Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events.

Vertical inheritance is foundational to Darwinian evolution, but fails to explain major innovations such as the rapid spread of antibiotic resistance among bacteria and the origin of photosynthesis in eukaryotes. While lateral gene transfer (LGT) is recognized as an evolutionary force in prokaryotes, the role of LGT in eukaryotic evolution is less clear. With the exception of the transfer of genes from organelles to the nucleus, a process termed endosymbiotic gene transfer (EGT), the extent of interdomain transfer from prokaryotes to eukaryotes is highly debated. A common critique of studies of interdomain LGT is the reliance on the topology of single-gene trees that attempt to estimate more than one billion years of evolution. We take a more conservative approach by identifying cases in which a single clade of eukaryotes is found in an otherwise prokaryotic gene tree (i.e. exclusive presence). Starting with a taxon-rich dataset of over 13,600 gene families and passing data through several rounds of curation, we identify and categorize the function of 306 interdomain LGT events into diverse eukaryotes, including 189 putative EGTs, 52 LGTs into Opisthokonta (i.e. animals, fungi and their microbial relatives), and 42 LGTs nearly exclusive to anaerobic eukaryotes. To assess differential gene loss as an explanation for exclusive presence, we compare branch lengths within each LGT tree to a set of vertically-inherited genes subsampled to mimic gene loss (i.e. with the same taxonomic sampling) and consistently find shorter relative distance between eukaryotes and prokaryotes in LGT trees, a pattern inconsistent with gene loss. Our methods provide a framework for future studies of interdomain LGT and move the field closer to an understanding of how best to model the evolutionary history of eukaryotes

Øysand research site: Geotechnical characterisation of deltaic sandy-silty soils

This paper describes the geology and geotechnical engineering properties of the fluvial and 18 deltaic gravelly-sandy-silty sediments at Øysand, Norway. Geophysical and geotechnical site 19 investigations carried out between 2016 and 2018 at the site are presented. Field testing included state-20 of-the-practice and state-of-the-art soil characterisation techniques such as total sounding, seismic 21 cone penetration testing, seismic flat dilatometer, multichannel analysis of surface waves, electrical 22 resistivity tomography, ground penetrating radar, piezometers, thermistors strings, slug tests, and 23 permeability tests using a newly developed CPT permeability probe from NGI. Several sampling 24 techniques were used at the site to assess sample quality. Laboratory testing consisted of index tests 25 and advanced triaxial tests with bender elements to estimate shear strength and stiffness. Data 26 interpretation, engineering soil properties and state variables derived from this analysis are presented, 27 along with comments on data quality. Engineering problems investigated at Øysand so far, are related 28 to: the impact of using different CPTU types, sample quality assessment by obtaining soils with state-29 of-the-practice and state-of-the-art techniques (such as gel push sampler and ground freezing), and 30 frost heave susceptibility

Somatic genome architecture and molecular evolution are decoupled in "young" linage-specific gene families in ciliates.

The evolution of lineage-specific gene families remains poorly studied across the eukaryotic tree of life, with most analyses focusing on the recent evolution of de novo genes in model species. Here we explore the origins of lineage-specific genes in ciliates, a ~1 billion year old clade of microeukaryotes that are defined by their division of somatic and germline functions into distinct nuclei. Previous analyses on conserved gene families have shown the effect of ciliates' unusual genome architecture on gene family evolution: extensive genome processing-the generation of thousands of gene-sized somatic chromosomes from canonical germline chromosomes-is associated with larger and more diverse gene families. To further study the relationship between ciliate genome architecture and gene family evolution, we analyzed lineage specific gene families from a set of 46 transcriptomes and 12 genomes representing x species from eight ciliate classes. We assess how the evolution lineage-specific gene families occurs among four groups of ciliates: extensive fragmenters with gene-size somatic chromosomes, non-extensive fragmenters with "large'' multi-gene somatic chromosomes, Heterotrichea with highly polyploid somatic genomes and Karyorelictea with 'paradiploid' somatic genomes. Our analyses demonstrate that: 1) most lineage-specific gene families are found at shallow taxonomic scales; 2) extensive genome processing (i.e., gene unscrambling) during development likely influences the size and number of young lineage-specific gene families; and 3) the influence of somatic genome architecture on molecular evolution is increasingly apparent in older gene families. Altogether, these data highlight the influences of genome architecture on the evolution of lineage-specific gene families in eukaryotes

Localisation of nitrate-reducing and highly abundant microbial communities in the oral cavity

This is the final version. Available on open access from Public Library of Science via the DOI in this record. Data Availability: All relevant data are within the paper and its Supporting Information filesThe nitrate (NO3-) reducing bacteria resident in the oral cavity have been implicated as key mediators of nitric oxide (NO) homeostasis and human health. NO3--reducing oral bacteria reduce inorganic dietary NO3- to nitrite (NO2-) via the NO3--NO2--NO pathway. Studies of oral NO3--reducing bacteria have typically sampled from either the tongue surface or saliva. The aim of this study was to assess whether other areas in the mouth could contain a physiologically relevant abundance of NO3- reducing bacteria, which may be important for sampling in clinical studies. The bacterial composition of seven oral sample types from 300 individuals were compared using a meta-analysis of the Human Microbiome Project data. This analysis revealed significant differences in the proportions of 20 well-established oral bacteria and highly abundant NO3--reducing bacteria across each oral site. The genera included Actinomyces, Brevibacillus, Campylobacter, Capnocytophaga, Corynebacterium, Eikenella, Fusobacterium, Granulicatella, Haemophilus, Leptotrichia, Microbacterium, Neisseria, Porphyromonas, Prevotella, Propionibacterium, Rothia, Selenomonas, Staphylococcus, Streptococcus and Veillonella. The highest proportion of NO3--reducing bacteria was observed in saliva, where eight of the bacterial genera were found in higher proportion than on the tongue dorsum, whilst the lowest proportions were found in the hard oral surfaces. Saliva also demonstrated higher intra-individual variability and bacterial diversity. This study provides new information on where samples should be taken in the oral cavity to assess the abundance of NO3--reducing bacteria. Taking saliva samples may benefit physiological studies, as saliva contained the highest abundance of NO3- reducing bacteria and is less invasive than other sampling methods. These results inform future studies coupling oral NO3--reducing bacteria research with physiological outcomes affecting human health

In Vivo assessment of a tissue-engineered vascular graft combining a biodegradable elastomeric scaffold and muscle-derived stem cells in a rat model

Limited autologous vascular graft availability and poor patency rates of synthetic grafts for bypass or replacement of small-diameter arteries remain a concern in the surgical community. These limitations could potentially be improved by a tissue engineering approach. We report here our progress in the development and in vivo testing of a stem-cell-based tissue-engineered vascular graft for arterial applications. Poly(ester urethane)urea scaffolds (length=10mm; inner diameter=1.2mm) were created by thermally induced phase separation (TIPS). Compound scaffolds were generated by reinforcing TIPS scaffolds with an outer electrospun layer of the same biomaterial (ES-TIPS). Both TIPS and ES-TIPS scaffolds were bulk-seeded with 10×106 allogeneic, LacZ-transfected, muscle-derived stem cells (MDSCs), and then placed in spinner flask culture for 48h. Constructs were implanted as interposition grafts in the abdominal aorta of rats for 8 weeks. Angiograms and histological assessment were performed at the time of explant. Cell-seeded constructs showed a higher patency rate than the unseeded controls: 65% (ES-TIPS) and 53% (TIPS) versus 10% (acellular TIPS). TIPS scaffolds had a 50% mechanical failure rate with aneurysmal formation, whereas no dilation was observed in the hybrid scaffolds. A smooth-muscle-like layer of cells was observed near the luminal surface of the constructs that stained positive for smooth muscle α-actin and calponin. LacZ+ cells were shown to be engrafted in the remodeled construct. A confluent layer of von Willebrand Factor-positive cells was observed in the lumen of MDSC-seeded constructs, whereas acellular controls showed platelet and fibrin deposition. This is the first evidence that MDSCs improve patency and contribute to the remodeling of a tissue-engineered vascular graft for arterial applications. © 2010 Mary Ann Liebert, Inc

Studying minijets via the pTp_T dependence of two-particle correlation in azimuthal angle ϕ\phi

Following my previous proposal that two-particle correlation functions can be used to resolve the minijet contribution to particle production in minimum biased events of high energy hadronic interactions, I study the $p_T$ and energy dependence of the correlation. Using HIJING Monte Carlo model, it is found that the correlation $c(\phi_1,\phi_2)$ in azimuthal angle $\phi$ between two particles with $p_T>p_T^{cut}$ resembles much like two back-to-back jets as $p_T^{cut}$ increases at high colliding energies due to minijet production. It is shown that $c(0,0)-c(0,\pi)$, which is related to the relative fraction of particles from minijets, increases with energy. The background of the correlation for fixed $p_T^{cut}$ also grows with energy due to the increase of multiple minijet production. Application of this analysis to the study of jet quenching in ultrarelativistic heavy ion collisions is also discussed.Comment: 11 pages Latex text and 8 ps figures, LBL-3349

Space-time Structure of Initial Parton Production in Ultrarelativistic Heavy Ion Collisions

The space and time evolution of initial parton production in ultrarelativistic heavy ion collisions is investigated within the framework of perturbative QCD which includes both initial and final state radiations. Uncertainty principle is used to relate the life time of a radiating parton to its virtuality and momentum. The interaction time of each hard or semihard parton scattering is also taken into account. For central $Au+Au$ collisions at $\sqrt{s}=200$ GeV, most of the partons are found to be produced within 0.5 fm/c after the total overlap of the two colliding nuclei. The local momentum distribution is approximately isotropical at that time. The implication on how to treat correctly the the secondary scattering in an ultimate parton cascading model is also discussed.Comment: 19 pages in REVTEX with 12 figures in separate uuencoded postscript files, LBL-3415

Multiple Interactions and the Structure of Beam Remnants

Recent experimental data have established some of the basic features of multiple interactions in hadron-hadron collisions. The emphasis is therefore now shifting, to one of exploring more detailed aspects. Starting from a brief review of the current situation, a next-generation model is developed, wherein a detailed account is given of correlated flavour, colour, longitudinal and transverse momentum distributions, encompassing both the partons initiating perturbative interactions and the partons left in the beam remnants. Some of the main features are illustrated for the Tevatron and the LHC.Comment: 69pp, 33 figure

Endothelial apoptotic activity of angiocidin is dependent on its polyubiquitin binding activity

We recently cloned the full-length cDNA of a tumour-associated protein. The recombinant protein expressed in bacteria and referred to as angiocidin has potent antitumour activity in vivo and in vitro. Angiocidin inhibits tumour growth and angiogenesis by inducing apoptosis in endothelial cells. Based on the sequence similarity of angiocidin to S5a, one of the major polyubiquitin recognition proteins in eukaryotic cells, we postulated that the antiendothelial activity of angiocidin could be due in part to its polyubiquitin binding activity. In support of this hypothesis, we show that angiocidin binds polyubiquitin in vivo with high affinity and colocalises with ubiquitinated proteins on the surface of endothelial cells. Binding is blocked with an antiubiquitin antibody. Angiocidin treatment of endothelial cells transfected with a proteasome fluorescent reporter protein showed a dose-dependent inhibition of proteasome activity and accumulation of polyubiquitinated proteins. Full-length angiocidin bound polyubiquitin while three angiocidin recombinant proteins whose putative polyubiquitin binding sites were mutated either failed to bind polyubiquitin or had significantly diminished binding activity. The in vitro apoptotic activity of these mutants correlated with their polyubiquitin binding activity. These data strongly argue that the apoptotic activity of angiocidin is dependent on its polyubiquitin binding activity