Automatic methyl assignment in large proteins by the MAGIC algorithm

Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein. Here, we propose methyl assignment by graphing inference construct, an exhaustive search algorithm with no peak network definition requirement. In order to overcome the combinatorial problem, the exhaustive search is performed locally, i.e. for a small number of methyls connected through-space according to experimental 3D methyl NOESY data. The local network approach drastically reduces the search space. Only the best local assignments are combined to provide the final output. Assignments that match the data with comparable scores are made available to the user for cross-validation by additional experiments such as methyl-amide NOEs. Several NMR datasets for proteins in the 25–50 kDa range were used during development and for performance evaluation against the manually assigned data. We show that the algorithm is robust, reliable and greatly speeds up the methyl assignment task.     

Occurrence of fenhexamid resistance in Botrytis cinerea from greenhouse strawberries in China

This study assessed the fenhexamid sensitivity of 143 Botrytis cinerea isolates collected from greenhouse strawberries in five regions of China between 2012 and 2013, and identified four isolates with moderate levels of resistance: two from the Xinjiang Uygur Autonomous Region and two from Hebei Province. The baseline fenhexamid sensitivity of B. cinerea exhibited a unimodal distribution with a mean EC₅₀ value of 0.20 ± 0.10 μg/ml (SD). The EC₅₀ values of the fenhexamid‐resistant isolates ranged from 0.05 to 0.40 μg/ml. Molecular analysis of the fenhexamid target gene erg27 revealed that the resistant isolates collected from Xinjiang (163‐6 and 163‐22) contained three mutations that led to amino acid changes (V365A, E368D and A378T) known to be associated with fenhexamid resistance, but that the isolates from Hebei lacked any mutations, indicating that an alternative mechanism could be responsible for their resistance. Most of the biological characteristics of the fenhexamid‐resistant isolates, such as mycelial growth, sclerotia production and pathogenicity, did not significantly differ from those of the sensitive ones (p ≤ .05), but it was noted that some of the resistant isolates exhibited reduced rates of sporulation and spore germination. In addition, the resistant isolates exhibited lower osmotic sensitivity than the sensitive ones. The study found no evidence of cross‐resistance with other fungicides, but that there was negative cross‐resistance with procymidone, iprodione, carbendazim and pyraclostrobin, which indicates that the inclusion of these fungicides within an integrated pest management (IPM) programme could help to minimize the risk of fenhexamid resistance developing in B. cinerea.     

许家窑遗址马科动物的死亡年龄

普氏野马(Equus przewalskii)和野驴(Equus hemionus)是许家窑遗址动物群中的优势属种。本文基于对这两种动物牙齿材料的测量与分析,确定了遗址中马科动物的死亡年龄,并对上、下文化层的死亡年龄分布进行了研究,以期探知古人类获取肉食资源的方式与特点。通过与马科动物在自然生存状态下以及死于不同原因(如疾病或营养衰竭、食肉动物猎杀、现代人类狩猎等)的年龄结构对比,结果表明:古人类在许家窑文化早期(下文化层)可能通过捡拾自然死亡的动物尸体、与食肉类动物抢夺猎物、主动狩猎等多种方式获取马科动物,而在许家窑文化晚期(上文化层)可能以主动狩猎作为获取马科动物的主要方式。此外,古人类在遗址的早期就可能已经具有捕获整个马科动物居群中任意年龄个体的能力,并能做出最优化判断,有选择地去捕猎脂肪和肉量较高的壮年动物群体。     

Shrub-encroachment induced alterations in input chemistry and soil microbial community affect topsoil organic carbon in an Inner Mongolian grassland

Shrub encroachment frequently occurs in arid and semi-arid grasslands worldwide and affects the regional carbon balance. Many previous studies have revealed the effects of shrub encroachment on bulk carbon content of grasslands, but molecular evidence is surprisingly lacking. In this study, we examined the chemical composition of plant tissues and soil organic carbon (SOC), and soil microbial communities to identify the effects of shrub (Caragana microphylla) encroachment on SOC storage in the top layer (0–10 cm) along a gradient of natural shrub cover in the grasslands of Inner Mongolia. We found that SOC in the shrub patches was derived mainly from leaves, whereas SOC in the grassy matrix was composed of a mixture of fresh root- and leaf-derived compounds. Compared with pure grassland, the SOC decreased by 29% in the shrub-encroached grasslands (SEGs), and this decrease was enhanced by increasing shrub cover. We also found that free lipids and lignin-derived phenols increased while the ratios of ω-C₁₈/∑C₁₈ and suberin/cutin decreased with increasing shrub cover. In addition, the ratios of fungal to bacterial phospholipid fatty acids (PLFAs) and gram-negative to gram-positive bacterial PLFAs decreased with increasing shrub cover. These results indicate that the encroachment of nitrogen-rich legume shrubs can lead to carbon loss by altering the chemical composition of plant inputs as well as the soil microbial community in grassland ecosystems.     

Intraspecific variation of trunk segmentation in the oryctocephalid trilobite Duyunaspis duyunensis from the Cambrian (Stage 4, Series 2) of South China

A detailed exploration of growth and trunk segmentation of the oryctocephalid trilobite, Duyunaspis duyunensis Chang & Chien in Zhou et al. 1977, from the lower Cambrian (Stage 4, Series 2) Balang Formation in western Hunan Province, South China, is presented. Because of the excellent preservation, the complete post‐protaspid ontogenetic series from merapsid degree 0 to the holaspid phase is described. The ontogenetic series reveals new information on morphological changes such as the migration of the posterior branch of the facial sutures (from proparian to opisthoparian) and contraction of the posteromedial notch in the pygidium. The abundance of articulated specimens available from a narrow stratigraphical interval makes this material singularly useful for studying the morphogenesis and post‐embryonic growth of D. duyunensis in comparison with other oryctocephalids. Strong evidence that multiple numbers of pygidial segment are recognized in each meraspid degree as well as in the holaspid period showed unusual intraspecific variability in the rate of trunk segmentation, providing insights into how Cambrian subisopygous trilobites controlled their body patterning, including size, shape and trunk segment number in both thorax and caudal plate during growth.     

The role of tamarisk in the spatial heterogeneity of soil resources in the northern Tarim Basin,Xinjiang, China

Plant and Soil - Noccaea caerulescens is a model plant for understanding metal hyperaccumulation as well as being a potential source of cultivars for phytoextraction. Sixty populations from...     

Physiological characterizations of three barley genotypes in response to low potassium stress

Plants adopt several strategies for fighting against low potassium (LK) stress. Our previous study identified some Tibetan wild barley accessions which show the higher LK tolerance than cultivated barley. However, the physiological mechanisms underlying the wild barley are not well understood. In this study, growth performance, elements content, SPAD value, photosynthetic parameters, and ATPase activities were measured to investigate the effect of LK stress on the two wild barley genotypes (XZ153 and XZ141) and one barley cultivar (ZD9) differing in LK tolerance. The results revealed that LK stress inhibited barley growth and induced reduction in dry weight, with XZ153 being least inhibited. Moreover, XZ153 had less reduction in photosynthetic rate, SPAD value, and K concentrations in the younger leaves under LK stress compared to the other two genotypes. Although the activities of H⁺/K⁺-ATPase and Ca²⁺/Mg²⁺-ATPase were increased significantly in all three genotypes in response to LK, the highest H⁺/K⁺-ATPase activity was observed in XZ153. The current results indicate that higher LK tolerance of XZ153 is partly attributed to its high capacity of transferring K from the old leaves to younger ones.