Molecular evolution and SSRs analysis based on the chloroplast genome of Callitropsis funebris

Chloroplast genome sequences have been used to understand evolutionary events and to infer efficiently phylogenetic relationships. Callitropsis funebris (Cupressaceae) is an endemic species in China. Its phylogenetic position is controversial due to morphological characters similar to those of Cupressus, Callitropsis, and Chamaecyparis. This study used next‐generation sequencing technology to sequence the complete chloroplast genome of Ca. funebris and then constructed the phylogenetic relationship between Ca. funebris and its related species based on a variety of data sets and methods. Simple sequence repeats (SSRs) and adaptive evolution analysis were also conducted. Our results showed that the monophyletic branch consisting of Ca. funebris and Cupressus tonkinensis is a sister to Cupressus, while Callitropsis is not monophyletic; Ca. nootkatensis and Ca. vietnamensis are nested in turn at the base of the monophyletic group Hesperocyparis. The statistical results of SSRs supported the closest relationship between Ca. funebris and Cupressus. By performing adaptive evolution analysis under the phylogenetic background of Cupressales, the Branch model detected three genes and the Site model detected 10 genes under positive selection; and the Branch‐Site model uncovered that rpoA has experienced positive selection in the Ca. funebries branch. Molecular analysis from the chloroplast genome highly supported that Ca. funebris is at the base of Cupressus. Of note, SSR features were found to be able to shed some light on phylogenetic relationships. In short, this chloroplast genomic study has provided new insights into the phylogeny of Ca. funebris and revealed multiple chloroplast genes possibly undergoing adaptive evolution.     

脐带间充质干细胞治疗熊去氧胆酸应答不佳的原发性胆汁性胆管炎的临床观察

目的探讨脐带间充质干细胞（UC-MSCs）输注治疗熊去氧胆酸（UDCA）应答不佳的原发性胆汁性胆管炎（PBC）患者的安全性和有效性，分析影响UC-MSCs疗效应答的相关因素。 方法选取解放军总医院第五医学中心2010年8月至2017年10月接受UC-MSCs输注治疗UDCA应答不佳的PBC患者29例。患者均以4周为间隔给予3次外周静脉输注细胞1.0×10⁶个/kg。通过实验室指标、生命体征及不良事件发生情况评估UC-MSCs治疗的安全性。通过患者临床症状、肝功指标和Child-Pugh评分评估治疗的有效性。以"巴黎Ⅰ标准"作为疗效标准，评价患者UC-MSCs治疗后的疗效应答情况，比较有效患者及无效患者基线临床症状和肝脏功能差异，分析影响UC-MSCs疗效的相关因素。采用独立样本t检验分析年龄；采用Mann-Whitney U检验比较两组UDCA治疗时间、激素治疗时间、实验室数据等，采用Wilcoxon秩和检验比较组间数据；采用χ²检验比较性别、临床症状和Child-Pugh分级等指标。多因素Cox回归分析对影响UC-MSCs疗效的相关因素。 结果1例患者在治疗后因合并严重感染出现高热，所有患者未出现UC-MSCs相关严重不良事件。UC-MSCs输注后与基线相比，患者的血清碱性磷酸酶（ALP）[281.00 （182.50，428.50）比201.00 （149.50，402.00）]、γ-谷氨酰转移酶（GGT）[156.00 （73.00，390.00）比84.00 （43.50，312.50）]、总胆固醇（TC）[5.10 （3.14，7.69）比3.94 （3.00，6.01）]均下降（P < 0.05）。其中，9例（31﹪）患者治疗后疗效明显，达到"巴黎Ⅰ标准"，与无效组患者基线相比，有效组患者天冬氨酸转氨酶（AST）[93.50 （77.75，100.75）比53.00 （46.00，78.00）]、ALP[342.00 （237.25，516.00）比185.00 （152.50，295.50）]、总胆红素（TBIL）[58.50 （33.45，69.33）比13.10 （11.25，20.25）]均下降（P < 0.05）。多因素Cox回归分析显示，血清TBIL是影响UC-MSCs疗效的重要独立因素[HR为0.817 （95﹪CI：0.715 ~ 0.935），P < 0.05]。 结论UC-MSCs输注对UDCA治疗应答不佳的PBC患者是安全可行的且耐受性良好，部分患者肝功能得到一定的改善。血清TBIL是影响UC-MSCs治疗疗效的独立重要因素，提示在疾病进展早期TBIL较低的阶段进行UC-MSCs治疗可能有效改善和减缓患者疾病进程。     

Postglacial population expansion of Dacrydium pectinatum(Podocarpaceae)in Hainan,southern China,based on cpDNA tmL-F nocoding sequence data

This study determined the sequences of chloro plast DNA(cpDNA)trnL-F non-coding regions of indiViduals of a tropical coniferous species,Dacrydium pectinatum,collected from 12 natural populations located in Hainan Province,southern China.Sequence length varied from 868 bp to 876 bp,indicating length polymorphism.Base composition in the sequences was high in A+T content between 64.17% and 64.95%.and no recombination event occurred (Rm=0).Thirty haplotypes were identified based on statistical parsimony algorithm by running the TCS program.Populations of D.pectinatum in Hainan were lacking genetic differentiation.Such a deduction was supported by the observed FST values(0.00),AMOVA(24.17% of molecular variance attributed to difference among populations,P＞0.05),high values of Nm(ranging from 1.92 to 2.50)and the branching structure in neighbor-joining(NJ)tree conin the TCS network of trnL-F haplotypes,and majority of the haplotypes coalesced near the tips in NJ tree.Gene genealogies of cpDNA haplotypes proposed a recent population expansion of D.pectinatum in Hainan,which was further supported by the results from Tajima's D test and mismatch distribution analysis.Our data.in COnjunction with geological and palynological evidences,showed that in the Holocene,due to global warming,refugee populations of D.pectinatum in Hainan might experience a range expansion.     

Adaptive Evolution in the GAF Domain of Phytochromes in Gymnosperms

The GAF domain of phytochrome is essential for photoconversion and signal transduction. In gymnosperms, it exists in all members of the phytochrome family that experience gene duplication. Maximum-likelihood models of codon substitution can provide a framework for constructing likelihood ratio tests of changes in selective pressure and make clear predictions about patterns of genetic change following gene duplication. In this study, 68 gymnosperm GAF sequences were analyzed to identify lineages and sites under positive selection. Our results indicate that (1) positive selection at a few sites (3.6%), rather than relaxation of selective constraints, has played a major role in the evolution of the gymnosperm GAF domain; (2) strong positive selective pressure tends to occur in the recent PHYP lineages of cogeneric species, but is absent in old lineages consisting of distantly related species; and (3) the selective pressure indicated by the ω ratio varies greatly among lineages and sites in the GAF domain.