This paper proposes a Petri net model for a commercial network processor (Intel IXP architecture) which is a multithreaded multiprocessor architecture. We consider and model three different applications viz., IPv4 forwarding, Network Address Translation, and IP Security running on IXP 2400/2850. A salient feature of the Petri net model is its ability to model the application, architecture and their interaction in great detail. The model is validated using the Intel proprietary tool (SDK 3.51 for IXP architecture) over a range of configurations.We conduct a detailed performance evaluation, identify the bottleneck resource, and propose a few architectural extensions and evaluate them in detail.

Network processors today consists of multiple parallel processors (microengines)

Gre, one of the conserved transcription factors in bacteria, modulates RnA polymerase (RnAp) activity to ensure processivity and fidelity of RNA synthesis. Gre factors regulate transcription by inducing the intrinsic-endonucleolytic activity of RnAp, allowing the enzyme to resume transcription from the paused and arrested sites. While Escherichia coli and a number of eubacteria harbor GreA and GreB, genus mycobacteria has a single Gre (GreA). to address the importance of the GreA in growth, physiology and gene expression of Mycobacterium smegmatis, we have constructed a conditional knockdown strain of GreA. the GreA depleted strain exhibited slow growth, drastic changes in cell surface phenotype, cell death, and increased susceptibility to front-line anti-tubercular drugs. transcripts and 2D-gel electrophoresis (2D-PAGE) analysis of the GreA conditional knock-down strain showed altered expression of the genes involved in transcription regulation. Among the genes analysed, expression of RnAp subunits (β, β' and ω), carD, hupB, lsr2, and nusA were affected to a large extent. Severe reduction in the expression of genes of rRnA operon in the knock-down strain reveal a role for GreA in regulating the core components of the translation process. Transcription is the central process in the cell. It is regulated by a variety of proteins at different stages. Many of these regulators control transcription by modulating the RNAP activity. The movement of RNAP along the template often gets interrupted by pauses resulting in backtracked RNAP. During backtracking, RNAP slides backwards along the DNA and the 3′ end of the newly synthesized RNA is disengaged from the active centre 1,2. In order to continue RNA extension from the 3′ end, bacteria have evolved strategies that serve to assist the backtracked RNAP to reinitiate elongation. The newly synthesized 3′ end of RNA is subjected to intrinsic cleavage by RNAP itself 3-6. Gre factors bind to the RNAP and assist transcript-cleavage 1,7-12. The absence of Gre would prolong or even prevent rescuing of backtracked RNAP complexes leading to a pause or arrest of transcription. This would limit overall rate and processivity of transcription and hence cell survival. Although Gre factors or their homologues are conserved in all forms of life, present understanding of their in vivo role in bacteria other than in E. coli is limited. Even in E. coli, a complete understanding of the effect of Gre mutants is hindered because of the presence of two Gre (GreA and GreB) and also the partial redundancy in function by the other secondary channel binding proteins such as DksA, Rnk and TraR 13-15. While GreA cleaves 2-3 nucleotide from 3′ end of RNA, GreB cleaves up to 9 nucleotide fragments. However, how the other secondary channel binding proteins complement their function is not clearly understood. It has been shown that GreA, GreB and DksA are mutually competing and exhibit functional redundancy 15. In E. coli, a double knockout of greA and greB did not show lethality, although colonies were s...

Social insects are models for phenotypic plasticity: the generation of different phenotypes from the same genotype. Ant queens and workers differ not only in their morphology and behaviour, but also in their fecundity and lifespan, which is often several times higher in queens. However, the gene regulatory mechanisms underlying these differences are not yet well understood. Since ant queens can live and reproduce for more than two decades, they need to protect their germline from the activity of transposable elements (TEs). This protection may be redundant in short-lived, often sterile workers. We have analysed the expression of two protective classes of smallRNAs, microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), in different tissues, castes, and age classes of the ant species Temnothorax rugatulus. We show that piRNAs are particularly active in the ovaries of queens. TEs are clear targets of the piRNAs in this ant species, and piRNA-specific sequence signatures in the ovaries of all queens regardless of age indicate that young and old queens have similarly active piRNA pathways. Interestingly, the reduced ovaries of the workers also showed the same level of piRNA activity. This was not only the case in young, fertile workers from queenless nests, but also in the presumably older foragers, which have almost completely regressed ovaries. These findings suggest that the germline in these ants is invariably protected by piRNA activity, irrespective of ovarian development. The brain and thorax of queens also contained piRNAs, but at lower levels, and the piRNA-specific ping-pong signatures were strongly reduced in these tissues. We also annotated and analysed miRNAs in different tissues. We confidently detected the expression of 304 miRNAs. Of these, 10 were enriched in the brain and three to the thorax, whereas 83 were specific to the ovaries. 105 miRNAs were found to be expressed in all three tissues. We also identified miRNAs whose expression potentially is related to ant caste, fecundity, and age, suggesting that caste-specific gene activity may be regulated in part by miRNAs. In contrast, our studies of piRNA activity indicate similar profiles across caste, fecundity and age groups, but strong tissue specificity with the highest piRNA mediated TE protection in the germline.