Mapping of HLA epitopes recognized by H-2-restricted cytotoxic T lymphocytes specific for HLA using recombinant genes and synthetic peptides

Immunization of DBA/2 (H-2d) mice with syngeneic P815 tumor cell transfectants that express HLA class I genes elicits CTL that recognize HLA in the context of H-2Kd molecules. Anti-HLA-CW3 CTL cross-react to a variable extent on the related alleles A3 and A24. Using a panel of target cells expressing native or recombinant HLA genes, we could map the epitope recognized by a CTL clone specific for CW3 to the second external (alpha 2) domain of CW3. Moreover, the epitope recognized by this clone could be mimicked by incubating P815 (HLA negative) target cells with a synthetic peptide corresponding to the C-terminal 12 amino acids of the CW3 alpha 2 domain (residues 171 to 182). Other independent anti-CW3 CTL clones with different fine specificities recognized the same CW3 peptide. In contrast, CTL clones specific for HLA-A24 or HLA-A3 that did not lyse P815-CW3 transfectants did not recognize this peptide. The CW3 peptide could be recognized on other tumor cell targets that were also of H-2d origin, but not on those of H-2b or H-2k origin. The requirement for the expression of H-2Kd by the target cells was directly demonstrated using L cell Kd transfectants. Our results suggest that the CTL response of DBA/2 mice immunized with P815-CW3 transfectants is predominantly Kd restricted and focused on epitopes contained within the 12 C-terminal amino acids of the alpha 2 domain.     

Competition between unrelated peptides recognized by H-2-Kd restricted T cells

P815 (H-2d) target cells incubated with synthetic peptides corresponding to region 170-182 of HLA or to region 141-161 of influenza nucleoprotein (NP) are lysed by DBA/2 derived cytolytic T cells (CTL) specific for HLA or by BALB/c derived CTL-specific for NP, respectively. Both peptide Ag are recognized in the context of Kd. We show herein that these unrelated, nonhomologous peptides clearly compete reciprocally for recognition by the appropriate Kd restricted CTL. In contrast, different NP peptides that are recognized by other CTL restricted by HLA-B37, H-2-Db or KK, either failed to compete or were much less efficient as competitors than NP peptides recognized in the context of Kd. The efficiency of a peptide as a competitor correlated with its potency as an Ag. The most efficient competitor was a variant peptide of NP 147-158 with R156 deleted, which had been previously shown to be 1,000 times more efficient as an Ag than its natural homolog. Our results suggest that peptides recognized by CTL in the context of the same MHC class I restriction element may bind to the same or interdependent site(s) on the restriction molecule.     

The freshwater planarian Dugesia sicula Lepori from Sardinia (Platyhelminthes,Tricladida)

Fissiparous strains of freshwater triclads of the Dugesia gonocephala group were collected from 12 localities in Sardinia all situated not more than 5 kilometers from the coast. Some environmental factors and the sexual status of the specimens were noted at the time of collection. During the laboratory rearing 30% of individuals of each strain became sexual (ex-fissiparous individuals). All the examined strains showed common karyological and morphological characteristics suggestive of the species Dugesia sicula Lepori. The chromosome complement, which was a constant 27+2–3 B chromosomes, was classified as aneutriploid, due to its clearly documented characteristics. The fissiparous populations of D. sicula appear to have a high degree of tolerance to variations in environmental factors, especially temperature. Within the D. gonocephala group this species has the broadest distribution in the Mediterranean region.     

Genome‐wide analyses of rice root development QTLs and development of an online resource, Rootbrowse

Genetic control of root development in rice is complex and the underlying mechanisms (constitutive and adaptive) are poorly understood. Lowland and upland varieties of indica and japonica rice with contrasting root development characteristics have been crossed, mapping populations developed and a number of QTLs in different chromosomes were identified. As these studies have used different sets of markers and many of the QTLs identified are long, it is difficult to exploit the varietal difference for improved root traits by marker assisted selection and for identification of concerned alleles. Intensive data mining of literature resulted in the identification 861 root development QTLs and associated microsatellite markers located on different chromosomes. The QTL and marker data generated and the genome sequence of rice were used for construction of a relational database, Rootbrowse, using MySQL relational database management system and Bio::DB::GFF schema. The data is viewed using GBrowse visualization tool. It graphically displays a section of the genome and all features annotated on it including the QTLs. The QTLs can be displayed along with SSR markers, protein coding genes and/or known root development genes for prediction of probable candidate genes.     

Mitochondrial Haplogroup U5b3: A Distant Echo of the Epipaleolithic in Italy and the Legacy of the Early Sardinians

There are extensive data indicating that some glacial refuge zones of southern Europe (Franco-Cantabria, Balkans, and Ukraine) were major genetic sources for the human recolonization of the continent at the beginning of the Holocene. Intriguingly, there is no genetic evidence that the refuge area located in the Italian Peninsula contributed to this process. Here we show, through phylogeographic analyses of mitochondrial DNA (mtDNA) variation performed at the highest level of molecular resolution (52 entire mitochondrial genomes), that the most likely homeland for U5b3—a haplogroup present at a very low frequency across Europe—was the Italian Peninsula. In contrast to mtDNA haplogroups that expanded from other refugia, the Holocene expansion of haplogroup U5b3 toward the North was restricted by the Alps and occurred only along the Mediterranean coasts, mainly toward nearby Provence (southern France). From there, ∼7,000–9,000 years ago, a subclade of this haplogroup moved to Sardinia, possibly as a result of the obsidian trade that linked the two regions, leaving a distinctive signature in the modern people of the island. This scenario strikingly matches the age, distribution, and postulated geographic source of a Sardinian Y chromosome haplogroup (I2a2-M26), a paradigmatic case in the European context of a founder event marking both female and male lineages.     

Cell cycle related proteins in hyperplasia of usual type in breast specimens of patients with and without breast cancer

Background  

Hyperplasia of usual type (HUT) is a common proliferative lesion associated with a slight elevated risk for subsequent development of breast cancer. Cell cycle-related proteins would be helpful to determine the putative role of these markers in the process of mammary carcinogenesis. The aim of this study was to analyze the expression of cell cycle related proteins in HUT of breast specimens of patients with and without breast cancer, and compare this expression with areas of invasive carcinomas.     

A case with mosaic partial duplication of 1q: prenatal and postmortem clinical and cytogenetic evaluations

Partial trisomy 1q including different segments of the long arm is a rare cytogenetic anomaly. Especially the cases with mosaic proximal tandem duplication of 1q included a longer fragment are very rare. Cases who have partial 1q trisomy showed large phenotypic variation due to the differences in size of the duplicated segments of 1q. The clinical phenotype of most cases is characterized by multiple congenital anomalies especially including central nervous system and developmental delay. We describe a prenatally diagnosed case with mild cerebral ventriculomegaly and karyotype with mosaic pure trisomy of chromosome 1q [(46,XX/46,XX,dup(1)(q21qter)]. Phenotypic postmortem examination showed cranial asymmetry, flat and broad nasal bridge, anteverted nostrils, hypertelorism, retrognathia, abnormal pinnae, hypoplasic thumbs, long fingers and toes, mediodorsal curvature of the 4th and 5th toes and posterior prominence of the heel was observed. Autopsy confirmed the ventriculomegaly. Postmortem chromosome preparation from skin culture, cord blood and intracardiac blood confirmed the mosaic pure trisomy of chromosome 1q.     

Karyology and karyotype analysis of diploid freshwater planarian populations of the Dugesia gonocephala group (Platyhelminthes,Tricladida) found in Sardinia

Karyology and karyotype analysis were carried out on freshwater planarian populations of the Dugesia gonocephala group. The strains studied were all diploid with chromosomic number 2n = 16; n = 8. They came from 12 sites mainly localized on the west of the island of Sardinia. Three karyotypes indicated with the letters A, B and C were found in which eight homomorphic pairs of chromosomes were easily identified. In karyotype A all chromosomes are metacentric. Ten populations of the twelve examined showed this karyotype which appears to be the most common. In karyotype B the seventh pair of chromosomes is submetacentric. This karyotype is quite common having been previously found in another eight Sardinian localities. Karyotype C differs from the others in having submetacentric third and seventh pairs of the chromosome complement. It was found in only one locality. The differences observed between these three karyotypes could be interpreted either as sign of differentiation at species level, or as an intraspecific variation due to chromosome mutations (pericentric inversions). This revised version was published online in July 2006 with corrections to the Cover Date.     

Characterisation and application of glycanases secreted by Aspergillus terreus CCMI 498 and Trichoderma viride CCMI 84 for enzymatic deinking of mixed office wastepaper

Two enzymatic extracts obtained from xylan-grown Aspergillus terreus CCMI 498 and cellulose-grown Trichoderma viride CCMI 84 were characterised for different glycanase activities. Both strains produce extracellular endoxylanase and endoglucanase enzymes. The enzymes optimal activity was found in the temperature range of 45–60 °C. Endoglucanase systems show identical activity profiles towards temperature, regardless of the strain and inducing substrate. Conversely, the endoxylanases produced by both strains showed maximal activity at different pH values (from 4.5 to 5.5), being the more acidic xylanase produced by T. viride grown on cellulose. The endoglucanase activities have an optimum pH at 4.5–5.0. The endoxylanase and endoglucanase activities exhibited high stability at 50 °C and pH 5.0. Mannanase, β-xylosidase, and amylase activities were also found, being the first two activities only present for T. viride extract. These two enzymatic extracts were used for mixed office wastepaper (MOW) deinking. When the enzymatic extract from T. viride was used, a further increase of 24% in ink removal was obtained by comparison with the control. Both enzymes contributed to the improvement of the paper strength properties and the obtained results clearly indicate that the effective use of enzymes for deinking can also contribute to the pulp and paper properties improvement.     

Effect of pH on the structure and aggregation of human glycodelin A. A comparison with beta-lactoglobulin A

The effect of pH on the structure of glycodelin A (GdA) and of beta-lactoglobulin A (beta-LgA) has been investigated by means of circular dichroism, steady state fluorescence, synchrotron radiation small angle X-ray scattering (SR-SAXS) and gel permeation chromatography. The comparison between GdA and beta-LgA shows that, at pH 7.0, both proteins are dimers with an extended content of beta-sheet conformation, but pH 2.0 and 9.0 yield a different secondary, tertiary and quaternary structural organisation. Whilst beta-LgA is a monomer, that conserves beta-sheet conformation at pH 2.0 and 9.0, GdA has a stable dimeric structure at alkaline pH, but at pH 2.0 increases its alpha-helix content and it aggregates soon. SR beam has been used to perform SAXS comparative measurements of the two proteins. SR-SAXS data provide the radius of gyration and the radii of the cross-section and of the thickness. GdA aggregation at acid pH has been characterised by calculating the distance distribution function (P(r)). Isoelectric focusing and chromatofocusing data show a different charge distribution on the surfaces of the two proteins, supporting the hypothesis that the presence of oligosaccharides deeply influences the conformational state and the aggregation process of GdA at different pH values. In particular, the presence of sialic acid residues, within the oligosaccharide moiety of the GdA, might be responsible for the differences observed between the two proteins.