A Conditional Yeast E1 Mutant Blocks the Ubiquitin–Proteasome Pathway and Reveals a Role for Ubiquitin Conjugates in Targeting Rad23 to the Proteasome

E1 ubiquitin activating enzyme catalyzes the initial step in all ubiquitin-dependent processes. We report the isolation of uba1-204, a temperature-sensitive allele of the essential Saccharomyces cerevisiae E1 gene, UBA1. Uba1-204 cells exhibit dramatic inhibition of the ubiquitin–proteasome system, resulting in rapid depletion of cellular ubiquitin conjugates and stabilization of multiple substrates. We have employed the tight phenotype of this mutant to investigate the role ubiquitin conjugates play in the dynamic interaction of the UbL/UBA adaptor proteins Rad23 and Dsk2 with the proteasome. Although proteasomes purified from mutant cells are intact and proteolytically active, they are depleted of ubiquitin conjugates, Rad23, and Dsk2. Binding of Rad23 to these proteasomes in vitro is enhanced by addition of either free or substrate-linked ubiquitin chains. Moreover, association of Rad23 with proteasomes in mutant and wild-type cells is improved upon stabilizing ubiquitin conjugates with proteasome inhibitor. We propose that recognition of polyubiquitin chains by Rad23 promotes its shuttling to the proteasome in vivo

Disease-Associated Mutant Ubiquitin Causes Proteasomal Impairment and Enhances the Toxicity of Protein Aggregates

Protein homeostasis is critical for cellular survival and its dysregulation has been implicated in Alzheimer's disease (AD) and other neurodegenerative disorders. Despite the growing appreciation of the pathogenic mechanisms involved in familial forms of AD, much less is known about the sporadic cases. Aggregates found in both familial and sporadic AD often include proteins other than those typically associated with the disease. One such protein is a mutant form of ubiquitin, UBB+1, a frameshift product generated by molecular misreading of a wild-type ubiquitin gene. UBB+1 has been associated with multiple disorders. UBB+1 cannot function as a ubiquitin molecule, and it is itself a substrate for degradation by the ubiquitin/proteasome system (UPS). Accumulation of UBB+1 impairs the proteasome system and enhances toxic protein aggregation, ultimately resulting in cell death. Here, we describe a novel model system to investigate how UBB+1 impairs UPS function and whether it plays a causal role in protein aggregation. We expressed a protein analogous to UBB+1 in yeast (Ubext) and demonstrated that it caused UPS impairment. Blocking ubiquitination of Ubext or weakening its interactions with other ubiquitin-processing proteins reduced the UPS impairment. Expression of Ubext altered the conjugation of wild-type ubiquitin to a UPS substrate. The expression of Ubext markedly enhanced cellular susceptibility to toxic protein aggregates but, surprisingly, did not induce or alter nontoxic protein aggregates in yeast. Taken together, these results suggest that Ubext interacts with more than one protein to elicit impairment of the UPS and affect protein aggregate toxicity. Furthermore, we suggest a model whereby chronic UPS impairment could inflict deleterious consequences on proper protein aggregate sequestration

Intelligent medium access control for the future wireless networks

Abstract Medium access control (MAC) in wireless ad hoc networks has received considerable attention for almost a couple of decades; however, there are still open problems which deserve thorough study in order to facilitate migration to the next generation broadband wireless communication systems. In ad hoc networks, a detected frame collision can be due to the so-called unreachability problem, where the destination station is situated either in the transmission or interference range of an emitting station and is unable to receive connection establishment frames from any of its neighboring stations. Unreachability might also be due to the inability of a radio station to respond to any connection establishment request, though when the unreachable station receives the connection establishment requests, however, it is prohibited from responding to the requests due to being situated in the interference range of the emitting neighbor. To investigate the impact of this problem, we have to be equipped with a proper analytical framework; therefore, as the first part of this thesis, a scalable framework called Parallel Space – Time Markov chain (PSTMC) is proposed, through which a finite load non-saturated ad hoc network can be easily modeled. At the first step, a single-hop ad hoc network is considered and the accuracy of the model is evaluated using extensive numerical results. Subsequently, the proposed framework is further extended to model multi-hop ad hoc networks. Several discussions are also given on how the framework can be deployed for an arbitrary network topology. One of the main key features of the PSTMC model is its remarkable scalability in modeling complex network configurations. In fact, it is shown that multi-hop ad hoc networks have bounded complexity in being modeled by the PSTMC framework due to its spectacular specifications. These features lead us to a powerful tool by which an arbitrary network topology can be studied. In addition, the proposed models clearly facilitate demonstrating the impact of the unreachability problem on the performance of multi-hop networks. The introduced framework shows how the unreachability problem degrades the achieved throughput and channel capacity by the contending radio stations depending on the deployed network topology. In the remainder of the thesis the unreachability problem in mobile ad hoc networks is tackled and a new MAC protocol to enhance the performance of the network is proposed. This MAC scheme is equipped with smart decision-making algorithms as well as adaptive management mechanisms to reduce the impact of the unreachability problem in single channel scenarios. Subsequently, the problem of concurrent radio resource management and contention resolution in multi-channel cognitive ad hoc networks is considered. In particular, a multi-channel technique for traffic distribution among a set of data channels without centralized control, which is enabled by a probabilistic channel selection algorithm as well as a multi-channel binary exponential backoff mechanism, is proposed. It is shown through simulations that the suggested scheme outperforms the existing MAC protocols in multi-channel environments as well as cognitive networks coexisting with primary users. A mathematical model is also introduced to study the performance of the multi-channel MAC protocol in a single-hop non-saturated wireless network

A self-organizing solution for interference avoidance in TDD underlay femtocells

In this paper, we draw our attention to the problem of interference avoidance in a macrocell-femtocell network. Further, macro user equipments operate in a Frequency Division Duplexing mode while all femtocells employ the macrocellular uplink spectrum in a Time Division Duplexing mode. We propose a self-adapting algorithm to tackle highly interfering MUEs through handover procedure. Results reveal that the proposed solution provides lower outage probability than closed and open access policies, without significant loss in terms of signal-to-noise-and-interference ratio