We present an efficient reduction from the Bounded integer programming (BIP) to the Subspace avoiding problem (SAP) in lattice theory. The reduction has some special properties with some interesting consequences. The first is the new upper time bound for BIP, poly(ϕ) · n n+o(n) (where n and ϕ are the dimension and the input size of the problem, respectively). This is the best bound up to now fo...

The unfolded protein response (UPR) is an intracellular signaling pathway that counteracts variable stresses that impair protein folding in the endoplasmic reticulum (ER). As such, the UPR is thought to be a homeostat that finely tunes ER protein folding capacity and ER abundance according to need. The mechanism by which the ER stress sensor Ire1 is activated by unfolded proteins and the role t...

Analysis of protein-protein interaction networks has revealed the presence of proteins with multiple interaction ligand proteins, such as hub proteins. For such proteins, multiple ligands would be predicted as interacting partners when predicting all-to-all protein-protein interactions (PPIs). In this work, to obtain a better understanding of PPI mechanisms, we focused on protein interaction su...

BIP is a component framework for constructing systems by superposing three layers of modeling: Behavior, Interaction, and Priority. Behavior is represented by labeled transition systems communicating through ports. Interactions are sets of ports. A synchronization between components is possible through the interactions specified by a set of connectors. When several interactions are possible, pr...

Protein-protein interactions underlie the fundamental processes of every cell. Certain proteins called chaperones specialize in protein folding, maturation, and degradation functions within a cell. BiP is the resident chaperone in the endoplasmic reticulum (ER) of eukaryotic cells. Following adverse cellular conditions, BiP acts as a mediator in returning the cell to homeostasis. Spatial locali...

Cells monitor protein folding by an inbuilt quality-control system in which incorrectly or misfolded folded proteins are tagged for degradation or sent back through a refolding cycle. However, continued accumulation of incorrectly folded proteins triggers the Unfolded Protein Response (UPR), which attempts to re-establish folding homeostasis or commits the cell to apoptosis. In this study, we d...

We have recently shown that an adenovirus carrying REIC/Dkk-3 (Ad-REIC) exhibits a potent tumor-specific cell-killing function for various human cancers. It has also become evident that some human cancers are resistant to Ad-REIC-induced apoptosis. The aim of the present study was to determine the molecular mechanisms of resistance to Ad-REIC. First, we isolated resistant clones from a human pr...

We have studied the possible mechanisms of endoplasmic reticulum (ER) export and retention by using natural residents of the plant ER. Under normal physiological conditions, calreticulin and the lumenal binding protein (BiP) are efficiently retained in the ER. When the ER retention signal is removed, truncated calreticulin is much more rapidly secreted than truncated BiP. Calreticulin carries t...

Reconstituted proteoliposomes derived from solubilized yeast microsomes are able to translocate a secreted yeast mating pheromone precursor (Brodsky, J. L., S. Hamamoto, D. Feldheim, and R. Schekman. 1993. J. Cell Biol. 120:95-107). Reconstituted proteoliposomes prepared from strains with mutations in the SEC63 or KAR2 genes are defective for translocation; the kar2 defect can be overcome by th...