Stochastic Gene Expression in a Lentiviral Positive Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity

Stochastic gene expression has been implicated in a variety of cellular processes, including cell differentiation and disease. In this issue of Cell, Weinberger et al. (2005) take an integrated computational-experimental approach to study the Tat transactivation feedback loop in HIV-1 and show that fluctuations in a key regulator, Tat, can result in a phenotypic bifurcation. This phenomenon is observed in an isogenic population where individual cells display two distinct expression states corresponding to latent and productive infection by HIV-1. These findings demonstrate the importance of stochastic gene expression in molecular "decision-making."Comment: Supplemental data available as q-bio.MN/060800

Quantitative analysis of cell types during growth and morphogenesis in Hydra

Tissue maceration was used to determine the absolute number and the distribution of cell types in Hydra. It was shown that the total number of cells per animal as well as the distribution of cells vary depending on temperature, feeding conditions, and state of growth. During head and foot regeneration and during budding the first detectable change in the cell distribution is an increase in the number of nerve cells at the site of morphogenesis. These results and the finding that nerve cells are most concentrated in the head region, diminishing in density down the body column, are discussed in relation to tissue polarity

Regular spherical dust spacetimes

Physical (and weak) regularity conditions are used to determine and classify all the possible types of spherically symmetric dust spacetimes in general relativity. This work unifies and completes various earlier results. The junction conditions are described for general non-comoving (and non-null) surfaces, and the limits of kinematical quantities are given on all comoving surfaces where there is Darmois matching. We show that an inhomogeneous generalisation of the Kantowski-Sachs metric may be joined to the Lemaitre-Tolman-Bondi metric. All the possible spacetimes are explicitly divided into four groups according to topology, including a group in which the spatial sections have the topology of a 3-torus. The recollapse conjecture (for these spacetimes) follows naturally in this approach.Comment: Minor improvements, additional references. Accepted by GR

Supplemental Data: Stochastic Gene Expression in a Lentiviral Positive Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity

Supplemental data for "Stochastic Gene Expression in a Lentiviral Positive Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity" [q-bio.MN/0608002, Cell. 2005 Jul 29;122(2):169-82].Comment: Supplemental data for q-bio.MN/060800

The Networked Nitrous Node: A Low-Power Field-Deployable COTS-based N2O gas sensor platform

We present a wireless nitrous oxide (N 2 O) gas sensor system consisting of a commercial high-current infrared N 2 O sensor wrapped in a “smart” sensor framework to make it suitable for battery-powered deployment. This framework consists of wireless mesh networking, data storage, additional environmental sensors, and a gas sensor power control circuit managed by a central microcontroller. The N 2 O sensor is the first order consumer of power and sampling N 2 O at approximately ten minute intervals yields an estimated system lifetime of 63 days when using four 18650 Li-ion batteries. The node stores data locally on SD card and wirelessly reports to a root PC that also stores data and displays to users in a simple graphical user interface. The system is composed of majority off-the-shelf components and any custom components were designed or programmed with open-source software. We expect these features will lead to this system being more easily understood, copied, and modified by engineers wishing to design similar sensor system frameworks and thereby allow even more power-prohibitive devices to be wirelessly deployed

State-by-State Report on Permanent Public Access to Electronic Government Information

The purpose of this study was to research what, if anything, state governments are doing to meet the enormous challenges of ensuring permanent public access to state electronic government information. A comprehensive survey was created and distributed to AALL authors in each of the fifty states, the District of Columbia and Puerto Rico. State authors completed the survey by December 2002 and, in addition, submitted a short executive summary based on their survey results. The survey reveals that only one state—Colorado—has enacted legislation that explicitly addresses permanent public access (effective August 15, 2003). No state, including Colorado, comprehensively addresses the challenges of permanent public access to and preservation of electronic government information. State records boards, state archives and state libraries are often aware of permanent public access issues and have often taken steps to preserve electronic information. They have sometimes taken steps to provide continuous public access or have developed guidelines for state agencies to provide such access. These efforts of state records boards, state archives and state libraries are often ineffective, however, because they lack a solid statutory foundation. Without comprehensive statutes supporting a system to coordinate and centralize permanent public access, state agencies thwart the positive efforts of state records boards, state archives and state libraries. The agencies fail to appreciate the need to ensure the full lifecycle of electronic government information, particularly Web-based publications and records. And any guidelines for permanent public access that target them do not solve the problem of agencies’ lack the expertise, personnel and funding. We envisioned that this project would be the first step in the advocacy process necessary to enact state laws that will prevent the loss of important state government information in electronic format. Toward this end, we sought to create a document that could be provided to legislators and other policymakers to educate them about the responsibility of state governments to ensure permanent public access to electronic information. An additional objective was to strengthen the GRC and WAO’s ties to AALL members at the local level, thereby forming a base of activists who could advocate for improved laws mandating permanent public access to state government information. Because AALL and other library organizations lack the manpower to tackle the problem of disappearing electronic government information in all states simultaneously, the Grant Team has identified key states to target for legislative activity

Performance of cages as large animal-exclusion devices in the deep sea

Sedimentary, deep-sea communities include megafaunal animals (e.g., sea cucumbers, brittle stars, crabs) and demersal fishes, collectively termed the large, motile epifauna (LME). Individuals of the LME are common, and their biomass approximates that of the macrofauna. Based on analogies with shallow-water animals, they are likely to be sources of mortality for the infauna and to create spatial and temporal heterogeneity in the community. Given present theories of deep-sea community organization, such effects could be important. Unfortunately, this hypothesis has not been tested because of the difficulty of conducting experiments in the deep sea and because tools for manipulating the LME have not been developed. We studied the suitability of exclusion cages for this purpose at 780 m depth in San Diego Trough. We placed 16 cages of two mesh sizes for 4.5 months over regions of the seafloor that appeared free of LME. Time-lapse photographs of a cage and a control plot coupled with observations of all cages at the end of the experiment indicated that small (1.27-cm × 1.27-cm square)-mesh cages were effective at excluding LME. Further, the cages were essentially free of cage artifacts that have been reported in shallow-water studies. Large, mobile and disruptive animals (e.g., fishes, crabs) did not establish long-term residence adjacent to or on the cages. Bio-fouling slightly reduced the open surface area of the cage mesh, potentially reducing flow through the cage, but the composition of surface sediments in terms of organic C and N, phytoplankton-derived pigments, and grain size was indistinguishable between cages and control areas. Activities of excess 234Th were significantly higher (average = 37%) inside of small-mesh cages, which might suggest enhanced particulate deposition inside cages. However, this measurement was an artifact of experimental manipulation. Particles that accumulated on the cage during the experiment were dislodged and settled to the seafloor when the cage was opened just prior to sampling. These particles would have been highly enriched in 234Th, and their inclusion in core samples artificially inflated the calculated sediment accumulation rates inside cages. Therefore, the cages performed well; they excluded the targeted LME without causing artifacts and thus should be useful for experimental study of a group of animals that may have substantial impact on the structure and organization of deep-sea communities