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| 2. |
- Bowman, John L, et al.
(author)
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Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome
- 2017
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In: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 171:2, s. 287-304.15
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Journal article (peer-reviewed)abstract
- The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.
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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 4. |
- Akiyama, Eiji, et al.
(author)
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SPIRAL STRUCTURE AND DIFFERENTIAL DUST SIZE DISTRIBUTION IN THE LkH alpha 330 DISK
- 2016
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In: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 152:6
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Journal article (peer-reviewed)abstract
- Dust trapping accelerates the coagulation of dust particles, and, thus, it represents an initial step toward the formation of planetesimals. We report H-band (1.6 mu m) linear polarimetric observations and 0.87 mm interferometric continuum observations toward a transitional disk around LkH alpha 330. As a. result, a pair of spiral arms were detected in the H-band emission, and an asymmetric (potentially arm-like) structure was detected in the 0.87 mm continuum emission. We discuss the origin of the spiral arm and the asymmetric structure. and suggest that a massive unseen planet is the most plausible explanation. The possibility of dust trapping and grain growth causing the asymmetric structure was also investigated through the opacity index (beta) by plotting the observed spectral energy distribution slope between 0.87 mm from our Submillimeter Array observation and 1.3 mm from literature. The results imply that grains are indistinguishable from interstellar medium-like dust in the east side (beta = 2.0 +/- 0.5) but are much smaller in the west side beta = 0.7(-0.4)(+0.5), indicating differential dust size distribution between the two sides of the disk. Combining the results of near-infrared and submillimeter observations, we conjecture that the spiral arms exist at the upper surface and an asymmetric structure resides in the disk interior. Future observations at centimeter wavelengths and differential polarization imaging in other bands (Y-K) with extreme AO imagers are required to understand how large dust grains form and to further explore the dust distribution in the disk.
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| 5. |
- Berger, Juerg, et al.
(author)
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Systematic identification of genes that regulate neuronal wiring in the Drosophila visual system
- 2008
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In: PLOS GENET. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 4:5, s. e1000085-
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Journal article (peer-reviewed)abstract
- Forward genetic screens in model organisms are an attractive means to identify those genes involved in any complex biological process, including neural circuit assembly. Although mutagenesis screens are readily performed to saturation, gene identification rarely is, being limited by the considerable effort generally required for positional cloning. Here, we apply a systematic positional cloning strategy to identify many of the genes required for neuronal wiring in the Drosophila visual system. From a large-scale forward genetic screen selecting for visual system wiring defects with a normal retinal pattern, we recovered 122 mutations in 42 genetic loci. For 6 of these loci, the underlying genetic lesions were previously identified using traditional methods. Using SNP-based mapping approaches, we have now identified 30 additional genes. Neuronal phenotypes have not previously been reported for 20 of these genes, and no mutant phenotype has been previously described for 5 genes. The genes encode a variety of proteins implicated in cellular processes such as gene regulation, cytoskeletal dynamics, axonal transport, and cell signalling. We conducted a comprehensive phenotypic analysis of 35 genes, scoring wiring defects according to 33 criteria. This work demonstrates the feasibility of combining large-scale gene identification with large-scale mutagenesis in Drosophila, and provides a comprehensive overview of the molecular mechanisms that regulate visual system wiring.
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| 6. |
- Davydova, Erna, et al.
(author)
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The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes
- 2021
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Journal article (peer-reviewed)abstract
- Post-translational methylation plays a crucial role in regulating and optimizing protein function. Protein histidine methylation, occurring as the two isomers 1- and 3-methylhistidine (1MH and 3MH), was first reported five decades ago, but remains largely unexplored. Here we report that METTL9 is a broad-specificity methyltransferase that mediates the formation of the majority of 1MH present in mouse and human proteomes. METTL9-catalyzed methylation requires a His-x-His (HxH) motif, where “x” is preferably a small amino acid, allowing METTL9 to methylate a number of HxH-containing proteins, including the immunomodulatory protein S100A9 and the NDUFB3 subunit of mitochondrial respiratory Complex I. Notably, METTL9-mediated methylation enhances respiration via Complex I, and the presence of 1MH in an HxH-containing peptide reduced its zinc binding affinity. Our results establish METTL9-mediated 1MH as a pervasive protein modification, thus setting the stage for further functional studies on protein histidine methylation.
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| 7. |
- Fitzer, Susan, et al.
(author)
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Established and emerging techniques for characterising the formation, structure and performance of calcified structures under ocean acidification
- 2019
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In: Oceanography and Marine Biology: An Annual Review 57. - Boca Raton, FL, USA : CRC Press. - 0078-3218. - 9780367134150 ; , s. 89-126
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Book chapter (peer-reviewed)abstract
- Ocean acidification (OA) is the decline in seawater pH and saturation levels of calcium carbonate (CaCO3) minerals that has led to concerns for calcifying organisms such as corals, oysters and mussels because of the adverse effects of OA on their biomineralisation, shells and skeletons. A range of cellular biology, geochemistry and materials science approaches have been used to explore biomineralisation. These techniques have revealed that responses to seawater acidification can be highly variable among species, yet the underlying mechanisms remain largely unresolved. To assess the impacts of global OA, researchers will need to apply a range of tools developed across disciplines, many of which are emerging and have not yet been used in this context. This review outlines techniques that could be applied to study OA-induced alterations in the mechanisms of biomineralisation and their ultimate effects on shells and skeletons. We illustrate how to characterise, quantify and monitor the process of biomineralisation in the context of global climate change and OA. We highlight the basic principles, as well as the advantages and disadvantages, of established, emerging and future techniques for OA researchers. A combination of these techniques will enable a holistic approach and better understanding of the potential impact of OA on biomineralisation and its consequences for marine calcifiers and associated ecosystems.
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| 8. |
- Horie, Masayuki, et al.
(author)
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Endogenous non-retroviral RNA virus elements in mammalian genomes.
- 2010
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 463:7277, s. 84-87
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Journal article (peer-reviewed)abstract
- Retroviruses are the only group of viruses known to have left a fossil record, in the form of endogenous proviruses, and approximately 8% of the human genome is made up of these elements. Although many other viruses, including non-retroviral RNA viruses, are known to generate DNA forms of their own genomes during replication, none has been found as DNA in the germline of animals. Bornaviruses, a genus of non-segmented, negative-sense RNA virus, are unique among RNA viruses in that they establish persistent infection in the cell nucleus. Here we show that elements homologous to the nucleoprotein (N) gene of bornavirus exist in the genomes of several mammalian species, including humans, non-human primates, rodents and elephants. These sequences have been designated endogenous Borna-like N (EBLN) elements. Some of the primate EBLNs contain an intact open reading frame (ORF) and are expressed as mRNA. Phylogenetic analyses showed that EBLNs seem to have been generated by different insertional events in each specific animal family. Furthermore, the EBLN of a ground squirrel was formed by a recent integration event, whereas those in primates must have been formed more than 40 million years ago. We also show that the N mRNA of a current mammalian bornavirus, Borna disease virus (BDV), can form EBLN-like elements in the genomes of persistently infected cultured cells. Our results provide the first evidence for endogenization of non-retroviral virus-derived elements in mammalian genomes and give novel insights not only into generation of endogenous elements, but also into a role of bornavirus as a source of genetic novelty in its host.
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| 9. |
- Kavallaris, Nikos I., et al.
(author)
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An analytic approach to the normalized Ricci flow-like equation
- 2010
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In: Nonlinear Analysis. - : Elsevier. - 0362-546X .- 1873-5215. ; 72:5, s. 2300-2317
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Journal article (peer-reviewed)abstract
- This paper is concerned with a parabolic equation with a non-local term defined on a compact two-dimensional Riemannian surface Ω. If the total mass of the solution, λ, is equal to 8π and Ω is the standard sphere S2, it is a Hamilton’s normalized Ricci flow. We obtain the global in time existence of the solution to this problem for 0<λ≤8π. If 0<λ<8π, the orbit is compact while for λ=8π, there is a time sequence along which the solution converges to a stationary solution.
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| 10. |
- Kavallaris, Nikos I., et al.
(author)
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An analytic approach to the normalized Ricci flow-like equation: Revisited
- 2015
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In: Applied Mathematics Letters. - : Elsevier BV. - 0893-9659 .- 1873-5452. ; 44, s. 30-33
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Journal article (peer-reviewed)abstract
- In this paper we revisit Hamilton's normalized Ricci flow, which was thoroughly studied via a PDE approach in Kavallaris and Suzuki (2010). Here we provide an improved convergence result compared to the one presented Kavallaris and Suzuki (2010) for the critical case λ=8π. We actually prove that the convergence towards the stationary normalized Ricci flow is realized through any time sequence.
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