Sir Edward Seaward's narrative of his shipwreck, and consequent discovery of certain islands in the Caribbean Sea: with a detail of many extraordinary and highly interesting events in his life, from the year 1733 to 1749, as written in his own diary.

Also attributed to William Ogilvie Porter.

Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage

The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the present study we have assessed the complexity of the transcriptome expressed in mouse macrophages before and after treatment with lipopolysaccharide, a global regulator of macrophage gene expression, using existing RIKEN 19K arrays. By comparison to array profiles of other cells and tissues, we identify a large set of macrophage-enriched genes, many of which have obvious functions in endocytosis and phagocytosis. In addition, a significant number of LPS-inducible genes were identified. The data suggest that macrophages are a complex source of mRNA for transcriptome studies. To assess complexity and identify additional macrophage expressed genes, cDNA libraries were created from purified populations of macrophage and dendritic cells, a functionally related cell type. Sequence analysis revealed a high incidence of novel mRNAs within these cDNA libraries. These studies provide insights into the depths of transcriptional complexity still untapped amongst products of inducible genes, and identify macrophage and dendritic cell populations as a starting point for sampling the inducible mammalian transcriptome.

Assessing computational tools for the discovery of transcription factor binding sites

The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.

Discovery of a new source of rifamycin antibiotics in marine sponge actinobacteria by phylogenetic prediction

Phylogenetic analysis of the ketosynthase (KS) gene sequences of marine sponge-derived Salinispora strains of actinobacteria indicated that the polyketide synthase (PKS) gene sequence most closely related to that of Salinispora was the rifamycin B synthase of Amycolatopsis mediterranei. This result was not expected from taxonomic species tree phylogenetics using 16S rRNA sequences. From the PKS sequence data generated from our sponge-derived Salinispora strains, we predicted that such strains might synthesize rifamycin-like compounds. Liquid chromatography-tandem mass spectrometry (LC/MS/MS) analysis was applied to one sponge-derived Salinispora strain to test the hypothesis of rifamycin synthesis. The analysis reported here demonstrates that this Salinispora isolate does produce compounds of the rifamycin class, including rifamycin B and rifamycin SV. A rifamycin-specific KS primer set was designed, and that primer set increased the number of rifamycin-positive strains detected by PCR screening relative to the number detectable using a conserved KS-specific set. Thus, the Salinispora group of actinobacteria represents a potential new source of rifamycins outside the genus Amycolatopsis and the first recorded source of rifamycins from marine bacteria.

Discovery of an MIT-like atracotoxin family: Spider venom peptides that share sequence homology but not pharmacological properties with AVIT family proteins

This project identified a novel family of six 66-68 residue peptides from the venom of two Australian funnel-web spiders, Hadronyche sp. 20 and H. infensa: Orchid Beach (Hexathelidae: Atracinae), that appear to undergo N- and/or C-terminal post-translational modifications and conform to an ancestral protein fold. These peptides all show significant amino acid sequence homology to atracotoxin-Hvf17 (ACTX-Hvf17), a non-toxic peptide isolated from the venom of H. versuta, and a variety of AVIT family proteins including mamba intestinal toxin 1 (MIT1) and its mammalian and piscine orthologs prokineticin 1 (PK1) and prokineticin 2 PK2). These AVIT family proteins target prokineticin receptors involved in the sensitization of nociceptors and gastrointestinal smooth muscle activation. Given their sequence homology to MITI, we have named these spider venom peptides the MIT-like atracotoxin (ACTX) family. Using isolated rat stomach fundus or guinea-pia ileum organ bath preparations we have shown that the prototypical ACTX-Hvf17, at concentrations up to 1 mu M, did not stimulate smooth muscle contractility, nor did it inhibit contractions induced by human PK1 (hPK1). The peptide also lacked activity on other isolated smooth muscle preparations including rat aorta. Furthermore, a FLIPR Ca2+ flux assay using HEK293 cells expressing prokineticin receptors showed that ACTX-Hvf17 fails to activate or block hPK1 or hPK2 receptors. Therefore, while the MIT-like ACTX family appears to adopt the ancestral disulfide-directed beta-hairpin protein fold of MIT1, a motif believed to be shared by other AVIT family peptides, variations in the amino acid sequence and surface charge result in a loss of activity on prokineticin receptors. (c) 2005 Elsevier Inc. All rights reserved.

Discovery of a large-scale wall in the direction of Abell 22

We report on the discovery of a large-scale wall in the direction of Abell 22. Using photometric and spectroscopic data from the Las Campanas Observatory and Anglo-Australian Telescope Rich Cluster Survey, Abell 22 is found to exhibit a highly unusual and striking redshift distribution. We show, by examining the galaxy distributions both in redshift space and on the colour-magnitude plane, that Abell 22 exhibits a foreground wall-like structure. A search for other galaxies and clusters in the nearby region using the 2dF Galaxy Redshift Survey data base suggests that the wall-like structure is a significant large-scale, non-virialized filament which runs between two other Abell clusters either side of Abell 22. The filament stretches over at least > 40 h(-1) Mpc in length and 10 h(-1) Mpc in width at the redshift of Abell 22.

Discovery of cyclotide-like protein sequences in graminaceous crop plants: Ancestral precursors of circular proteins?

Cyclotides are peptides from plants of the Rubiaceae and Violaceae families that have the unusual characteristic of a macrocylic backbone. They are further characterized by their incorporation of a cystine knot in which two disulfides, along with the intervening backbone residues, form a ring through which a third disulfide is threaded. The cyclotides have been found in every Violaceae species screened to date but are apparently present in only a few Rubiaceae species. The selective distribution reported so far raises questions about the evolution of the cyclotides within the plant kingdom. In this study, we use a combined bioinformatics and expression analysis approach to elucidate the evolution and distribution of the cyclotides in the plant kingdom and report the discovery of related sequences widespread in the Poaceae family, including crop plants such as rice ( Oryza sativa), maize ( Zea mays), and wheat ( Triticum aestivum), which carry considerable economic and social importance. The presence of cyclotide-like sequences within these plants suggests that the cyclotides may be derived from an ancestral gene of great antiquity. Quantitative RT-PCR was used to show that two of the discovered cyclotide-like genes from rice and barley ( Hordeum vulgare) have tissue-specific expression patterns.

Discovery of ultracompact dwarf galaxies in the Virgo Cluster

We have discovered nine ultracompact dwarf galaxies (UCDs) in the Virgo Cluster, extending samples of these objects outside the Fornax Cluster. Using the Two Degree Field (2dF) multifiber spectrograph on the Anglo-Australian Telescope, the new Virgo members were found among 1500 color-selected, starlike targets with 16: 0 < b(j) < 20.2 in a 2 degrees diameter field centered on M87 (NGC 4486). The newly found UCDs are comparable to the UCDs in the Fornax Cluster, with sizes less than or similar to 100 pc, -12.9 < M-B < -10.7, and exhibiting red absorption-line spectra, indicative of an older stellar population. The properties of these objects remain consistent with the tidal threshing model for the origin of UCDs from the surviving nuclei of nucleated dwarf elliptical galaxies disrupted in the cluster core but can also be explained as objects that were formed by mergers of star clusters created in galaxy interactions. The discovery that UCDs exist in Virgo shows that this galaxy type is probably a ubiquitous phenomenon in clusters of galaxies; coupled with their possible origin by tidal threshing, the UCD population is a potential indicator and probe of the formation history of a given cluster. We also describe one additional bright UCD with M-B = -12.0 in the core of the Fornax Cluster. We find no further UCDs in our Fornax Cluster Spectroscopic Survey down to bj 19.5 in two additional 2dF fields extending as far as 3 degrees from the center of the cluster. All six Fornax bright UCDs identified with 2dF lie within 0.degrees 5 (projected distance of 170 kpc) of the central elliptical galaxy NGC 1399.

Expression-based strategies for discovery of genes involved in testis and ovary development

In recent years, strategies for gene identification based on differential gene expression have become increasingly popular, due in part to the development of microarray technology. These strategies are particularly well suited to the identification of genes involved in sex determination and gonadal development, which unlike the development of other organ systems, proceeds along two very different alternative courses, depending on the sex of the embryo. We have used a high-throughput, array-based expression screen to identify several genes expressed sex-specifically in developing mouse gonads. One of these, vanin 1, appears to play a role in mediating migration of mesonephric cells into the male genital ridge. Progress in characterizing other genes arising from the screen is discussed.

Isolation, characterization and discovery of new alleles of sHsp genes in durum wheat (Triticum durum Desf.)

Gli organismi vegetali mostrano una notevole capacità di adattamento alle condizioni di stress e lo studio delle componenti molecolari alla base dell'adattamento in colture cerealicole di interesse alimentare, come il frumento, è di particolare interesse per lo studio di varietà che consentano una buona produzione con basso input anche in condizioni ambientali non ottimali. L'esposizione delle colture cerealicole a stress termico durante determinate fasi del ciclo vitale influisce negativamente sulla resa e sulla qualità, a questo fine è necessario chiarire le basi genetiche e molecolari della termotolleranza per identificare geni e alleli vantaggiosi da impiegare in programmi di incrocio volti al miglioramento genetico. Numerosi studi dimostrano il coinvolgimento delle sHSP a localizzazione cloroplastica (in frumento sHSP26) nel meccanismo di acquisizione della termotolleranza e la loro interazione con diverse componenti del fotosistema II (PSII) che determinerebbe un’azione protettiva in condizioni di stress termico e altri tipi di stress. Lo scopo del progetto è quello di caratterizzare in frumento duro nuove varianti alleliche correlate alla tolleranza a stress termico mediate l'utilizzo del TILLING (Target Induced Local Lesion In Genome), un approccio di genetica inversa che prevede la mutagenesi e l'identificazione delle mutazioni indotte in siti di interesse. Durante la tesi sono state isolate e caratterizzate 3 sequenze geniche complete per smallHsp26 denominate TdHsp26-A1; TdHsp26-A2; TdHsp26-B1 e un putativo pseudogene denominato TdHsp26-A3. I geni isolati sono stati usati come target in analisi di TILLING in due popolazioni di frumento duro mutagenizzate con EMS (EtilMetanoSulfonato). Nel nostro studio sono stati impiegati due differenti approcci di TILLING: un approccio di TILLING classico mediante screening con High Resolution Melting (HRM) e un approccio innovativo che sfrutta un database di TILLING recentemente sviluppato. La popolazione di mutanti cv. Kronos è stata analizzata per la presenza di mutazioni in tutti e tre i geni individuati mediante ricerca online nel database di TILLING, il quale sfrutta la tecnica dell’exome capture sulla popolazione di TILLING seguito da sequenziamento ad alta processività. Attraverso questa tecnica sono state individuate, nella popolazione mutagenizzata di frumento duro cv. Kronos, 36 linee recanti mutazioni missenso. Contemporaneamente lo screening con HRM, effettuato su 960 genotipi della libreria di TILLING di frumento duro cv. Cham1 ha consentito di individuare mutazioni in una regione di 211bp di interesse funzionale del gene TdHsp26-B1, tra le quali 3 linee mutanti recanti mutazioni missenso in omozigosi. Alcune mutazioni missenso individuate sui due geni TdHsp26-A1 e TdHsp26-B1 sono state confermate in vivo nelle piante delle rispettive linee mutanti generando marcatori codominanti KASP (Kompetitive Allele Specific PCR) con cui è stato possibile verificare anche il grado di zigosità di tali mutazioni. Al fine di ridurre il numero di mutazioni non desiderate nelle linee risultate più interessanti, è stato eseguito il re-incrocio dei mutanti con i relativi parentali wild type ed inoltre sono stati generati alcuni doppi mutanti che consentiranno di comprendere meglio i meccanismi molecolari presieduti da questa classe genica. Gli individui F1 degli incroci sono stati poi genotipizzati con i medesimi marcatori KASP specifici per la mutazione di interesse per verificare la buona riuscita dell’incrocio. Questo approccio ha permesso di individuare ed implementare risorse genetiche utili ad intraprendere studi funzionali relativi al ruolo di smallHSP plastidiche implicate nella acquisizione di termotolleranza in frumento duro e di generare marcatori potenzialmente utili in futuri programmi di breeding.