASD and one of typically developing (TD) children were presented with pictures showing hand-object interactions and asked what the individual was doing and why. In half of the “why” trials the observed grip was congruent with the function of the object (“why-use” trials), in the other half it corresponded to the grip typically used to move that object (“why-place” trials). The results showed that children with ASD have no difficulties in reporting the goals of individual motor acts. In contrast they made several errors in the why task with all errors occurring in the “why-place” trials. In the second experiment the same two groups of children saw pictures showing a hand-grip congruent with the object use, but within a context suggesting either the use of the object or its placement into a container. Here children with ASD performed as TD children, correctly indicating the agent''s intention. In conclusion, our data show that understanding others'' intentions can occur in two ways: by relying on motor information derived from the hand-object interaction, and by using functional information derived from the object''s standard use. Children with ASD have no deficit in the second type of understanding, while they have difficulties in understanding others'' intentions when they have to rely exclusively on motor cues.     

Understanding atherosclerosis through mouse genetics

During the past year studies with mouse models have significantly clarified our understanding of atherosclerosis. Noteworthy achievements include: the discovery of a number of novel genes and pathways; new evidence emphasizing the role of lymphocytes in atherogenesis; the development of mouse models exhibiting advanced lesions with evidence of thrombosis; and new results indicating an anti-atherogenic effect of testosterone.     

Understanding biology through intelligent systems

A report on the Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB), Edmonton, Canada, 3-7 August 2002.     

Transfer of orlistat through oil-water interfaces

The transfer of radiolabelled orlistat ([14C]orlistat), a potent gastrointestinal lipase inhibitor, through an oil-water interface from a single oil droplet to an aqueous phase was investigated, using an oil drop tensiometer. The absolute transfer fluxes were found to be very low, even in the presence of micellar concentrations of bile salts, which increased their values from 0.2 to 2.5 and 6.5 pmol cm(-2) min(-1) in the presence of 0, 4 and 15 mM NaTDC, respectively. Adding either a lipid emulsion or pure human pancreatic lipase (HPL) or human serum albumin or beta-lactoglobulin had no effect on the flux of transfer of orlistat. The presence of colipase or a mixture of colipase and HPL was found, however, to reduce the flux of orlistat transfer, probably because it partly covered the single oil drop surface, even in the presence of bile salts. Using a finely emulsified system, we investigated the partitioning of orlistat between the aqueous and oil phases, in the absence or presence of bile salts above their CMC (4 mM NaTDC, final concentration). Under these emulsified conditions, orlistat was found to be mostly associated with the oil phase, since more than 98.8% of the total radioactivity was recovered after decantation with the oil phase. The low transfer rates of orlistat, as well as its partitioning coefficient between the oil and the aqueous phases, should help us to better understand the inhibitory effects of orlistat on lipid digestion in humans.     

Transfer of porcine embryos through mini-laparotomy

The aim of this experiment was to examine the suitability of mini-laparotomy for transferring embryos in pigs. Expanded blastocysts collected from estrus-induced prepuberal gilts were transferred to the uterus of synchronous recipients. Each recipient received 18 embryos transferred unilaterally either by conventional laparotomy (n = 20), mini-laparotomy (n = 15) or laparoscopy (n = 14). The mini-laparotomy consisted of a midventral incision of 4 cm enabling the surgeon to grasp a uterine horn with two fingers and exteriorize about 3 cm of it. To close the suture wound, only three or four interrupted skin sutures are required. Pregnancy rates after conventional surgery, mini-laparotomy and laparoscopy were 60.67 and 21%, respectively. Corresponding litter size was 7.4, 6.2 and 6.0 and total embryo survival 25, 23 and 7%. The differences in pregnancy rate and total embryo survival between conventional and mini-surgery were negligible, whereas between laparoscopy and the other two techniques it was significant. It may be concluded that, with a little practice, the time saving and less traumatic mini-laparotomy is a practicable alternative to conventional surgery.     

Understanding human T-cell-mediated immunoregulation through herpesviruses

Human herpesviruses have coevolved with humans over millions of years, and adaptation of latent infection within the cells of the immune system is a unique characteristic of many of these viruses. Following primary infection, these herpesviruses establish an asymptomatic-persistent infection in healthy individuals that is strictly controlled by virus-specific CD8(+) and CD4(+) T cells. Here, we provide a brief overview of how the human immune system interacts with these latent viruses and regulates the lifelong host-virus relationship in healthy virus carriers. Extensive studies on T-cell-mediated immune regulation over the last decade has allowed researchers to successfully translate these findings into the clinical setting to treat various herpesvirus-associated diseases in transplant patients and individuals with virus-associated malignancies. It is highly likely that these newly emerging T-cell-based therapeutic and diagnostic technologies will revolutionize the clinical management of patients with herpesvirus-associated diseases.     

Understanding signal transduction through functional proteomics

The study of signal transduction provides fundamental information regarding the regulation of all biologic processes that support the normal function of life. Functional proteomics, a rapidly emerging discipline that aims to understand the expression, function and regulation of the entire set of proteins in a given cell type, tissue or organism, offers unprecedented opportunity for signal transduction research in terms of understanding cellular behavior and regulation at the systems level. Indeed, swift progress in the area of proteomics has demonstrated the major impact of proteomic approaches on signal transduction and biomedical research. In this review, recent and innovative applications of functional proteomics in determining changes in protein contents, modifications, activities and interactions underpinning signaling transduction pathways are discussed.     

Understanding type 1 diabetes through proteomics

Introduction: Auto-immunity against pancreatic beta-cells leads to an absolute shortage of the hormone insulin, resulting in hyperglycemia and the onset of type 1 diabetes (T1D). Proteomic approaches have been used to elucidate the mechanisms of beta-cell dysfunction and death.

Areas covered: In the present review, we discuss discoveries in the beta-cell proteome that have contributed to better insights in the role of the beta-cell in T1D. Techniques, such as 2D-DIGE and MALDI imaging, together with new approaches for sample preparation, including laser capture microdissection and immunopeptidomics, have resulted in novel mechanistic insights in the pathogenesis of T1D. We describe how proteomic studies in beta-cell lines as well as isolated islets from animal models and humans have discovered intracellular signaling pathways leading to beta-cell destruction, the generation of neo-antigens through post-translational modifications of beta-cell antigens as well as better biomarkers of disease progression.

Expert commentary: Proteomics has contributed to the discovery of beta-cell neo-autoantigen generation through post-translational modifications, hybrid insulin peptide formation and the generation of defective ribosomal gene products. These concepts are revolutionizing our insights in the pathogenesis of T1D, acknowledging a central role for the beta-cell in its own destruction.     

Understanding protein folding through peptide models

From the time it was recognized that proteins are made up primarily of secondary structures, theories of protein folding have used secondary structural elements as important building blocks. Peptides have played a central role in elucidating the factors that stabilize individual elements of secondary structure and are now being employed to study higher levels of organization. The control of conformation in peptides has taken on new relevance with the realization that protein folding plays a central role in many disease states.     

Understanding mouse models of disease through metabolomics

Metabolomics is widely applicable to a number of fields including toxicology, plant metabolism and functional genomics. In the area of functional genomics, a number of studies have demonstrated the potential of this approach, which combines high-throughput metabolite profiling with computer-assisted pattern recognition approaches. In this review, recent applications of metabolomics to understanding mouse models of disease are considered. This includes studies on the impact of mouse strain on disease models, as well as metabolic profiling of cardiovascular, metabolic and neurodegenerative diseases. This versatile tool is set to increase in popularity as functional genomic approaches produce more mouse models for phenotyping.     

Understanding splicing regulation through RNA splicing maps

Alternative splicing is a highly regulated process that greatly increases the proteome diversity and plays an important role in cellular differentiation and disease. Interactions between RNA-binding proteins (RBPs) and pre-mRNA are the principle regulator of splicing decisions. Findings from recent genome-wide studies of protein-RNA interactions have been combined with assays of the global effects of RBPs on splicing to create RNA splicing maps. These maps integrate information from all pre-mRNAs regulated by single RBPs to identify the global positioning principles guiding splicing regulation. Recent studies using this approach have identified a set of positional principles that are shared between diverse RBPs. Here, we discuss how insights from RNA splicing maps of different RBPs inform the mechanistic models of splicing regulation.     

Understanding mutations and protein stability through tripeptides

A novel methodology to predict the local conformational changes in a protein as a consequence of missense mutations is proposed. A pentapeptide at the locus of mutation plays the dominant role and it is analyzed in terms of tripeptides. A measure for spatial and temporal fluctuations in a pentapeptide is devised and validated. The method does not involve any prior knowledge of structural templates from sequence homology studies. Structural deformations can be predicted with about 70-80% reliability in any protein. Disease causing mutations and benign mutations have been addressed. In particular, p53, retinoblastoma protein and lipoprotein lipase are studied in detail.     

Understanding protein flexibility through dimensionality reduction.

This work shows how to decrease the complexity of modeling flexibility in proteins by reducing the number of dimensions necessary to model important macromolecular motions such as the induced-fit process. Induced fit occurs during the binding of a protein to other proteins, nucleic acids, or small molecules (ligands) and is a critical part of protein function. It is now widely accepted that conformational changes of proteins can affect their ability to bind other molecules and that any progress in modeling protein motion and flexibility will contribute to the understanding of key biological functions. However, modeling protein flexibility has proven a very difficult task. Experimental laboratory methods, such as x-ray crystallography, produce rather limited information, while computational methods such as molecular dynamics are too slow for routine use with large systems. In this work, we show how to use the principal component analysis method, a dimensionality reduction technique, to transform the original high-dimensional representation of protein motion into a lower dimensional representation that captures the dominant modes of motions of proteins. For a medium-sized protein, this corresponds to reducing a problem with a few thousand degrees of freedom to one with less than fifty. Although there is inevitably some loss in accuracy, we show that we can obtain conformations that have been observed in laboratory experiments, starting from different initial conformations and working in a drastically reduced search space.     

Understanding stem cell-mediated brain repair through neuroimaging

Transplantation of stem cells into the damaged brain can lead to behavioral recovery. However, at present, the mechanisms by which these cells exert their beneficial effects are still poorly understood. Survival, migration and differentiation are but a few of the factors that are thought to be involved in stem cell-mediated brain repair. It is hoped that neuroimaging, by MRI and PET, will provide serial in vivo assessments of transplanted cells that can lead to a greater understanding of the mechanisms involved in brain repair.