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- Edqvist, Per-Henrik D, et al.
(författare)
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Axon-bearing and axon-less horizontal cell subtypes are generated consecutively during chick retinal development from progenitors that are sensitive to follistatin
- 2008
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Ingår i: BMC Developmental Biology. - 1471-213X. ; 8, s. 46-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:Horizontal cells are retinal interneurons that modulate the output from photoreceptors. A rich literature on the morphological classification and functional properties of HCs in different animals exists, however, the understanding of the events underlying their development is still limited. In most vertebrates including chicken, two main horizontal cell (HC) subtypes are identified based on the presence or absence of an axon.RESULTS:In this work we have molecularly characterized three HC subtypes based on Lim1, Isl1, GABA and TrkA, a classification that is consistent with three chick HC subtypes previously defined by morphology. The axon-bearing and axon-less HC subpopulations molecularly defined by Lim1 and Isl1, are born consecutively on embryonic day (E) 3-4 and E4-5, respectively, and exhibit temporally distinguishable periods of migration. Their relative numbers are not adjusted by apoptosis. A sharp decrease of high endogenous levels of the activin-inhibitor follistatin at E3 coincides with the appearance of the Lim1 positive cells. Extending the follistatin exposure of the HC retinal progenitor cells by injection of follistatin at E3 increased the number of both Lim1- and Isl1 positive HCs when analysed at E9.CONCLUSION:The results imply that the axon-bearing and axon-less HC subgroups are defined early and are generated consecutively from a retinal progenitor cell population that is sensitive to the inhibitory action of follistatin. The results are consistent with a model wherein added follistatin causes HC-generating progenitors to proliferate beyond the normal period of HC generation, thus producing extra HCs of both types that migrate to the HC layer.
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| 4. |
- Lundstedt-Enkel, Katrin, et al.
(författare)
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Different multivariate approaches to material discovery, process development, PAT and environmental process monitoring
- 2006
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Ingår i: Chemometrics and Intelligent Laboratory Systems. - : Elsevier BV. - 0169-7439 .- 1873-3239. ; 84:1-2, s. 201-207
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Tidskriftsartikel (refereegranskat)abstract
- The aim with the present paper is to illustrate the use of multivariate strategies (i.e. integration of different multivariate methods) with five examples, four from the pharmaceutical industry and one from environmental research. In the first part, two examples wherein hierarchical models are applied to quality control (QC) and process control are discussed. In the second part a more complex problem and a strategy for material discovery/development are presented wherein a combination of multivariate calibration, multivariate analysis and multivariate design is needed. In the third part, a process analytical/optimization problem is illustrated with a two-step process, demanding that different multivariate tools are combined in a sequential way so that a useful model can be established and the process can be understood. In the final part the usefulness of principal component analysis followed by soft independent modelling of class analogy is illustrated with an example from environmental process monitoring. The five examples from quite different areas show that the chemometric tools are even more powerful if used integrated. However, different strategies and combinations of the tools have to be applied, depending on the problem and the aim.
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| 5. |
- Lundstedt-Enkel, Katrin, et al.
(författare)
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QSBMR - Quantitative Structure Biomagnification Relationships : Physicochemical and Structural Descriptors Important for the Biomagnification of Organochlorines and Brominated Flame Retardants
- 2006
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Ingår i: Journal of Chemometrics. - : Wiley. - 0886-9383 .- 1099-128X. ; 20:8-10, s. 392-401
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this project is to establish models to predict the biomagnification of contaminants present in Baltic Sea biota. In this paper a quantitative model that we term QSBMR-Quantitative Structure Biomagnification Relationships is presented. This model describes the relationship between the biomagnification factors (BMFs) for several organochlorines (OCs) and brominated flame retardants (BFRs), for example, polychlorinated biphenyls (PCBs), polybrominated diphenylethers (PBDEs) and hexabromocyclododecane (HBCD), and their descriptors, for example, physico-chemical properties and structural descriptors. The concentrations of contaminants in herring (Clupea harengus) muscle and guillemot (Uria aalge) egg from the Baltic Sea were used. The BMFs were calculated with the randomly sampled ratios (RSR) method that denotes the BMFs with a measure of the variation. In order to describe the physico-chemical properties and chemical structures, approximately 100 descriptors for the contaminants were generated: (a), by using the software (TSAR); (b) finding log Kow values from the literature, and (c) creating binary fingerprint variables that described the position of the chlorine and bromine for the respective PCB and PBDE molecules. Partial least squares (PLS) regression was used to model the relationship between the contaminants' BMF and the descriptors and the resulting QSBMR revealed that more than 20 descriptors in combination were important for the biomagnification of OCs and BFRs between herring and guillemot. The model including all contaminants (R2X=0.73, R2Y=0.87 and Q2=0.63, three components) explained approximately as much of the variation as the model with the PCBs alone (R2X=0.83, R2Y=0.87 and Q2=0.58, two components). The model with the BFRs alone (R2X=0.68, R2Y=0.88 and Q2 = 0.41, two components) had a slightly lower Q2 than the model including all contaminants. For validation, a training set of seven contaminants was selected by multivariate design (MVD) and a model was established. This model was then used to predict the BMFs of the test set (seven contaminants not included in the model). The resulting R2 for the regression Observed BMF versus Predicted BMF was high (0.65). The good models showed that descriptors important for the biomagnification of OCs and BFRs had been used. These types of models will be useful for in silico predictions of the biomagnification of new, not yet investigated, compounds as an aid in risk assessments.
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| 8. |
- Muthas, Daniel, et al.
(författare)
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Focused hierarchical design of peptide libraries - follow the lead
- 2007
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Ingår i: Journal of Chemometrics. - : Wiley. - 0886-9383 .- 1099-128X. ; 21:10-11, s. 486-495
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Tidskriftsartikel (refereegranskat)abstract
- A novel design strategy based on the hierarchical design of experiments (HDoE) method named focused hierarchical design of experiments (FHDoE) is presented. FHDoE combine two design layers and use focused substitutions to increase the probability of obtaining active peptides when designing libraries through a selection of compounds biased towards a lead structure. Increasing the number of peptides with measurable activity will increase the information gained and the likelihood of constructing good quantitative structure-activity relationship (QSAR) models. The utility of the novel design method is verified using two different approaches. First, a library designed with the novel FHDoE method was compared with libraries generated from classical positional scanning techniques (e.g., alanine scan) as well as with general and centered minimum analog peptide sets (MAPS) libraries by using an example found in the literature. Secondly, the same design strategies were applied to a dataset of 58 angiotensin converting enzyme (ACE) dipeptide inhibitors. QSAR models were generated from designed sublibraries and the activities of the remaining compounds were predicted. These two examples show that the use of FHDoE renders peptide libraries close in physicochemical space to the native ligand, yielding a more thorough screening of the area of interest as compared to the classical positional scans and fractional factorial design (FFD). It is also shown that an FHDoE library of six dipeptides could produce a QSAR model that better described the requisites of high activity ACE inhibitors than could QSAR models built from either a nine-dipeptide library designed with MAPS or a 58-dipeptide library.
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