System Support for Bandwidth Management and Content Adaptation in Internet Applications

This paper describes the implementation and evaluation of an operating system module, the Congestion Manager (CM), which provides integrated network flow management and exports a convenient programming interface that allows applications to be notified of, and adapt to, changing network conditions. We describe the API by which applications interface with the CM, and the architectural considerations that factored into the design. To evaluate the architecture and API, we describe our implementations of TCP; a streaming layered audio/video application; and an interactive audio application using the CM, and show that they achieve adaptive behavior without incurring much end-system overhead. All flows including TCP benefit from the sharing of congestion information, and applications are able to incorporate new functionality such as congestion control and adaptive behavior.Comment: 14 pages, appeared in OSDI 200

Scaling all-pairs overlay routing

This paper presents and experimentally evaluates a new algorithm for efficient one-hop link-state routing in full-mesh networks. Prior techniques for this setting scale poorly, as each node incurs quadratic (n[superscript 2]) communication overhead to broadcast its link state to all other nodes. In contrast, in our algorithm each node exchanges routing state with only a small subset of overlay nodes determined by using a quorum system. Using a two round protocol, each node can find an optimal one-hop path to any other node using only n[superscript 1.5] per-node communication. Our algorithm can also be used to find the optimal shortest path of arbitrary length using only n[superscript 1.5] logn per-node communication. The algorithm is designed to be resilient to both node and link failures. We apply this algorithm to a Resilient Overlay Network (RON) system, and evaluate the results using a large-scale, globally distributed set of Internet hosts. The reduced communication overhead from using our improved full-mesh algorithm allows the creation of all-pairs routing overlays that scale to hundreds of nodes, without reducing the system's ability to rapidly find optimal routes.National Science Foundation (U.S.).National Science Foundation (U.S.). Graduate Research Fellowship Progra

Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community.

The candidate phyla radiation (CPR) comprises a large monophyletic group of bacterial lineages known almost exclusively based on genomes obtained using cultivation-independent methods. Within the CPR, Gracilibacteria (BD1-5) are particularly poorly understood due to undersampling and the inherent fragmented nature of available genomes. Here, we report the first closed, curated genome of a gracilibacterium from an enrichment experiment inoculated from the Gulf of Mexico and designed to investigate hydrocarbon degradation. The gracilibacterium rose in abundance after the community switched to dominance by Colwellia Notably, we predict that this gracilibacterium completely lacks glycolysis, the pentose phosphate and Entner-Doudoroff pathways. It appears to acquire pyruvate, acetyl coenzyme A (acetyl-CoA), and oxaloacetate via degradation of externally derived citrate, malate, and amino acids and may use compound interconversion and oxidoreductases to generate and recycle reductive power. The initial genome assembly was fragmented in an unusual gene that is hypervariable within a repeat region. Such extreme local variation is rare but characteristic of genes that confer traits under pressure to diversify within a population. Notably, the four major repeated 9-mer nucleotide sequences all generate a proline-threonine-aspartic acid (PTD) repeat. The genome of an abundant Colwellia psychrerythraea population has a large extracellular protein that also contains the repeated PTD motif. Although we do not know the host for the BD1-5 cell, the high relative abundance of the C. psychrerythraea population and the shared surface protein repeat may indicate an association between these bacteria.IMPORTANCE CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved an unusual repeat region that would be invisible without genome curation. The nucleotide sequence is apparently under strong diversifying selection, but the amino acid sequence is under stabilizing selection. The amino acid repeat also occurs in a surface protein of a coexisting bacterium, suggesting colocation and possibly interdependence

Latonduines A and B, New Alkaloids Isolated from the Marine Sponge Stylissa carteri:??? Structure Elucidation, Synthesis, and Biogenetic Implications

Part of research collaboration results between Fac Mar Fish UNHAS and EOS UBCLatonduines A (6) and B (7), two new alkaloids with unprecedented heterocyclic skeletons, have been isolated from the Indonesian marine sponge Stylissa carteri. The structures of the latonduines were elucidated by analysis of spectroscopic data and confirmed by the total synthesis of latonduine A (6). It is proposed that ornithine is the biogenetic precursor to the aminopyrimidine fragment of the latonduines