| 1. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)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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| 2. |
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| 3. |
- Anderson, Craig, 1976, et al.
(författare)
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In situ ecological development of a bacteriogenic iron oxide-producing microbial community from a subsurface granitic rock environment
- 2006
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Ingår i: Geobiology. - : Wiley. - 1472-4677 .- 1472-4669. ; 4:1, s. 29-42
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Tidskriftsartikel (refereegranskat)abstract
- The initial development and diversity of an in situ subsurface microbial community producing bacteriogenic iron oxides (BIOS) were investigated at the initiation of biofilm growth (2-month period) and after a 1-year period of undisturbed growth. Water chemistry data, samples of iron encrusted biofilm material and groundwater were collected from BRIC (BIOS reactor, in situ, continuous flow) apparatuses installed 297 m below sea level at the Äspö Hard Rock Laboratory (HRL) in south eastern Sweden. Comparisons between the BIOS BRIC system and an anaerobic control (AC) BRIC revealed that water mixing at the inflow leads to profuse development of BIOS related to a slightly elevated level of O2 (up to 0.3 mg L-1 at the transition zone between BIOS development and non-development) and elevated Eh (>120 mV) in the first 70 mm of water depth. Decreases in dissolved and particulate iron were connected to the visible appearance of BIOS biofilms. The basic phylogenetic diversity of this site was evaluated using amplified ribosomal DNA restriction enzyme analysis (ARDRA), denaturing gradient gel electrophoresis (DGGE) and partial sequencing of 16S rDNA. From 67 clones that were positive for 16S rDNA inserts, a total of 42 different ARDRA profiles were recognized, representing four bacterial phyla and 14 different metabolic lifestyles. DGGE profiles indicated that there are differences in the representative bacteria when considering either BIOS biofilms or groundwater. DGGE also indicated that the DNA extraction protocols and any polymerase chain reaction biases were consistent. Bacterial metabolic groups associated with indirect metal adsorption and reduction along with bacteria utilizing many alternative electron acceptors were strongly represented within the clones. This study indicates that the microbial diversity of BIOS is greater than previously thought.
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| 4. |
- Hung, Craig L. H., et al.
(författare)
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An assessment of the risks associated with polychlorinated biphenyls found in the stomach contents of stranded Indo-Pacific Humpback Dolphins (Sousa chinensis) and Finless Porpoises (Neophocaena phocaenoides) from Hong Kong waters
- 2006
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Ingår i: Chemosphere. - : Elsevier. - 0045-6535 .- 1879-1298. ; 63:5, s. 845-852
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Tidskriftsartikel (refereegranskat)abstract
- The risks to Indo-Pacific Humpback Dolphins and Finless Porpoises associated with polychlorinated biphenyls (PCBs) were assessed. Stomach contents from twelve stranded Humpback Dolphins and sixteen stranded Finless Porpoises were collected. Concentrations of total and isomer-specific PCBs in the stomach contents were determined using dual-column gas chromatography equipped with electron capture detectors (GC-ECD). Risks due to the PCBs were assessed in three scenarios, based on total PCBs (summation of 41 PCB congeners), total toxicity equivalency (TEQs) and PCB 118, using the toxicity reference values (TRVs) as the threshold effects benchmarks. The calculated risk quotients (RQs) showed that risks due to PCBs were generally low or negligible. Specifically, RQs from total TEQs and total PCBs for Finless Porpoises are below one, suggesting that PCBs should be a low risk for the Finless Porpoise in Hong Kong waters. However, the Humpback Dolphin has RQs larger than 1 for total TEQs and total PCBs when the 95th percentile data were used in the evaluation. This indicates that further investigation may be needed to examine more closely the potential impact of toxic contaminants in the habitat of the Humpback Dolphin.
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| 5. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)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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| 6. |
- Malkoch, Michael, et al.
(författare)
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Synthesis of well-defined hydrogel networks using Click chemistry
- 2006
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Ingår i: Chemical Communications. - 1359-7345 .- 1364-548X. ; :26, s. 2774-2776
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Tidskriftsartikel (refereegranskat)abstract
- New PEG-based hydrogel materials have been synthesized by Click chemistry and shown to result in well-defined networks having significantly improved mechanical properties; the selectivity of the azide/ acetylene coupling reaction also allows for the incorporation of various additives and functional groups leading to chemical tailoring of the hydrogels.
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| 7. |
- Mikkelsen, Tarjei, et al.
(författare)
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Initial sequence of the chimpanzee genome and comparison with the human genome
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 437:7055, s. 69-87
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Tidskriftsartikel (refereegranskat)abstract
- Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.
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| 8. |
- Sallis, James F, et al.
(författare)
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Neighborhood environments are related to physical activity among adults in 11 countries
- 2009
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Ingår i: American Journal of Preventive Medicine. - 0749-3797 .- 1873-2607. ; 36:6, s. 484-490
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundUnderstanding environmental correlates of physical activity can inform policy changes. Surveys were conducted in 11 countries using the same self-report environmental variables and the International Physical Activity Questionnaire, allowing analyses with pooled data.MethodsThe participating countries were Belgium, Brazil, Canada, Colombia, China (Hong Kong), Japan, Lithuania, New Zealand, Norway, Sweden, and the U.S., with a combined sample of 11,541 adults living in cities. Samples were reasonably representative, and seasons of data collection were comparable. Participants indicated whether seven environmental attributes were present in their neighborhood. Outcomes were measures of whether health-related guidelines for physical activity were met. Data were collected in 2002–2003 and analyzed in 2007. Logistic regression analyses evaluated associations of physical activity with environmental attributes, adjusted for age, gender, and clustering within country.ResultsFive of seven environmental variables were significantly related to meeting physical activity guidelines, ranging from access to low-cost recreation facilities (OR=1.16) to sidewalks on most streets (OR=1.47). A graded association was observed, with the most activity–supportive neighborhoods having 100% higher rates of sufficient physical activity compared to those with no supportive attributes.ConclusionsResults suggest neighborhoods built to support physical activity have a strong potential to contribute to increased physical activity. Designing neighborhoods to support physical activity can now be defined as an international public health issue.
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