| 1. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 2. |
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| 3. |
- Casar Borota, Olivera, et al.
(författare)
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Corticotroph Aggressive Pituitary Tumors and Carcinomas Frequently Harbor ATRX Mutations
- 2021
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Ingår i: Journal of Clinical Endocrinology & Metabolism. - : The Endocrine Society. - 0021-972X .- 1945-7197. ; 106:4, s. 1183-1194
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Tidskriftsartikel (refereegranskat)abstract
- Context: Aggressive pituitary tumors (APTs) are characterized by unusually rapid growth and lack of response to standard treatment. About 1% to 2% develop metastases being classified as pituitary carcinomas (PCs). For unknown reasons, the corticotroph tumors are overrepresented among APTs and PCs. Mutations in the alpha thalassemia/mental retardation syndrome X-linked (ATRX) gene, regulating chromatin remodeling and telomere maintenance, have been implicated in the development of several cancer types, including neuroendocrine tumors. Objective: To study ATRX protein expression and mutational status of the ATRX gene in APTs and PCs. Design: We investigated ATRX protein expression by using immunohistochemistry in 30 APTs and 18 PCs, mostly of Pit-1 and T-Pit cell lineage. In tumors lacking ATRX immunolabeling, mutational status of the ATRX gene was explored. Results: Nine of the 48 tumors (19%) demonstrated lack of ATRX immunolabelling with a higher proportion in patients with PCs (5/18; 28%) than in those with APTs (4/30;13%). Lack of ATRX was most common in the corticotroph tumors, 7/22 (32%), versus tumors of the Pit-1 lineage, 2/24 (8%). Loss-of-function ATRX mutations were found in all 9 ATRX immunonegative cases: nonsense mutations (n = 4), frameshift deletions (n = 4), and large deletions affecting 22-28 of the 36 exons (n = 3). More than 1 ATRX gene defect was identified in 2 PCs. Conclusion: ATRX mutations occur in a subset of APTs and are more common in corticotroph tumors. The findings provide a rationale for performing ATRX immunohistochemistry to identify patients at risk of developing aggressive and potentially metastatic pituitary tumors.
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| 4. |
- Kennedy, S. A., et al.
(författare)
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Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D
- 2020
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.
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| 5. |
- Leloudas, G., et al.
(författare)
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The normal Type Ia SN 2003hv out to very late phases
- 2009
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 505:1, s. 265-279
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Tidskriftsartikel (refereegranskat)abstract
- Aims: We study a thermonuclear supernova (SN), emphasizing very late phases. Methods: An extensive dataset for SN 2003hv that covers the flux evolution from maximum light to day +786 is presented. This includes 82 epochs of optical imaging, 24 epochs of near-infrared (NIR) imaging, and 10 epochs of optical spectroscopy. These data are combined with published nebular-phase IR spectra, and the observations are compared to model light curves and synthetic nebular spectra. Results: SN 2003hv is a normal Type Ia supernova (SN Ia) with photometric and spectroscopic properties consistent with its rarely observed B-band decline-rate parameter, Δ m15(B) = 1.61 ± 0.02. The blueshift of the most isolated [Fe ii] lines in the nebular-phase optical spectrum appears consistent with those observed in the IR at similar epochs. At late times there is a prevalent color evolution from the optical toward the NIR bands. We present the latest-ever detection of a SN Ia in the NIR in Hubble Space Telescope images. The study of the ultraviolet/optical/infrared (UVOIR) light curve reveals that a substantial fraction of the flux is “missing” at late times. Between 300 and 700 days past maximum brightness, the UVOIR light curve declines linearly following the decay of radioactive 56Co, assuming full and instantaneous positron trapping. At 700 days we detect a possible slowdown of the decline in optical-bands, mainly in the V-band. Conclusions: The data are incompatible with a dramatic infrared catastrophe (IRC). However, the idea that an IRC occurred in the densest regions before 350 days can explain the missing flux from the UVOIR wavelengths and the flat-topped profiles in the NIR. We argue that such a scenario is possible if the ejecta are clumpy. The observations suggest that positrons are most likely trapped in the ejecta. Based on observations collected at the European Southern Observatory, Paranal, Chile (ESO Programmes 073.D-0294(AB), 074.D-0259(BC) and 075.D-0116(AB)), Cerro Tololo Inter-American Observatory, Lick Observatory, Las Campanas Observatory, Siding Spring Observatory, and the Hubble Space Telescope. Tables 3, 4, and Appendix A are only available in electronic form at http://www.aanda.org
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| 6. |
- Stritzinger, M. D., et al.
(författare)
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The Carnegie Supernova Project I : Photometry data release of low-redshift stripped-envelope supernovae
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 609
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Tidskriftsartikel (refereegranskat)abstract
- The first phase of the Carnegie Supernova Project (CSP-I) was a dedicated supernova follow-up program based at the Las Campanas Observatory that collected science data of young, low-redshift supernovae between 2004 and 2009. Presented in this paper is the CSP-I photometric data release of low-redshift stripped-envelope core-collapse supernovae. The data consist of optical (uBgVri) photometry of 34 objects, with a subset of 26 having near-infrared (YJH) photometry. Twenty objects have optical pre-maximum coverage with a subset of 12 beginning at least five days prior to the epoch of B-band maximum brightness. In the near-infrared, 17 objects have pre-maximum observations with a subset of 14 beginning at least five days prior to the epoch of J-band maximum brightness. Analysis of this photometric data release is presented in companion papers focusing on techniques to estimate host-galaxy extinction and the light-curve and progenitor star properties of the sample. The analysis of an accompanying visual-wavelength spectroscopy sample of similar to 150 spectra will be the subject of a future paper.
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| 7. |
- Hahlin, Axel, et al.
(författare)
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Determination of small-scale magnetic fields on Sun-like stars in the near-infrared using CRIRES
- 2023
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 675
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Tidskriftsartikel (refereegranskat)abstract
- Aims: We aim to characterise the small-scale magnetic fields of a sample of 16 Sun-like stars and investigate the capabilities of the newly upgraded near-infrared (NIR) instrument CRIRES+ at the Very Large Telescope in the context of small-scale magnetic field studies. Our targets also had their magnetic fields studied with optical spectra, which allowed us to compare magnetic field properties at different spatial scales on the stellar surface and to contrast small-scale magnetic field measurements at different wavelengths.Methods: We analysed the Zeeman broadening signature for six magnetically sensitive and insensitive Fe I lines in the H-band to measure small-scale magnetic fields on the stellar surfaces of our sample. We used polarised radiative transfer modelling and non-local thermodynamic equilibrium departure coefficients in combination with Markov chain Monte Carlo sampling to determine magnetic field characteristics and non-magnetic stellar parameters. We used two different approaches to describe the small-scale magnetic fields. The first is a two-component model with a single magnetic region and a free magnetic field strength. The second model contains multiple magnetic components with fixed magnetic field strengths.Results: We found average magnetic field strengths ranging from & SIM;0.4 kG down to < 0.1 kG. The results align closely with other results from high-resolution NIR spectrographs, such as SPIRou. It appears that the typical magnetic field strength in the magnetic region is slightly stronger than 1.3 kG, and for most stars in our sample, this strength is between 1 and 2 kG. We also found that the small-scale fields correlate with the large-scale fields and that the small-scale fields are at least ten times stronger than the large-scale fields inferred with Zeeman Doppler imaging. The two- and multi-component models produce systematically different results, as the strong fields from the multi-component model increase the obtained mean magnetic field strength. When comparing our results with the optical measurements of small-scale fields, we found a systematic offset two to three times stronger than fields in the optical results. This discrepancy cannot be explained by uncertainties in stellar parameters. Care should therefore be taken when comparing results obtained at different wavelengths until a clear cause can be established.
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| 8. |
- Malick, Michael J., et al.
(författare)
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Growth and survival in relation to body size of juvenile pink salmon in the northern Gulf of Alaska
- 2011
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Ingår i: Marine and Coastal Fisheries. - 1942-5120. ; 3:1, s. 261-270
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Tidskriftsartikel (refereegranskat)abstract
- The abundance of anadromous salmon is partially determined by size-selective mortality during the early marine life phase. Consequently, identifying the growth patterns of juvenile salmon during this life phase is important in understanding the dynamics of salmon populations. We examined patterns of early marine growth in juvenile pink salmon Oncorhynchus gorbuscha released by four hatcheries in Prince William Sound (PWS), Alaska, and explored how these patterns related to marine survival. Since larger individuals are thought to experience reduced mortality, we partitioned the data into weight-based quartiles and compared growth rates (% body weight/d) of all fish, the largest fish (top 25%), and the smallest fish (bottom 25%). Sampling occurred during summer 1997–2004 in PWS, the inshore Gulf of Alaska (GOA), and the offshore GOA. Growth rates varied significantly among years and sampling locations; however, the growth rate patterns were markedly similar among size-groups and hatcheries. Growth rates tended to be high in 1997, 2002, and 2004 and lower in 1998, 2001, and 2003. Fish sampled in the offshore GOA typically had faster growth rates than those sampled elsewhere, although this was less pronounced for the largest fish. For all size-groups, the relationship between survival and growth rate was strongest for fish captured in the offshore GOA and weakest for those captured in PWS, indicating that the likelihood of survival is greater for juveniles that migrate offshore earlier. The strength of the growth rate–survival relationship for pink salmon captured in the offshore GOA was similar among all size-groups, suggesting that once fish migrate offshore they are less vulnerable to size-selective predation.
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| 9. |
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| 10. |
- Pignata, Giuliano, et al.
(författare)
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SN 2009bb : A PECULIAR BROAD-LINED TYPE Ic SUPERNOVA
- 2011
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 728:1, s. 14-
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Tidskriftsartikel (refereegranskat)abstract
- Ultraviolet, optical, and near-infrared photometry and optical spectroscopy of the broad-lined Type Ic supernova (SN) 2009bb are presented, following the flux evolution from -10 to +285 days past B-band maximum. Thanks to the very early discovery, it is possible to place tight constraints on the SN explosion epoch. The expansion velocities measured from near maximum spectra are found to be only slightly smaller than those measured from spectra of the prototype broad-lined SN 1998bw associated with GRB 980425. Fitting an analytical model to the pseudobolometric light curve of SN 2009bb suggests that 4.1 +/- 1.9M(circle dot) of material was ejected with 0.22 +/- 0.06 M(circle dot) of it being (56)Ni. The resulting kinetic energy is 1.8 +/- 0.7 x 10(52) erg. This, together with an absolute peak magnitude of M(B) = -18.36 +/- 0.44, places SN 2009bb on the energetic and luminous end of the broad-lined Type Ic (SN Ic) sequence. Detection of helium in the early time optical spectra accompanied with strong radio emission and high metallicity of its environment makes SN 2009bb a peculiar object. Similar to the case for gamma-ray bursts (GRBs), we find that the bulk explosion parameters of SN 2009bb cannot account for the copious energy coupled to relativistic ejecta, and conclude that another energy reservoir (a central engine) is required to power the radio emission. Nevertheless, the analysis of the SN 2009bb nebular spectrum suggests that the failed GRB detection is not imputable to a large angle between the line-of-sight and the GRB beamed radiation. Therefore, if a GRB was produced during the SN 2009bb explosion, it was below the threshold of the current generation of gamma-ray instruments.
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