SwePub - sökning: WFRF:(Chen Xin 1980)

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1.	Chen, Xin, 1980, et al. (författare) Dataset for suppressors of amyloid-beta toxicity and their functions in recombinant protein production in yeast 2022 Ingår i: Data in Brief. - : Elsevier BV. - 2352-3409. ; 42 Tidskriftsartikel (refereegranskat)abstract The production of recombinant proteins at high levels often induces stress-related phenotypes by protein misfolding or aggregation. These are similar to those of the yeast Alzheimer's disease (AD) model in which amyloid-beta peptides (A beta 42) were accumulated [1,2] . We have previously identified suppressors of A beta 42 cytotoxicity via the genome-wide synthetic genetic array (SGA) [3] and here we use them as metabolic engineering targets to evaluate their potentiality on recombinant protein production in yeast Saccharomyces cerevisiae. In order to investigate the mechanisms linking the genetic modifications to the improved recombinant protein production, we perform systems biology approaches (transcriptomics and proteomics) on the resulting strain and intermediate strains. The RNAseq data are preprocessed by the nf-core/RNAseq pipeline and analyzed using the Platform for Integrative Analysis of Omics (PIANO) package [4] . The quantitative proteome is analyzed on an Orbitrap Fusion Lumos mass spectrometer interfaced with an Easy-nLC1200 liquid chromatography (LC) system. LC-MS data files are processed by Proteome Discoverer version 2.4 with Mascot 2.5.1 as a database search engine. The original data presented in this work can be found in the research paper titled "Suppressors of Amyloid-beta Toxicity Improve Recombinant Protein Produc-tion in yeast by Reducing Oxidative Stress and Tuning Cellu-lar Metabolism", by Chen et al. [5] . (C) 2022 The Author(s). Published by Elsevier Inc.
2.	Chen, Xin, 1980, et al. (författare) Suppressors of amyloid-β toxicity improve recombinant protein production in yeast by reducing oxidative stress and tuning cellular metabolism 2022 Ingår i: Metabolic Engineering. - : Elsevier BV. - 1096-7176 .- 1096-7184. ; 72, s. 311-324 Tidskriftsartikel (refereegranskat)abstract High-level production of recombinant proteins in industrial microorganisms is often limited by the formation of misfolded proteins or protein aggregates, which consequently induce cellular stress responses. We hypothesized that in a yeast Alzheimer's disease (AD) model overexpression of amyloid-β peptides (Aβ42), one of the main peptides relevant for AD pathologies, induces similar phenotypes of cellular stress. Using this humanized AD model, we previously identified suppressors of Aβ42 cytotoxicity. Here we hypothesize that these suppressors could be used as metabolic engineering targets to alleviate cellular stress and improve recombinant protein production in the yeast Saccharomyces cerevisiae. Forty-six candidate genes were individually deleted and twenty were individually overexpressed. The positive targets that increased recombinant α-amylase production were further combined leading to an 18.7-fold increased recombinant protein production. These target genes are involved in multiple cellular networks including RNA processing, transcription, ER-mitochondrial complex, and protein unfolding. By using transcriptomics and proteomics analyses, combined with reverse metabolic engineering, we showed that reduced oxidative stress, increased membrane lipid biosynthesis and repressed arginine and sulfur amino acid biosynthesis are significant pathways for increased recombinant protein production. Our findings provide new insights towards developing synthetic yeast cell factories for biosynthesis of valuable proteins.
3.	Lakshmana, Tilak Rajesh, 1980, et al. (författare) Partial joint processing for frequency selective channels 2010 Ingår i: IEEE Vehicular Technology Conference. - 1550-2252. - 9781424435746 Konferensbidrag (refereegranskat)abstract In this paper, we consider a static cluster of base stations where joint processing is allowed in the downlink. The partial joint processing scheme is a user-centric approach where subclusters or active sets of base stations are dynamically defined for each user in the cluster. In frequency selective channels, the definition of the subclusters or active set thresholding of base stations can be frequency adaptive (per resource block) or non-adaptive (averaged over all the resource blocks). Frequency adaptive thresholding improves the average sum-rate of the cluster, but at the cost of an increased user data interbase information exchange with respect to the non-adaptive frequency thresholding case. On the other hand, the channel state information available at the transmitter side to design the beamforming matrix is very limited and rank deficiency problems arise for low values of active set thresholding and users located close to the base station. To solve this problem, an algorithm is proposed that defines a cooperation area over the cluster where the partial joint processing scheme can be performed, frequency adaptive or non-adaptive, for a given active set threshold value.
4.	Agarwal, Nisha Rani, 1987, et al. (författare) Non-Linear Microscopy of Mitochondrial Damage and Abnormal Lipid Metabolism in Beta-Amyloid Expressing Yeast 2015 Ingår i: Biophysical Journal. - 0006-3495 .- 1542-0086. ; 108:2, s. 325A-325A Konferensbidrag (övrigt vetenskapligt/konstnärligt)
5.	Busayavalasa, Kiran, et al. (författare) The Nup155-mediated organisation of inner nuclear membrane proteins is independent of Nup155 anchoring to the metazoan nuclear pore complex 2012 Ingår i: Journal of Cell Science. - : The Company of Biologists. - 0021-9533 .- 1477-9137. ; 125:18, s. 4214-4218 Tidskriftsartikel (refereegranskat)abstract The nuclear envelope (NE), an important barrier between the nucleus and the cytoplasm, is composed of three structures: the outer nuclear membrane, which is continuous with the ER, the inner nuclear membrane (INM), which interfaces with chromatin, and nuclear pore complexes (NPCs), which are essential for the exchange of macromolecules between the two compartments. The NPC protein Nup155 has an evolutionarily conserved role in the metazoan NE formation; but the in vivo analysis of Nup155 has been severely hampered by the essential function of this protein in cell viability. Here, we take advantage of the hypomorphicity of RNAi systems and use a combination of protein binding and rescue assays to map the interaction sites of two neighbouring NPC proteins Nup93 and Nup53 on Nup155, and to define the requirements of these interactions in INM protein organization. We show that different parts of Drosophila Nup155 have distinct functions: the Nup155 beta-propeller anchors the protein to the NPC, whereas the alpha-solenoid part of Nup155 is essential for the correct localisation of INM proteins lamin-B receptor (LBR) and otefin. Using chromatin extracts from semisynchronized cells, we also provide evidence that the Nup155 alpha-solenoid has a chromatin-binding activity that is stronger at the end of mitosis. Our results argue that the role of Nup155 in INM protein localisation is not mediated through the NPC anchoring activity of the protein and suggest that regions other than Nup155 beta-propeller are necessary for the targeting of proteins to the INM.
6.	Chen, Xin, 1980, et al. (författare) Amyloid-beta peptide-induced cytotoxicity and mitochondrial dysfunction in yeast 2015 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 15:6 Tidskriftsartikel (refereegranskat)abstract Alzheimer's disease (AD) is the most common neurodegenerative disease, characterized by deposits of amyloid-beta(A beta) peptides. However, the underlying molecular mechanisms of neuron cell dysfunction and cell death in AD still remain poorly understood. Yeast Saccharomyces cerevisiae shares many conserved biological processes with all eukaryotic cells, including human neurons. Thanks to relatively simple and quick genetic and environmental manipulations, the large knowledge base and data collections, this organism has become a valuable tool to unravel fundamental intracellular mechanisms underlying neurodegeneration. In this study, we have used yeast as a model system to study the effects of intracellular A beta peptides and we found that cells constitutively producing native A beta directed to the secretory pathway exhibited a lower growth rate, lower biomass yield, lower respiratory rate, increased oxidative stress, hallmarks of mitochondrial dysfunction and ubiquitin-proteasome system dysfunction. These findings are relevant for better understanding the role of A beta in cell stress and cell damage.
7.	Chen, Xin, 1980, et al. (författare) FMN reduces Amyloid-beta toxicity in yeast by regulating redox status and cellular metabolism 2020 Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1 Tidskriftsartikel (refereegranskat)abstract Alzheimer's disease (AD) is defined by progressive neurodegeneration, with oligomerization and aggregation of amyloid-beta peptides (A beta) playing a pivotal role in its pathogenesis. In recent years, the yeast Saccharomyces cerevisiae has been successfully used to clarify the roles of different human proteins involved in neurodegeneration. Here, we report a genome-wide synthetic genetic interaction array to identify toxicity modifiers of A beta 42, using yeast as the model organism. We find that FMN1, the gene encoding riboflavin kinase, and its metabolic product flavin mononucleotide (FMN) reduce A beta 42 toxicity. Classic experimental analyses combined with RNAseq show the effects of FMN supplementation to include reducing misfolded protein load, altering cellular metabolism, increasing NADH/(NADH+NAD(+)) and NADPH/(NADPH+NADP(+)) ratios and increasing resistance to oxidative stress. Additionally, FMN supplementation modifies Htt103QP toxicity and alpha-synuclein toxicity in the humanized yeast. Our findings offer insights for reducing cytotoxicity of A beta 42, and potentially other misfolded proteins, via FMN-dependent cellular pathways.Saccharomyces cerevisiae is a model organism to study proteins involved in neurodegeneration. Here, the authors performed a yeast genome-wide synthetic genetic interaction array (SGA) to screen for toxicity modifiers of A beta 42 and identify riboflavin kinase and its metabolic product flavin mononucleotide as modulators that alleviate cellular A beta 42 toxicity, which is supported by further experimental analyses.
8.	Chen, Xin, 1980, et al. (författare) Graphene Oxide Attenuates Toxicity of Amyloid-β Aggregates in Yeast by Promoting Disassembly and Boosting Cellular Stress Response 2023 Ingår i: Advanced Functional Materials. - 1616-3028 .- 1616-301X. ; 33:45 Tidskriftsartikel (refereegranskat)abstract Alzheimer's disease (AD) is the most prevalent neurodegenerative disease, with the aggregation of misfolded amyloid-β (Aβ) peptides in the brain being one of its histopathological hallmarks. Recently, graphene oxide (GO) nanoflakes have attracted significant attention in biomedical areas due to their capacity of suppressing Aβ aggregation in vitro. The mechanism of this beneficial effect has not been fully understood in vivo. Herein, the impact of GO on intracellular Aβ42 aggregates and cytotoxicity is investigated using yeast Saccharomyces cerevisiae as the model organism. This study finds that GO nanoflakes can effectively penetrate yeast cells and reduce Aβ42 toxicity. Combination of proteomics data and follow-up experiments show that GO treatment alters cellular metabolism to increases cellular resistance to misfolded protein stress and oxidative stress, and reduces amounts of intracellular Aβ42 oligomers. Additionally, GO treatment also reduces HTT103QP toxicity in the Huntington's disease (HD) yeast model. The findings offer insights for rationally designing GO nanoflakes-based therapies for attenuating cytotoxicity of Aβ42, and potentially of other misfolded proteins involved in neurodegenerative pathology.
9.	Chen, Xin, 1980, et al. (författare) Improved resource allocation strategy in SU-CoMP network 2011 Ingår i: The Journal of China Universities of Posts and Telecommunications. - 2210-5123. ; 18:4, s. 7-12 Tidskriftsartikel (refereegranskat)abstract Coordinated Multi-Point transmission and reception (CoMP) for single user, named as SU-CoMP, is considered as an efficient approach tomitigate inter-cell interference in Orthogonal Frequency Division Multiple Access (OFDMA) systems. Two prevalent approaches in SU-CoMP areCoordinated Scheduling (CS) and Joint Processing (JP). Although JP in SU-CoMP has been proved to achieve a great link performanceimprovement for the cell-edge user, efficient Resource Allocation (RA) on the system level is quite needed. However, so far limited work has beendone considering JP, and most existing schemes achieved the improvement of cell-edge performance at cost of the cell-average performancedegradation compared to the single cell RA. In this paper, a two-phase strategy is proposed for SU-CoMP networks. CS and JP are combined toimprove both cell-edge and cell-average performance. Compared to the single cell RA, simulation results demonstrate that, the proposed strategyleads to both higher cell-average and cell-edge throughput.
10.	Chen, Xin, 1980, et al. (författare) Interplay of Energetics and ER Stress Exacerbates Alzheimer's Amyloid-beta (A beta) Toxicity in Yeast 2017 Ingår i: Frontiers in Molecular Neuroscience. - : Frontiers Media SA. - 1662-5099. ; 10 Tidskriftsartikel (refereegranskat)abstract Alzheimer's disease (AD) is a progressive neurodegeneration. Oligomers of amyloid-beta peptides (A beta) are thought to play a pivotal role in AD pathogenesis, yet the mechanisms involved remain unclear. Two major isoforms of A beta associated with AD are A beta 40 and A beta 42, the latter being more toxic and prone to form oligomers. Here, we took a systems biology approach to study two humanized yeast AD models which expressed either A beta 40 or A beta 42 in bioreactor cultures. Strict control of oxygen availability and culture pH, strongly affected chronological lifespan and reduced variations during cell growth. Reduced growth rates and biomass yields were observed upon A beta 42 expression, indicating a redirection of energy from growth to maintenance. Quantitative physiology analyses furthermore revealed reduced mitochondria' functionality and ATP generation in A beta 42 expressing cells, which matched with observed aberrant mitochondria' structures. Genome-wide expression level analysis showed that A beta 42 expression triggered strong ER stress and unfolded protein responses. Equivalent expression of A beta 40, however, induced only mild ER stress, which resulted in hardly affected physiology. Using AD yeast models in well controlled cultures strengthened our understanding on how cells translate different A beta toxicity signals into particular cell fate programs, and further enhance their potential as a discovery platform to identify possible therapies.
11.	Chen, Xin, 1980, et al. (författare) Optimal and Efficient Power Allocation for OFDM Non-Coherent Cooperative Transmission 2012 Ingår i: IEEE Wireless Communications and Networking Conference, WCNC. - 1525-3511. - 9781467304375 ; , s. 1584-1589 Konferensbidrag (refereegranskat)abstract In this paper, we study the subchannel (SC) power allocation for orthogonal frequency division multiplexing (OFDM) multiple access points (APs) systems with non-coherent cooperative transmission. The objective is to maximize the total capacity under per-AP power constraints. It can be proved that the optimal solution can be obtained by the combination of an optimal SC partition search and the power allocation across SCs for each feasible partition. Existing work exhaustively searched the optimal SC partition and used Lagrange dual method to compute the power allocation across SCs. Since the entire complexity increases exponentially with the number of SCs, the existing method is unsuitable for practical implementation. In this paper, we propose a novel optimal power allocation algorithm for non-coherent cooperative transmission with a much lower complexity. Firstly, a concept of “cut-off SC” is proposed for searching the optimal SC partition. Then, an efficient optimal power allocation algorithm across SCs is proposed for any given cut-off SC. Simulation results demonstrate that the proposed algorithm is optimal with a polynomial complexity, and ends within an acceptable number of iterations.
12.	Chen, Xin, 1980, et al. (författare) Role of frameshift ubiquitin B protein in Alzheimer's disease 2016 Ingår i: Wiley Interdisciplinary Reviews: Systems Biology and Medicine. - : Wiley. - 1939-5094 .- 1939-005X. ; 8:4, s. 300-313 Forskningsöversikt (refereegranskat)abstract Alzheimer's disease (AD) is the most common neurodegenerative disease and is characterized by accumulation of misfolded and aggregated proteins. Since the ubiquitin-proteasome system (UPS) is the major intracellular protein quality control (PQC) system in eukaryotic cells, it is likely involved in the etiology of AD. The frameshift form of ubiquitin (Ubb+1) accumulates in the neuritic plaques and neurofibrillary tangles in patients with AD. Ubb+1 accumulates in an age-dependent manner as a result of RNA-polymerase mediated molecular misreading during transcription, which allows the formation of mutant proteins in the absence of gene mutations. The accumulation of the Ubb+1 protein may act as an endogenous reporter for proteasome dysfunction and a growing number of studies have shown that Ubb+1 may play more important pathogenic roles in AD etiology than previously hypothesized. The yeast Saccharomyces cerevisiae shares many conserved biological processes with all eukaryotic cells, including human neurons. This organism has been regarded as a model system for investigating the fundamental intracellular mechanisms, including those underlying neurodegeneration. We propose here that yeast systems biology approaches, combined with cell and molecular biology approaches will increase the relevant knowledge needed for advancement and elucidation of mechanisms and complex traits, which could provide new targets for therapeutic intervention in AD. WIREs Syst Biol Med 2016, 8:300–313. doi: 10.1002/wsbm.1340. For further resources related to this article, please visit the WIREs website.
13.	Chen, Xin, 1980, et al. (författare) UBB+1 reduces amyloid-beta cytotoxicity by activation of autophagy in yeast 2021 Ingår i: Aging. - : Impact Journals, LLC. - 1945-4589. ; 13:21, s. 23953-23980 Tidskriftsartikel (refereegranskat)abstract UBB+1 is a mutated version of ubiquitin B peptide caused by a transcriptional frameshift due to the RNA polymerase II "slippage". The accumulation of UBB+1 has been linked to ubiquitin-proteasome system (UPS) dysfunction and neurodegeneration. Alzheimer's disease (AD) is defined as a progressive neurodegeneration and aggregation of amyloid-beta peptides (A beta) is a prominent neuropathological feature of AD. In our previous study, we found that yeast cells expressing UBB+1 at lower level display an increased resistance to cellular stresses under conditions of chronological aging. In order to examine the molecular mechanisms behind, here we performed genome-wide transcriptional analyses and molecular/cellular biology assays. We found that low UBB+1 expression activated the autophagy pathway, increased vacuolar activity, and promoted transport of autophagic marker ATG8p into vacuole. Furthermore, we introduced low UBB+1 expression to our humanized yeast AD models, that constitutively express A beta 42 and A beta 40 peptide, respectively. The co-expression of UBB+1 with A beta 42 or A beta 40 peptide led to reduced intracellular A beta levels, ameliorated viability, and increased chronological life span. In an autophagy deficient background strain (atg1 Delta), intracellular A beta levels were not affected by UBB+1 expression. Our findings offer insights for reducing intracellular A beta toxicity via autophagydependent cellular pathways under low level of UBB+1 expression.
14.	Johansson, Magnus, 1983, et al. (författare) PUFA-induced cell death is mediated by Yca1p-dependent and -independent pathways, and is reduced by vitamin C in yeast 2016 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 16:2 Tidskriftsartikel (refereegranskat)abstract Polyunsaturated fatty acids (PUFA) such as linoleic acid (LA, n-6, C18:2) and gamma-linolenic acid (GLA, n-6, C18: 3) are essential and must be obtained from the diet. There has been a growing interest in establishing a bio-sustainable production of PUFA in several microorganisms, e.g. in yeast Saccharomyces cerevisiae. However, PUFAs can also be toxic to cells because of their susceptibility to peroxidation. Here we investigated the negative effects of LA and GLA production on S. cerevisiae by characterizing a strain expressing active Delta 6 and Delta 12 desaturases from the fungus Mucor rouxii. Previously, we showed that the PUFA-producing strain has low viability, down-regulated genes for oxidative stress response, and decreased proteasome activity. Here we show that the PUFA strain accumulates high levels of reactive oxygen species (ROS) and lipid peroxides, and accumulates damaged proteins. The PUFA strain also showed great increase in metacaspase Yca1p activity, suggesting cells could die by caspase-mediated cell death. When treated with antioxidant vitamin C, ROS, lipid peroxidation and protein carbonylation were greatly reduced, and the activity of the metacaspase was significantly decreased too, ultimately doubling the lifespan of the PUFA strain. When deleting YCA1, the caspase-like activity and the oxidative stress decreased and although the lifespan was slightly prolonged, the phenotype could not be fully reversed, pointing that Yca1p was not the main executor of cell death.
15.	Li, Jingya, 1986, et al. (författare) Downlink Radio Resource Allocation for Coordinated Cellular OFDMA Networks 2010 Ingår i: IEICE Transactions on Communications. - 1745-1345. ; E93B:12, s. 3480-3488 Tidskriftsartikel (refereegranskat)abstract Base station coordination is considered as a promising technique to mitigate inter-cell interference and improve the cell-edge performance in cellular orthogonal frequency division multiple-access (OFDMA) networks. The problem to design an efficient radio resource allocation scheme for coordinated cellular OFDMA networks incorporating base station coordination has been only partially investigated. In this contribution, a novel radio resource allocation algorithm with universal frequency reuse is proposed to support base station coordinated transmission. Firstly, with the assumption of global coordination between all base station sectors in the network, a coordinated subchannel assignment algorithm is proposed. Then, by dividing the entire network into a number of disjoint coordinated clusters of base station sectors, a reduced-feedback algorithm for subchannel assignment is proposed for practical use. The utility function based on the user average throughput is used to balance the efficiency and fairness of wireless resource allocation. System level simulation results demonstrate that the reduced-feedback subchannel assignment algorithm significantly improves the cell-edge average throughput and the fairness index of users in the network, with acceptable degradation of cell-average performance.
16.	Li, Jingya, 1986, et al. (författare) Joint Scheduling and Power Control in Coordinated Multi-Point Clusters 2011 Ingår i: IEEE Vehicular Technology Conference. - 1550-2252. - 9781424483273 ; , s. Art. no. 6092837- Konferensbidrag (refereegranskat)abstract In this paper, we address the problem of designing a joint scheduling and power control algorithm in a downlink coordinated multi-point (CoMP) cluster supporting CoMP joint transmission. The objective is to maximize the cell-edge throughput under per-point power constraints. By an analytical derivation, binary power control is proved to be the optimal solution for any given selected user group. Utilizing this analytical result, a centralized and a semi-distributed version of joint user selection and power control algorithms are proposed. Compared to algorithms without considering joint transmission and algorithms without considering power control, simulation results show that the proposed algorithms achieve a good trade-off between joint transmission and interference coordination, which helps to improve the cell-edge performance.
17.	Li, Jingya, 1986, et al. (författare) Resource allocation for OFDMA systems with multi-cell joint transmission 2012 Ingår i: 2012 IEEE 13th International Workshop on Signal Processing Advances in Wireless Communications, SPAWC 2012. Cesme, 17-20 June 2012. - 9781467309714 ; , s. 179-183 Konferensbidrag (refereegranskat)abstract This paper considers the downlink resource allocation of a coordinated multi-cell cluster in OFDMA systems with universal frequency reuse. Multi-cell joint transmission is considered via zero-forcing precoding. Furthermore, joint optimization of the user selection and power allocation across multiple subchannels and multiple cells is studied. The objective is to maximize the weighted sum rate under per-base-station power constraints. Based on general duality theory, two iterative resource allocation algorithms are proposed and compared with the optimal solution, which requires an exhaustive search of all possible combinations of users over all subchannels. Simulation results show that the two proposed algorithms achieve a performance very close to the optimal, with much lower computational complexity. In addition, we show that joint user set selection across multiple subchannels significantly improves the system performance in terms of the weighted sum rate.
18.	Meza, Eugenio, 1975, et al. (författare) Development of a method for heat shock stress assessment in yeast based on transcription of specific genes 2021 Ingår i: Yeast. - : Wiley. - 1097-0061 .- 0749-503X. ; 38:10, s. 549-565 Tidskriftsartikel (refereegranskat)abstract All living cells, including yeast cells, are challenged by different types of stresses in their environments and must cope with challenges such as heat, chemical stress, or oxidative damage. By reversibly adjusting the physiology while maintaining structural and genetic integrity, cells can achieve a competitive advantage and adapt environmental fluctuations. The yeast Saccharomyces cerevisiae has been extensively used as a model for study of stress responses due to the strong conservation of many essential cellular processes between yeast and human cells. We focused here on developing a tool to detect and quantify early responses using specific transcriptional responses. We analyzed the published transcriptional data on S. cerevisiae DBY strain responses to 10 different stresses in different time points. The principal component analysis (PCA) and the Pearson analysis were used to assess the stress response genes that are highly expressed in each individual stress condition. Except for these stress response genes, we also identified the reference genes in each stress condition, which would not be induced under stress condition and show stable transcriptional expression over time. We then tested our candidates experimentally in the CEN.PK strain. After data analysis, we identified two stress response genes (UBI4 and RRP) and two reference genes (MEX67 and SSY1) under heat shock (HS) condition. These genes were further verified by real-time PCR at mild (42°C), severe (46°C), to lethal temperature (50°C), respectively.
19.	Muñoz Arellano, Ana Joyce, 1983, et al. (författare) Different expression levels of human mutant ubiquitin B+1 (UBB+1) can modify chronological lifespan or stress resistance of saccharomyces cerevisiae 2018 Ingår i: Frontiers in Molecular Neuroscience. - : Frontiers Media SA. - 1662-5099. ; 11 Tidskriftsartikel (refereegranskat)abstract The ubiquitin-proteasome system (UPS) is the main pathway responsible for the degradation of misfolded proteins, and its dysregulation has been implicated in several neurodegenerative diseases, including Alzheimer’s disease (AD). UBB+1, a mutant variant of ubiquitin B, was found to accumulate in neurons of AD patients and it has been linked to UPS dysfunction and neuronal death. Using the yeast Saccharomyces cerevisiae as a model system, we constitutively expressed UBB+1to evaluate its effects on proteasome function and cell death, particularly under conditions of chronological aging. We showed that the expression of UBB+1caused inhibition of the three proteasomal proteolytic activities (caspase-like (β1), trypsin-like (β2) and chymotrypsin-like (β5) activities) in yeast. Interestingly, this inhibition did not alter cell viability of growing cells. Moreover, we showed that cells expressing UBB+1at lower level displayed an increased capacity to degrade induced misfolded proteins. When we evaluated cells during chronological aging, UBB+1expression at lower level, prevented cells to accumulate reactive oxygen species (ROS) and avert apoptosis, dramatically increasing yeast life span. Since proteasome inhibition by UBB+1has previously been shown to induce chaperone expression and thus protect against stress, we evaluated our UBB+1model under heat shock and oxidative stress. Higher expression of UBB+1caused thermotolerance in yeast due to induction of chaperones, which occurred to a lesser extent at lower expression level of UBB+1(where we observed the phenotype of extended life span). Altering UPS capacity by differential expression of UBB+1protects cells against several stresses during chronological aging. This system can be valuable to study the effects of UBB+1on misfolded proteins involved in neurodegeneration and aging.
20.	Souza-Moreira, Tatiana M., et al. (författare) Screening of 2A peptides for polycistronic gene expression in yeast 2018 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 18:5 Tidskriftsartikel (refereegranskat)abstract A complexity of pathway expression in yeast compared to prokaryotes is the need for separate promoters and terminators for each gene expressed. Single transcript expression and separated protein production is possible via the use of 2A viral peptides, but detailed characterization to assess their suitability and applications is needed. The present work aimed to characterize multiple 2A peptide sequences to determine suitability for metabolic engineering applications in Saccharomyces cerevisiae. We screened 22 peptides placed between fluorescent protein sequences. Cleaving efficiency was calculated by western blot intensity of bands corresponding to the cleaved and uncleaved forms of the reporter. Three out of the 22 sequences showed high cleavage efficiency: 2A peptide from Equine rhinitis B virus (91%), Porcine teschovirus-1 (85%) and Operophtera brumata cypovirus-18 (83%). Furthermore, expression of the released protein was comparable to its monocistronic expression. As a proof-of-concept, the triterpene friedelin was successfully produced in the same yeast strain by expressing its synthase with the truncated form of HMG1 linked by the 2A peptide of ERBV-1, with production titers comparable to monocistronic expression (via separate promoters). These results suggest that these peptides could be suitable for expression and translation of multiple proteins in metabolic engineering applications in S. cerevisiae.
21.	Tedersoo, Leho, et al. (författare) Global diversity and geography of soil fungi 2014 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6213, s. artikel nr 1256688- Tidskriftsartikel (refereegranskat)abstract Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.
22.	Wang, Yanyan, 1989, et al. (författare) CRISPR/Cas9-mediated point mutations improve alpha-amylase secretion in Saccharomyces cerevisiae 2022 Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 22:1 Tidskriftsartikel (refereegranskat)abstract The rapid expansion of the application of pharmaceutical proteins and industrial enzymes requires robust microbial workhorses for high protein production. The budding yeast Saccharomyces cerevisiae is an attractive cell factory due to its ability to perform eukaryotic post-translational modifications and to secrete proteins. Many strategies have been used to engineer yeast platform strains for higher protein secretion capacity. Herein, we investigated a line of strains that have previously been selected after UV random mutagenesis for improved alpha-amylase secretion. A total of 42 amino acid altering point mutations identified in this strain line were reintroduced into the parental strain AAC to study their individual effects on protein secretion. These point mutations included missense mutations (amino acid substitution), nonsense mutations (stop codon generation), and frameshift mutations. For comparison, single gene deletions for the corresponding target genes were also performed in this study. A total of 11 point mutations and seven gene deletions were found to effectively improve alpha-amylase secretion. These targets were involved in several bioprocesses, including cellular stresses, protein degradation, transportation, mRNA processing and export, DNA replication, and repair, which indicates that the improved protein secretion capacity in the evolved strains is the result of the interaction of multiple intracellular processes. Our findings will contribute to the construction of novel cell factories for recombinant protein secretion. Systematic characterization of point mutations from evolved strains using CRISPR/Cas9 technology revealed a set of gene alterations that improved recombinant protein secretion in Saccharomyces cerevisiae.
23.	Wang, Yanyan, 1989, et al. (författare) Expression of antibody fragments in Saccharomyces cerevisiae strains evolved for enhanced protein secretion 2021 Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 20:1 Tidskriftsartikel (refereegranskat)abstract Monoclonal antibodies, antibody fragments and fusion proteins derived thereof have revolutionized the practice of medicine. Major challenges faced by the biopharmaceutical industry are however high production costs, long processing times and low productivities associated with their production in mammalian cell lines. The yeast Saccharomyces cerevisiae, a well-characterized eukaryotic cell factory possessing the capacity of posttranslational modifications, has been industrially exploited as a secretion host for production of a range of products, including pharmaceuticals. However, due to the incompatible surface glycosylation, few antibody molecules have been functionally expressed in S. cerevisiae. Here, three non-glycosylated antibody fragments from human and the Camelidae family were chosen for expression in a S. cerevisiae strain (HA) previously evolved for high α-amylase secretion. These included the Fab fragment Ranibizumab (Ran), the scFv peptide Pexelizumab (Pex), and a nanobody consisting of a single V-type domain (Nan). Both secretion and biological activities of the antibody fragments were confirmed. In addition, the secretion level of each protein was compared in the wild type (LA) and two evolved strains (HA and MA) with different secretory capacities. We found that the secretion of Ran and Nan was positively correlated with the strains’ secretory capacity, while Pex was most efficiently secreted in the parental strain. To investigate the mechanisms for different secretion abilities in these selected yeast strains for the different antibody fragments, RNA-seq analysis was performed. The results showed that several bioprocesses were significantly enriched for differentially expressed genes when comparing the enriched terms between HA.Nan vs. LA.Nan and HA.Pex vs. LA.Pex, including amino acid metabolism, protein synthesis, cell cycle and others, which indicates that there are unique physiological needs for each antibody fragment secretion.

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