| 1. |
- Hoorn, C., et al.
(författare)
-
Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity
- 2010
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 330:6006, s. 927-931
-
Tidskriftsartikel (refereegranskat)abstract
- The Amazonian rainforest is arguably the most species-rich terrestrial ecosystem in the world, yet the timing of the origin and evolutionary causes of this diversity are a matter of debate. We review the geologic and phylogenetic evidence from Amazonia and compare it with uplift records from the Andes. This uplift and its effect on regional climate fundamentally changed the Amazonian landscape by reconfiguring drainage patterns and creating a vast influx of sediments into the basin. On this "Andean" substrate, a region-wide edaphic mosaic developed that became extremely rich in species, particularly in Western Amazonia. We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.
|
|
| 2. |
- Hoorn, C., et al.
(författare)
-
Origins of Biodiversity Response
- 2011
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 331:6016, s. 399-400
-
Tidskriftsartikel (refereegranskat)
|
|
| 3. |
- Beltran-Pardo, Eliana, et al.
(författare)
-
Sequence analysis of the DNA-repair gene rad51 in the tardigrades Milnesium cf. tardigradum, Hypsibius dujardini and Macrobiotus cf. harmsworthi
- 2013
-
Ingår i: Journal of limnology. - 1129-5767 .- 1723-8633. ; 72:s1, s. 80-91
-
Tidskriftsartikel (refereegranskat)abstract
- Tardigrades are known for being resistant to extreme conditions, including tolerance to ionising and UV radiation in both the hydratedand the dehydrated state. It is known that these factors may cause damage to DNA. It has recently been shown that single and double DNAstrand breaks occur when tardigrades are maintained for a long time in the anhydrobiotic state. This may suggest that perhaps tardigrades rely on efficient DNA repair mechanisms. Among all proteins that comprise the DNA repair system, recombinases such as RecA or Rad51 have a very important function: DNA exchange activity. This enzyme is used in the homologous recombination and allows repair of thedamaged strand using homologous non-damaged strands as a template. In this study, Rad51 induction was evaluated by western blot in Milnesium cf. tardigradum, after exposure to gamma radiation. The Rad51 protein was highly induced by radiation, when compared to the control. The rad51 genes were searched in three tardigrades: Milnesium cf. tardigradum, Hypsibius dujardini and Macrobiotus cf. harmsworthi. The gene sequences were obtained by preparing and sequencing transcriptome libraries for H. dujardini and M. cf. harmsworthi and designing rad51 degenerate primers specific for M. cf. tardigradum. Comparison of Rad51 putative proteins from tardigrades with other organisms showed that they are highly similar to the corresponding sequence from the nematode Trichinella spiralis. A structure-based sequence alignment from tardigrades and other organisms revealed that putative Rad51 predicted proteins from tardigrades contain the expected motifs for these important recombinases. In a cladogram tree based on this alignment, tardigrades tend to cluster together suggesting that they have selective differences in these genes that make them diverge between species. Predicted Rad51 structures from tardigrades were also compared with crystalline structure of Rad51 in Saccharomyces cerevisiae. These results reveal that S. cerevisiae Rad51 structure is very similar to that of the three analysed tardigrades. On the other hand the predicted structure of Rad51 from M. cf. harmsworthi and H. dujardini are closer related to each other, than each of them to that of M. cf. tardigradum.
|
|
| 4. |
- Chockalingam, P. S., et al.
(författare)
-
Elevated aggrecanase activity in a rat model of joint injury is attenuated by an aggrecanase specific inhibitor
- 2011
-
Ingår i: Osteoarthritis and Cartilage. - : Elsevier BV. - 1063-4584. ; 19:3, s. 315-323
-
Tidskriftsartikel (refereegranskat)abstract
- Objective: To evaluate aggrecanase activity after traumatic knee injury in a rat model by measuring the level of aggrecanase-generated Ala-Arg-Gly-aggrecan (ARG-aggrecan) fragments in synovial fluid, and compare with ARG-aggrecan release into joint fluid following human knee injury. To evaluate the effect of small molecule inhibitors on induced aggrecanase activity in the rat model. Method: An enzyme-linked immunosorbent assay (ELISA) was developed to measure ARG-aggrecan levels in animal and human joint fluids. A rat model of meniscal tear (MT)-induced joint instability was used to assess ARG-aggrecan release into joint fluid and the effects of aggrecanase inhibition. Synovial fluids were also obtained from patients with acute joint injury or osteoarthritis and assayed for ARG-aggrecan. Results: Joint fluids from human patients after knee injury showed significantly enhanced levels of ARG-aggrecan compared to uninjured reference subjects. Similarly, synovial fluid ARG-aggrecan levels increased following surgically-induced joint instability in the rat MT model, which was significantly attenuated by orally dosing the animals with AGG-523, an aggrecanase specific inhibitor. Conclusions: Aggrecanase-generated aggrecan fragments were rapidly released into human and rat joint fluids after injury to the knee and remained elevated over a prolonged period. Our findings in human and preclinical models strengthen the connection between aggrecanase activity in joints and knee injury and disease. The ability of a small molecule aggrecanase inhibitor to reduce the release of aggrecanase-generated aggrecan fragments into rat joints suggests that pharmacologic inhibition of aggrecanase activity in humans may be an effective treatment for slowing cartilage degradation following joint injury. (C) 2010 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.
|
|
| 5. |
- Jönsson, Ingemar, 1959-, et al.
(författare)
-
Tolerance to gamma-irradiation in eggs of the tardigrade Richtersius coronifer depends on stage of development
- 2013
-
Ingår i: Journal of limnology. - 1129-5767 .- 1723-8633. ; 72:s1, s. 73-79
-
Tidskriftsartikel (refereegranskat)abstract
- Tardigrades are known as one of the most radiation tolerant animals on Earth, and several studies on tolerance in adult tardigrades have been published. In contrast, very few studies on radiation tolerance of embryonic stages have been reported. Here we report a study on tolerance to gamma irradiation in eggs of the eutardigrade Richtersius coronifer. Irradiation of eggs collected directly from a natural substrate (moss) showed a clear dose-response, with a steep decline in hatchability at doses up to 0.4 kGy followed by a relatively constant hatchability around 25% up to 2 kGy, and a decline to ca. 5% at 4 kGy above which no eggs hatched. Analysis of the time required for eggs to hatch after irradiation (residual development time) showed that hatching of eggs after exposure to high doses of gamma radiation was associated with short residual development time. Since short residual development time means that the egg was irradiated at a late developmental stage, this suggests that eggs were more tolerant to radiation late in development. This was also confirmed in another experiment in which stage of development at irradiation was controlled. No eggs irradiated at the early developmental stage hatched, and only one egg at middle stage hatched, while eggs irradiated in the late stage hatched at a rate indistinguishable from controls. This suggests that the eggs are more sensitive to radiation in the early stages of development, or that tolerance to radiation is acquired only late in development, shortly before the eggs hatch, hypotheses that are not mutually exclusive. Our study emphasizes the importance of considering specific cell cycle phases and developmental stages in studies of tolerance to radiation in tardigrades, and the potential importance of embryonic studies in revealing the mechanisms behind the radiation tolerance of tardigrades and other cryptobiotic animals.
|
|
| 6. |
- López, A., et al.
(författare)
-
Laboratory characterization and astrophysical detection of vibrationally excited states of vinyl cyanide in Orion-KL
- 2014
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 572
-
Tidskriftsartikel (refereegranskat)abstract
- Context. We perform a laboratory characterization in the 18–1893 GHz range and astronomical detection between 80–280 GHz in Orion-KL with IRAM-30 m of CH2CHCN (vinyl cyanide) in its ground and vibrationally excited states. Aims. Our aim is to improve the understanding of rotational spectra of vibrationally excited vinyl cyanide with new laboratory data and analysis. The laboratory results allow searching for these excited state transitions in the Orion-KL line survey. Furthermore, rotational lines of CH2CHCN contribute to the understanding of the physical and chemical properties of the cloud. Methods. Laboratory measurements of CH2CHCN made on several different frequency-modulated spectrometers were combined into a single broadband 50–1900 GHz spectrum and its assignment was confirmed by Stark modulation spectra recorded in the 18–40 GHz region and by ab-initio anharmonic force field calculations. For analyzing the emission lines of vinyl cyanide detected in Orion-KL we used the excitation and radiative transfer code (MADEX) at LTE conditions. Results. Detailed characterization of laboratory spectra of CH2CHCN in nine different excited vibrational states: ?11 = 1, ?15 = 1, 2) ⇔ (?10 = 1,?15 = 1) ⇔ (?11 = 1,?14 = 1), and ?11 = 4 are determined, as well as the detection of transitions in the ?11 = 2and ?11 = 2, ?10 = 1 ⇔ (?11 = 1,?15 = 1), ?11 = 3/?15 = 2/?14 = 1, (?11 = 1,?10 = 1) ⇔ (?11 = 2,?15 = 1), ?9 = 1, (?11 = 1,?15 = The rotational transitions of the ground state of this molecule emerge from four cloud components of hot core nature, which trace the ?11 = 3 states for the first time in Orion-KL and of those in the ?10 = 1 ⇔ (?11 = 1,?15 = 1) dyad of states for the first time in space. physical and chemical conditions of high mass star forming regions in the Orion-KL Nebula. The lowest energy vibrationally excited states of vinyl cyanide, such as ?11 = 1 (at 328.5 K), ?15 = 1 (at 478.6 K), ?11 = 2 (at 657.8 K), the ?10 = 1 ⇔ (?11 = 1,?15 = 1) dyad (at 806.4/809.9 K), and ?11 = 3 (at 987.9 K), are populated under warm and dense conditions, so they probe the hottest parts of the Orion-KL source. The vibrational temperatures derived for the ?11 = 1, ?11 = 2, and ?15 = 1 states are 252 ± 76K, 242 ± 121K, column density of CH2CHCN in the ground state is (3.0 ± 0.9) × 1015 cm−2. We report the detection of methyl isocyanide (CH3NC) and 227 ± 68K, respectively; all of them are close to the mean kinetic temperature of the hot core component (210K). The total for the first time in Orion-KL and a tentative detection of vinyl isocyanide (CH2CHNC). We also give column density ratios between the cyanide and isocyanide isomers, obtaining a N(CH3NC)/N(CH3CN) ratio of 0.002. Conclusions. Laboratory characterization of many previously unassigned vibrationally excited states of vinyl cyanide ranging from microwave to THz frequencies allowed us to detect these molecular species in Orion-KL. Column density, rotational and vibrational temperatures for CH2CHCN in their ground and excited states, and the isotopologues have been constrained by means of a sample of more than 1000 lines in this survey.
|
|
| 7. |
- Beltran-Pardo, Eliana A., et al.
(författare)
-
Sequence analysis of the DNA-repair gene rad51 in the tardigrades Milnesium cf. tardigradum, Hypsibius dujardini and Macrobiotus cf. harmsworthi
- 2013
-
Ingår i: Journal of limnology. - : PAGEPress Publications. - 1129-5767 .- 1723-8633. ; 72, s. 80-91
-
Tidskriftsartikel (refereegranskat)abstract
- Tardigrades are known for being resistant to extreme conditions, including tolerance to ionising and UV radiation in both the hydrated and the dehydrated state. It is known that these factors may cause damage to DNA. It has recently been shown that single and double DNA strand breaks occur when tardigrades are maintained for a long time in the anhydrobiotic state. This may suggest that perhaps tardigrades rely on efficient DNA repair mechanisms. Among all proteins that comprise the DNA repair system, recombinases such as RecA or Rad51 have a very important function: DNA exchange activity. This enzyme is used in the homologous recombination and allows repair of the damaged strand using homologous non-damaged strands as a template. In this study, Rad51 induction was evaluated by western blot in Milnesium cf. tardigradum, after exposure to gamma radiation. The Rad51 protein was highly induced by radiation, when compared to the control. The rad51 genes were searched in three tardigrades: Milnesium cf. tardigradum, Hypsibius dujardini and Macrobiotus cf. harmsworthi. The gene sequences were obtained by preparing and sequencing transcriptome libraries for H. dujardini and M. cf. harmsworthi and designing rad51 degenerate primers specific for M. cf. tardigradum. Comparison of Rad51 putative proteins from tardigrades with other organisms showed that they are highly similar to the corresponding sequence from the nematode Trichinella spiralis. A structure-based sequence alignment from tardigrades and other organisms revealed that putative Rad51 predicted proteins from tardigrades contain the expected motifs for these important recombinases. In a cladogram tree based on this alignment, tardigrades tend to cluster together suggesting that they have selective differences in these genes that make them diverge between species. Predicted Rad51 structures from tardigrades were also compared with crystalline structure of Rad51 in Saccharomyces cerevisiae. These results reveal that S. cerevisiae Rad51 structure is very similar to that of the three analysed tardigrades. On the other hand the predicted structure of Rad51 from M. cf. harmsworthi and H. dujardini are closer related to each other, than each of them to that of M. cf. tardigradum.
|
|
| 8. |
- Bermúdez, Eduardo, et al.
(författare)
-
Improved homology model of cyclohexanone monooxygenase from Acinetobacter calcoaceticus based on multiple templates
- 2014
-
Ingår i: Computational biology and chemistry. - : Elsevier BV. - 1476-9271 .- 1476-928X. ; 49, s. 14-22
-
Tidskriftsartikel (refereegranskat)abstract
- A new homology model of cyclohexanone monooxygenase (CHMO) from Acinetobacter calcoaceticus is derived based on multiple templates, and in particular the crystal structure of CHMO from Rhodococcus sp. The derived model was fully evaluated, showing that the quality of the new structure was improved over previous models. Critically, the nicotinamide cofactor is included in the model for the first time. Analysis of several molecular dynamics snapshots of intermediates in the enzymatic mechanism led to a description of key residues for cofactor binding and intermediate stabilization during the reaction, in particular Arg327 and the well known conserved motif (FxGxxxHxxxW) in Baeyer-Villiger monooxygenases, in excellent agreement with known experimental and computational data. © 2014 Elsevier Ltd.
|
|
| 9. |
- Caspeta-Guadarrama, Luis, 1974, et al.
(författare)
-
Enzymatic hydrolysis at high-solids loadings for the conversion of agave bagasse to fuel ethanol
- 2014
-
Ingår i: Applied Energy. - : Elsevier BV. - 1872-9118 .- 0306-2619. ; 113, s. 277-286
-
Tidskriftsartikel (refereegranskat)abstract
- Agave bagasse is the lignocellulosic residue accumulated during the production of alcoholic beverages in Mexico and is a potential feedstock for the production of biofuels. A factorial design was used to investigate the effect of temperature, residence time and concentrations of acid and ethanol on ethanosolv pretreatment and enzymatic hydrolysis of agave bagasse. This method and the use of a stirred in-house-made mini-reactor increased the digestibility of agave bagasse from 30% observed with the dilute-acid method to 98%; also allowed reducing the quantity of enzymes used to hydrolyze samples with solid loadings of 30%. w/w and glucose concentrations up to 225. g/L were obtained in the enzymatic hydrolysates. Overall this process allows the recovery of 91% of the total fermentable sugars contained in the agave bagasse (0.51. g/g) and 69% of total lignin as co-product (0.11. g/g). The maximum ethanol yield under optimal conditions using an industrial yeast strain for the fermentation was 0.25. g/g of dry agave bagasse, which is 86% of the maximum theoretical (0.29. g/g). The effect of the glucose concentration and solid loading on the conversion of cellulose to glucose is discussed, in addition to prospective production of about 50. million liters of fuel ethanol using agave bagasse residues from the tequila industry as a potential solution to the disposal problems.
|
|
| 10. |
|
|
