JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture

BACKGROUND: Whole-genome sequencing projects are rapidly producing an enormous number of new sequences. Consequently almost every family of proteins now contains hundreds of members. It has thus become necessary to develop tools, which classify protein sequences automatically and also quickly and reliably. The difficulty of this task is intimately linked to the mechanism by which protein sequences diverge, i.e. by simultaneous residue substitutions, insertions and/or deletions and whole domain reorganisations (duplications/swapping/fusion). RESULTS: Here we present a novel approach, which is based on random sampling of sub-sequences (probes) out of a set of input sequences. The probes are compared to the input sequences, after a normalisation step; the results are used to partition the input sequences into homogeneous groups of proteins. In addition, this method provides information on diagnostic parts of the proteins. The performance of this method is challenged by two data sets. The first one contains the sequences of prokaryotic lyases that could be arranged as a multiple sequence alignment. The second one contains all proteins from Swiss-Prot Release 36 with at least one Src homology 2 (SH2) domain – a classical example for proteins with modular architecture. CONCLUSION: The outcome of our method is robust, highly reproducible as shown using bootstrap and resampling validation procedures. The results are essentially coherent with the biology. This method depends solely on well-established publicly available software and algorithms

High-Luminosity Hydrogen Jet Target Development

This research was sponsored by the National Science Foundation Grant NSF PHY-931478

The H_2O Jet Target

This research was sponsored by the National Science Foundation Grant NSF PHY-931478

Pcr Primers for the Amplification of Mitochondrial Small Subunit Ribosomal DNA of Lichen-forming Ascomycetes

Four primers for the amplification of mitochondrial DNA of lichenforming ascomycetes are presented. The primers match the conserved regions U2, U4, and U6, respectively, of mitochondrial small subunit (SSU) ribosomal DNA (rDNA). Polymerase chain reaction using different combinations of the primers produced single amplification products from DNA of eight lichen-forming fungal species but did not amplify DNA of two axenic cultured algal species. The amplification product obtained from Lobaria pulmonaria was sequenced and the 894-bp sequence was compared with the mitochondrial SSU rDNA sequence of Podospora anserine. The two sequences revealed more than 76% identity in the conserved regions U3 to U5 demonstrating that we amplified mitochondrial DNA. The primers matching U2 and U6 yielded amplification products of 800-1000 bp depending on the species examined. The variation observed suggests that mitochondrial SSU rDNA may be useful for phylogenetic analyses of lichen-forming ascomycete

Identification of dominant bacterial phylotypes in a cadmium-treated forest soil

The presence of heavy metals in soils can lead to changes in microbial community structure, characterized by the dominance of groups that are able to tolerate contamination. Such groups may provide good microbial indicators of heavy-metal pollution in soil. Through terminal restriction fragment length polymorphism (T-RFLP) profiling, changes in the bacterial community structure of an acidic forest soil that had been incubated with cadmium (Cd) for 30 days were investigated. T-RFLP revealed, in particular, three operational taxonomic units (OTUs) strongly dominating in relative abundance in the contaminated soil. By cloning of the amplified 16S rRNA genes and partial sequencing of 25 clones, these three dominant OTUs were phylogenetically characterized. One dominant OTU in the cadmium-contaminated soil was derived from Betaproteobacteria, genus Burkholderia, and the other two were from uncultured members of the class Actinobacteria, closely related to the genus Streptomyces. To confirm T-RFLP data, four primers were designed on the basis of this study's dominant sequences, targeting the OTUs corresponding to Burkholderia or Actinobacteria. Real-time PCR showed that Burkholderia target sequences were more abundant in cadmium-treated soil (7.8 × 107± 3.0 × 107 targets g−1 soil) than in untreated soil (4.0 × 106± 8.9 × 105 targets g−1 soil). It was concluded that the genus Burkholderia includes species that may be particularly dominant under cadmium contaminatio

Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense

There are a variety of bacterial defense strategies to survive in a hostile environment. Generation of extracellular polysaccharides has proved to be a simple but effective strategy against the host's innate immune system. A comparative genomics approach led us to identify a new protein family termed Stealth, most likely involved in the synthesis of extracellular polysaccharides. This protein family is characterized by a series of domains conserved across phylogeny from bacteria to eukaryotes. In bacteria, Stealth (previously characterized as SacB, XcbA, or WefC) is encoded by subsets of strains mainly colonizing multicellular organisms, with evidence for a protective effect against the host innate immune defense. More specifically, integrating all the available information about Stealth proteins in bacteria, we propose that Stealth is a D-hexose-1-phosphoryl transferase involved in the synthesis of polysaccharides. In the animal kingdom, Stealth is strongly conserved across evolution from social amoebas to simple and complex multicellular organisms, such as Dictyostelium discoideum, hydra, and human. Based on the occurrence of Stealth in most Eukaryotes and a subset of Prokaryotes together with its potential role in extracellular polysaccharide synthesis, we propose that metazoan Stealth functions to regulate the innate immune system. Moreover, there is good reason to speculate that the acquisition and spread of Stealth could be responsible for future epidemic outbreaks of infectious diseases caused by a large variety of eubacterial pathogens. Our in silico identification of a homologous protein in the human host will help to elucidate the causes of Stealth-dependent virulence. At a more basic level, the characterization of the molecular and cellular function of Stealth proteins may shed light on fundamental mechanisms of innate immune defense against microbial invasion

The untapped potential of macrofossils in ancient plant DNA research.

The rapid development of ancient DNA (aDNA) analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa is now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of palaeogenomic studies still focuses on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for palaeogenomic analyses: Plant remains such as needles, leaves, wood, seeds or fruits that are deposited in natural archives, such as lake sediments, permafrost or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research

Telomere Length Homeostasis Is Achieved via a Switch between Telomerase- Extendible and -Nonextendible States

AbstractTelomerase counteracts telomere erosion that stems from incomplete chromosome end replication and nucleolytic processing. A precise understanding of telomere length homeostasis has been hampered by the lack of assays that delineate the nonuniform telomere extension events of single chromosome molecules. Here, we measure telomere elongation at nucleotide resolution in Saccharomyces cerevisiae. The number of nucleotides added to a telomere in a single cell cycle varies between a few to more than 100 nucleotides and is independent of telomere length. Telomerase does not act on every telomere in each cell cycle, however. Instead, it exhibits an increasing preference for telomeres as their lengths decline. Deletion of the telomeric proteins Rif1 or Rif2 gives rise to longer telomeres by increasing the frequency of elongation events. Thus, by taking a molecular snapshot of a single round of telomere replication, we demonstrate that telomere length homeostasis is achieved via a switch between telomerase-extendible and -nonextendible states

Essays on reputation and repeated games

textThis dissertation consists of three essays on reputation and repeated games. Reputation models typically assume players have full memory of past events, yet in many applications this assumption does not hold. In the first chapter, I explore two different relaxations of the assumption that history is perfectly observed in the context of Ely and Välimäki's (2003) mechanic game, where reputation (with full history observation) is clearly bad for all players. First I consider "limited history," where short-run players see only the most recent T periods. For large T, the full history equilibrium behavior always holds due to an "echo" effect (for high discount factors); for small T, the repeated static equilibrium exists. Second I consider "fading history," where short-run players randomly sample past periods with probabilities that "fade" toward zero for older periods. When fading is faster than a fairly lax threshold, the long-run player always acts myopically, a result that holds more generally for reputation games where the long-run player has a strictly dominant stage game action. This finding suggests that reputational incentives may be too weak to affect long-run player behavior in some realistic word-of-mouth environments. The second chapter develops general theoretical tools to study incomplete information games where players observe only finitely many recent periods. I derive a recursive characterization of the set of equilibrium payoffs, which allows analysis of both stationary and (previously unexplored) non-stationary equilibria. I also introduce "quasi-Markov perfection," an equilibrium refinement which is a necessary condition of any equilibrium that is "non-fragile" (purifiable), i.e., robust to small, additively separable and independent perturbations of payoffs. These tools are applied to two examples. The first is a product choice game with 1-period memory of the firm's actions, obtaining a complete characterization of the exact minimum and maximum purifiable equilibrium payoffs for almost all discount factors and prior beliefs on an "honest" Stackelberg commitment type, which shows that non-stationary equilibria expand the equilibrium set. The second is the same game with long memory: in all stationary and purifiable equilibria, the long-run player obtains exactly the Stackelberg payoff so long as the memory is longer than a threshold dependent on the prior. These results show that the presence of the honest type (even for arbitrarily small prior beliefs) qualitatively changes the equilibrium set for any fixed discount factor above a threshold independent of the prior, thereby not requiring extreme patience. The third chapter studies the question of why drug trafficking organizations inflict violence on each other, and why conflict breaks out under some government crackdowns and not others, in a repeated games context. Violence between Mexican drug cartels soared following the government's anti-cartel offensive starting in 2006, but not under previous crackdowns. I construct a theoretical explanation for these observations and previous empirical research. I develop a duopoly model where the firms have the capacity to make costly attacks on each other. The firms use the threat of violence to incentivize inter-cartel cooperation, and under imperfect monitoring, violence occurs on the equilibrium path of a high payoff equilibrium. When a "corrupt" government uses the threat of law enforcement as a punishment for uncooperative behavior, violence is not needed as frequently to achieve high payoffs. When government cracks down indiscriminately, the firms may return to frequent violence as a way of ensuring cooperation and high payoffs, even if the crackdown makes drug trafficking otherwise less profitable.Economic