How the global structure of protein interaction networks evolves

Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can be estimated from available Saccharomyces cerevisiae genome data and are sufficiently high to affect network structure on short time scales. For instance, more than 100 interactions may be added to the yeast network every million years, a substantial fraction of which adds previously unconnected proteins to the network. Highly connected proteins show a greater rate of interaction turnover than proteins with few interactions. From these observations one can explain ? without natural selection on global network structure ? the evolutionary sustenance of the most prominent network feature, the distribution of the frequency P(d) of proteins with d neighbors, which is a broad-tailed distribution. This distribution is independent of the experimental approach providing nformation on network structure

Draft Final Report

This report contains reviews of various city ordinances, which include plans to improve design regulations along the overlay zone. Also includes a mention of the Waller Creek Citizens' Advisory Committee.EXECUTIVE SUMMARY: The Colorado River corridor from Tom Miller Dam, through Lady Bird Lake and then eastward beyond Longhorn Dam is undoubtedly the most significant community asset in central Austin. This incredibly beautiful stretch of river provides a wide range of benefits to our city including fantastic scenic vistas, wonderful urban recreational opportunities, and serene open spaces that gives our center city a unique character among Texas cities. In addition to providing our drinking water, the river and lake are a major economic asset drawing folks to Austin both to work and play downtown. It is also a fragile beauty that can quickly be overwhelmed if development along its shores is not carefully planned and regulated to provide a balance between accommodating growth in the urban core and preserving the character of the river corridor and the lakefront. Development along the banks of the lake in the 1970’s and early 1980’s drew attention to the need to establish a clear vision of what the community wanted along the lakefront. The 1985 Town Lake Corridor Study and the 1986 Waterfront Overlay ordinance gave the task force the necessary planning guidelines and land development tools to assess what would constitute harmonious development along the lakefront preserving the unique quality of this river corridor. While the original Waterfront Overlay ordinance was largely successful, recent development pressure along the shoreline of Lady Bird Lake has brought into question whether the current Waterfront Overlay ordinance is adequate to protect and enhance the lakefront, especially since the 1986 ordinance underwent a code rewrite in 1999 that made some significant changes. In response to this concern, the City Council charged the Waterfront Overlay Taskforce with reviewing the current situation. The essential finding from the Taskforce’s eight month review is that the current code has been significantly weakened by the changes in the ordinance that have been adopted since 1986 and in particular the 1999 recodification of the ordinance has removed significant protections and incentives to promote community benefits and enhancement of the waterfrontWaller Creek Working Grou

Statistical analysis of simple repeats in the human genome

The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of interspersed, mobile elements hundreds of base pairs (bp) long, among which the Alu families. A link between homo- and di-polymeric tracts and mobile elements has been recently highlighted. In particular, the mobility of Alu repeats, which form 10% of the human genome, has been correlated with the length of poly(A) tracts located at one end of the Alu. These tracts have a rigid and non-bendable structure and have an inhibitory effect on nucleosomes, which normally compact the DNA. We performed a statistical analysis of the genome-wide distribution of lengths and inter--tract separations of poly(X) and poly(XY) tracts in the human genome. Our study shows that in humans the length distributions of these sequences reflect the dynamics of their expansion and DNA replication. By means of general tools from linguistics, we show that the latter play the role of highly-significant content-bearing terms in the DNA text. Furthermore, we find that such tracts are positioned in a non-random fashion, with an apparent periodicity of 150 bases. This allows us to extend the link between repetitive, highly mobile elements such as Alus and low-complexity words in human DNA. More precisely, we show that Alus are sources of poly(X) tracts, which in turn affect in a subtle way the combination and diversification of gene expression and the fixation of multigene families

Human tribbles-1 controls proliferation and chemotaxis of smooth muscle cells via MAPK signaling pathways

Migration and proliferation of smooth muscle cells are key to a number of physiological and pathological processes, including wound healing and the narrowing of the vessel wall.Previous work has shown links between inflammatory stimuli and vascular smooth muscle cell proliferation and migration through mitogen activated protein kinase (MAPK) activation, though the molecular mechanisms of this process are poorly understood. Here we report that tribbles-1, a recently described modulator of MAPK activation controls vascular smooth muscle cell proliferation and chemotaxis via the Jun Kinase pathway. Our findings demonstrate that this regulation takes place via direct interactions between tribbles-1 and MKK4/SEK1, a Jun activator kinase. The activity of this kinase is dependent on tribbles-1 levels, whilst the activation and the expression of MKK4/SEK1 is not. In addition, tribbles-1 expression is elevated in human atherosclerotic arteries compared to non-atherosclerotic controls, suggesting that this protein may pay a role in disease in vivo. In summary, the data presented here suggest an important regulatory role for trb-1 in vascular smooth muscle cell biology

HELIN Consortium OPAC Report

Report of the HELIN OPAC Task Force, a group appointed by the HELIN Directors to review the Innovative Interfaces online public access catalog under 2006 release driven by WebPAC Pro. The task force met during the fall of 2006

HELIN Federated Search Task Force Final Report

Final report of the HELIN Federated Search Task Force, a group appointed by the HELIN Reference Committee at the request of the HELIN Directors to investigate and report on available federated search engines, which allow users simultaneously to search multiple databases. The task force was not asked to recommend a specific one for licensing by HELIN member libraries and did not do so

HELIN Task Force on Electronic Archiving Report

Report of the HELIN Electronic Archiving Task Force, appointed from the HELIN Serials Committee and the HELIN Collection Development Committee

Polarized point sources in the LOFAR Two-meter Sky Survey: A preliminary catalog

The polarization properties of radio sources at very low frequencies (h45m–15h30m right ascension, 45°–57° declination, 570 square degrees). We have produced a catalog of 92 polarized radio sources at 150 MHz at 4.′3 resolution and 1 mJy rms sensitivity, which is the largest catalog of polarized sources at such low frequencies. We estimate a lower limit to the polarized source surface density at 150 MHz, with our resolution and sensitivity, of 1 source per 6.2 square degrees. We find that our Faraday depth measurements are in agreement with previous measurements and have significantly smaller errors. Most of our sources show significant depolarization compared to 1.4 GHz, but there is a small population of sources with low depolarization indicating that their polarized emission is highly localized in Faraday depth. We predict that an extension of this work to the full LOTSS data would detect at least 3400 polarized sources using the same methods, and probably considerably more with improved data processing