Showing papers by "Lixin Zhang published in 2001"

Raf-1 promotes cell survival by antagonizing apoptosis signal-regulating kinase 1 through a MEK-ERK independent mechanism.

Abstract: The Ser/Thr kinase Raf-1 is a protooncogene product that is a central component in many signaling pathways involved in normal cell growth and oncogenic transformation. Upon activation, Raf-1 phosphorylates mitogen-activated protein kinase kinase (MEK), which in turn activates mitogen-activated protein kinase/extracellular signal-regulated kinases (MAPK/ERKs), leading to the propagation of signals. Depending on specific stimuli and cellular environment, the Raf-1--MEK--ERK cascade regulates diverse cellular processes such as proliferation, differentiation, and apoptosis. Here, we describe a MEK--ERK-independent prosurvival function of Raf-1. We found that Raf-1 interacts with the proapoptotic, stress-activated protein kinase ASK1 (apoptosis signal-regulating kinase 1) in vitro and in vivo. Deletion analysis localized the Raf-1 binding site to the N-terminal regulatory fragment of ASK1. This interaction allows Raf-1 to act independently of the MEK--ERK pathway to inhibit apoptosis. Furthermore, catalytically inactive forms of Raf-1 can mimic the wild-type effect, raising the possibility of a kinase-independent function of Raf-1. Thus, Raf-1 may promote cell survival through its protein-protein interactions in addition to its established MEK kinase function.

The Impulse memory controller

Abstract: Impulse is a memory system architecture that adds an optional level of address indirection at the memory controller. Applications can use this level of indirection to remap their data structures in memory. As a result, they can control how their data is accessed and cached, which can improve cache and bus utilization. The Impulse design does not require any modification to processor, cache, or bus designs since all the functionality resides at the memory controller. As a result, Impulse can be adopted in conventional systems without major system changes. We describe the design of the Impulse architecture and how an Impulse memory system can be used in a variety of ways to improve the performance of memory-bound applications. Impulse can be used to dynamically create superpages cheaply, to dynamically recolor physical pages, to perform strided fetches, and to perform gathers and scatters through indirection vectors. Our performance results demonstrate the effectiveness of these optimizations in a variety of scenarios. Using Impulse can speed up a range of applications from 20 percent to over a factor of 5. Alternatively, Impulse can be used by the OS for dynamic superpage creation; the best policy for creating superpages using Impulse outperforms previously known superpage creation policies.

Rubisco activase: an enzyme with a temperature‐dependent dual function?

Abstract: Summary Heat treatment of intact spinach leaves was found to induce a unique thylakoid membrane association of an approximately 40 kDa stromal protein. This protein was identified as rubisco activase. Most of the rubisco activase was sequestered to the thylakoid membrane, particularly to the stroma-exposed regions, during the first 10 min of heat treatment at 42∞C. At lower temperatures (38‐40∞C) the association of rubisco activase with the thylakoid membrane occurred more slowly. The temperaturedependent association of rubisco activase with the thylakoid membrane was due to a conformational change in the rubisco activase itself, not to heat-induced alterations in the thylakoid membrane. Association of the 41 kDa isoform of rubisco activase occurred first, followed by the binding of the 45 kDa isoform to the thylakoid membrane. Fractionation of thylakoid membranes revealed a specific association of rubisco activase with thylakoid-bound polysomes. Our results suggest a temperaturedependent dual function for rubisco activase. At optimal temperatures it functions in releasing inhibitory sugar phosphates from the active site of Rubisco. During a sudden and unexpected exposure of plants to heat stress, rubisco activase is likely to manifest a second role as a chaperone in association with thylakoid-bound ribosomes, possibly protecting, as a first aid, the thylakoid associated protein synthesis machinery against heat inactivation.

Reevaluating online superpage promotion with hardware support

Abstract: Typical translation lookaside buffers (TLBs) can map a far smaller region of memory than application footprints demand, and the cost of handling TLB misses therefore limits the performance of an increasing number of applications. This bottleneck can be mitigated by the use of superpages, multiple adjacent virtual memory pages that can be mapped with a single TLB entry that extend TLB reach without significantly increasing size or cost. We analyze hardware/software tradeoff for dynamically creating superpages. This study extends previous work by using execution-driven simulation to compare creating superpages via copying with remapping pages within the memory controller and by examining how the tradeoffs change when moving front a single-issue to a superscalar processor model. We find that remapping-based promotion outperforms copying-based promotion, often significantly. Copying-based promotion is slightly more effective on superscalar processors than on single-issue processors, and the relative performance of remapping-based promotion on the two platform is application-dependent.

Memory system support for dynamic cache line assembly

Abstract: The effectiveness of cache-based memory hierarchies depends on the presence of spatial and temporal locality in applications. Memory accesses of many important applications have predictable behavior but poor locality. As a result, the performance of these applications suffers from the increasing gap between processor and memory performance. In this paper, we describe a novel mechanism provided by the Impulse memory controller called Dynamic Cache Line Assembly that can be used by applications to improve memory performance. This mechanism allows applications to gather on-the-fly data spread through memory into contiguous cache lines, which creates spatial data locality where none exists naturally. We have used dynamic cache line assembly to optimize a random access loop and an implementation of Fast Fourier Transform (FFTW). Detailed simulation results show that the use of dynamic cache line assembly improves the performance of these benchmarks by up to a factor of 3.2 and 1.4, respectively.

Isolated nucleic acid molecule encoding a regulator of fungal gene expression

Abstract: The invention relates to regulators of fungal gene expression and their use in commercial and medical applications. More particularly, the invention relates to regulators of fungal genes involved in production of enzymes, secondary metabolites and other useful products, as well as to regulators of genes involved in fungal invasion. The invention provides novel regulators of fungal gene expression, and methods for using regulator genes in commercial and medical applications.

Maintenance of functional photosystem II by D1 protein turnover

Abstract: Water splitting of oxygenic photosynthesis produces various radicals and active oxygen species with harmful effects on PSII. Such photodamage to PSII occurs at all light intensities. Damaged PSII centers, however, do not usually accumulate in the thylakoid membrane due to a rapid and efficient repair mechanism. A grant design of PSII protects most of the protein components with the damage targeted to only one protein, the reaction center D1 protein. Repair of PSII via turnover of the D1 protein is a complex process. Central for such turnover and repair is a regulated reversible phosphorylation of PSII proteins, changes between dimer/monomer organization of PSII, migration of PS II between grana and stroma-exposed thylakoid domains, partial PSII disassembly and a multistep highly specific proteolysis of the D1 protein. Replacement of the damaged D1 with a new copy requires targeting of ribosome psbA mRNA complexes to the thylakoid membrane and subsequent light-regulated translation elongation. Concomitantly with D1 elongation, the protein is inserted into the thylakoid membrane, probably via a cpSecY-related translocation channel. Before termination of translation the nascent D1 chain starts interacting with other PSII proteins, particularly with the D2 protein, the presence of which seems to be a prerequisite for D1 elongation to be completed. CP47 is next integrated into the complex and finally, after termination of translation and maturation of the D1 protein, the CP43 protein is associated. Various assembly steps of PSII are highly regulated and require proper redox conditions and maintenance of the trans-thylakoid proton gradient.

Novel regulators of fungal gene expression

Abstract: The invention relates to regulators of fungal gene expression and their use in commercial and medical applications. More particularly, the invention relates to regulators of fungal genes involved in production of enzymes, secondary metabolites and other useful products, as well as to regulators of genes involved in fungal invasion. The invention provides novel regulators of fungal gene expression, and methods for using regulator genes in commercial and medical applications.

Assembly of Photosystem II in chloroplast psbEFLJ operon mutants

Abstract: Assembly and/or stabilization of the PSII complex has been studied in tobacco psbEFLJ operon mutants, each type lacking one of the genes. The core of PSII consists of the D1 and D2 proteins, the cytochrome b559, the chlorophyll a binding complexes CP43 and CP47 and a number of smaller proteins including the psbL and psbJ gene products. Cytochrome b559 is a thylakoid membrane-embedded heme protein and is composed of two subunits, a and b , encoded by the chloroplast psbE and psbF genes. Two-dimensional blue-native gel electrophoresis was used to study the assembly of thylakoid protein complexes in psbEFLJ operon mutants. All proteins encoded by the operon, PsbE, PsbF, PsbL and PsbJ are necessary for normal assembly of PSII core monomer. No PSII assemblies were observed in ?psbE mutants whereas the ?psbF mutants allowed transient D1/D2 heterodimer to be detected in thylakoid membranes. PsbL appeared to be particularly needed for stable assembly of CP43 into PSII core. When PsbJ protein was missing, the amount and stability of PSII complexes are strongly reduced. PSI, LHCII and cytochome b6f complexes were normally assembled in all mutants. Thylakoid membrane organization was severly altered in ?psbE and ?psbF mutants with significantly lower amount of grana stacks composed of only a few appressed thylakoids.