scholarly journals Endosymbiotic Gene Transfer in Tertiary Plastid-Containing Dinoflagellates

2013 ◽  
Vol 13 (2) ◽  
pp. 246-255 ◽  
Author(s):  
Fabien Burki ◽  
Behzad Imanian ◽  
Elisabeth Hehenberger ◽  
Yoshihisa Hirakawa ◽  
Shinichiro Maruyama ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Host Genome ◽  
Data Sets ◽  
Transcriptome Data ◽  
Endosymbiotic Gene Transfer ◽  
Low Level ◽  
Long Period ◽  
Host Nucleus ◽  
Endosymbiotic Origin

ABSTRACTPlastid establishment involves the transfer of endosymbiotic genes to the host nucleus, a process known as endosymbiotic gene transfer (EGT). Large amounts of EGT have been shown in several photosynthetic lineages but also in present-day plastid-lacking organisms, supporting the notion that endosymbiotic genes leave a substantial genetic footprint in the host nucleus. Yet the extent of this genetic relocation remains debated, largely because the long period that has passed since most plastids originated has erased many of the clues to how this process unfolded. Among the dinoflagellates, however, the ancestral peridinin-containing plastid has been replaced by tertiary plastids on several more recent occasions, giving us a less ancient window to examine plastid origins. In this study, we evaluated the endosymbiotic contribution to the host genome in two dinoflagellate lineages with tertiary plastids. We generated the first nuclear transcriptome data sets for the “dinotoms,” which harbor diatom-derived plastids, and analyzed these data in combination with the available transcriptomes for kareniaceans, which harbor haptophyte-derived plastids. We found low level of detectable EGT in both dinoflagellate lineages, with only 9 genes and 90 genes of possible tertiary endosymbiotic origin in dinotoms and kareniaceans, respectively, suggesting that tertiary endosymbioses did not heavily impact the host dinoflagellate genomes.

scholarly journals Genomic perspectives on the birth and spread of plastids

2015 ◽  
Vol 112 (33) ◽  
pp. 10147-10153 ◽  
Author(s):  
John M. Archibald
Keyword(s):  
Gene Transfer ◽  
Deep Structure ◽  
The Other ◽  
Endosymbiotic Gene Transfer ◽  
Microbial Eukaryotes ◽  
Eukaryotic Genes ◽  
History Of ◽  
Potential Impact ◽  
Cyanobacterial Genes ◽  
Endosymbiotic Origin

The endosymbiotic origin of plastids from cyanobacteria was a landmark event in the history of eukaryotic life. Subsequent to the evolution of primary plastids, photosynthesis spread from red and green algae to unrelated eukaryotes by secondary and tertiary endosymbiosis. Although the movement of cyanobacterial genes from endosymbiont to host is well studied, less is known about the migration of eukaryotic genes from one nucleus to the other in the context of serial endosymbiosis. Here I explore the magnitude and potential impact of nucleus-to-nucleus endosymbiotic gene transfer in the evolution of complex algae, and the extent to which such transfers compromise our ability to infer the deep structure of the eukaryotic tree of life. In addition to endosymbiotic gene transfer, horizontal gene transfer events occurring before, during, and after endosymbioses further confound our efforts to reconstruct the ancient mergers that forged multiple lines of photosynthetic microbial eukaryotes.

The Roots of Mountains

1944 ◽  
Vol 81 (2) ◽  
pp. 77-80
Author(s):  
G. F. S. Hills
Keyword(s):  
Intermediate Layer ◽  
Plastic Medium ◽  
Low Level ◽  
Long Period ◽  
The Alps ◽  
Mountain Chain

The two Palaeozoic ranges, the Caledonian and the Hercynian, were comparable in size with the Alps. In his chapter on the European Altaids, F. E. Suess1 says “Recent investigations have brought evidence that the original Variscan mountain chain of which now only scanty remains are left, was once not inferior in size and extension to the Alps to-day”. The remains of both ranges are now at a low level, and it was for some time tacitly accepted that that low level was due to denudation through the long period since they were formed. That low level is not, however, consistent with isostatic theory. Isostatic theory requires that a mountain must have strong roots immersed in a heavier plastic medium so that in effect the chain and its roots float “hydrostatically” in that medium. Accordingly if a layer h km. thick and density p is removed from the top of the range, the level of the range will fall by h (1 − /σ) where σ is the density of the plastic medium. If p = 2·6 for granite, and σ = 2·85 for the intermediate layer, the level will fall by − km.

scholarly journals Phylogenetic evidence of headful packaging strategy in gene transfer agents

2020 ◽  
Author(s):  
Emma Esterman ◽  
Yuri I. Wolf ◽  
Roman Kogay ◽  
Eugene V. Koonin ◽  
Olga Zhaxybayeva
Keyword(s):  
Gene Transfer ◽  
Rhodobacter Capsulatus ◽  
Large Subunit ◽  
Dna Packaging ◽  
Host Genome ◽  
Bacterial And Archaeal Communities ◽  
History Of ◽  
Viral Dna Packaging ◽  
Packaging Strategy ◽  
Transfer Agents

AbstractGene transfer agents (GTAs) are virus-like particles encoded and produced by many bacteria and archaea. Unlike viruses, GTAs package fragments of the host genome instead of the genes that encode the components of the GTA itself. As a result of this non-specific DNA packaging, GTAs can transfer genes within bacterial and archaeal communities. GTAs clearly evolved from viruses and are thought to have been maintained in prokaryotic genomes due to the advantages associated with their DNA transfer capacity. The most-studied GTA is produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), which packages random portions of the host genome at a lower DNA density than usually observed in tailed bacterial viruses. How the DNA packaging properties of RcGTA evolved from those of the ancestral virus remains unknown. To address this question, we reconstructed the evolutionary history of the large subunit of the terminase (TerL), a highly conserved enzyme used by viruses and GTAs to package DNA. We found that RcGTA-like TerLs grouped within viruses that employ the headful packaging strategy. Because distinct mechanisms of viral DNA packaging correspond to differences in the TerL amino acid sequence, our finding suggests that RcGTA evolved from a headful packaging virus. Headful packaging is the least sequence-specific mode of DNA packaging, which would facilitate the switch from packaging of the viral genome to packaging random pieces of the host genome during GTA evolution.

scholarly journals Expression of a foreign gene in cats reconstituted with retroviral vector infected autologous bone marrow

Blood ◽  
1991 ◽  
Vol 78 (1) ◽  
pp. 237-245 ◽  
Author(s):  
CD Jr Lothrop ◽  
ZS al-Lebban ◽  
GP Niemeyer ◽  
JB Jones ◽  
MG Peterson ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Bone Marrow ◽  
Gene Transfer ◽  
Autologous Bone Marrow ◽  
Retroviral Vectors ◽  
Retroviral Vector ◽  
Foreign Gene ◽  
Large Animal ◽  
Low Level ◽  
Autologous Bone

Abstract A Moloney murine leukemia virus based retroviral vector was used to transfer the bacterial neomycin resistance gene (neoR) into feline hematopoietic cells. We reconstituted four cats that had been lethally irradiated with autologous bone marrow that had been infected with the N2 or SAX retroviral vector. Bone marrow cells from all four cats expressed the neoR gene 30 days posttransplant and three of four cats still had the neoR gene and a low level of drug resistant colony- forming unit granulocyte-macrophage after more than 200 days. Two of the four cats unexpectedly developed diabetes mellitus 90 days posttransplantation. The expression of a foreign gene in cats, albeit at a low level, demonstrates that retroviral vectors can be used for gene transfer in noninbred large animal species and may be useful for gene therapy of humans. The development of diabetes mellitus in two of the subjects emphasizes the value of animal models for the study of possible deleterious effects of retroviral vector-mediated gene transfer.

scholarly journals CoMM: A Collaborative Mixed Model That Integrates GWAS and eQTL Data Sets to Investigate the Genetic Architecture of Complex Traits

2019 ◽  
Vol 13 ◽  
pp. 117793221988143 ◽  
Author(s):  
Kar-Fu Yeung ◽  
Yi Yang ◽  
Can Yang ◽  
Jin Liu
Keyword(s):  
Gene Expression ◽  
Association Study ◽  
Genetic Variants ◽  
Complex Traits ◽  
Mixed Model ◽  
Genome Wide Association Study ◽  
Data Sets ◽  
Transcriptome Data ◽  
Data Set ◽  
Expression Levels

Genome-wide association study (GWAS) analyses have identified thousands of associations between genetic variants and complex traits. However, it is still a challenge to uncover the mechanisms underlying the association. With the growing availability of transcriptome data sets, it has become possible to perform statistical analyses targeted at identifying influential genes whose expression levels correlate with the phenotype. Methods such as PrediXcan and transcriptome-wide association study (TWAS) use the transcriptome data set to fit a predictive model for gene expression, with genetic variants as covariates. The gene expression levels for the GWAS data set are then ‘imputed’ using the prediction model, and the imputed expression levels are tested for their association with the phenotype. These methods fail to account for the uncertainty in the GWAS imputation step, and we propose a collaborative mixed model (CoMM) that addresses this limitation by jointly modelling the multiple analysis steps. We illustrate CoMM’s ability to identify relevant genes in the Northern Finland Birth Cohort 1966 data set and extend the model to handle the more widely available GWAS summary statistics.

scholarly journals New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

2019 ◽  
Vol 36 (4) ◽  
pp. 757-765 ◽  
Author(s):  
Jürgen F H Strassert ◽  
Mahwash Jamy ◽  
Alexander P Mylnikov ◽  
Denis V Tikhonenkov ◽  
Fabien Burki
Keyword(s):  
Phylogenetic Signal ◽  
Evolutionary Origin ◽  
Phylogenetic Position ◽  
Aquatic Environments ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Transcriptome Data ◽  
Phylogenetic Reconstructions ◽  
Phylogenomic Analyses ◽  
Alignment Length

AbstractThe resolution of the broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these “orphan” groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome data sets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker “TSAR” to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

scholarly journals The Measurement of Long-Period Oscillations at Sacramento Peak Observatory and South Pole

1983 ◽  
Vol 66 ◽  
pp. 43-54
Author(s):  
Robin Stebbins ◽  
Christopher Wilson
Keyword(s):  
Data Analysis ◽  
Solar Limb ◽  
Data Sets ◽  
South Pole ◽  
Sacramento Peak ◽  
Long Period ◽  
Peak Observatory ◽  
South Pole Telescope ◽  
Sacramento Peak Observatory ◽  
A Site

AbstractA program to measure long-period brightness oscillations at the solar limb has been pursued at Sacramento Peak Observatory for several years. Past improvements in observing technique and data analysis are reviewed. The encouraging results aid in the verification of the reality and the origin of oscillatory signals. However, the main stumbling block to this and other observational programs is the length of observing sequences imposed by the day/night cycle. The South Pole has received considerable attention as a site where extended observations might be possible. Currently, the Sacramento Peak program is developing a South Pole telescope designed for the observing technique and data analysis proven in Sunspot. A review of pertinent South Pole site parameters is given here for other workers who may be considering South Pole observations. Observing sequences longer than 150 hr are possible, though rare. Data sets of this duration are very attractive for solar oscillation studies.

scholarly journals Assessing Geographical Origin of Gentiana Rigescens Using Untargeted Chromatographic Fingerprint, Data Fusion and Chemometrics

Molecules ◽  
2019 ◽  
Vol 24 (14) ◽  
pp. 2562 ◽  
Author(s):  
Shen ◽  
Yu ◽  
Wang
Keyword(s):  
Data Fusion ◽  
Geographical Origin ◽  
Data Sets ◽  
Classification Models ◽  
Hplc Fingerprint ◽  
Low Level ◽  
Level Data ◽  
Stems And Leaves ◽  
Gentiana Rigescens ◽  
Fingerprint Data

Gentiana rigescens Franchet, which is famous for its bitter properties, is a traditional drug of chronic hepatitis and important raw materials for the pharmaceutical industry in China. In the study, high-performance liquid chromatography (HPLC), coupled with diode array detector (DAD) and chemometrics, were used to investigate the chemical geographical variation of G. rigescens and to classify medicinal materials, according to their grown latitudes. The chromatographic fingerprints of 280 individuals and 840 samples from rhizomes, stems, and leaves of four different latitude areas were recorded and analyzed for tracing the geographical origin of medicinal materials. At first, HPLC fingerprints of underground and aerial parts were generated while using reversed-phase liquid chromatography. After the preliminary data exploration, two supervised pattern recognition techniques, random forest (RF) and orthogonal partial least-squares discriminant analysis (OPLS-DA), were applied to the three HPLC fingerprint data sets of rhizomes, stems, and leaves, respectively. Furthermore, fingerprint data sets of aerial and underground parts were separately processed and joined while using two data fusion strategies (“low-level” and “mid-level”). The results showed that classification models that are based OPLS-DA were more efficient than RF models. The classification models using low-level data fusion method built showed considerably good recognition and prediction abilities (the accuracy is higher than 99% and sensibility, specificity, Matthews correlation coefficient, and efficiency range from 0.95 to 1.00). Low-level data fusion strategy combined with OPLS-DA could provide the best discrimination result. In summary, this study explored the latitude variation of phytochemical of G. rigescens and developed a reliable and accurate identification method for G. rigescens that were grown at different latitudes based on untargeted HPLC fingerprint, data fusion, and chemometrics. The study results are meaningful for authentication and the quality control of Chinese medicinal materials.

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