The SUMO project I. A survey of multiple populations in globular clusters

We present a general overview and the first results of the SUMO project (a SUrvey of Multiple pOpulations in Globular Clusters). The objective of this survey is the study of multiple stellar populations in the largest sample of globular clusters homogeneously analysed to date. To this aim we obtained high signal-to-noise (S/N>50) photometry for main sequence stars with mass down to ~0.5 M_SUN in a large sample of clusters using both archival and proprietary U, B, V, and I data from ground-based telescopes. In this paper, we focus on the occurrence of multiple stellar populations in twenty three clusters. We have defined a new photometric index cubi= (U-B)-(B-I), that turns out to be very effective for identifying multiple sequences along the red giant branch (RGB). We found that in the V-cubi diagram all clusters presented in this paper show broadened or multimodal RGBs, with the presence of two or more components. We found a direct connection with the chemical properties of different sequences, that display different abundances of light elements (O, Na, C, N, and Al). The cubi index is also a powerful tool to identify distinct sequences of stars along the horizontal branch and, for the first time in the case of NGC104 (47 Tuc), along the asymptotic giant branch. Our results demonstrate that i) the presence of more than two stellar populations is a common feature among globular clusters, as already highlighted in previous work; ii) multiple sequences with different chemical contents can be easily identified by using standard Johnson photometry obtained with ground-based facilities; iii) in the study of GC multiple stellar populations the cubi index is alternative to spectroscopy, and has the advantage of larger statistics.Comment: 23 pages, 20 figures, accepted for publication in MNRA

Characterization of regulatory sequences in alternative promoters of hypermethylated genes associated with tumor resistance to cisplatin

The development of cisplatin resistance in human cancers is controlled by multiple genes and leads to therapeutic failure. Hypermethylation of specific gene promoters is a key event in clinical resistance to cisplatin. Although the usage of multiple promoters is frequent in the transcription of human genes, the role of alternative promoters and their regulatory sequences have not yet been investigated in cisplatin resistance genes. In a new approach, we hypothesized that human cancers exploit the specific transcription factor-binding sites (TFBS) and CpG islands (CGIs) located in the alternative promoters of certain genes to acquire platinum drug resistance. To provide a useful resource of regulatory elements associated with cisplatin resistance, we investigated the TFBS and CGIs in 48 alternative promoters of 14 hypermethylated cisplatin resistance genes previously reported. CGIs prone to methylation were identified in 28 alternative promoters of 11 hypermethylated genes. The majority of alternative promoters harboring CGIs (93%) were clustered in one phylogenetic subclass, whereas the ones lacking CGIs were distributed in two unrelated subclasses. Regulatory sequences, initiator and TATA-532 prevailed over TATA-8 and were found in all the promoters. B recognition element (BRE) sequences were present only in alternative promoters harboring CGIs, but CCAAT and TAACC were found in both types of alternative promoters, whereas downstream promoter element sequences were significantly less frequent. Therefore, it was hypothesized that BRE and CGI sequences co-localized in alternative promoters of cisplatin resistance genes may be used to design molecular markers for drug resistance. A more extensive knowledge of alternative promoters and their regulatory elements in clinical resistance to cisplatin is likely to usher novel avenues for sensitizing human cancers to treatment.Cancer Prevention and Research Institute of Texas (CPRIT; no. RP130266

Agarose gel serum protein electrophoresis in cats with and without lymphoma and preliminary results of tandem mass fingerprinting analysis

<b>Background</b>: Serum electrophoretic profiles in cats are poorly characterized with respect to the protein components of the globulin fractions, and interpretation of the electrophoretograms has routinely been done in ignorance of the identity of the proteins found within each fraction. <b>Objectives</b>: To compare the protein fractions from serum protein electrophoresis (SPE) in healthy cats and those with lymphoma and to confirm some component proteins in the major fractions after feline SPE, using tandem mass fingerprinting analysis (TMFA). <b>Methods</b>: Total protein was measured and agarose gel SPE performed on blood collected from 14 healthy cats and 14 with lymphoma. The absolute protein concentration within each fraction was compared between the two groups. Bands corresponding to the SPE fractions were excised from two controls and a lymphoma cat and analysed by liquid chromatography coupled to mass spectrometry. Results were compared to sequences in the NCBI protein database. <b>Results</b>: Median albumin concentrations were significantly decreased in lymphoma cats and median beta globulin concentrations were elevated. Narrow electrophoretic spikes were present in the beta/gamma fraction in 3 lymphoma cats. Following TMFA, multiple proteins were identified from each fraction and their mobility agreed with results from previous studies generated using alternative techniques. Inter–alpha (globulin) inhibitor 4 was identified in feline serum for the first time. <b>Conclusions</b>: Cats with lymphoma had lower median albumin and higher beta globulin concentrations than healthy cats. Despite the limitations of 1D agarose gel SPE, TMFA provided preliminary data to confirm the protein components of the various fractio

Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. Methods: RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. Results: Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. Conclusions: Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation

Members of the zinc finger protein gene family sharing a conserved N-terminal module

We report the isolation of human members of a subfamily of structurally related finger protein genes. These potentially encode polypeptides containing finger motifs of the Krüppel type at the C-terminus, and a conserved amino acid module at the N-terminus; because of its invariant location the latter is referred to as finger preceding box (FPB). The FPB, detected also in previously described finger proteins from human, mouse and Xenopus, extends over approximately 65 amino acids and appears to be composed of two contiguous modules: FPB-A (residues 1-42) and FPB-B (residues 43-65). The latter is absent in some of the members analyzed. Elements A and B and the zinc finger domain are encoded by separate exons in the ZNF2 gene, a human member of this sub-family. The positioning of introns within this gene is remarkable. One intron flanks and a second interrupts the first codon of the FPB-A and FPB-B modules, respectively. A third intron occurs a few nucleotides downstream of FPB-B marking its separation from the remainder of the coding sequences. This organization, together with the absence of FPB-B in some cDNAs, supports the hypothesis that mRNAs encoding polypeptides that include one, both or none of the FPB-A and FPB-B modules may be assembled through alternative splicing pathways. Northern analyses showed that members of his sub-family are expressed as multiple transcripts in several cell lines. The sequences of distinct cDNAs homologous to the ZNF2 gene indicate that alternative splicing events adjoin either coding or non oding xons to the FPB sequences. © 1991 Oxford University Press

Genome-wide landscape of alternative splicing events in brachypodium distachyon

Recently, Brachypodium distachyon has emerged as a model plant for studying monocot grasses and cereal crops. Using assembled expressed transcript sequences and subsequent mapping to the corresponding genome, we identified 1219 alternative splicing (AS) events spanning across 2021 putatively assembled transcripts generated from 941 genes. Approximately, 6.3% of expressed genes are alternatively spliced in B. distachyon. We observed that a majority of the identified AS events were related to retained introns (55.5%), followed by alternative acceptor sites (16.7%).We also observed a low percentage of exon skipping (5.0%) and alternative donor site events (8.8%). The 'complex event' that consists of a combination of two or more basic splicing events accounted for ~14.0%. Comparative AS transcript analysis revealed 163 and 39 homologous pairs between B. distachyon and Oryza sativa and between B. distachyon and Arabidopsis thaliana, respectively. In all, we found 16 AS transcripts to be conserved in all 3 species. AS events and related putative assembled transcripts annotation can be systematically browsed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/plant/). © The Author 2012

An asymmetric approach to preserve common intervals while sorting by reversals

Dias Vieira Braga M, Gautier C, Sagot M-F. An asymmetric approach to preserve common intervals while sorting by reversals. Algorithms for Molecular Biology. 2009;4(1):16.Background: The reversal distance and optimal sequences of reversals to transform a genome into another are useful tools to analyse evolutionary scenarios. However, the number of sequences is huge and some additional criteria should be used to obtain a more accurate analysis. One strategy is searching for sequences that respect constraints, such as the common intervals (clusters of co-localised genes). Another approach is to explore the whole space of sorting sequences, eventually grouping them into classes of equivalence. Recently both strategies started to be put together, to restrain the space to the sequences that respect constraints. In particular an algorithm has been proposed to list classes whose sorting sequences do not break the common intervals detected between the two inital genomes A and B. This approach may reduce the space of sequences and is symmetric (the result of the analysis sorting A into B can be obtained from the analysis sorting B into A). Results: We propose an alternative approach to restrain the space of sorting sequences, using progressive instead of initial detection of common intervals (the list of common intervals is updated after applying each reversal). This may reduce the space of sequences even more, but is shown to be asymmetric. Conclusions: We suggest that our method may be more realistic when the relation ancestor-descendant between the analysed genomes is clear and we apply it to do a better characterisation of the evolutionary scenario of the bacterium Rickettsia felis with respect to one of its ancestors

New insight in lymnaeid snails (Mollusca, Gastropoda) as intermediate hosts of Fasciola hepatica (Trematoda, Digenea) in Belgium and Luxembourg

<b>Background</b><p></p> The present study aims to assess the epidemiological role of different lymnaeid snails as intermediate hosts of the liver fluke Fasciola hepatica in Belgium and Luxembourg.<p></p> <b>Methods</b><p></p> During summer 2008, 7103 lymnaeid snails were collected from 125 ponds distributed in 5 clusters each including 25 ponds. Each cluster was located in a different biogeographic area of Belgium and Luxembourg. In addition, snails were also collected in sixteen other biotopes considered as temporary wet areas. These snails were identified as Galba truncatula (n = 2474) (the main intermediate host of F. hepatica in Europe) and Radix sp. (n = 4629). Moreover, several biological and non-biological variables were also recorded from the different biotopes. DNA was extracted from each snail collected using Chelex® technique. DNA samples were screened through a multiplex PCR that amplifies lymnaeid internal transcribed spacer 2 gene sequences (500–600 bp) (acting as an internal control) and a 124 bp fragment of repetitive DNA from Fasciola sp.<p></p> <b>Results</b><p></p> Lymnaeid snails were found in 75 biotopes (53.2%). Thirty individuals of G. truncatula (1.31%) and 7 of Radix sp. (0.16%) were found to be positive for Fasciola sp. The seven positive Radix sp. snails all belonged to the species R. balthica (Linnaeus, 1758). Classification and regression tree analysis were performed in order to better understand links and relative importance of the different recorded factors. One of the best explanatory variables for the presence/absence of the different snail species seems to be the geographic location, whereas for the infection status of the snails no obvious relationship was linked to the presence of cattle.<p></p> <b>Conclusions</b><p></p> Epidemiological implications of these findings and particularly the role of R. balthica as an alternative intermediate host in Belgium and Luxembourg were discussed