DNA, Data and Ethics

The biophysical differences between different kinds of DNA data banks are described. The different ethical implications of DNA fingerprint data banks, data banks of known gene sequences, and data banks of total genomic sequences are considered. Ethical approaches using the concept of the common good and those based on human rights are evaluated in the context of DNA data. Additional theological considerations are discussed. In conclusion, a 'one size fits all' approach to bioethics in this area is rejected

Reproductive strategies of six perennial plant species in relation to a successional series

Data are presented on the phenology of dry weight allocation of plant tissue to major component parts for six herbaceous perennials, in relation to a successional sequence. Individual reproductive effort is shown to be constant throughout the succession. Reproductive effort at the population level however is shown to be highest in an early successional quarry site and lowest in an ungrazed grassland site. Populations from the successionally more advanced scrub site generally show a level of reproductive effort between the other two. Significant intra-specific differences between populations from the three sites are demonstrated for mean total plant dry weight, time of anthesis, leaf area and stem length. These are interpreted as plastic responses to environmental variables and the level of competition. Leaf palatability experiments show that leaves taken from different parts of the succession are not different in their palatability to a generalised herbivore

Genesis of ancestral haplotypes: RNA modifications and reverse transcription–mediated polymorphisms

Understanding the genesis of the block haplotype structure of the genome is a major challenge. With the completion of the sequencing of the Human Genome and the initiation of the HapMap project the concept that the chromosomes of the mammalian genome are a mosaic, or patchwork, of conserved extended block haplotype sequences is now accepted by the mainstream genomics research community. Ancestral Haplotypes (AHs) can be viewed as a recombined string of smaller Polymorphic Frozen Blocks (PFBs). How have such variant extended DNA sequence tracts emerged in evolution? Here the relevant literature on the problem is reviewed from various fields of molecular and cell biology particularly molecular immunology and comparative and functional genomics. Based on our synthesis we then advance a testable molecular and cellular model. A critical part of the analysis concerns the origin of the strand biased mutation signatures in the transcribed regions of the human and higher primate genome, A-to-G versus T-to-C (ratio ~1.5 fold) and C-to-T versus G-to-A (≥1.5 fold). A comparison and evaluation of the current state of the fields of immunoglobulin Somatic Hypermutation (SHM) and Transcription-Coupled DNA Repair focused on how mutations in newly synthesized RNA might be copied back to DNA thus accounting for some of the genome-wide strand biases (e.g., the A-to-G vs T-to-C component of the strand biased spectrum). We hypothesize that the genesis of PFBs and extended AHs occurs during mutagenic episodes in evolution (e.g., retroviral infections) and that many of the critical DNA sequence diversifying events occur first at the RNA level, e.g., recombination between RNA strings resulting in tandem and dispersed RNA duplications (retroduplications), RNA mutations via adenosine-to-inosine pre-mRNA editing events as well as error prone RNA synthesis. These are then copied back into DNA by a cellular reverse transcription process (also likely to be error-prone) that we have called "reverse transcription-mediated long DNA conversion." Finally we suggest that all these activities and others can be envisaged as being brought physically under the umbrella of special sites in the nucleus involved in transcription known as "transcription factories."

A rigidity property of asymptotically simple spacetimes arising from conformally flat data

Given a time symmetric initial data set for the vacuum Einstein field equations which is conformally flat near infinity, it is shown that the solutions to the regular finite initial value problem at spatial infinity extend smoothly through the critical sets where null infinity touches spatial infinity if and only if the initial data coincides with Schwarzschild data near infinity.Comment: 37 page

Human DNA tumor viruses evade uracil-mediated antiviral immunity

It is estimated that approximately 15% of tumors worldwide are caused by viruses [1]. These oncogenic viruses are classified as either RNA (RTVs) or DNA tumor viruses (DTVs) [1]. There are two human RTVs: hepatitis C virus (HCV) and human T-cell lymphotropic virus-1 (HTLV-1), and five human DTVs: human papilloma virus (HPV), hepatitis B virus (HBV), Epstein–Barr virus (EBV), Kaposi sarcoma-associated herpesvirus (KSHV), and Merkel cell polyomavirus (MCPyV) [1]. These tumor viruses (TVs) establish lifelong infection and evade host immunity using several strategies. While not all TV infections cause disease, viral modes of established latency and persistence perturb normal cellular processes, sometimes leading to cancer [1]. Particularly interesting are mechanisms to evade uracil-mediated antiviral immunity, which can be detrimental to the host genome

Modular Cosmology, Thermal Inflation, Baryogenesis and Predictions for Particle Accelerators

Modular cosmology is plagued by overproduction of unwanted relics, gravitinos and especially moduli, at relatively low energy scales. Thermal inflation provides a compelling solution to this moduli problem, but invalidates most baryogenesis scenarios. We propose a simple model in which the MSSM plus neutrino mass term $(LH_u)^2$ is supplemented by a minimal flaton sector to drive the thermal inflation, and make two crucial assumptions: the flaton vacuum expectation value generates the $\mu$-term of the MSSM and $m_L^2 + m_{H_u}^2 < 0$. The second assumption is particularly interesting in that it violates a well known constraint, implying that there exists a nearby deep non-MSSM vacuum, and provides a clear signature of our model which can be tested at future particle accelerators. We show that our model leads to thermal inflation followed by Affleck-Dine leptogenensis along the $LH_u$ flat direction. A key feature of our leptogenesis scenario is that the $H_uH_d$ flat direction is also induced to temporarily acquire a large value, playing a crucial role in the leptogenesis, as well as dynamically shielding the field configuration from the deep non-MSSM minimum, ensuring that the fields relax into our MSSM vacuum.Comment: v3; 19 pages, 3 figures; added a reference for section

Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA

This paper examines the influence of the Raf Kinase Inhibitor Protein (RKIP) on the Extracellular signal Regulated Kinase (ERK) signalling pathway [5] through modelling in a Markovian process algebra, PEPA [11]. Two models of the system are presented, a reagent-centric view and a pathway-centric view. The models capture functionality at the level of subpathway, rather than at a molecular level. Each model affords a different perspective of the pathway and analysis. We demonstrate the two models to be formally equivalent using the timing-aware bisimulation defined over PEPA models and discuss the biological significance