Analysis of horizontal genetic transfer in red algae in the post-genomics age

The recently published genome of the unicellular red alga revealed a gene-rich, intron-poor species, which is surprising for a free-living mesophile. Of the 8,355 predicted protein-coding regions, up to 773 (9.3%) were implicated in horizontal genetic transfer (HGT) events involving other prokaryote and eukaryote lineages. A much smaller number, up to 174 (2.1%) showed unambiguous evidence of vertical inheritance. Together with other red algal genomes, nearly all published in 2013, these data provide an excellent platform for studying diverse aspects of algal biology and evolution. This novel information will help investigators test existing hypotheses about the impact of endosymbiosis and HGT on algal evolution and enable comparative analysis within a more-refined, hypothesis-driven framework that extends beyond HGT. Here we explore the impacts of this infusion of red algal genome data on addressing questions regarding the complex nature of algal evolution and highlight the need for scalable phylogenomic approaches to handle the forthcoming deluge of sequence information

The origin of plastids

Organelles, called plastids, are the main sites of photosynthesis in eukaryotic cells. Chloroplasts, as well as any other pigment containing cytoplasmic organelles that enables the harvesting and conversion of light and carbon dioxide into food and energy, are plastids. Found mainly in eukaryotic cells, plastids can be grouped into two distinctive types depending on their membrane structure: primary plastids and secondary plastids. Primary plastids are found in most algae and plants, and secondary, more-complex plastids are typically found in plankton, such as diatoms and dinoflagellates. Exploring the origin of plastids is an exciting field of research because it enhances our understanding of the basis of photosynthesis in green plants, our primary food source on planet Earth

Quantum dot polarized light sources

The design, operation and performance of quantum dot spin-polarized vertical cavity surface emitting lasers (VCSELs) and single-photon sources are described and discussed. The effects of spin-induced gain anisotropy on output polarization and threshold current reduction have been studied along with the high-frequency response in a spin-polarized VCSEL. While the output circular polarization in a VCSEL follows the out-of-plane magnetization characteristics of the ferromagnetic spin injector, the output polarization of the spin-polarized single-photon source shows a switching behavior which is explained by invoking the exciton fine structure in the quantum dots and the effects of electron–hole exchange splitting due to in-plane quantum dot rotational asymmetry.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90780/1/0268-1242_26_1_014002.pd

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R

A frequent bottleneck in interpreting pylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of rnonophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R. package for classifying phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa based on tip labels (i.e., leaves) on a tree, with customisable options to assess clades within the context of the whole tree. Using simulated and empirical datasets, we demonstrate the potential and scalability of PhySortR in analysis of thousands of phylogenetic trees without a priori assumption of tree-rooting, and in yielding readily interpretable trees that unambiguously satisfy the query. PhySortR is a command line tool that is freely available and easily automatable

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

PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas

<p>Abstract</p> <p>Background</p> <p>Phylogenomic pipelines generate a large collection of phylogenetic trees that require manual inspection to answer questions about gene or genome evolution. A notable application of phylogenomics is to photosynthetic organelle (plastid) endosymbiosis. In the case of primary endosymbiosis, a heterotrophic protist engulfed a cyanobacterium, giving rise to the first photosynthetic eukaryote. Plastid establishment precipitated extensive gene transfer from the endosymbiont to the nuclear genome of the 'host'. Estimating the magnitude of this endosymbiotic gene transfer (EGT) and determining the functions of the prokaryotic genes remain controversial issues. We used phylogenomics to study EGT in the model green alga <it>Chlamydomonas reinhardtii</it>. To facilitate this procedure, we developed PhyloSort to rapidly search large collection of trees for monophyletic relationships. Here we present PhyloSort and its application to estimating EGT in <it>Chlamydomonas</it>.</p> <p>Results</p> <p>PhyloSort is an open-source tool to sort phylogenetic trees by searching for user specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units in a phylogenomic context. Using PhyloSort, we identified 897 <it>Chlamydomonas </it>genes of putative cyanobacterial origin, of which 531 had bootstrap support values ≥ 50% for the grouping of the algal and cyanobacterial homologs.</p> <p>Conclusion</p> <p>PhyloSort can be applied to quantify the number of genes that support different evolutionary hypotheses such as a taxonomic classification or endosymbiotic or horizontal gene transfer events. In our application, we demonstrate that cyanobacteria account for 3.5–6% of the protein-coding genes in the nuclear genome of <it>Chlamydomonas</it>.</p

Endosymbiont or host: who drove mitochondrial and plastid evolution?

The recognition that mitochondria and plastids are derived from alphaproteobacterial and cyanobacterial endosymbionts, respectively, was one of the greatest advances in modern evolutionary biology. Researchers have yet however to provide detailed cell biological descriptions of how these once free-living prokaryotes were transformed into intracellular organelles. A key area of study in this realm is elucidating the evolution of the molecular machines that control organelle protein topogenesis. Alcock et al. (Science 2010, 327 [5966]:649-650) suggest that evolutionary innovations that established the mitochondrial protein sorting system were driven by the alphaproteobacterial endosymbiont (an "insiders' perspective"). In contrast, here we argue that evolution of mitochondrial and plastid topogenesis may better be understood as an outcome of selective pressures acting on host cell chromosomes (the "outsiders' view")

Giant infiltrating lipoma of the thigh: a rare case report and literature review

Giant infiltrating lipoma of thigh, infrequently observed. Subcutaneous and gastrointestinal lipomas are not infrequently encountered, but huge, encapsulated or infiltrating lipomas of the thigh are rarely observed. They are of interest because causing functional limitation and due to their tendency to recur after surgical removal and their potential hazard of malignant transformation. The clinical findings and surgical management of a 72 year old man with a large infiltrating lipoma of thigh are reported here