FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3

The International HapMap Project has recently made available genotypes and frequency data for phase 3 (NCBI build 36, dbSNPb129) of the HapMap providing an enriched genotype dataset for approximately 1.6 million single nucleotide polymorphisms (SNPs) from 1,115 individuals with ancestry from parts of Africa, Asia, Europe, North America and Mexico. In the present study, we aim to facilitate pharmacogenetics studies by providing a database of SNPs with high population differentiation through a genomewide test on allele frequency variation among 11 HapMap3 samples. Common SNPs with minor allele frequency greater than 5¢ from each of 11 HapMap3 samples were included in the present analysis. The population differentiation is measured in terms of fixation index (Fst), and the SNPs with Fst values over 0.5 were defined as highly differentiated SNPs. Our tests were carried out between all pairs of the 11 HapMap3 samples or among subgroups with the same continental ancestries. Altogether we carried out 64 genomewide Fst tests and identified 28,215 highly differentiated SNPs for 49 different combinations of HapMap3 samples in the current database.     

Novel MUC1 aptamer selectively delivers cytotoxic agent to cancer cells in vitro

Chemotherapy is a primary treatment for cancer, but its efficacy is often limited by the adverse effects of cytotoxic agents. Targeted drug delivery may reduce the non-specific toxicity of chemotherapy by selectively directing anticancer drugs to tumor cells. MUC1 protein is an attractive target for tumor-specific drug delivery owning to its overexpression in most adenocarcinomas. In this study, a novel MUC1 aptamer is exploited as the targeting ligand for carrying doxorubicin (Dox) to cancer cells. We developed an 86-base DNA aptamer (MA3) that bound to a peptide epitope of MUC1 with a K(d) of 38.3 nM and minimal cross reactivity to albumin. Using A549 lung cancer and MCF-7 breast cancer cells as MUC1-expressing models, MA3 was found to preferentially bind to MUC1-positive but not MUC1-negative cells. An aptamer-doxorubicin complex (Apt-Dox) was formulated by intercalating doxorubicin into the DNA structure of MA3. Apt-Dox was found capable of carrying doxorubicin into MUC1-positive tumor cells, while significantly reducing the drug intake by MUC1-negative cells. Moreover, Apt-Dox retained the efficacy of doxorubicin against MUC1-positive tumor cells, but lowered the toxicity to MUC1-negative cells (P<0.01). The results suggest that the MUC1 aptamer may have potential utility as a targeting ligand for selective delivery of cytotoxic agent to MUC1-expressing tumors.     

Discovery of novel 2-substituted-4-phenoxypyridine derivatives as potential antitumor agents

A series of 2-substituted-4-phenoxypyridine derivatives were designed, synthesized, and evaluated for their antiproliferative activity against 4 cancer cell lines (A549, HT-29, H460, and U87MG) in vitro. Most compounds showed moderate to excellent potency. Nine tyrosine kinases (c-Met, Flt-3, ALK, VEGFR-2, VEGFR-3, PDGFR-α, PDGFR-β, c-Kit, and EGFR) were used to evaluate the inhibitory activities with the most promising analogue 39, which showed the Flt-3/c-Met IC₅₀ values of 2.18/2.61?nM. Structure-activity relationship studies indicated that n-Pr served as R¹ group showed a higher preference, and stronger mono-EWGs on the phenyl ring (such as R²?=?4-F) was benefited to the potency.     

All five host-range variants of Xanthomonas citri carry one pthA homolog with 17.5 repeats that determines pathogenicity on citrus, but none determine host-range variation

Citrus canker disease is caused by five groups of Xanthomonas citri strains that are distinguished primarily by host range: three from Asia (A, A*, and A(w)) and two that form a phylogenetically distinct clade and originated in South America (B and C). Every X. citri strain carries multiple DNA fragments that hybridize with pthA, which is essential for the pathogenicity of wide-host-range X. citri group A strain 3213. DNA fragments that hybridized with pthA were cloned from a representative strain from all five groups. Each strain carried one and only one pthA homolog that functionally complemented a knockout mutation of pthA in 3213. Every complementing homolog was of identical size to pthA and carried 17.5 nearly identical, direct tandem repeats, including three new genes from narrow-host-range groups C (pthC), A(w) (pthAW), and A* (pthA*). Every noncomplementing paralog was of a different size; one of these was sequenced from group A* (pthA*-2) and was found to have an intact promoter and full-length reading frame but with 15.5 repeats. None of the complementing homologs nor any of the noncomplementing paralogs conferred avirulence to 3213 on grapefruit or suppressed avirulence of a group A* strain on grapefruit. A knockout mutation of pthC in a group C strain resulted in loss of pathogenicity on lime, but the strain was unaffected in ability to elicit an HR on grapefruit. This pthC- mutant was fully complemented by pthA, pthB, or pthC. Analysis of the predicted amino-acid sequences of all functional pthA homologs and nonfunctional paralogs indicated that the specific sequence of the 17th repeat may be essential for pathogenicity of X. citri on citrus.     

秦岭西段地区蝴蝶群落多样性与环境因子相关性

为了探讨秦岭西段地区蝴蝶群落多样性与生境类型、季节和环境因子之间的关系,本文于2020–2021年对该地区不同季节不同生境的蝴蝶群落进行了系统调查,基于调查结果,对α多样性进行了趋势和外推分析,对β多样性进行了非度量多维尺度分析(non-metric multidimensional scaling,NMDS)和聚类分析,运用广义加性模型(generalized additive model,GAM)对多样性指数与主要环境因子的关系进行了拟合分析。结果表明,本次调查共观测到蝴蝶8,898头,隶属于5科84属169种,其中个体数量最多的是粉蝶科,有3,671头,物种数最多的是蛱蝶科,有80种。α多样性分析结果显示,在不同生境类型中,针阔混交林的物种多样性指数最高;在不同季节中,夏季的物种多样性指数最高。β多样性分析结果显示,针阔混交林和落叶阔叶林的蝴蝶群落组成相似性最高,不同季节间蝴蝶群落物种组成相似性较低,春季和夏季蝴蝶群落明显聚集,秋季蝴蝶群落更为分散。广义加性模型拟合曲线表明,较高的植被异质性可维持蝴蝶群落的多样性;环境温度处于24–30℃之间时,Pielou均匀度指数较高,蝴蝶群...     

模拟海平面上升对海滨木槿渗透调节的影响

通过模拟海平面上升对海滨木槿主要渗透调节物质可溶性蛋白、可溶性糖和淀粉的影响发现,可溶性糖和可溶性蛋白均随水淹时间的延长呈现先升高后下降的变化,且变化较一致。而淀粉则呈先升高后下降再升高的N型曲线变化。另外通过对各个处理的分析比较发现,海滨木槿在海水淹浸35 cm·d^-1和6 h·d^-1环境下在渗透调节水平上仍然表现出较强的抗性。研究发现海滨木槿水淹胁迫程度较小的情况下可溶性糖与可溶性蛋白含量呈显著正相关,可溶性糖与淀粉呈显著负相关,说明海滨木槿在一定程度的水淹胁迫下主要渗透调节物质具有协同性,且水淹第21 d后存在可溶性糖向淀粉转化的可能。     

Morphological and molecular characterization of free-floating and attached green macroalgae Ulva spp. in the Yellow Sea of China

During the summer of 2008 and 2009, massive algal blooms repeatedly broke out in the Yellow Sea of China. These were undoubtedly caused by the accumulations of one or more species in the macroalgal genus Ulva. In previous reports, morphological observation indicated that the species involved in this phenomenon is Ulva prolifera but molecular analyses indicated that the species belongs to an Ulva linza–procera–prolifera (LPP) clade. Correct identification of the bloom species is required to understand and manage the blooms, but the taxonomic status of the bloom species remains unclear. In the current study, the taxonomic status of 22 selected specimens from the Yellow Sea was assessed by using both morphological and molecular (ITS and rbcL sequences) data. In addition, 5S rDNA analyses were performed for those samples clustering in the LPP clade, and phylogenetic tree and ribotype analyses were constructed for determining the possible origin of the bloom. Three free-floating and two attached Ulva species were distinguished and described: Ulva compressa Linnaeus and Ulva pertusa Kjellman were found in free-floating samples; U. linza Linnaeus was found on rocks; and U. prolifera O.F. Müller was found in both habitats. Diversity in free-floating Ulva of the Yellow Sea appears to be greater than previously thought. The dominant free-floating Ulva species, U. prolifera, was not closely related to local populations attached to rocks but was closely related to populations from Japan.     

Elevated temperature is more effective than elevated [CO2] in exposing genotypic variation in Telopea speciosissima growth plasticity: implications for woody plant populations under climate change

Intraspecific variation in phenotypic plasticity is a critical determinant of plant species capacity to cope with climate change. A long‐standing hypothesis states that greater levels of environmental variability will select for genotypes with greater phenotypic plasticity. However, few studies have examined how genotypes of woody species originating from contrasting environments respond to multiple climate change factors. Here, we investigated the main and interactive effects of elevated [CO₂] (C_E) and elevated temperature (T_E) on growth and physiology of Coastal (warmer, less variable temperature environment) and Upland (cooler, more variable temperature environment) genotypes of an Australian woody species Telopea speciosissima. Both genotypes were positively responsive to C_E (35% and 29% increase in whole‐plant dry mass and leaf area, respectively), but only the Coastal genotype exhibited positive growth responses to T_E. We found that the Coastal genotype exhibited greater growth response to T_E (47% and 85% increase in whole‐plant dry mass and leaf area, respectively) when compared with the Upland genotype (no change in dry mass or leaf area). No intraspecific variation in physiological plasticity was detected under C_E or T_E, and the interactive effects of C_E and T_E on intraspecific variation in phenotypic plasticity were also largely absent. Overall, T_E was a more effective climate factor than C_E in exposing genotypic variation in our woody species. Our results contradict the paradigm that genotypes from more variable climates will exhibit greater phenotypic plasticity in future climate regimes.