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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Chen, Jian, et al.
(författare)
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Zika virus infects renal proximal tubular epithelial cells with prolonged persistency and cytopathic effects
- 2017
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Ingår i: Emerging Microbes & Infections. - : NATURE PUBLISHING GROUP. - 2222-1751. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Zika virus (ZIKV) infection can cause fetal developmental abnormalities and Guillain-Barre syndrome in adults. Although progress has been made in understanding the link between ZIKV infection and microcephaly, the pathology of ZIKV, particularly the viral reservoirs in human, remains poorly understood. Several studies have shown that compared to serum samples, patients' urine samples often have a longer duration of ZIKV persistency and higher viral load. This finding suggests that an independent viral reservoir may exist in the human urinary system. Despite the clinical observations, the host cells of ZIKV in the human urinary system are poorly characterized. In this study, we demonstrate that ZIKV can infect renal proximal tubular epithelial cells (RPTEpiCs) in immunodeficient mice in vivo and in both immortalized and primary human renal proximal tubular epithelial cells (hRPTEpiCs) in vitro. Importantly, ZIKV infection in mouse kidneys caused caspase-3-mediated apoptosis of renal cells. Similarly, in vitro infection of immortalized and primary hRPTEpiCs resulted in notable cytopathic effects. Consistent with the clinical observations, we found that ZIKV infection can persist with prolonged duration in hRPTEpiCs. RNA-Seq analyses of infected hRPTEpiCs revealed a large number of transcriptional changes in response to ZIKV infection, including type I interferon signaling genes and anti-viral response genes. Our results suggest that hRPTEpiCs are a potential reservoir of ZIKV in the human urinary system, providing a possible explanation for the prolonged persistency of ZIKV in patients' urine.
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| 4. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 5. |
- Wang, Longxin, et al.
(författare)
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Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis)
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- The Quercus variabilis, a deciduous broadleaved tree species, holds significant ecological and economical value. While a chromosome-level genome for this species has been made available, it remains riddled with unanchored sequences and gaps. In this study, we present a nearly complete comprehensive telomere-to-telomere (T2T) and haplotype-resolved reference genome for Q. variabilis. This was achieved through the integration of ONT ultra-long reads, PacBio HiFi long reads, and Hi-C data. The resultant two haplotype genomes measure 789 Mb and 768 Mb in length, with a contig N50 of 65 Mb and 56 Mb, and were anchored to 12 allelic chromosomes. Within this T2T haplotype-resolved assembly, we predicted 36,830 and 36,370 protein-coding genes, with 95.9% and 96.0% functional annotation for each haplotype genome. The availability of the T2T and haplotype-resolved reference genome lays a solid foundation, not only for illustrating genome structure and functional genomics studies but also to inform and facilitate genetic breeding and improvement of cultivated Quercus species.
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| 6. |
- Ahmed, Jawwad, et al.
(författare)
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Efficient Inter-Thread Scheduling Scheme for Long-Reach Passive Optical Networks
- 2013
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Ingår i: IEEE Communications Magazine. - 0163-6804 .- 1558-1896. ; 51:2, s. S35-S43
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Tidskriftsartikel (refereegranskat)abstract
- These days there is a clear trend toward extending the reach of passive optical networks to cover large geographical areas, which enables reduction of the number of central offices and hence has the potential of cost saving in network operation. On the other hand, this reach extension necessitates the design of efficient dynamic bandwidth allocation schemes in order to tackle performance degradation caused by the increased propagation delay in long reach PONs. Among many existing approaches, the multi-thread-based DBA scheme where several bandwidth allocation processes are performed in parallel is considered one of the most effective options to improve network performance in LRPONs. We have found that without proper intercommunication between the overlapped threads, multi-thread DBA may lose efficiency and even perform worse than the conventional single-thread algorithm. With this in mind, this article reviews different inter-thread scheduling schemes for LR-PONs, and proposes a novel approach of integrating the key ideas of the existing ones. Extensive simulation results confirm that our proposed scheme can significantly improve DBA performance for LR-PONs under a variety of scenarios with consideration of different values of network load and reach.
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| 7. |
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| 8. |
- Chen, Biao, et al.
(författare)
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Efficient and fine scheduling algorithm for bandwidth allocation in Ethernet passive optical networks
- 2006
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Ingår i: IEEE Journal of Selected Topics in Quantum Electronics. - 1077-260X .- 1558-4542. ; 12:4, s. 653-660
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Tidskriftsartikel (refereegranskat)abstract
- A novel fine scheduling algorithm is introduced for upstream bandwidth allocation in an Ethernet-based passive optical network. This scheduling algorithm consists of an inter optical network unit (ONU) scheduler at the optical line terminal (OLT) and an intra-ONU scheduler at each ONU. In the inter-ONU scheduling, a novel GATE/REPORT approach is introduced to eliminate the unused remainders without transmission delay and maximize the utilization of bandwidth. Our novel intra-ONU scheduler gives fair bandwidth allocation to the queues of different priorities for each user in a hierarchical and decentralized way. Numerical results have shown that our overall scheduling algorithm can fulfill various requirements of delay and throughput for the transmission of multimedia traffic for each end user..
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| 9. |
- Chen, Jiajia, et al.
(författare)
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A novel algorithm for intra-ONU bandwidth allocation in ethernet passive optical networks
- 2005
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Ingår i: IEEE Communications Letters. - 1089-7798 .- 1558-2558. ; 9:9, s. 850-852
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Tidskriftsartikel (refereegranskat)abstract
- A novel decentralized algorithm is introduced for the intra-ONU bandwidth allocation in an Ethernet Passive Optical Network (EPON). The algorithm is of low computational complexity, and can guarantee both the priority and fairness of the differentiated services. Simulation results are presented and compared with those of two existing bandwidth allocation algorithms.
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| 10. |
- Chen, Jiajia, et al.
(författare)
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A novel hierarchical algorithm for intra-ONU scheduling in an ethernet passive optical network
- 2005
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Ingår i: Network Architectures, Management, and Applications III. - : SPIE. ; , s. W220-W220
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Konferensbidrag (refereegranskat)abstract
- The quality of service (QoS) requirements of end users and services are totally different, and thus the multi-oriented (user-oriented and service-oriented) scheduling for access networks based on a remote scheduling system especially for EPONs is desired to replace the single-oriented (user-oriented or service-oriented) scheduling. In this paper we introduce a novel hierarchical algorithm of intra-ONU scheduling for multi-oriented QoS, which can guarantee both the priority of the differentiated services and the fairness of the different users. Numerical results have shown that our overall scheduling algorithm can fulfill various requirements of delay and throughput for the transmission of multimedia traffic for each end user.
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