A simple model of unbounded evolutionary versatility as a largest-scale trend in organismal evolution

The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but empirical and theoretical arguments undermine this belief. Natural selection results in organisms that are well adapted to their local environments, but it is not clear how local adaptation can produce a global trend. In this paper, I present a simple computational model, in which local adaptation to a randomly changing environment results in a global trend towards increasing evolutionary versatility. In this model, for evolutionary versatility to increase without bound, the environment must be highly dynamic. The model also shows that unbounded evolutionary versatility implies an accelerating evolutionary pace. I believe that unbounded increase in evolutionary versatility is a large-scale trend in evolution. I discuss some of the testable predictions about organismal evolution that are suggested by the model

REPARATION : ribosome profiling assisted (re-)annotation of bacterial genomes

Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence composition and often underestimate the complexity of the proteome. We developed RibosomeE Profiling Assisted (re-)AnnotaTION (REPARATION), a de novo machine learning algorithm that takes advantage of experimental protein synthesis evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation (https://github.com/Biobix/ REPARATION). REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds based on a growth curve model to screen for spurious ORFs. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel (small) ORFs including variants of previously annotated ORFs and >70% of all (variants of) annotated protein coding ORFs were predicted by REPARATION to be translated. Our predictions are supported by matching mass spectrometry proteomics data, sequence composition and conservation analysis. REPARATION is unique in that it makes use of experimental translation evidence to intrinsically perform a de novo ORF delineation in bacterial genomes irrespective of the sequence features linked to open reading frames

Ribosome signatures aid bacterial translation initiation site identification

Background: While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information, developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. These patterns are typically lost in standard ribosome profiling analysis pipelines, when reads from footprints are adjusted to determine the specific codon being translated. Results: Utilising these signatures in combination with nucleotide sequence information, we build a model capable of predicting translation initiation sites and demonstrate its high accuracy using N-terminal proteomics. Applying this to prokaryotic translatomes, we re-annotate translation initiation sites and provide evidence of N-terminal truncations and extensions of previously annotated coding sequences. These re-annotations are supported by the presence of structural and sequence-based features next to N-terminal peptide evidence. Finally, our model identifies 61 novel genes previously undiscovered in the Salmonella enterica genome. Conclusions: Signatures within ribosome profiling read length distributions can be used in combination with nucleotide sequence information to provide accurate genome-wide identification of translation initiation sites

A Single-Molecule Hershey-Chase Experiment

Ever since Hershey and Chase used phages to establish DNA as the carrier of genetic information in 1952, the precise mechanisms of phage DNA translocation have been a mystery. While bulk measurements have set a time scale for in vivo DNA translocation during bacteriophage infection, measurements of DNA ejection by single bacteriophages have only been made in vitro. Here, we present direct visualization of single bacteriophages infecting individual Escherichia coli cells. For bacteriophage lambda, we establish a mean ejection time of roughly 5 minutes with significant cell-to-cell variability, including pausing events. In contrast, corresponding in vitro single-molecule ejections take only 10 seconds to reach completion and do not exhibit significant variability. Our data reveal that the velocity of ejection for two different genome lengths collapses onto a single curve. This suggests that in vivo ejections are controlled by the amount of DNA ejected, in contrast with in vitro DNA ejections, which are governed by the amount of DNA left inside the capsid. This analysis provides evidence against a purely intrastrand repulsion based mechanism, and suggests that cell-internal processes dominate. This provides a picture of the early stages of phage infection and sheds light on the problem of polymer translocation

The Matter of Chinese Painting, Case studies of 8th century murals

In the first part of this study a context is set for the research, and translations of classic and modern Chinese written sources are included. In the second part I have explored the technical and material aspects of Chinese painting, starting with a set of murals in three Tang tombs all dating to 706 CE. The tombs were excavated during the nineteen seventies in the Xi’an area of the central Chinese province of Shaanxi. I have collected samples of paint layers and ground layers from these tombs, and have analysed them. The study resulted in a new set of reference materials, because the data that I collected are not challenged in time or geographical location. Other paintings were however examined and compared to broaden the reach of the study. To give just one example: Works in the collection of the Freer and Sackler Gallery in Washington D.C. were included, because they are well documented in the conservation archive of the research department, which contains data that has been collected over many years and by several specialists.Universiteit LeidenThe research was supported by: Hulsewé-Wasniewski Foundation; The Research School for Asian, African and Amer-Indian Studies, [CNWS]; The Netherlands Foundation for the advancement of Tropical Research, [WOTRO]; Leiden University Fund, [LUF]; Henry Luce Foundation; The Netherlands Institute of Cultural Heritage, [ICN]Niet-projectgebonden publicaties talen en culturen van Chin

Parting the Mists

Wong, Aida Yuen. 2006. Parting the Mists, Discovering Japan and the Rise of National-Style Painting in Modern China. Series: Asian Interactions and Comparisons Honolulu: University of Hawai’i Press. ISBN 978 o 8248 2952

Self-organized Critical Model Of Biological Evolution

A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process where the change in fitness after mutation follows a Gaussian distribution with mean $x>0$ and standard deviation $\sigma$. Scaling behaviors are observed in our numerical simulation, indicating that the model is self-organized critical. Besides, the numerical experiment suggests that models with different $x$ and $\sigma$ belong to the same universality class. PACS numbers: 87.10.+e, 05.40.+jComment: 8 pages in REVTEX 3.0 with 4 figures (Figures available on request by sending e-mail to [email protected]

Getting better : Nurse practitioner’s research for quality improvement in cardiac surgery

This thesis describes the efforts to reduce complications during and after cardiac surgery and to enhance the quality of patient care during the in-hospital stay after surgery. Several important topics for daily patient care will be addressed. In light of this goal, the scope and aims of the research described in this thesis are to improve patient outcomes after cardiac surgery by researching the following early perioperative and long-term postoperative issues. 1) The effects of a protocol on cessation of anticoagulants and platelet-inhibiting medication on perioperative blood loss. 2) The effect of a novel approach to preventing postoperative wound infections: applying negative topical pressure on a closed wound. 3) Improving pain management after cardiac surgery with a nurse-driven pain protocol. 4) Improving knowledge about the management of rare complications after cardiac surgery by investigating and describing the diagnosis and management of atrio-esophageal fistula after the totally thoracoscopic maze procedure and of prosthetic valve endocarditis with Propionibacterium acnes (P. acnes)