The PPGMRPP repetitive epitope of the Sm autoantigen: Antigenic specificity induced by conformational changes. Application of the Sequential Oligopeptide Carriers (SOCs)

The PPGMRPP sequence, found in several copies in the Sm and U1RNPautoantigens, is the main target of anti-Sm and anti-U1RNP antibodies insystemic lupus erythematosus (SLE) and mixed connective tissue disease(MCTD) patient's sera. It is also recognized, to a lower extent, byanti-Ro/SSA and anti-La/SSB specificities. The PPGMRPP-NH₂peptide amide and the PPGMRPP peptide, which is bound to a pentamericsequential oligopeptide carrier (SOC₅), were examined by¹H-NMR spectroscopy and ELISA assays, using sera from patientswith autoimmune rheumatic diseases. Among the three main conformers foundfor the free PPGMRPP, the extended one was also identified for PPGMRPP-NH₂ and (PPGMRPP)₅-SOC₅.This can be attributed to the absence of ionic interactions between theArg-guanidinium and the carboxylate group in the amide andSOC₅-bound forms of the peptide. Immunoassays using sera fromvarious specificities showed an enhanced anti-Sm and anti-U1RNP recognitionof PPGMRPP-NH₂ and(PPGMRPP)₅-SOC₅, and lowering of the anti-Ro/SSAand anti-La/SSB reactivity. The presence of multiple conformers of freePPGMRPP may explain the unexpected cross-reactivity to the anti-Ro/Lapositive sera, while the prevalence of the extended conformation inPPGMRPP-NH₂ and (PPGMRPP)₅-SOC₅is mainly responsible for the enhanced recognition from the anti-Sm andanti-U1RNP autoantibodies. It is concluded that the antigenic specificity ofPPGMRPP-NH₂ and (PPGMRPP)₅-SOC₅ ismainly induced by conformational changes resulting from the conversion ofthe C-terminal carboxylate group to the amide form.     

Arsonoliposomes: effect of lipid composition on their stability and morphology

The influence of the lipid composition of arsonoliposomes on their membrane integrity was investigated to evaluate whether it is possible to combine their action with drugs that can be encapsulated in their aqueous interior. This was investigated by measuring the retention of vesicle-encapsulated calcein (100 mM) during incubation, in the absence and presence of serum proteins. Liposomes containing various concentrations of arsonolipid (with the palmitoyl side chain) as well as egg-lecithin (phosphatidylcholine, PC) and cholesterol (lipid/chol 2:1 mol:mol) were prepared. In some experiments, PC was replaced by the synthetic phospholipid DSPC. All PC/arsonoliposomes tested are stable after 24 h of incubation in buffer at 37 degrees C. After incubation in the presence of serum proteins, arsonoliposomes that contain low amounts of arsonolipid (up to 5 mol% of the lipid content without cholesterol) are stable, whereas increased release of calcein is observed when vesicle arsonolipid concentration is raised (from 5 to 15 mol%). Further increase of arsonolipid content results in immediate decrease of calcein latency while the remaining calcein is rapidly released during incubation. DSPC/arsonoliposomes are comparably more stable, and membrane integrity is independent of the vesicle arsonolipid content, in the range investigated (15-40 mol% of the lipid content without cholesterol). Thereby, we conclude that more stable arsonoliposomes that incorporate high arsonolipid concentrations may be produced when PC is replaced by DSPC. The latter arsonoliposomes provide a system that may be used for combining arsonolipid activity with the activity of other drugs.     

A Sequence Alignment-Independent Method for Protein Classification

Annotation of the rapidly accumulating body of sequence data relies heavily on the detection of remote homologues and functional motifs in protein families. The most popular methods rely on sequence alignment. These include programs that use a scoring matrix to compare the probability of a potential alignment with random chance and programs that use curated multiple alignments to train profile hidden Markov models (HMMs). Related approaches depend on bootstrapping multiple alignments from a single sequence. However, alignment-based programs have limitations. They make the assumption that contiguity is conserved between homologous segments, which may not be true in genetic recombination or horizontal transfer. Alignments also become ambiguous when sequence similarity drops below 40%. This has kindled interest in classification methods that do not rely on alignment. An approach to classification without alignment based on the distribution of contiguous sequences of four amino acids (4-grams) was developed. Interest in 4-grams stemmed from the observation that almost all theoretically possible 4-grams (20(4)) occur in natural sequences and the majority of 4-grams are uniformly distributed. This implies that the probability of finding identical 4-grams by random chance in unrelated sequences is low. A Bayesian probabilistic model was developed to test this hypothesis. For each protein family in Pfam-A and PIR-PSD, a feature vector called a probe was constructed from the set of 4-grams that best characterised the family. In rigorous jackknife tests, unknown sequences from Pfam-A and PIR-PSD were compared with the probes for each family. A classification result was deemed a true positive if the probe match with the highest probability was in first place in a rank-ordered list. This was achieved in 70% of cases. Analysis of false positives suggested that the precision might approach 85% if selected families were clustered into subsets. Case studies indicated that the 4-grams in common between an unknown and the best matching probe correlated with functional motifs from PRINTS. The results showed that remote homologues and functional motifs could be identified from an analysis of 4-gram patterns.     

Insularity affects head morphology,bite force and diet in a Mediterranean lizard

Island environments differ with regard to numerous features from the mainland and may induce large‐scale changes in most aspects of the biology of an organism. In this study, we explore the effect of insularity on the morphology and performance of the feeding apparatus, a system crucial for the survival of organisms. To this end, we examined the head morphology and feeding ecology of island and mainland populations of the Balkan green lizard, Lacerta trilineata. We predicted that head morphology, performance and diet composition would differ between sexes and habitats as a result of varying sexual and natural selection pressures. We employed geometric morphometrics to test for differences in head morphology, measured bite forces and analysed the diet of 154 adult lizards. Morphological analyses revealed significant differences between sexes and also between mainland and island populations. Relative to females, males had larger heads, a stronger bite and consumed harder prey than females. Moreover, island lizards differed in head shape, but not in head size, and, in the case of males, demonstrated a higher bite force. Islanders had a wider food niche breadth and included more plant material in their diet. Our findings suggest that insularity influences feeding ecology and, through selection on bite force, head morphology. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 469–484.     

Distribution Patterns and Conservation Perspectives of the Endemic Flora of Peloponnese (Greece)

An inventory of the endemic vascular plants of the Peloponnese (395 species and subspecies) has been created based on literature, herbarium and field data. Endemics?? distribution patterns, altitudinal distribution and habitat specificity were investigated. A rarity score for each endemic has been calculated based on its population size, geographic range and habitat specificity. The main mountainous areas of the Peloponnese are largely congruent to the hotspots of endemism. Altitudinal range and niche breadth of the endemics were positively correlated to their range size. The elevational gradient of the endemic species richness showed a hump-shaped pattern, in contrast to the monotonically decreasing pattern of total species richness. Endemic species were found to support boundary theory, while total species richness distribution followed the Rapoport??s elevational rule. The elevational distribution of the average rarity score and the average weighted threat of the endemics resulted in low values for mid-elevation intervals and increased values for low and high altitude areas, indicating that conservation efforts should focus on the two extremes of the elevational gradient. Area prioritization methods were applied using a rarity/complementarity based algorithm with two species weighting schemes. Their results were largely congruent confirming the significance of the main mountainous areas for the conservation of the endemics. Spatial overlap among selected grid cells using the rarity/complementarity analysis and Natura 2000 network was found to be low. Our results revealed the conservation importance of at least one new area located on Kythera Island.     

Validation of rat reference genes for improved quantitative gene expression analysis using low density arrays

Real-time PCR has become increasingly important in gene expression profiling research, and it is widely agreed that normalized data are required for accurate estimates of messenger RNA (mRNA) expression. With increased gene expression profiling in preclinical research and toxicogenomics, a need for reference genes in the rat has emerged, and the studies in this area have not yet been thoroughly evaluated. The purpose of our study was to evaluate a panel of rat reference genes for variation of gene expression in different tissue types. We selected 48 known target genes based on their putative invariability. The gene expression of all targets was examined in 11 types of rat tissues using TaqMan low density array (LDA) technology. The variability of each gene was assessed using a two-step statistical model. The analysis of mean expression using multiple reference genes was shown to provide accurate and reliable normalized expression data. The least five variable genes from each specific tissue were recommended for future tissue-specific studies. Finally, a subset of investigated rat reference genes showing the least variation is recommended for further evaluation using the LDA platform. Our work should considerably enhance a researcher's ability to simply and efficiently identify appropriate reference genes for given experiments.     

Global similarity and local divergence in human and mouse gene co-expression networks

Background  

A genome-wide comparative analysis of human and mouse gene expression patterns was performed in order to evaluate the evolutionary divergence of mammalian gene expression. Tissue-specific expression profiles were analyzed for 9,105 human-mouse orthologous gene pairs across 28 tissues. Expression profiles were resolved into species-specific coexpression networks, and the topological properties of the networks were compared between species.     

Palaeoenvironmental conditions preceding the Messinian Salinity Crisis: A case study from Gavdos Island

The Messinian pre-evaporitic sedimentary succession of Gavdos Island (Metochia section) is a nearly uninterrupted succession of marine sediments, dominated by finely laminated diatomaceous marls, which are cyclically alternating with clayey diatomites and white diatomites. The qualitative and quantitative analysis of the planktonic foraminiferal fauna allowed the recognition of nine bioevents, which have been astronomically dated for the Mediterranean. The base of the diatomitic succession in Gavdos Island is dated at 6.722 Ma and the top at 6.015 Ma. The studied section contains benthic foraminiferal genera characteristic of an outer shelf to slope environment. The qualitative and quantitative analysis of this microfauna revealed three benthic foraminiferal fossil assemblages and the occurrence of allochthonous species transported into the bathyal environment by current activity. The cyclical pattern of the benthic foraminifera assemblages indicates that the studied sediments have been affected by repeated episodes of basin restriction characterized by low diversity benthic foraminifera populations, and a limited planktonic foraminifer association typified by shallow, surface-dwelling forms. This restriction was partly due to Antarctic cooling, which produced palaeo-Mediterranean sea-level oscillations during the Early Messinian, as a prelude to closure of the Atlantic connections. The relative impact of climatic versus tectonic control on sedimentation patterns within this basin is discussed.     

SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing

SOP3 is a web-based software tool for designing oligonucleotide primers for use in the analysis of single nucleotide polymorphisms (SNPs). Accessible via the Internet, the application is optimized for developing the PCR and sequencing primers that are necessary for Pyrosequencing. The application accepts as input gene name, SNP reference sequence number, or chromosomal nucleotide location. Output can be parsed by gene name, SNP reference number, heterozygosity value, location, chromosome, or function. The location of an individual polymorphism, such as an intron, exon, or 5' or 3' untranslated region is indicated, as are whether nucleotide changes in an exon are associated with a change in an amino acid sequence. SOP3 presents for each entry a set of forward and biotinylated reverse PCR primers as well as a sequencing primer for use during the analysis of SNPs by Pyrosequencing. Theoretical pyrograms for each allele are calculated and presented graphically. The method has been tested in the development of Pyrosequencing assays for determining SNPs and for deletion/insertion polymorphisms in the human genome. Of the SOP3-designed primer sets that were tested, a large majority of the primer sets have successfully produced PCR products and Pyrosequencing data.