Testing bespoke management of foraging habitat for European turtle doves Streptopelia turtur

Agri-environment schemes (AES) are increasingly being employed to mitigate biodiversity loss in agricultural environments. The European Turtle Dove Streptopelia turtur is an obligate granivorous bird in rapid decline within both the UK (−96% since 1970) and across continental Europe (−77% since 1980), despite widespread uptake of AES. Here, we assess the efficacy of a potentially new, sown agri-environment option designed to provide abundant, accessible seed for S. turtur during the breeding season. During summer 2011 we compared vegetation structure and seed provision on trial plots to control habitat types (existing agri-environment options thought to potentially provide S. turtur foraging habitat) to assess whether trial plots performed better for foraging S. turtur than control habitats. In September 2011 all trial plots were topped (cut) and half of a subset of trial plots were then scarified (60% of soil surface disturbed). Vegetation structure on topped, and topped and scarified trial plots was measured during summer 2012 to determine which management regime was most effective in maintaining suitable sward structure and seed provision into the second year. No control habitat type produced as much seed important in S. turtur diet as trial plots at any point during year one. Trial plots provided accessible vegetation structure early in the season with no difference in vegetation metrics between trial plots and previously published data on S. turtur foraging locations. However, to allow later access, management is required during mid-June to open up the sward through localized topping or scarification. Vegetation structure during year two was generally too dense to attract foraging S. turtur. However, scarifying trial plots during the September following sowing encouraged self-seeding of Fumaria. officinalis (a plant species historically forming a significant proportion of S. turtur diet during the breeding season) into the second year, with this species present in 16% of scarified trial plots compared to only 4% of topped trial plots during year two. Thus, autumn scarification, possibly followed by topping or scarification of part of the trial plots in June, is necessary for trial plots to provide more seed and access for S. turtur than existing agri-environment options during year two. We recommend modifications to our original seed mix in order to reduce vegetation density and improve vegetation structure. The study provides an example of the need to strike the right balance between food abundance and accessibility, through vegetation structure, when designing agri-environment scheme management options that provide food for birds.     

“首届中国孤儿药研发论坛”专家观点（续）

对 2015 年 4 月 25 日召开的“首届中国孤儿药研发论坛”与会专家对话内容进行归纳总结,旨在为从事罕见病诊断和孤儿药研发工作的人士提供信息参考。来自产、学、研领域的专家从研发、临床、审评、投资、媒体等角度探讨了中国孤儿药研发策略。     

4-Demethylwyosine Synthase from Pyrococcus abyssi Is a Radical-S-adenosyl-l-methionine Enzyme with an Additional [4Fe-4S]+2 Cluster That Interacts with the Pyruvate Co-substrate

Wybutosine and its derivatives are found in position 37 of tRNA encoding Phe in eukaryotes and archaea. They are believed to play a key role in the decoding function of the ribosome. The second step in the biosynthesis of wybutosine is catalyzed by TYW1 protein, which is a member of the well established class of metalloenzymes called “Radical-SAM.” These enzymes use a [4Fe-4S] cluster, chelated by three cysteines in a CX₃CX₂C motif, and S-adenosyl-l-methionine (SAM) to generate a 5′-deoxyadenosyl radical that initiates various chemically challenging reactions. Sequence analysis of TYW1 proteins revealed, in the N-terminal half of the enzyme beside the Radical-SAM cysteine triad, an additional highly conserved cysteine motif. In this study we show by combining analytical and spectroscopic methods including UV-visible absorption, Mössbauer, EPR, and HYSCORE spectroscopies that these additional cysteines are involved in the coordination of a second [4Fe-4S] cluster displaying a free coordination site that interacts with pyruvate, the second substrate of the reaction. The presence of two distinct iron-sulfur clusters on TYW1 is reminiscent of MiaB, another tRNA-modifying metalloenzyme whose active form was shown to bind two iron-sulfur clusters. A possible role for the second [4Fe-4S] cluster in the enzyme activity is discussed.     

Habitat modeling used to predict relative abundance of bobcats in Iowa

We combined observations of bobcats (Lynx rufus) from bowhunters with remotely-sensed data to build models that describe habitat and relative abundance of this species in the agricultural landscape of Iowa, USA. We calculated landscape composition and configuration from publicly available land cover, census, road, hydrologic, and elevation data. We used multiple regression models to examine county-level associations between several explanatory variables and relative abundance of bobcats reported by surveyed bowhunters in each county. The most influential explanatory variables in the models were metrics associated with the presence of grassland, including Conservation Reserve, along with configuration of this perennial habitat with forests, although human population density and abundance of eastern cottontails (Sylvilagus floridanus) also correlated with abundance of bobcats. Validation of predictions against 3 years of independent data provided confidence in the models, with 66% of predictions within 1 bobcat/1,000 hunter-hours and 95% within 5 bobcats/1,000 hunter-hours of observed values. Once we accounted for landscape differences, no residual spatial trend was evident, despite relatively recent bobcat recolonization of Iowa. Models suggested that future range expansion of the bobcat population may be possible in some northern Iowa counties where habitat composition is similar to counties in southern Iowa where bobcats are abundant. Results from the county-level model have been useful to the Iowa Department of Natural Resources in evaluating the expansion of this once rare species and for delineating harvest opportunities. © 2011 The Wildlife Society.     

Further in vitro exploration fails to support the allosteric three-site model

Ongoing debate in the ribosome field has focused on the role of bound E-site tRNA and the Shine-Dalgarno-anti-Shine-Dalgarno (SD-aSD) interaction on A-site tRNA interactions and the fidelity of tRNA selection. Here we use an in vitro reconstituted Escherichia coli translation system to explore the reported effects of E-site-bound tRNA and SD-aSD interactions on tRNA selection events and find no evidence for allosteric coupling. A large set of experiments exploring the role of the E-site tRNA in miscoding failed to recapitulate the observations of earlier studies (Di Giacco, V., Márquez, V., Qin, Y., Pech, M., Triana-Alonso, F. J., Wilson, D. N., and Nierhaus, K. H. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 10715-10720 and Geigenmüller, U., and Nierhaus, K. H. (1990) EMBO J. 9, 4527-4533); the frequency of miscoding was unaffected by the presence of E-site-bound cognate tRNA. Moreover, our data provide clear evidence that the reported effects of the SD-aSD interaction on fidelity can be attributed to the binding of ribosomes to an unanticipated site on the mRNA (in the absence of the SD sequence) that provides a cognate pairing codon leading naturally to incorporation of the purported "noncognate" amino acid.     

The Mechanism of Pre-transfer Editing in Yeast Mitochondrial Threonyl-tRNA Synthetase

Accurate translation of mRNA into protein is a fundamental biological process critical for maintaining normal cellular functions. To ensure translational fidelity, aminoacyl-tRNA synthetases (aaRSs) employ pre-transfer and post-transfer editing activities to hydrolyze misactivated and mischarged amino acids, respectively. Whereas post-transfer editing, which requires either a specialized domain in aaRS or a trans-protein factor, is well described, the mechanism of pre-transfer editing is less understood. Here, we show that yeast mitochondrial threonyl-tRNA synthetase (MST1), which lacks an editing domain, utilizes pre-transfer editing to discriminate against serine. MST1 misactivates serine and edits seryl adenylate (Ser-AMP) in a tRNA-independent manner. MST1 hydrolyzes 80% of misactivated Ser-AMP at a rate 4-fold higher than that for the cognate threonyl adenylate (Thr-AMP) while releasing 20% of Ser-AMP into the solution. To understand the mechanism of pre-transfer editing, we solved the crystal structure of MST1 complexed with an analog of Ser-AMP. The binding of the Ser-AMP analog to MST1 induces conformational changes in the aminoacylation active site, and it positions a potential hydrolytic water molecule more favorably for nucleophilic attack. In addition, inhibition results reveal that the Ser-AMP analog binds the active site 100-fold less tightly than the Thr-AMP analog. In conclusion, we propose that the plasticity of the aminoacylation site in MST1 allows binding of Ser-AMP and the appropriate positioning of the hydrolytic water molecule.     

Substrate specificity of bacterial prolyl-tRNA synthetase editing domain is controlled by a tunable hydrophobic pocket

Aminoacyl-tRNA synthetases catalyze the covalent attachment of amino acids onto their cognate tRNAs. High fidelity in this reaction is crucial to the accurate decoding of genetic information and is ensured, in part, by proofreading of the newly synthesized aminoacyl-tRNAs. Prolyl-tRNA synthetases (ProRS) mischarge tRNA(Pro) with alanine or cysteine due to their smaller or similar sizes relative to cognate proline. Mischarged Ala-tRNA(Pro) is hydrolyzed by an editing domain (INS) present in most bacterial ProRSs. In contrast, the INS domain is unable to deacylate Cys-tRNA(Pro), which is hydrolyzed exclusively by a freestanding trans-editing domain known as YbaK. Here, we have used computational and experimental approaches to probe the molecular basis of INS domain alanine specificity. We show that the methyl side chain of alanine binds in a well defined hydrophobic pocket characterized by conserved residues Ile-263, Leu-266, and Lys-279 and partially conserved residue Thr-277 in Escherichia coli ProRS. Site-specific mutation of these residues leads to a significant loss in Ala-tRNA(Pro) hydrolysis, and altering the size of the pocket modulates the substrate specificity. Remarkably, one ProRS INS domain variant displays a complete switch in substrate specificity from alanine to cysteine. The mutually exclusive aminoacyl-tRNA substrate specificities of the WT and engineered INS domains is consistent with the evolution of two distinct editing domains that function to clear Ala-tRNA(Pro) and Cys-tRNA(Pro) in vivo.     

与耳聋相关的线粒体tRNA突变

线粒体tRNA基因突变是导致感音神经性耳聋的原因之一．有些tRNA突变可直接造成耳聋的发生,称之为原发突变．如tRNA^Leu(UUR) A3243G等突变与综合征型耳聋相关,而tRNA^Ser(UCN) T7511C等突变则与非综合征型耳聋相关．此外,继发突变如tRNA^Thr G15927A等突变则对原发突变起协同作用,影响耳聋的表型表达．这些突变可引起tRNA二级结构改变,从而影响线粒体蛋白质合成,降低细胞内ATP的产生,由此引起的线粒体功能障碍可导致耳聋的发生．主要讨论与耳聋相关的线粒体tRNA突变及其致聋机理．     

Long‐term population trends in three grassland insect groups: a comparative analysis of 1951 and 2009

Development of farming practices has caused drastic changes in European agricultural landscapes during the past 50 years. As a consequence of these changes, insect diversity is widely expected to decline. We performed a comparative analysis with long‐term data of three insect groups: Auchenorrhyncha, Heteroptera and Orthoptera. In 2009, we revisited nine grassland sites in northern Germany that were originally sampled in 1951 using the same techniques and during a similar time frame. We found that the insect community exhibited no consistent trends between years. Species richness of Auchenorrhyncha and Heteroptera increased on plot level as well as on landscape level but remained unchanged for Orthoptera. Abundance of Auchenorrhyncha and Orthoptera significantly decreased, while Heteroptera increased. There is a strong trend towards homogeneity in community composition for Heteroptera and a weak one for Auchenorrhyncha. The frequency and abundance of species preferring disturbed and/or eutrophic habitats increased, whereas the number of species preferring low‐productive habitats declined. This trend is especially pronounced in Auchenorrhyncha. Generalistic species were more abundant in relative proportions as well as in absolute numbers. We hypothesize that these trends arise from alterations of Central European landscapes because of agricultural intensification over the last several decades.     

中国1,334种兰科植物就地保护状况评价

作者通过对中国543个自然保护区内兰科植物数据的分析,对我国1,334种兰科植物的就地保护状况进行了逐一评价。我们根据有记录分布保护区的数量,通过专家咨询的方式,将兰科植物就地保护水平划分为"有效保护"、"较好保护"、"一般保护"、"较少保护"、"保护状况不明"和"未予评价"6个等级。结果发现:有676种兰科植物在自然保护区内得到了不同程度的就地保护,占所评价兰科植物总数的51.9%;但有626种兰科植物保护状况不明,尚未受到就地保护,占总数的46.9%。另外有32种仅分布在香港、澳门和台湾地区,本研究中未予评价,约占总数的2.4%。根据评价结果,就兰科植物就地保护中存在的基础调查不足、受关注程度低、受保护率低等问题进行了深入的讨论,提出5条有针对性的建议对策:(1)加强兰科植物的调查监测;(2)提高兰科植物的保护级别与受关注程度;(3)进一步完善兰科自然保护区建设;(4)规范自然保护区综合科学考察;(5)定期评价我国兰科植物保护成效。