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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. |
- Bandelt, HJ, et al.
(författare)
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Quasi-median graphs from sets of partitions
- 2002
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Ingår i: Discrete Applied Mathematics. - 0166-218X .- 1872-6771. ; 122:23-35, s. 23-35
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- In studies of molecular evolution, one is typically confronted with the task of inferring a phylogenetic tree from a set X of sequences of length n over a finite alphabet Lambda. For studies that invoke parsimony, it has been found helpful to consider the quasi-median graph generated by X in the Hamming graph Lambda(n). Although a great deal is already known about quasi-median graphs (and their algebraic counterparts), little is known about the quasi-median generation in Lambda(n) starting from a set X of vertices. We describe the vertices of the quasi-median graph generated by X in terms of the coordinatewise partitions of X. In particular, we clarify when the generated quasi-median graph is the so-called relation graph associated with X. This immediately characterizes the instances where either a block graph or the total Hamming graph is generated.
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| 4. |
- Cieslik, D, et al.
(författare)
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Connectivity calculus
- 2003
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Ingår i: Applied Mathematics Letters. - 0893-9659 .- 1873-5452. ; 16:3, s. 395-399
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Tidskriftsartikel (refereegranskat)abstract
- Given a finite hypergraph H = (V, E) and, for each e E E, a collection of nonempty subsets pi(e) of e, Mobius inversion is used to establish a recursive formula for the number of connected components of the hypergraph H = (V, boolean OR(eis an element ofE)pi(e)). As shown elsewhere, this formula is an essential ingredient in the context of a certain divide-and-conquer strategy that allows us to define a dynamical programming scheme solving Steiner's problem for graphs in linear time (however, with a constant depending hyperexponentially on their tree width).
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| 6. |
- Dress, A., et al.
(författare)
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Six points suffice : How to check for metric consistency
- 2001
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Ingår i: European journal of combinatorics (Print). - : Elsevier BV. - 0195-6698 .- 1095-9971. ; 22:4, s. 465-474
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Tidskriftsartikel (refereegranskat)abstract
- In many areas of data analysis, it is desirable to have tools at hand for analyzing the structure of distance tables-or, in more mathematical terms, of finite metric spaces. One such tool, known as split decomposition theory has proven particularly useful in this respect. Tbe class of so-called totally decomposable metrics forms a cornerstone for this theory, and much work has been devoted to their study. Recently, it has become apparent that a particular subclass of these metrics, the consistent metrics, are also of fundamental importance. In this paper, we give a six-point characterization of consistent metrics amongst the totally decomposable ones.
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| 8. |
- Huber, Katharina T, et al.
(författare)
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Pruned median networks : A technique for reducing the complexity of median networks
- 2001
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 19:2, s. 302-310
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Tidskriftsartikel (refereegranskat)abstract
- Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by tree-like bifurcating evolutionary models. These observations might result from processes of-species diversification and/or processes of sequence evolution that are not tree-like. In these Cases, bifurcating tree representations provide poor visualization of phylogenetic signals in sequence data. In this paper, we use median networks to study DNA sequence substitution patterns in plant nuclear and chloroplast markers. We describe how to prune median networks to obtain so called pruned median networks. These simpler networks may help to provide a useful framework for investigating the phylogenetic complexity of recently diverged taxa with hybrid origins.
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| 9. |
- Huber, Katharina T., et al.
(författare)
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Reconstructing the evolutionary history of polyploids from multilabeled trees
- 2006
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 23:9, s. 1784-1791
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Tidskriftsartikel (refereegranskat)abstract
- In recent studies, phylogenetic networks have been derived from so-called multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were constructed using sophisticated techniques in phylogenetic analysis, the presented networks were inferred using ad hoc arguments that cannot be easily extended to larger, more complicated examples. In this paper, we present a general method for constructing such networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties. To illustrate the applicability of our method, we discuss its use in reconstructing the evolutionary history of plant allopolyploids. We conclude with a discussion concerning possible future directions. The network construction method has been implemented and is freely available for use from http://www.uea.ac.uk/similar to a043878/padre.html.
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| 10. |
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