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81.
Anna Barbanti Hector Torrado Enrique Macpherson Luca Bargelloni Rafaella Franch Carlos Carreras Marta Pascual 《Molecular ecology resources》2020,20(3):795-806
High‐throughput sequencing has revolutionized population and conservation genetics. RAD sequencing methods, such as 2b‐RAD, can be used on species lacking a reference genome. However, transferring protocols across taxa can potentially lead to poor results. We tested two different IIB enzymes (AlfI and CspCI) on two species with different genome sizes (the loggerhead turtle Caretta caretta and the sharpsnout seabream Diplodus puntazzo) to build a set of guidelines to improve 2b‐RAD protocols on non‐model organisms while optimising costs. Good results were obtained even with degraded samples, showing the value of 2b‐RAD in studies with poor DNA quality. However, library quality was found to be a critical parameter on the number of reads and loci obtained for genotyping. Resampling analyses with different number of reads per individual showed a trade‐off between number of loci and number of reads per sample. The resulting accumulation curves can be used as a tool to calculate the number of sequences per individual needed to reach a mean depth ≥20 reads to acquire good genotyping results. Finally, we demonstrated that selective‐base ligation does not affect genomic differentiation between individuals, indicating that this technique can be used in species with large genome sizes to adjust the number of loci to the study scope, to reduce sequencing costs and to maintain suitable sequencing depth for a reliable genotyping without compromising the results. Here, we provide a set of guidelines to improve 2b‐RAD protocols on non‐model organisms with different genome sizes, helping decision‐making for a reliable and cost‐effective genotyping. 相似文献
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Selwyn Hoeks Mark A. J. Huijbregts Michela Busana Michael B. J. Harfoot Jens-Christian Svenning Luca Santini 《Ecography》2020,43(12):1752-1763
Large carnivores can exert top–down effects in ecosystems, but the size of these effects are largely unknown. Empirical investigation on the importance of large carnivores for ecosystem structure and functioning presents a number of challenges due to the large spatio-temporal scale and the complexity of such dynamics. Here, we applied a mechanistic global ecosystem model to investigate the influence of large-carnivore removal from undisturbed ecosystems. First, we simulated large-carnivore removal on the global scale to inspect the geographic pattern of top–down control and to disentangle the functional role of large carnivores in top–down control in different environmental contexts. Second, we conducted four small-scale ecosystem simulation experiments to understand direct and indirect changes in food-web structure under different environmental conditions. We found that the removal of top–down control exerted by large carnivores (> 21 kg) can trigger large trophic cascades, leading to an overall decrease in autotroph biomass globally. Furthermore, the loss of large carnivores resulted in an increase of mesopredators. The magnitude of these changes was positively related to primary productivity (NPP), in line with the ‘exploitation ecosystem hypothesis’. In addition, we found that seasonality in NPP dampened the magnitude of change following the removal of large carnivores. Our results reinforce the idea that large carnivores play a fundamental role in shaping ecosystems, and further declines and extinctions can trigger substantial ecosystem responses. Our findings also support previous studies suggesting that natural ecosystem dynamics have been severely modified and are still changing as a result of the widespread decline and extinction of large carnivores. 相似文献
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Ventura Luigi Gnetti Letizia Rossi Maurizio Tiseo Marcello Giordano Giovanna Corradi Massimo Silva Mario Milanese Gianluca Minari Roberta Leonetti Alessandro Cattadori Sara Ampollini Luca Carbognani Paolo Mozzoni Paola 《Molecular biology reports》2021,48(4):3485-3494
Molecular Biology Reports - Benign metastasizing leiomyoma (BML) is a rare disease characterized by extrauterine benign leiomyomatosis in patients with a previous or concomitant history of uterine... 相似文献
87.
Luana Lionetto Martina Ulivieri Matilde Capi Donatella De Bernardini Francesco Fazio Andrea Petrucca Leda Marina Pomes Ottavia De Luca Giovanna Gentile Barbara Casolla Martina Curto Gerardo Salerno Serena Schillizzi Maria Simona Torre Iolanda Santino Monica Rocco Paolo Marchetti Antonio Aceti Marina Borro 《生物化学与生物物理学报:疾病的分子基础》2021,1867(3):166042
Immune dysregulation is a hallmark of patients infected by SARS-CoV2 and the balance between immune reactivity and tolerance is a key determinant of all stages of infection, including the excessive inflammatory state causing the acute respiratory distress syndrome. The kynurenine pathway (KP) of tryptophan (Trp) metabolism is activated by pro-inflammatory cytokines and drives mechanisms of immune tolerance. We examined the state of activation of the KP by measuring the Kyn:Trp ratio in the serum of healthy subjects (n = 239), and SARS-CoV2-negative (n = 305) and -positive patients (n = 89). Patients were recruited at the Emergency Room of St. Andrea Hospital (Rome, Italy). Kyn and Trp serum levels were assessed by HPLC/MS-MS. Compared to healthy controls, both SARS-CoV2-negative and -positive patients showed an increase in the Kyn:Trp ratio. The increase was larger in SARS-CoV2-positive patients, with a significant difference between SARS-CoV2-positive and -negative patients. In addition, the increase was more prominent in males, and positively correlated with age and severity of SARS-CoV2 infection, categorized as follows: 1 = no need for intensive care unit (ICU); 2 ≤ 3 weeks spent in ICU; 3 ≥ 3 weeks spent in ICU; and 4 = death. The highest Kyn:Trp values were found in SARS-CoV2-positive patients with severe lymphopenia. These findings suggest that the Kyn:Trp ratio reflects the level of inflammation associated with SARS-CoV2 infection, and, therefore, might represent a valuable biomarker for therapeutic intervention. 相似文献
88.
Marrucci Luca Iraldo Fabio Daddi Tiberio 《The International Journal of Life Cycle Assessment》2021,26(3):575-590
The International Journal of Life Cycle Assessment - The EU Ecolabel is a voluntary scheme that aims to reduce the overall environmental impact of organisations to boost sustainable consumption in... 相似文献
89.
Chromatin investigation in the nucleus using a phasor approach to structured illumination microscopy
Isotta Cainero Elena Cerutti Mario Faretta Gaetano Ivan Dellino Pier Giuseppe Pelicci Paolo Bianchini Giuseppe Vicidomini Alberto Diaspro Luca Lanzanò 《Biophysical journal》2021,120(12):2566-2576
Chromatin in the nucleus is organized in functional sites at variable level of compaction. Structured illumination microscopy (SIM) can be used to generate three-dimensional super-resolution (SR) imaging of chromatin by changing in phase and in orientation a periodic line illumination pattern. The spatial frequency domain is the natural choice to process SIM raw data and to reconstruct an SR image. Using an alternative approach, we demonstrate that the additional spatial information encoded in the knowledge of the position of the illumination pattern can be efficiently decoded using a generalized version of separation of photon by lifetime tuning (SPLIT) that does not require lifetime measurements. In the resulting SPLIT-SIM, the SR image is obtained by isolating a fraction of the intensity corresponding to the center of the diffraction-limited point spread function. This extends the use of the SPLIT approach from stimulated emission depletion microscopy to SIM. The SPLIT-SIM algorithm is based only on phasor analysis and does not require deconvolution. We show that SPLIT-SIM can be used to generate SR images of chromatin organizational motifs with tunable resolution and can be a valuable tool for the imaging of functional sites in the nucleus. 相似文献
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