| 1. |
- Hagman, C, et al.
(author)
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Reproducibility of tryptic digestion investigated by quantitative fourier transform ion cyclotron resonance mass spectrometry
- 2005
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 4:2, s. 394-399
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Journal article (peer-reviewed)abstract
- In this study, the reproducibility of tryptic digestion of complex solutions was investigated using liquid chromatography Fourier transform ion cyclotron resonance (LC FT-ICR) mass spectrometry. Tryptic peptides, from human cerebrospinal fluid, (CSF) were labeled with Quantification-Using-Enhanced-Signal-Tags (QUEST)-markers, or 1-([H-4]nicotinoyloxy)- and 1-([D-4]nicotinoyloxy)-succinimide ester markers. The analysis was performed on abundant proteins with respect-to-intensity ratios and sequence coverage and obtained by comparing differently labeled components from one or different pools. To interpret the dynamics in the proteome, one must be able to estimate the error introduced in each experimental steps. The intra sample variation due to derivatization was approximately 10%. The inter sample variation depending on derivatization and tryptic digestion was not more than approximately 30%. These experimental observations provide a range for the up- and clown-regulations that are possible to study with electrospray ionization LC FT-ICR mass spectrometry.
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| 2. |
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| 4. |
- Bentz, Maria, et al.
(author)
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Membrane protein identification: N-terminal labeling of nontryptic membrane protein peptides facilitates database searching
- 2008
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 7:2, s. 659-665
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Journal article (peer-reviewed)abstract
- Membrane proteins are fairly refractory to digestion especially by trypsin, and less specific proteases, such as elastase and pepsin, are much more effective. However, database searching using nontryptic peptides is much less effective because of the lack of charge localization at the N and C termini and the absence of sequence specificity. We describe a method for N-terminal-specific labeling of peptides from nontryptic digestions of membrane proteins, which facilitates Mascot database searching and can be used for relative quantitation. The conditions for digestion have been optimized to obtain peptides of a suitable length for mass spectrometry (MS) fragmentation. We show the effectiveness of the method using a plasma membrane preparation from a leukemia cell line and demonstrate a large increase in the number of membrane proteins, with small extra-membranar domains being identified in comparison to previous published methods.
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| 5. |
- Bentz, Maria
(author)
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Membrane protein proteomics - Novel method for membrane protein identification and quantification
- 2007
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Doctoral thesis (other academic/artistic)abstract
- Membrane proteins are fairly refractory to digestion especially by trypsin. Less specific proteases like elastase and pepsin are much more effective. However database searching using non-tryptic peptides is much less effective due to the lack of charge localisation at the N- and C-termini and the absence of sequence specificity. We describe a method for N-terminal specific labelling of peptides from non-tryptic digestions of membrane proteins which facilitates database searching and can be used for relative quantitation. The conditions for digestion using the non-specific enzyme Proteinase K have been optimised to obtain peptides of a suitable length for MS fragmentation. We show the effectiveness of the identification of membrane proteins using a plasma membrane preparation from a leukaemia cell line and demonstrate a large increase in the number of membrane proteins with small extra-membranar domains being identified in comparison to previous published methods. Our method was then further developed for relative quantitation of membrane proteins. We describe this by using membrane preparations from Bacillus subtilis grown with and without the presents of 0.5% glucose and an isotopic labelling strategy. The results show good reproducibility of the calculated fold changes of the identified peptides within the same protein. The method was then applied on plasma membrane proteins from cancer cells grown with and without the presence of oxygen. The aim was to find biomarkers for tissue hypoxia.
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| 6. |
- Cappadona, Salvatore, et al.
(author)
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Wavelet-based method for noise characterization and rejection in high-performance liquid chromatography coupled to mass spectrometry
- 2008
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In: Analytical Chemistry. - : American Chemical Society (ACS). - 1520-6882 .- 0003-2700. ; 80:13, s. 4960-4968
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Journal article (peer-reviewed)abstract
- We present a new method for rejecting noise from HPLC-MS data sets. The algorithm reveals peptides at low concentrations by minimizing both the chemical and the random noise. The goal is reached through a systematic approach to characterize and remove the background. The data are represented as two-dimensional maps, in order to optimally exploit the complementary dimensions of separation of the peptides offered by the LC-MS technique. The virtual chromatograms, reconstructed from the spectrographic data, have proved to be more suitable to characterize the noise than the raw mass spectra. By means of wavelet analysis, it was possible to access both the chemical and the random noise, at different scales of the decomposition. The novel approach has proved to efficiently distinguish signal from noise and to selectively reject the background while preserving low-abundance peptides.
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| 7. |
- Fazey, Ioan, et al.
(author)
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Transforming knowledge systems for life on Earth : Visions of future systems and how to get there
- 2020
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In: Energy Research & Social Science. - : Elsevier. - 2214-6296 .- 2214-6326. ; 70
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Journal article (peer-reviewed)abstract
- Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
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| 8. |
- Jakobsson, Johan, et al.
(author)
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Targeted transgene expression in rat brain using lentiviral vectors.
- 2003
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In: Journal of Neuroscience Research. - : Wiley. - 1097-4547 .- 0360-4012. ; 73:6, s. 876-885
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Journal article (peer-reviewed)abstract
- Direct gene transfer to the adult brain is dependent on vectors that transduce non-dividing cells, such as lentiviral vectors. Another aspect of the development of gene therapy to the brain is the need for cell-specific transgene expression. Expression from vesicular stomatitis virus G-protein (VSV-G) pseudotyped lentiviral vectors has been reported to be mainly neuron specific in the brain. We constructed cell-specific lentiviral vectors using the neuron-specific enolase (rNSE) or the glial fibrillary acidic protein (hGFAP) promoters and compared them to the ubiquitous human cytomegalovirus promoter (hCMV), a hybrid CMV/-actin promoter (CAG) and the promoter for human elongation factor 1 (EF1). Our results showed that the hGFAP promoter was expressed only in glial cells, whereas rNSE was purely neuron specific, showing that VSV-G is pantropic in the rat striatum. We conclude that the VSV-G allows transduction of both glial and neuronal cells and the promoter dictates in what cell type the transgene will be expressed. The expression of transgenes exclusively in astrocytes would allow for local delivery of secreted transgene products, such as glial cell line-derived neurotrophic factor (GDNF), circumventing the anterograde transport that may induce unwanted side effects.
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| 9. |
- Marini, Lorenzo, et al.
(author)
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Climate drivers of bark beetle outbreak dynamics in Norway spruce forests
- 2017
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In: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. ; 40:12, s. 1426-1435
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Journal article (peer-reviewed)abstract
- Bark beetles are among the most devastating biotic agents affecting forests globally and several species are expected to be favored by climate change. Given the potential interactions of insect outbreaks with other biotic and abiotic disturbances, and the potentially strong impact of changing disturbance regimes on forest resources, investigating climatic drivers of destructive bark beetle outbreaks is of paramount importance. We analyzed 17 time-series of the amount of wood damaged by Ips typographus, the most destructive pest of Norway spruce forests, collected across 8 European countries in the last three decades. We aimed to quantify the relative importance of key climate drivers in explaining timber loss dynamics, also testing for possible synergistic effects. Local outbreaks shared the same drivers, including increasing summer rainfall deficit and warm temperatures. Large availability of storm-felled trees in the previous year was also strongly related to an increase in timber loss, likely by providing an alternative source of breeding material. We did not find any positive synergy among outbreak drivers. On the contrary, the occurrence of large storms reduced the positive effect of warming temperatures and rainfall deficit. The large surplus of breeding material likely boosted I. typographus population size above the density threshold required to colonize and kill healthy trees irrespective of other climate triggers. Importantly, we found strong negative density dependence in I. typographus that may provide a mechanism for population decline after population eruptions. Generality in the effects of complex climatic events across different geographical areas suggests that the large-scale drivers can be used as early warning indicators of increasing local outbreak probability. Ecography
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