| 1. |
- Birney, Ewan, et al.
(author)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Clark, Eric, et al.
(author)
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Foreword
- 2009
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In: National Geographic countries of the world. - 9781426303890 ; , s. 4-5
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Book chapter (pop. science, debate, etc.)
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| 3. |
- Clark, Eric, et al.
(author)
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Isolating Connections - Connecting Isolations
- 2009
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In: Geografiska Annaler. Series B. Human Geography. - 1468-0467. ; 91B:4, s. 311-323
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Research review (peer-reviewed)abstract
- The varied and distinct ways we connect can facilitate or impose isolation, our own or someone else's. Different forms of isolation are themselves interconnected and sometimes enrich our connecting. The relation between isolation and connection, we argue, is one of complementarity, like Calvino's 'two inseparable and complementary functions of life ... syntony, or participation in the world around us ... [and] focalization or constructive concentration.' Solitude sought can enhance connections. Imposed isolation weakens connections in ways both obvious and subtle. This contrast between sought and imposed underscores the influence of hierarchy and socially produced inequities, excesses of which fragment the social ties that could constrain or diminish these same inequities. Deep inequity degrades the quality of both connections and isolation, at significant costs to our health, ecology, economy, cultural diversity, and political vitality. From this vantage point, we cull ways to improve our syntony and our focalization, fulfilling by expressing those shared egalitarian moral sentiments that motivate connections of solidarity partly in the interest of being "left alone".
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| 4. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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In: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Research review (peer-reviewed)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.
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| 5. |
- Clark, Andrew G., et al.
(author)
-
Evolution of genes and genomes on the Drosophila phylogeny
- 2007
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 6. |
- Clark, Eric
(author)
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Book review
- 2005
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In: Geografiska Annaler. Series A. Physical Geography. - 0435-3676. ; 87:4, s. 300-302
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Review (other academic/artistic)
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| 7. |
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| 8. |
- Clark, Eric, et al.
(author)
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Ecologically unequal exchange and landesque capital on Kinmen Island
- 2009
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In: Asia-Pacific Forum. - 1729-2980. ; 44, s. 148-167
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Journal article (peer-reviewed)abstract
- Two conceptual tools in historical analyses of environmental issues and political ecologies have gained much attention in recent years: ecologically unequal exchange and landesque capital. The former narrows in on how societal relations of power allow for the physical transfer of environmental degradation—upon which our daily consumption rests—to places far away from our environmentally clean (and therefore often presumed sustainable) homes, cities and regions. The latter focuses instead on the power of human activity to improve environmental conditions, commonly in terms of soil fertility, biodiversity, land cover, carrying capacity, resilience vis-à-vis ecological degradation, or other dimensions of sustainability. One draws attention to the geographically uneven and ecologically detrimental consequences of human activities, while the other draws attention to the potential of human activities to reinforce the resilience and sustainability of social-ecological systems. There is an interesting tension between these processes which calls for closer inspection. The purpose of this paper is to bring them together in the same empirical analysis.
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| 9. |
- Clark, Eric, et al.
(author)
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Island development
- 2009
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In: International encyclopedia of human geography. - 9780080449111 ; 5, s. 607-610
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Book chapter (peer-reviewed)
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| 10. |
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