Suppressive effect of glutamic acid decarboxylase 65-specific autoimmune B lymphocytes on processing of T cell determinants located within the antibody epitope

Type 1 diabetes is a T cell-mediated disease in which B cells serve critical Ag-presenting functions. In >95% of type 1 diabetic patients the B cell response to the glutamic acid decarboxylase 65 (GAD65) autoantigen is exclusively directed at conformational epitopes residing on the surface of the native molecule. We have examined how the epitope specificity of Ag-presenting autoimmune B cell lines, derived from a type 1 diabetic patient, affects the repertoire of peptides presented to DRB1*0401-restricted T cell hybridomas. The general effect of GAD65-specific B cells was to enhance Ag capture and therefore Ag presentation. The enhancing effect was, however, restricted to T cell determinants located outside the B cell epitope region, because processing/presentation of T cell epitopes located within the autoimmune B cell epitope were suppressed in a dominant fashion. A similar effect was observed when soluble Abs formed immune complexes with GAD65 before uptake and processing by splenocytes. Thus, GAD65-specific B cells and the Abs they secrete appear to modulate the autoimmune T cell repertoire by down-regulating T cell epitopes in an immunodominant area while boosting epitopes in distant or cryptic regions.     

Regeneration in planarians and other worms: New findings,new tools,and new perspectives

Molecular biology, recombinant DNA techniques, and new methods of cell lineage have reignited the interest of planarians and other worms (mainly annelids and nemerteans) as invertebrate model systems of regeneration. Here, the mean results produced in the last five years are reviewed, an update of the genes and molecules involved in planarian regeneration is provided, and a new morphallactic-epimorphic model of pattern formation is suggested. Moreover, and most importantly, we highlight the new strides brought upon by genomic/proteomic analyses, RNA interference (RNAi) to inactivate gene function, and Bromodeoxyuridine (BrdU) cell labelling. The raising hope to obtain transformed neoblasts and transgenic planarians is also stressed. Altogether, such approaches will eventually lead to solve the long-standing open questions on regeneration which still baffles us. Finally, we warn against overlooking the evident links between regeneration processes and those controlling the daily wear and tear of tissues and cells. Both processes act, at least in planarians, upon a unique stem-cell endowed with an unrivaled developmental potential in the animal kingdom-the neoblast. This cell could be considered the forebear and a model system for stem-cell analysis.     

Principal component analysis of gene frequencies and the origin of Basques

The genetic peculiarity of the Basque population has long been noted. We aim to describe Basque distinctiveness in space and assess the internal Basque heterogeneity. All these aspects are relevant to the question of the origin of Basques. After a thorough literature search, a data base was created containing all the available data on gene frequencies in the Iberian Peninsula and France. Twenty-nine systems, comprising 71 alleles, were used to carry out a principal component (PC) analysis. The results show a sharp peak in the first PC in the Basque area, which remains even when the geographic scope is widened to include western Europe. As demonstrated by “wombling” analysis, the steeper slope in the first PC is found to the east of the Basque area, along the Pyrenees. Measures of genetic heterogeneity (such as F_ST values) within the Basque country, as compared to those for non-Basques, do not show a particular internal substructuration in the Basque population. The genetic results support a scenario in which the Basques are the product of in situ differentiation around the time of the Last Glacial Maximum (18,000 B .P .), in agreement with archaeological and linguistic data. Isolation from the surrounding populations has allowed the differentiation to last for millennia, but has erased the differences existing among Basques. © 1994 Wiley-Liss, Inc.     

Computational comparison of microtubule-stabilising agents laulimalide and peloruside with taxol and colchicine

Microtubule-stabilising agents laulimalide and peloruside have been compared with tubulin-interacting drugs paclitaxel and colchicine by different computational approaches. Docking and QSAR-based programs point to a favourable interaction with the beta tubulin paclitaxel binding site, although an additional, preferred binding site has been found at the alpha subunit of tubulin. All together provides a plausible rationalisation of the singular binding features of these microtubule stabilisers and paves the way for future structural studies.     

Insights into the western Bantu dispersal: mtDNA lineage analysis in Angola

Africa is the homeland of humankind and it is known to harbour the highest levels of human genetic diversity. However, many continental regions, especially in the sub-Saharan side, still remain largely uncharacterized (i.e. southwest and central Africa). Here, we examine the mitochondrial DNA (mtDNA) variation in a sample from Angola. The two mtDNA hypervariable segments as well as the 9-bp tandem repeat on the COII/tRNA^lys intergenic region have allowed us to allocate mtDNAs to common African haplogroups. Angola lies in the southern end of the putative western branch of the Bantu expansion, where it met the local Khoisan populations. Angolan mtDNA lineages show basically a Bantu substrate with no traces of Khoisan lineages. Roughly, more than half of the southwestern mtDNA pool can be assigned to west Africa, ~25% to central Africa and a significant 16% to east Africa, which points to the western gene pool having contributed most to the mtDNA lineages in Angola. We have also detected signals of extensive gene flow from southeast Africa. Our results suggest that eastern and western Bantu expansion routes were not independent from each other, and were connected south of the rainforest and along the southern African savannah. In agreement with historical documentation, the analysis also showed that the Angola mtDNA genetic pool shows affinities with the African lineages from Brazil, the main American destination of the slaves from Angola, although not all lineages in Brazil can be accounted for by the Angolan mtDNA pool.     

Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage

Monoamine oxidase A (MAOA) is the X-linked gene responsible for deamination and subsequent degradation of several neurotransmitters and other amines. Among other activities, the gene has been shown to play a role in locomotion, circadian rhythm, and pain sensitivity and to have a critical influence on behavior and cognition. Previous studies have reported a non-neutral evolution of the gene attributable to positive selection in the human lineage. To determine whether this selection was human-exclusive or shared with other species, we performed a population genetic analysis of the pattern of nucleotide variation in non-human species, including bonobo, chimpanzee, gorilla, and orangutan. Footprints of positive selection were absent in all analyzed species, suggesting that positive selection has been recent and unique to humans. To determine which human-unique genetic changes could have been responsible for this differential evolution, the coding region of the gene was compared between human, chimpanzee, and gorilla. Only one human exclusive non-conservative change is present in the gene: Glu151Lys. This human substitution affects protein dimerization according to a three-dimensional structural model that predicts a non-negligible functional shift. This is the only candidate position at present to have been selected to fixation in humans during an episode of positive selection. Divergence analysis among species has shown that, even under positive selection in the human lineage, the MAOA gene did not experience accelerated evolution in any of the analyzed lineages, and that tools such as K_a/K_s would not have detected the selective history of the gene.     

Comparative Analysis of <Emphasis Type="Italic">Alu</Emphasis> Insertion Sequences in the APP 5′ FlankingRegion in Humans and Other Primates

Overexpression of the amyloid precursor protein gene (APP) may play a role in the neuropathology of Alzheimers disease. Therefore, elucidating the mechanisms involved in APP gene regulation is of primary importance, and various cis-acting regulatory elements located in 5 distal regions are known to play a main role. Some of them lie within Alu elements, one of which (Alu1) is only found in humans and apes while the other (Alu2) has a much older history and is also found in rhesus. These Alu insertions harbor sequence motifs that may act as cis-regulatory elements, which may cause differences in APP regulation among primate species and whose functionality may be ascertained through their conservation in a comparative analysis. We have performed a comparative analysis of the region comprising the two Alu elements of the APP promoter in several primates, including humans. We have found a significant decrease in nucleotide diversity in the Alu2 element (inserted in all the species analyzed) compared to the Alu1 (inserted only in apes). This finding can be interpreted as a constriction in the Alu2 sequence variation as a consequence of a functional role of this element in the APP expression. The present results suggest a wider extension of the regulatory elements than the known short consensus regulatory sequences. Moreover, the different conservation of two highly similar and neighboring sequences suggests that, besides the importance of the sequence motifs, their position in relation to the gene suggests that they have played a role in being recruited as regulatory elements.     

Comparative Genetics of Functional Trinucleotide Tandem Repeats in Humans and Apes

Several human neurodegenerative disorders are caused by the expansion of polymorphic trinucleotide repeat regions. Many of these loci are functional short tandem repeats (STRs) located in brain-expressed genes, and their study is thus relevant from both a medical and an evolutionary point of view. The aims of our study are to infer the comparative pattern of variation and evolution of this set of loci in order to show species-specific features in this group of STRs and on their potential for expansion (therefore, an insight into evolutionary medicine) and to unravel whether any human-specific feature may be identified in brain-expressed genes involved in human disease. We analyzed the variability of the normal range of seven expanding STR CAG/CTG loci (SCA1, SCA2, SCA3-MJD, SCA6, SCA8, SCA12, and DRPLA) and two nonexpanding polymorphic CAG loci (KCNN3 and NCOA3) in humans, chimpanzees, gorillas, and orangutans. The study showed a general conservation of the repetitive tract and of the polymorphism in the four species and high heterogeneity among loci distributions. Humans present slightly larger alleles than the rest of species but a more relevant difference appears in variability levels: Humans are the species with the largest variance, although only for the expanding loci, suggesting a relationship between variability levels and expansion potential. The sequence analysis shows high levels of sequence conservation among species, a lack of correspondence between interruption patterns and variability levels, and signs of conservative selective pressure for some of the STR loci. Only two loci (SCA1 and SCA8) show a human specific distribution, with larger alleles than the rest of species. This could account, at the same time, for a human-specific trait and a predisposition to disease through expansion.This article contains online supplementary material.     

Observation of a parental inversion variant in a rare Williams–Beuren syndrome family with two affected children

The Williams–Beuren syndrome (WBS) region at 7q11.23 is subject to several genomic rearrangements, one of which, the WBSinv-1 variant, is an inversion polymorphism. The WBSinv-1 chromosome has been shown to occur frequently in parents of individuals with WBS, implying that it predisposes the region to the WBS deletion. Here we investigate two WBS families with multiple affected children, and show that in one family, both siblings have a deletion on a WBSinv-1 chromosome background that arose due to interchromosomal recombination. These results suggest that the two WBS deletions in this family were independent events, and that there is likely a significant increase in the risk of deletion of the WBS region associated with the WBSinv-1 chromosome. The rarity of multiplex WBS families would suggest that the overall risk of having a child with WBS is still relatively low; however, families with an existing member with WBS may choose to opt for WBSinv-1 testing and genetic counseling.