Phylogenetic significance of the kinethmoid‐associated Y‐shaped ligament and long intercostal ligaments in the Cypriniformes (Actinopterygii: Ostariophysi)

Liao, T.Y. & Kullander, S.O. (2012). Phylogenetic significance of the kinethmoid‐associated Y‐shaped ligament and long intercostal ligaments in the Cypriniformes (Actinopterygii: Ostariophysi). —Zoologica Scripta, 42, 71–87. The phylogenetic significance of the Y‐shaped and long intercostal ligaments in the Cypriniformes is examined using character optimization in 184 species representing 20 non‐ostariophysan teleost species, five ostariophysan orders, seven cypriniform families and 14 cyprinid subfamilies. Character states were optimized on the phylogenetic trees of previous studies. Given the topology of Saitoh et al. (2011) , the Y‐shaped ligament, connecting the kinethmoid to the ethmoid complex, is shown to be a synapomorphy for the Cyprinidae, with reversals observed in the Cyprininae, Danioninae, Gobioninae and Psilorhynchinae. The condition of the Y‐shaped ligament is consistent within most subfamilies with a few exceptions. Despite the exceptions, the Y‐shaped ligament may be considered as a diagnostic character distinguishing cyprinid subfamilies with otherwise similar morphology, that is, the Danioninae and Opsariichthyinae. The long intercostal ligament, connecting five to eight ribs and ascending from the subdistal end of the fifth rib, is present in the Catostomidae and all cyprinid subfamilies, except for the Psilorhynchinae and two developmentally truncated genera, Danionella and Paedocypris. In addition to these two cypriniforme families, the long intercostal ligament is homoplastically present in some catfishes. Given the topology of Saitoh et al. (2011) , presence of the long intercostal ligament is a synapomorphy of Cyprinidae+Catostomidae. Some shorter ligaments are also present in the Cypriniformes and Chilodus gracilis (Characiformes), near the base of the anterior ribs and only occurring anterodorsally to the putative line of the long intercostal ligament even when it is absent.     

杂交构树UDP-葡萄糖脱氢酶基因编码蛋白的亚细胞定位及其启动子5'端缺失片段的功能分析

为了研究杂交构树UDP-葡萄糖脱氢酶基因（DDBJ，BpUGDH基因登录号为LC457701）启动子不同区域的表达活性，利用5'端缺失及同源重组实验技术，将5个不同长度的BpUGDH启动子5'端缺失片段与GUS基因连接，并通过农杆菌介导法瞬时转化烟草；同时，为了定位BpUGDH基因编码的蛋白在细胞中表达的具体位置，利用GFP报告基因融合目的基因进行蛋白质的亚细胞定位。结果显示：BpUGDH基因启动子-244 bp以内的序列均能介导GUS基因的诱导表达，并且-973、-465、-355、-281和-244 bp之间的区域可能对BpUGDH基因启动子的活性发挥着至关重要的作用。另外，BpUGDH基因编码蛋白的亚细胞定位结果显示：BpUGDH位于叶绿体中。     

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

Recent modifications and improvements to standard nucleic acid force fields have attempted to fix problems and issues that have been observed as longer timescale simulations have become routine. Although previous work has shown the ability to fold the UUCG stem–loop structure, until now no group has attempted to quantify the performance of current force fields using highly converged structural populations of the tetraloop conformational ensemble. In this study, we report the use of multiple independent sets of multidimensional replica exchange molecular dynamics (M-REMD) simulations with different initial conditions to generate well-converged conformational ensembles for the tetranucleotides r(GACC) and r(CCCC), as well as the larger UUCG tetraloop motif. By generating what is to our knowledge the most complete RNA structure ensembles reported to date for these systems, we remove the coupling between force field errors and errors due to incomplete sampling, providing a comprehensive comparison between current top-performing MD force fields for RNA. Of the RNA force fields tested in this study, none demonstrate the ability to correctly identify the most thermodynamically stable structure for all three systems. We discuss the deficiencies present in each potential function and suggest areas where improvements can be made. The results imply that although “short” (nsec-μsec timescale) simulations may stay close to their respective experimental structures and may well reproduce experimental observables, inevitably the current force fields will populate alternative incorrect structures that are more stable than those observed via experiment.