| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are 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 monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- Thomas, HS, et al.
(författare)
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- 2019
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swepub:Mat__t
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| 5. |
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| 6. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 7. |
- George, Julie, et al.
(författare)
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Comprehensive genomic profiles of small cell lung cancer
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 524:7563, s. 47-U73
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Tidskriftsartikel (refereegranskat)abstract
- We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Dex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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| 8. |
- Abramson, Alex, et al.
(författare)
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Ingestible transiently anchoring electronics for microstimulation and conductive signaling
- 2020
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 6:35
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Tidskriftsartikel (refereegranskat)abstract
- Ingestible electronic devices enable noninvasive evaluation and diagnosis of pathologies in the gastrointestinal (GI) tract but generally cannot therapeutically interact with the tissue wall. Here, we report the development of an orally administered electrical stimulation device characterized in ex vivo human tissue and in in vivo swine models, which transiently anchored itself to the stomach by autonomously inserting electrically conductive, hooked probes. The probes provided stimulation to the tissue via timed electrical pulses that could be used as a treatment for gastric motility disorders. To demonstrate interaction with stomach muscle tissue, we used the electrical stimulation to induce acute muscular contractions. Pulses conductively signaled the probes' successful anchoring and detachment events to a parenterally placed device. The ability to anchor into and electrically interact with targeted GI tissues controlled by the enteric nervous system introduces opportunities to treat a multitude of associated pathologies.
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| 9. |
- Ademuyiwa, Adesoji O., et al.
(författare)
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Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
- 2016
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Ingår i: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
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Tidskriftsartikel (refereegranskat)abstract
- Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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| 13. |
- Annamalai, Alagappan, et al.
(författare)
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Sn/Be Sequentially co-doped Hematite Photoanodes for Enhanced Photoelectrochemical Water Oxidation : Effect of Be2+ as co-dopant
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- For ex-situ co-doping methods, sintering at high temperatures enables rapid diffusion of Sn4+ and Be2+ dopants into hematite (alpha-Fe2O3) lattices, without altering the nanorod morphology or damaging their crystallinity. Sn/Be co-doping results in a remarkable enhancement in photocurrent (1.7 mA/cm(2)) compared to pristine alpha-Fe2O3 (0.7 mA/cm(2)), and Sn4+ mono-doped alpha-Fe2O3 photoanodes (1.0 mA/cm(2)). From first-principles calculations, we found that Sn4+ doping induced a shallow donor level below the conduction band minimum, which does not contribute to increase electrical conductivity and photocurrent because of its localized nature. Additionally, Sn4+-doping induce local micro-strain and a decreased Fe-O bond ordering. When Be2+ was co-doped with Sn4+-doped alpha-Fe2O3 photoanodes, the conduction band recovered its original state, without localized impurities peaks, also a reduction in micro-strain and increased Fe-O bond ordering is observed. Also the sequence in which the ex-situ co-doping is carried out is very crucial, as Be/Sn co-doping sequence induces many under-coordinated O atoms resulting in a higher micro-strain and lower charge separation efficiency resulting undesired electron recombination. Here, we perform a detailed systematic characterization using XRD, FESEM, XPS and comprehensive electrochemical and photoelectrochemical studies, along with sophisticated synchrotron diffraction studies and extended X-ray absorption fine structure.
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| 15. |
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| 16. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 17. |
- Du, Yong, et al.
(författare)
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Investigation of the Heteroepitaxial Process Optimization of Ge Layers on Si (001) by RPCVD
- 2021
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Ingår i: Nanomaterials. - : MDPI AG. - 2079-4991. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- This work presents the growth of high-quality Ge epilayers on Si (001) substrates using a reduced pressure chemical vapor deposition (RPCVD) chamber. Based on the initial nucleation, a low temperature high temperature (LT-HT) two-step approach, we systematically investigate the nucleation time and surface topography, influence of a LT-Ge buffer layer thickness, a HT-Ge growth temperature, layer thickness, and high temperature thermal treatment on the morphological and crystalline quality of the Ge epilayers. It is also a unique study in the initial growth of Ge epitaxy; the start point of the experiments includes Stranski-Krastanov mode in which the Ge wet layer is initially formed and later the growth is developed to form nuclides. Afterwards, a two-dimensional Ge layer is formed from the coalescing of the nuclides. The evolution of the strain from the beginning stage of the growth up to the full Ge layer has been investigated. Material characterization results show that Ge epilayer with 400 nm LT-Ge buffer layer features at least the root mean square (RMS) value and it's threading dislocation density (TDD) decreases by a factor of 2. In view of the 400 nm LT-Ge buffer layer, the 1000 nm Ge epilayer with HT-Ge growth temperature of 650 degrees C showed the best material quality, which is conducive to the merging of the crystals into a connected structure eventually forming a continuous and two-dimensional film. After increasing the thickness of Ge layer from 900 nm to 2000 nm, Ge surface roughness decreased first and then increased slowly (the RMS value for 1400 nm Ge layer was 0.81 nm). Finally, a high-temperature annealing process was carried out and high-quality Ge layer was obtained (TDD=2.78 x 10(7) cm(-2)). In addition, room temperature strong photoluminescence (PL) peak intensity and narrow full width at half maximum (11 meV) spectra further confirm the high crystalline quality of the Ge layer manufactured by this optimized process. This work highlights the inducing, increasing, and relaxing of the strain in the Ge buffer and the signature of the defect formation.
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| 18. |
- Du, Yong, et al.
(författare)
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Review of Highly Mismatched III-V Heteroepitaxy Growth on (001) Silicon
- 2022
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Ingår i: Nanomaterials. - : MDPI AG. - 2079-4991. ; 12:5
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Forskningsöversikt (refereegranskat)abstract
- Si-based group III-V material enables a multitude of applications and functionalities of the novel optoelectronic integration chips (OEICs) owing to their excellent optoelectronic properties and compatibility with the mature Si CMOS process technology. To achieve high performance OEICs, the crystal quality of the group III-V epitaxial layer plays an extremely vital role. However, there are several challenges for high quality group III-V material growth on Si, such as a large lattice mismatch, highly thermal expansion coefficient difference, and huge dissimilarity between group III-V material and Si, which inevitably leads to the formation of high threading dislocation densities (TDDs) and anti-phase boundaries (APBs). In view of the above-mentioned growth problems, this review details the defects formation and defects suppression methods to grow III-V materials on Si substrate (such as GaAs and InP), so as to give readers a full understanding on the group III-V hetero-epitaxial growth on Si substrates. Based on the previous literature investigation, two main concepts (global growth and selective epitaxial growth (SEG)) were proposed. Besides, we highlight the advanced technologies, such as the miscut substrate, multi-type buffer layer, strain superlattice (SLs), and epitaxial lateral overgrowth (ELO), to decrease the TDDs and APBs. To achieve high performance OEICs, the growth strategy and development trend for group III-V material on Si platform were also emphasized.
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| 19. |
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| 20. |
- Gao, Jinlong, et al.
(författare)
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Visualization of instantaneous structure and dynamics of large-scale turbulent flames stabilized by a gliding arc discharge
- 2019
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Ingår i: Proceedings of the Combustion Institute. - : Elsevier BV. - 1540-7489. ; 37:4, s. 5629-5636
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Tidskriftsartikel (refereegranskat)abstract
- A burner design with integrated electrodes was used to couple a gliding arc (GA) discharge to a high-power and large-scale turbulent flame for flame stabilization. Simultaneous OH and CH2O planar laser-induced fluorescence (PLIF) and CH PLIF measurements were conducted to visualize instantaneous structures of the GA-assisted flame. Six different regions of the GA-assisted flame were resolved by the multi-species PLIF measurements, including the plasma core, the discharge-induced OH region, the post-flame OH region, the flame front, the preheat CH2O region and the fresh gas mixture. Specifically, the OH profile was observed to be ring-shaped around the gliding arc discharge channel. The formaldehyde (CH2O) was found to be widely distributed in the entire measurement volume even at a low equivalence ratio of 0.4, which suggest that long-lived species from the gliding arc discharge have induced low-temperature oxidations of CH4. The CH layer coincides with the interface of the OH and CH2O regions and indicates that the flame front and the discharge channel are spatially separated by a distance of 3-5 mm. These results reveal that the discharge column acts as a movable pilot flame, providing active radicals and thermal energy to sustain the flame. High-speed video photography was also employed to record the dynamics of the GA-assisted flame. This temporally resolved data was used to study the ignition and propagation behaviors of the flame in response to a temporally modulated burst-mode discharge. The results indicate that turbulent flame can be sustained by matching temporal parameters of the high-voltage bursts to the extinction time of flame.
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| 21. |
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| 22. |
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| 23. |
- Kong, Yi, et al.
(författare)
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Elastic and thermodynamic properties of the Ni-B system studied by first-principles calculations and experimental measurements
- 2010
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Ingår i: Calphad. - : Elsevier BV. - 0364-5916 .- 1873-2984. ; 34:2, s. 245-251
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Tidskriftsartikel (refereegranskat)abstract
- The elastic and thermodynamic properties of NiB, Ni2B, Ni3B, orthorhombic Ni4B3(O-Ni4B3), monoclinic Ni4B3(M-Ni4B3), and Ni23B6, are calculated via first-principles method for the Ni-B system. The ground state energies, the full sets of elastic constants and the associated macroscopic elastic parameters of these Ni-B alloys are computed for the first time. Taking contributions from lattice vibrations and thermally excited electrons into account, thermodynamic properties at finite temperatures are then predicted. In addition, we measure the molar heat capacity at constant pressure for NiB and compare the results with the theoretical predictions. Various calculations demonstrate that the first-principles calculation can be used to clarify the diverse experimental data, and provide reliable thermodynamic data. (C) 2010 Elsevier Ltd. All rights reserved.
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| 24. |
- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 25. |
- Li, Cai, et al.
(författare)
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Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment
- 2014
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Ingår i: GigaScience. - 2047-217X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adelie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. Results: Phylogenetic dating suggests that early penguins arose similar to 60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from similar to 1 million years ago to similar to 100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. Conclusions: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
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