Insights into a dinoflagellate genome through expressed sequence tag analysis

BACKGROUND: Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and photosynthetic organelles (plastids) that have been gained and lost multiple times. We generated EST sequences from non-normalized and normalized cDNA libraries from a culture of the toxic species Alexandrium tamarense to elucidate dinoflagellate evolution. Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging. RESULTS: Approximately 20% of the 6,723 unique (11,171 total 3'-reads) ESTs data could be annotated using Blast searches against GenBank. Several putative dinoflagellate-specific mRNAs were identified, including one novel plastid protein. Dinoflagellate genes, similar to other eukaryotes, have a high GC-content that is reflected in the amino acid codon usage. Highly represented transcripts include histone-like (HLP) and luciferin binding proteins and several genes occur in families that encode nearly identical proteins. We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X. We speculate this histone may be retained for its role in DNA double-strand break repair. CONCLUSION: This is the most extensive collection to date of ESTs from a toxic dinoflagellate. These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production

Quantum walks with spatiotemporal fractal disorder

We investigate the transport and entanglement properties exhibited by quantum walks with coin operators concatenated in a space-time fractal structure. Inspired by recent developments in photonics, we choose the paradigmatic Sierpinski gasket. The 0-1 pattern of the fractal is mapped into an alternation of the generalized Hadamard-Fourier operators. In fulfilling the blank space on the analysis of the impact of disorder in quantum walk properties -- specifically, fractal deterministic disorder --, our results show a robust effect of entanglement enhancement as well as an interesting novel road to superdiffusive spreading with a tunable scaling exponent attaining effective ballistic diffusion. Namely, with this fractal approach it is possible to obtain an increase in quantum entanglement without jeopardizing spreading. Alongside those features, we analyze further properties such as the degree of interference and visibility. The present model corresponds to a new application of fractals in an experimentally feasible setting, namely the building block for the construction of photonic patterned structures.Comment: 16 pages, 9 figure

Quantum walks in two dimensions: controlling directional spreading with entangling coins and tunable disordered step operator

We study a 2-D disordered time-discrete quantum walk based on 1-D `generalized elephant quantum walk' where an entangling coin operator is assumed and which paves the way to a new set of properties. We show that considering a given disorder in one direction, it is possible to control the degree of spreading and entanglement in the other direction. This observation helps assert that the random quantum walks of this ilk serve as a controllable decoherence channel with the degree of randomness being the tunable parameter and highlight the role of dimensionality in quantum systems regarding information and transport.Comment: 16 pages, 19 figure

CD4 T follicular cells and B cells

© 2023 Wiley-VCH GmbH.Regulatory and effector cell responses to Plasmodium vivax, the most common human malaria parasite outside Africa, remain understudied in naturally infected populations. Here, we describe peripheral CD4 + T- and B-cell populations during and shortly after an uncomplicated P. vivax infection in 38 continuously exposed adult Amazonians. Consistent with previous observations, we found an increased frequency in CD4 + CD45RA - CD25 + FoxP3 + T regulatory cells that express the inhibitory molecule CTLA-4 during the acute infection, with a sustained expansion of CD21 - CD27 - atypical memory cells within the CD19 + B-cell compartment. Both Th1- and Th2-type subsets of CXCR5 + ICOS hi PD-1 + circulating T follicular helper (cTfh) cells, which are thought to contribute to antibody production, were induced during P. vivax infection, with a positive correlation between overall cTfh cell frequency and IgG antibody titers to the P. vivax blood-stage antigen MSP1 19 . We identified significant changes in cell populations that had not been described in human malaria, such as an increased frequency of CTLA-4 + T follicular regulatory cells that antagonize Tfh cells, and a decreased frequency of circulating CD24 hi CD27 + B regulatory cells in response to acute infection. In conclusion, we disclose a complex immunoregulatory network that is critical to understand how naturally acquired immunity develops in P. vivax malaria.publishersversionepub_ahead_of_prin

Gene discovery in an invasive tephritid model pest species, the Mediterranean fruit fly, Ceratitis capitata

<p>Abstract</p> <p>Background</p> <p>The medfly, <it>Ceratitis capitata</it>, is a highly invasive agricultural pest that has become a model insect for the development of biological control programs. Despite research into the behavior and classical and population genetics of this organism, the quantity of sequence data available is limited. We have utilized an expressed sequence tag (EST) approach to obtain detailed information on transcriptome signatures that relate to a variety of physiological systems in the medfly; this information emphasizes on reproduction, sex determination, and chemosensory perception, since the study was based on normalized cDNA libraries from embryos and adult heads.</p> <p>Results</p> <p>A total of 21,253 high-quality ESTs were obtained from the embryo and head libraries. Clustering analyses performed separately for each library resulted in 5201 embryo and 6684 head transcripts. Considering an estimated 19% overlap in the transcriptomes of the two libraries, they represent about 9614 unique transcripts involved in a wide range of biological processes and molecular functions. Of particular interest are the sequences that share homology with <it>Drosophila </it>genes involved in sex determination, olfaction, and reproductive behavior. The medfly <it>transformer2 </it>(<it>tra2</it>) homolog was identified among the embryonic sequences, and its genomic organization and expression were characterized.</p> <p>Conclusion</p> <p>The sequences obtained in this study represent the first major dataset of expressed genes in a tephritid species of agricultural importance. This resource provides essential information to support the investigation of numerous questions regarding the biology of the medfly and other related species and also constitutes an invaluable tool for the annotation of complete genome sequences. Our study has revealed intriguing findings regarding the transcript regulation of <it>tra2 </it>and other sex determination genes, as well as insights into the comparative genomics of genes implicated in chemosensory reception and reproduction.</p

A pig multi-tissue normalised cDNA library: large-scale sequencing, cluster analysis and 9K micro-array resource generation

<p>Abstract</p> <p>Background</p> <p>Domestic animal breeding and product quality improvement require the control of reproduction, nutrition, health and welfare in these animals. It is thus necessary to improve our knowledge of the major physiological functions and their interactions. This would be greatly enhanced by the availability of expressed gene sequences in the databases and by cDNA arrays allowing the transcriptome analysis of any function.</p> <p>The objective within the AGENAE French program was to initiate a high-throughput cDNA sequencing program of a 38-tissue normalised library and generate a diverse microarray for transcriptome analysis in pig species.</p> <p>Results</p> <p>We constructed a multi-tissue cDNA library, which was normalised and subtracted to reduce the redundancy of the clones. Expressed Sequence Tags were produced and 24449 high-quality sequences were released in EMBL database. The assembly of all the public ESTs (available through SIGENAE website) resulted in 40786 contigs and 54653 singletons. At least one Agenae sequence is present in 11969 contigs (12.5%) and in 9291 of the deeper-than-one-contigs (22.8%). Sequence analysis showed that both normalisation and subtraction processes were successful and that the initial tissue complexity was maintained in the final libraries. A 9K nylon cDNA microarray was produced and is available through CRB-GADIE. It will allow high sensitivity transcriptome analyses in pigs.</p> <p>Conclusion</p> <p>In the present work, a pig multi-tissue cDNA library was constructed and a 9K cDNA microarray designed. It contributes to the Expressed Sequence Tags pig data, and offers a valuable tool for transcriptome analysis.</p

Identification of Differentially Expressed MicroRNAs in Osteosarcoma

A limited number of reports have investigated the role of microRNAs in osteosarcoma. In this study, we performed miRNA expression profiling of osteosarcoma cell lines, tumor samples, and normal human osteoblasts. Twenty-two differentially expressed microRNAs were identified using high throughput real-time PCR analysis, and 4 (miR-135b, miR-150, miR-542-5p, and miR-652) were confirmed and validated in a different group of tumors. Both miR-135b and miR-150 have been previously shown to be important in cancer. We hypothesize that dysregulation of differentially expressed microRNAs may contribute to tumorigenesis. They might also represent molecular biomarkers or targets for drug development in osteosarcoma