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| 2. |
- Tuskan, G A, et al.
(författare)
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The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 313:5793, s. 1596-604
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Tidskriftsartikel (refereegranskat)abstract
- We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
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| 4. |
- 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. |
- Aryal, M. M., et al.
(författare)
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Understanding of nuclear quadrupole interactions of Cl-35, Br-79 and I-129 and binding energies of solid halogens at first-principles level
- 2007
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Ingår i: Hyperfine Interactions. - : Springer Science and Business Media LLC. - 0304-3843 .- 1572-9540. ; 176:1-3, s. 51-57
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Tidskriftsartikel (refereegranskat)abstract
- This paper deals with the understanding at a first-principles level of the nuclear quadrupole interaction (NQI) parameters of solid chlorine, bromine and iodine as well as the intermolecular binding of these molecules in the solid. The electronic structure investigations that we have carried out to study these properties of the solid halogens are based on the Hartree-Fock Cluster approach using the Roothaan variational procedure with electron correlation effects included using many-body perturbation theory with the empty orbitals used in the perturbation theory investigations for the excited states. The results of our investigations provide good agreement with the measured NQI parameters primarily from the Hartree-Fock one electron wave-functions with many-body effects making minor contributions. The binding (dissociation) energies for the molecules with the solid state environment on the other hand arises from intermolecular many body effects identified as the Van der Waals attraction with one-electron Hartree-Fock contribution being repulsive in nature.
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| 7. |
- Sodergren, Erica, et al.
(författare)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 8. |
- Terashima, N., et al.
(författare)
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2D-NMR (HSQC) difference spectra between specifically C-13-enriched and unenriched protolignin of Ginkgo biloba obtained in the solution state of whole cell wall material
- 2009
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Ingår i: Holzforschung. - 1437-434X .- 0018-3830. ; 63:4, s. 379-384
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Tidskriftsartikel (refereegranskat)abstract
- In the structural analysis of lignins by C-13-NMR, signal overlap limits definitive assignment and accurate intensity measurement. Selective labeling by C-13-enrichment of a specific carbon in lignin enhances its signal intensity in the spectrum. Further enhancement of the specifically labeled carbons can be realized via difference spectra created from the enriched and unenriched samples. Difference 2D C-13-H-1 correlation (HSQC) NMR spectra, derived from the spectra of specifically C-13-enriched lignin model polymers (so-called dehydrogenation polymers) and their unenriched counterparts, take advantage of the enhanced dispersion afforded by both C-13 and H-1 chemical shifts, diminishing the difficulties arising from the signal-overlap problem and aiding in definitive signal assignments. In this research, protolignin in xylem cell walls was specifically C-13-enriched at all of the individual phenylpropanoid side-chain carbons by feeding C-13-enriched coniferins to growing stems of Ginkgo biloba. The whole xylem fractions containing C-13-enriched and unenriched protolignins were dissolved in a mixture of N-methylimidazole and DMSO, and then acetylated. Solution state 2D-NMR (HSQC) spectra of the acetylated whole cell wall were acquired. Difference spectra between the walls containing C-13-enriched and unenriched lignins afforded simplified 2D spectra in which well-separated signals were assigned exclusively to the specifically enriched carbons. This novel NMR technique provides a useful tool for elucidation of entire protolignin in the cell wall of ginkgo xylem.
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| 9. |
- van de Merwe, JP, et al.
(författare)
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Diagnostic Criteria, Classification, and Nomenclature for Painful Bladder Syndrome/Interstitial Cystitis: An ESSIC Proposal.
- 2008
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Ingår i: European Urology. - : Elsevier BV. - 0302-2838. ; 53:1, s. 60-67
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Tidskriftsartikel (refereegranskat)abstract
- Abstract Objectives Because the term “interstitial cystitis” (IC) has different meanings in different centers and different parts of the world, the European Society for the Study of Interstitial Cystitis (ESSIC) has worked to create a consensus on definitions, diagnosis, and classification in an attempt to overcome the lack of international agreement on various aspects of IC. Methods ESSIC has discussed definitions, diagnostic criteria, and disease classification in four meetings and extended e-mail correspondence. Results It was agreed to name the disease bladder pain syndrome (BPS). BPS would be diagnosed on the basis of chronic pelvic pain, pressure, or discomfort perceived to be related to the urinary bladder accompanied by at least one other urinary symptom such as persistent urge to void or urinary frequency. Confusable diseases as the cause of the symptoms must be excluded. Classification of BPS types might be performed according to findings at cystoscopy with hydrodistention and morphologic findings in bladder biopsies. The presence of other organ symptoms as well as cognitive, behavioral, emotional, and sexual symptoms, should be addressed. Conclusions The name IC has become misleading and is replaced by BPS. This name is in line with recent nomenclature recommendations by the European Association of Urology and is based on the axial structure of the International Association for the Study of Pain classification. To facilitate the change of the name, ESSIC agreed to include IC in the overall term (BPS/IC) during this transition period. Take Home Message The European Society for the Study of Interstitial Cystitis recommends that the name “interstitial cystitis” be changed to “bladder pain syndrome.” A specific definition, diagnostic criteria, and patient evaluation standard are provided.
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