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21.
Tomas Sinkunas Giedrius Gasiunas Sakharam P Waghmare Mark J Dickman Rodolphe Barrangou Philippe Horvath Virginijus Siksnys 《The EMBO journal》2013,32(3):385-394
Clustered regularly interspaced short palindromic repeats (CRISPR)‐encoded immunity in Type I systems relies on the Cascade (CRISPR‐associated complex for antiviral defence) ribonucleoprotein complex, which triggers foreign DNA degradation by an accessory Cas3 protein. To establish the mechanism for adaptive immunity provided by the Streptococcus thermophilus CRISPR4‐Cas (CRISPR‐associated) system (St‐CRISPR4‐Cas), we isolated an effector complex (St‐Cascade) containing 61‐nucleotide CRISPR RNA (crRNA). We show that St‐Cascade, guided by crRNA, binds in vitro to a matching proto‐spacer if a proto‐spacer adjacent motif (PAM) is present. Surprisingly, the PAM sequence determined from binding analysis is promiscuous and limited to a single nucleotide (A or T) immediately upstream (?1 position) of the proto‐spacer. In the presence of a correct PAM, St‐Cascade binding to the target DNA generates an R‐loop that serves as a landing site for the Cas3 ATPase/nuclease. We show that Cas3 binding to the displaced strand in the R‐loop triggers DNA cleavage, and if ATP is present, Cas3 further degrades DNA in a unidirectional manner. These findings establish a molecular basis for CRISPR immunity in St‐CRISPR4‐Cas and other Type I systems. 相似文献
22.
Jinshu Chi Mats B. Nilsson Hjalmar Laudon Anders Lindroth Jrgen Wallerman Johan E. S. Fransson Natascha Kljun Tomas Lundmark Mikaell Ottosson Lfvenius Matthias Peichl 《Global Change Biology》2020,26(4):2353-2367
The boreal biome exchanges large amounts of carbon (C) and greenhouse gases (GHGs) with the atmosphere and thus significantly affects the global climate. A managed boreal landscape consists of various sinks and sources of carbon dioxide (CO2), methane (CH4), and dissolved organic and inorganic carbon (DOC and DIC) across forests, mires, lakes, and streams. Due to the spatial heterogeneity, large uncertainties exist regarding the net landscape carbon balance (NLCB). In this study, we compiled terrestrial and aquatic fluxes of CO2, CH4, DOC, DIC, and harvested C obtained from tall‐tower eddy covariance measurements, stream monitoring, and remote sensing of biomass stocks for an entire boreal catchment (~68 km2) in Sweden to estimate the NLCB across the land–water–atmosphere continuum. Our results showed that this managed boreal forest landscape was a net C sink (NLCB = 39 g C m?2 year?1) with the landscape–atmosphere CO2 exchange being the dominant component, followed by the C export via harvest and streams. Accounting for the global warming potential of CH4, the landscape was a GHG sink of 237 g CO2‐eq m?2 year?1, thus providing a climate‐cooling effect. The CH4 flux contribution to the annual GHG budget increased from 0.6% during spring to 3.2% during winter. The aquatic C loss was most significant during spring contributing 8% to the annual NLCB. We further found that abiotic controls (e.g., air temperature and incoming radiation) regulated the temporal variability of the NLCB whereas land cover types (e.g., mire vs. forest) and management practices (e.g., clear‐cutting) determined their spatial variability. Our study advocates the need for integrating terrestrial and aquatic fluxes at the landscape scale based on tall‐tower eddy covariance measurements combined with biomass stock and stream monitoring to develop a holistic understanding of the NLCB of managed boreal forest landscapes and to better evaluate their potential for mitigating climate change. 相似文献
23.
Pieler R Sanchez-Cabo F Hackl H Thallinger GG Trajanoski Z 《Bioinformatics (Oxford, England)》2004,20(12):1971-1973
SUMMARY: ArrayNorm is a user-friendly, versatile and platform-independent Java application for the visualization, normalization and analysis of two-color microarray data. A variety of normalization options were implemented to remove the systematic and random errors in the data, taking into account the experimental design and the particularities of every slide. In addition, ArrayNorm provides a module for statistical identification of genes with significant changes in expression. AVAILABILITY: The package is freely available for academic and non-profit institutions from http://genome.tugraz.at 相似文献
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In-gel digestion of proteins isolated by gel electrophoresis is a cornerstone of mass spectrometry (MS)-driven proteomics. The 10-year-old recipe by Shevchenko et al. has been optimized to increase the speed and sensitivity of analysis. The protocol is for the in-gel digestion of both silver and Coomassie-stained protein spots or bands and can be followed by MALDI-MS or LC-MS/MS analysis to identify proteins at sensitivities better than a few femtomoles of protein starting material. 相似文献
27.
Elevational species richness gradients in a hyperdiverse insect taxon: a global meta‐study on geometrid moths 下载免费PDF全文
Jan Beck Christy M. McCain Jan C. Axmacher Louise A. Ashton Florian Bärtschi Gunnar Brehm Sei‐Woong Choi Oldrich Cizek Robert K. Colwell Konrad Fiedler Cristina L. Francois Steven Highland Jeremy D. Holloway Jurie Intachat Tomas Kadlec Roger L. Kitching Sarah C. Maunsell Thomas Merckx Akihiro Nakamura Erica Odell Weiguo Sang Pagi S. Toko Jaroslav Zamecnik Yi Zou Vojtech Novotny 《Global Ecology and Biogeography》2017,26(4):412-424
28.
Rui Faria Pragya Chaube Hernn E. Morales Tomas Larsson Alan R. Lemmon Emily M. Lemmon Marina Rafajlovi Marina Panova Mark Ravinet Kerstin Johannesson Anja M. Westram Roger K. Butlin 《Molecular ecology》2019,28(6):1375-1393
Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients. 相似文献
29.
Petr Kelbich Karel Hrach Jan Spicka Petr Vachata Tomas Radovnicky Eva Hanuljakova Jan Krejsek 《Current issues in molecular biology》2022,44(8):3666
Laboratory analysis of basic cerebrospinal fluid (CSF) parameters is considered as essential for any CSF evaluation. It can provide rapidly very valuable information about the status of the central nervous system (CNS). Our retrospective study evaluated parameters of basic CSF analysis in cases of either infectious or non-infectious CNS involvement. Neutrophils are effector cells of innate immunity. Predominance of neutrophils was found in 98.2% of patients with purulent inflammation in CNS. Lymphocytes are cellular substrate of adaptive immunity. We found their predominance in 94.8% of patients with multiple sclerosis (MS), 66.7% of patients with tick-borne encephalitis (TBE), 92.2% of patients with neuroborreliosis, 83.3% of patients with inflammatory response with oxidative burst of macrophages in CNS and 75.0% of patients with malignant infiltration of meninges (MIM). The simultaneous assessment of aerobic and anaerobic metabolism in CSF using the coefficient of energy balance (KEB) allows us to specify the type of inflammation in CNS. We found predominantly aerobic metabolism (KEB > 28.0) in 100.0% CSF of patients with normal CSF findings and in 92.8% CSF of patients with MS. Predominant faintly anaerobic metabolism (28.0 > KEB > 20.0) in CSF was found in 71.8% patients with TBE and in 64.7% patients with neuroborreliosis. Strong anaerobic metabolism (KEB < 10.0) was found in the CSF of 99.1% patients with purulent inflammation, 100.0% patients with inflammatory response with oxidative burst of macrophages and in 80.6% patients with MIM. Joint evaluation of basic CSF parameters provides sufficient information about the immune response in the CSF compartment for rapid and reliable diagnosis of CNS involvement. 相似文献
30.
Lucia Mala Mikulas Hank Petr Stastny Frantisek Zahalka Kevin R. Ford Piotr Zmijewski David Bujnovsky Miroslav Petr Tomas Maly 《Biology of sport / Institute of Sport》2023,40(1):265
Body composition (BC) and inter-limb anthropometric asymmetries (LA) may influence the physical performance of soccer players. This study aimed to determine differences in BC and LA among soccer across four performance levels. The study involved 110 male soccer players participating in Czech senior teams who were grouped into four different performance levels (i.e. G1: national team, G2: 1st division, G3: 2nd division, G4: 3rd division). The following BC and LA parameters were compared among groups: body height, body mass, absolute fat-free mass, relative fat-free mass (FFMrel), percentage of fat mass (FM), total body water (TBW), intracellular water (ICW), extracellular water (ECW), phase angle, and bilateral muscle mass differences in the upper and lower extremities. Significant differences were observed in BC parameters among all groups (λ = 0.06, F75,246 = 5.38, p = 0.01, ηp2 = 0.62). High-performance players (i.e. G1, G2) had significantly (p < 0.01) lower FM than lower performance players (i.e. G3, G4). The lowest values of FFMrel, relative TBW, relative ICW and ECW were detected in the lowest-performance players (i.e. G4). Significantly lower bilateral muscle mass differences were detected in G1 players (2.71 ± 1.26%; p < 0.01) compared with G4 players (3.95 ± 1.17%). G1 and G2 players had a higher proportion of muscle mass in the torso (p < 0.01) and upper limbs than G3 and G4 (p < 0.01). Elite and high-performance players have better BC and lower inter-limb anthropometric asymmetries compared with low-performance level players. 相似文献