Identification of the Active Sites in the Methyltransferases of a Transcribing dsRNA Virus

Many double-stranded RNA (dsRNA) viruses are capable of transcribing and capping RNA within a stable icosahedral viral capsid. The turret of turreted dsRNA viruses belonging to the family Reoviridae is formed by five copies of the turret protein, which contains domains with both 7-N-methyltransferase and 2′-O-methyltransferase activities, and serves to catalyze the methylation reactions during RNA capping. Cypovirus of the family Reoviridae provides a good model system for studying the methylation reactions in dsRNA viruses. Here, we present the structure of a transcribing cypovirus to a resolution of ~ 3.8 Å by cryo-electron microscopy. The binding sites for both S-adenosyl-l-methionine and RNA in the two methyltransferases of the turret were identified. Structural analysis of the turret in complex with RNA revealed a pathway through which the RNA molecule reaches the active sites of the two methyltransferases before it is released into the cytoplasm. The pathway shows that RNA capping reactions occur in the active sites of different turret protein monomers, suggesting that RNA capping requires concerted efforts by at least three turret protein monomers. Thus, the turret structure provides novel insights into the precise mechanisms of RNA methylation.     

Cryo-EM structures of cardiac thin filaments reveal the 3D architecture of troponin

Troponin is an essential component of striated muscle and it regulates the sliding of actomyosin system in a calcium-dependent manner. Despite its importance, the structure of troponin has been elusive due to its high structural heterogeneity. In this study, we analyzed the 3D structures of murine cardiac thin filaments using a cryo-electron microscope equipped with a Volta phase plate (VPP). Contrast enhancement by a VPP enabled us to reconstruct the entire repeat of the thin filament. We determined the orientation of troponin relative to F-actin and tropomyosin, and characterized the interactions between troponin and tropomyosin. This study provides a structural basis for understanding the molecular mechanism of actomyosin system.     

Biosensors based on peptide exposure show single molecule conformations in live cells

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Effect and design of buffer zones in the Nordic climate: The influence of width, amount of surface runoff, seasonal variation and vegetation type on retention efficiency for nutrient and particle runoff

Loss of nutrients and sediments from agricultural runoff causes eutrophication in surface water. Vegetated buffer zones adjacent to a stream can effectively remove and retain nutrients and sediments. It is, therefore, important to study design criteria which optimise the effect of buffer zones (BZ). This paper describes the influence of four criteria: (i) buffer zone width, (ii) amount of surface runoff water entering the BZ, (iii) seasonal variation and (iv) vegetation type. These parameters were studied after simulated and natural runoff at four different sites in Southern Norway with cold temperate climate. Surface runoff was collected before entering and after passing the BZs. The simulation experiments were short-term experiments carried out over a few days in 1992 and 1993. In the natural runoff experiments, volume proportional mixed samples were collected after each runoff period during 1992–1999. The results show significantly higher removal efficiency (in %) from 10 m wide BZs compared to 5 m widths, however, the specific retention (per m²) is higher in 5 m BZ. Buffer zones can receive particle runoff over several days without a significant decrease in their removal level. Retention efficiency between summer and autumn varied depending on the measured parameter (phosphorus, particles and nitrogen), and there were no significant differences in removal efficiency between summer and winter. The results show no significant differences between forest buffer zones (FBZ) and grass buffer zones (GBZ) regarding their retention efficiency for nitrogen and phosphorus. There was significantly higher retention efficiency in FBZ for particles. Average removal efficiencies from both simulated and natural runoff experiments varied from 60–89%, 37–81% and 81–91% for phosphorus, nitrogen and particles, respectively.     

珠江口伶仃洋中华白海豚栖息地利用对海岸线等变迁的响应

沿岸鲸豚类栖息地易受人类活动的干扰，导致其分布和核心栖息地发生变化。珠江口-漠阳江口中华白海豚种群是目前所知全球范围内最大的种群，其中伶仃洋水域是其重要的栖息地。近年来，珠江口伶仃洋周边城市发展带来的人类活动增加，白海豚的生存压力日益增大，分析伶仃洋中华白海豚对栖息地环境变化的响应，研究对应的保护策略显得非常迫切。以多源陆地资源卫星Landsat为数据源，通过影像分析近43年珠江口伶仃洋围填海造成的海域流失，结合近20年来采用截线抽样法收集的海豚观测数据，运用含障碍核插值（Kernel interpolation with barriers）方法，分析白海豚的分布及核心栖息地的变化。结果显示：1986-2015年期间，研究区域内流失的海域面积为344.08km²；目击分布离人工海岸线的平均距离大于自然海岸线的平均距离，目击分布到自然海岸线和人工海岸线的平均距离均在减小，表明过去20年白海豚的栖息地使用选择发生了一些变化，被迫适应人类活动的干扰；1997-2016年白海豚的分布范围呈现先增加后减小，白海豚栖息地使用的重心偏向伶仃洋东部水域，核心栖息地趋向主航道和无人海岛附近水域萎缩，可能是海豚因海域食物资源减少而迫不得已的选择。不同时期，珠江口中华白海豚国家级自然保护区所覆盖的核心栖息地比例呈递减趋势，占比由79.9%下降到49.4%，当前有必要对保护区范围和功能区作出一些优化调整，以适应栖息地使用的变化格局。     

Mapping QTL for production traits in segregating Piétrain pig populations using genome‐wide association study results of F2 crosses

In this study, genome‐wide association study (GWAS) results of porcine F2 crosses were used to map QTL in outcross Piétrain populations. For this purpose, two F2 crosses (Piétrain × Meishan, n = 304; Piétrain × Wild Boar, n = 291) were genotyped with the PorcineSNP60v2 BeadChip and phenotyped for the dressing yield, carcass length, daily gain and drip loss traits. GWASs were conducted in the pooled F2 cross applying single marker mixed linear models. For the investigated traits, between two and five (in total 15) QTL core regions, spanning 250 segregating SNPs around a significant trait‐associated peak SNP, were identified. The SNPs within the QTL core regions were subsequently tested for trait association in two outcross Piétrain populations consisting of 771 progeny‐tested boars and 210 sows with their own performance records. In the sow (boar) dataset, five (eight) of the 15 mapped QTL were validated. Hence, many QTL mapped in the F2 crosses (with Piétrain as a common founder breed) are still segregating in the current Piétrain breed. This confirms the usefulness of existing F2 crosses for mapping QTL that are still segregating in the recent founder breed generation. The approach utilizes the high power of an F2 cross to map QTL in a breeding population for which it is not guaranteed that they would be found using a GWAS in this population.     

Genetic diversity and molecular fingerprinting of Prunus cerasus var. austera from central Italy

In central Italy, Prunus cerasus var. austera is cultivated as small stands or scattered trees in marginal areas for the production of jam and wine. Thanks to the healthy attributes of its products and its ability to grow in different environmental conditions, this variety has gained new interest in the development of marginal areas. We assessed the level of the genetic variability of P. cerasus var. austera germplasm from central Italy and identified a ‘core collection’ representative of the present genetic diversity. A total of 161 trees, morphologically identified as var. austera, and one tree, identified as var. caproniana were collected and genotyped by 14 SSRs. Two individuals provided by a commercial plant nursery, one of P. cerasus var. caproniana and one of P. cerasus var. austera, were used as control. Thirteen SSRs presented private alleles in austera. Seven individuals morphologically identified as austera revealed private alleles specific to caproniana. The PCoA and Bayesian clustering analysis showed a main genetic group including var. austera, while a second group included all the caproniana-like genotypes. A core collection of 31 trees (46% of austera genotypes) was selected. This study can be considered as a starting point for future investigations on this variety.