DIA-Based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia

Drug resistance is a critical obstacle to effective treatment in patients with chronic myeloid leukemia. To understand the underlying resistance mechanisms in response to imatinib mesylate (IMA) and adriamycin (ADR), the parental K562 cells were treated with low doses of IMA or ADR for 2 months to generate derivative cells with mild, intermediate, and severe resistance to the drugs as defined by their increasing resistance index. PulseDIA-based (DIA [data-independent acquisition]) quantitative proteomics was then employed to reveal the proteome changes in these resistant cells. In total, 7082 proteins from 98,232 peptides were identified and quantified from the dataset using four DIA software tools including OpenSWATH, Spectronaut, DIA-NN, and EncyclopeDIA. Sirtuin signaling pathway was found to be significantly enriched in both ADR-resistant and IMA-resistant K562 cells. In particular, isocitrate dehydrogenase (NADP(+)) 2 was identified as a potential drug target correlated with the drug resistance phenotype, and its inhibition by the antagonist AGI-6780 reversed the acquired resistance in K562 cells to either ADR or IMA. Together, our study has implicated isocitrate dehydrogenase (NADP(+)) 2 as a potential target that can be therapeutically leveraged to alleviate the drug resistance in K562 cells when treated with IMA and ADR.     

In-depth Profiling and Quantification of the Lysine Acetylome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer

Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death worldwide with limited therapeutic options. Comprehensive investigation of protein posttranslational modifications in HCC is still limited. Lysine acetylation is one of the most common types of posttranslational modification involved in many cellular processes and plays crucial roles in the regulation of cancer. In this study, we analyzed the proteome and K-acetylome in eight pairs of HCC tumors and normal adjacent tissues using a timsTOF Pro instrument. As a result, we identified 9219 K-acetylation sites in 2625 proteins, of which 1003 sites exhibited differential acetylation levels between tumors and normal adjacent tissues. Interestingly, many novel tumor-specific K-acetylation sites were characterized, for example, filamin A (K865), filamin B (K697), and cofilin (K19), suggesting altered activities of these cytoskeleton-modulating molecules, which may contribute to tumor metastasis. In addition, we observed an overall suppression of protein K-acetylation in HCC tumors, especially for enzymes from various metabolic pathways, for example, glycolysis, tricarboxylic acid cycle, and fatty acid metabolism. Moreover, the expression of deacetylase sirtuin 2 (SIRT2) was upregulated in HCC tumors, and its role of deacetylation in HCC cells was further explored by examining the impact of SIRT2 overexpression on the proteome and K-acetylome in Huh7 HCC cells. SIRT2 overexpression reduced K-acetylation of proteins involved in a wide range of cellular processes, including energy metabolism. Furthermore, cellular assays showed that overexpression of SIRT2 in HCC cells inhibited both glycolysis and oxidative phosphorylation. Taken together, our findings provide valuable information to better understand the roles of K-acetylation in HCC and to treat this disease by correcting the aberrant acetylation patterns.     

接种丛枝菌根真菌对云南石漠化土壤呼吸的影响

为探明"丛枝菌根（Arbuscular mycorrhiza，AM）真菌-植物-土壤"耦合作用对石漠化土壤呼吸季节动态的影响，采用LI-6400-09土壤呼吸室和便携式光合作用测量系统，对圆柏（Sabina chinensis）接种摩西斗管囊霉（Funneliformis mosseae，FM）、根内根孢囊霉（Rhizophagus intraradices，RI）2种AM菌种处理下土壤呼吸季节动态进行野外连续定位观测，并探究AM真菌接种处理下石漠化土壤呼吸速率与植物生长、土壤理化性质之间的关系。结果表明：（1）相较于对照，接种AM真菌对石漠化生境土壤呼吸季节动态产生了显著影响（P<0.01）。AM真菌处理具有较高的土壤呼吸季节变化幅度，即根内根孢囊霉处理土壤呼吸速率（1.55-9.10 μmol m^-2 s^-1）显著高于摩西斗管囊霉（1.62-8.29 μmol m^-2 s^-1）和对照（1.23-4.46 μmol m^-2 s^-1）；（2） AM真菌接种处理下土壤温湿度变化对土壤呼吸的影响显著大于对照，即土壤温度与水分对土壤呼吸的平均解释量大小顺序为：RI （44.84%；52.35%）>FM （17.18%；41.65%）>CK （2.66%；16.55%）；（3）2种菌种处理下土壤呼吸速率均与土壤有机质、硝态氮、全氮、速效钾、树高、胸径及根系生物量呈显著或极显著正相关（P<0.01或0.05），而与pH呈极显著负相关（P<0.01），但对照处理土壤呼吸速率除与pH呈显著负相关（P<0.05）外，与其它土壤理化指标相关性不显著；（4）土壤温度和水分、硝态氮、铵态氮、有机质、易氧化有机碳、速效钾、全氮及全磷对土壤呼吸变化的贡献最大，而胸径、树高、有效磷、微生物生物量、根系生物量及pH的影响次之。因此，"AM真菌-寄主植物-土壤"相互作用对石漠化生境土壤呼吸季节动态的影响，主要取决于不同AM真菌接种处理对土壤微气候（如含水量）、碳素（有机质、易氧化有机碳）、无机氮库（铵态氮、硝态氮）、根系生物量及磷钾养分可利用性的调控。     

模拟根系分泌物输入对高寒退化草地土壤微生物残体的影响

微生物残体是稳定土壤碳库的重要来源，对退化生境碳的固持和积累具有重要意义。植物根系分泌物作为植物-土壤-微生物"交流"的媒介，是调控土壤微生物残体迁移转化的关键。因此，以极度退化草地土壤为对象，以氨基糖为标志物，模拟研究了不同氮浓度（低氮-LN：0.1 gN/kg；高氮-HN：0.2 gN/kg）和多样性（3种化合物、9种化合物）根系分泌物输入对土壤微生物残体的影响。结果表明：（1）根系分泌物输入可显著增加高寒退化草地土壤微生物残体含量，且主要由真菌残体贡献。其中高氮和低多样性处理增加最明显，微生物残体和真菌残体分别增加了101.14%，125.16%，而低氮和高多样性处理微生物残体和真菌残体仅增加了35.79%，33.51%。（2）根系分泌物的输入可增加土壤β-葡萄糖苷酶、土壤磷酸酶和过氧化物酶活性，促进微生物的生长，而降低β-N-乙酰氨基葡萄糖苷酶活性，减少微生物残体的分解。（3）回归分析结果显示，土壤微生物残体与土壤环境的C/N呈显著负相关，与微生物生物量C/N呈显著正相关。上述结果表明，在未来退化草地恢复中，可充分利用模拟根系分泌物输入的土壤固碳策略，即通过提高土壤氮的有效性，促进微生物的生长，加快代谢周转，进一步提高微生物残体含量。     

高效合成葡萄糖二酸酿酒酵母工程菌的构建

葡萄糖二酸是天然存在的一种重要二元酸,其在医疗保健和化工工业等领域具有很高的实际应用价值,因此被称为“最具价值的生物炼制产品之一”。以酿酒酵母(Saccharomyces cerevisiae)为底盘微生物,文中考察了过量表达肌醇转运蛋白Itr1、融合表达肌醇加氧酶和葡萄糖醛酸脱氢酶以及弱化表达葡萄糖6-磷酸脱氢酶基因ZWF1三种策略对葡萄糖二酸产量的影响。研究结果显示,过量表达肌醇转运蛋白Itr1使葡萄糖二酸产量在摇瓶发酵条件下较出发菌株Bga-3提高了26%;MIOX4-Udh融合蛋白的表达使葡萄糖二酸的产量较Bga-3菌株提高了40%;在此基础上,弱化表达葡萄糖6-磷酸脱氢酶基因ZWF1后,葡萄糖二酸的产量达5.5 g/L,较相同发酵条件下Bga-3菌株提高了60%。在5 L发酵罐中,该菌株葡萄糖二酸的最高产量达10.85 g/L,较Bga-3菌株提高了80%。由此可见,上述代谢改造策略的应用在很大程度上提高了葡萄糖二酸的途径效率和产量,为通过代谢工程方法在酿酒酵母中合成其他化合物的研究提供了参考。     

An evaluation of a novel estimator of linkage disequilibrium

The analysis of systems involving many loci is important in population and quantitative genetics. An important problem is the study of linkage disequilibrium (LD), a concept relevant in genome-enabled prediction of quantitative traits and in exploration of marker–phenotype associations. This article introduces a new estimator of a LD parameter (ρ²) that is much easier to compute than a maximum likelihood (or Bayesian) estimate of a tetra-choric correlation. We examined the conjecture that the sampling distribution of the estimator of ρ² could be less frequency dependent than that of the estimator of r², a widely used metric for assessing LD. This was done via an empirical evaluation of LD in 806 Holstein–Friesian cattle using 771 single-nucleotide polymorphism (SNP) markers and of HapMap III data on 21 991 SNPs (chromosome 3) observed in 88 unrelated individuals from Tuscany. Also, 1600 haplotypes over a region of 1 Mb simulated under the coalescent were used to estimate LD using the two measures. Subsequently, a simulation study compared the new estimator with that of r² using several scenarios of LD and allelic frequencies. From these studies, it is concluded that ρ² provides a useful metric for the study of LD as the distribution of its estimator is less frequency dependent than that of the standard estimator of r².     

Ecological succession among iron-oxidizing bacteria

Despite over 125 years of study, the factors that dictate species dominance in neutrophilic iron-oxidizing bacterial (FeOB) communities remain unknown. In a freshwater wetland, we documented a clear ecological succession coupled with niche separation between the helical stalk-forming Gallionellales (for example, Gallionella ferruginea) and tubular sheath-forming Leptothrix ochracea. Changes in the iron-seep community were documented using microscopy and cultivation-independent methods. Quantification of Fe-oxyhydroxide morphotypes by light microscopy was coupled with species-specific fluorescent in situ hybridization (FISH) probes using a protocol that minimized background fluorescence caused by the Fe-oxyhydroxides. Together with scanning electron microscopy, these techniques all indicated that Gallionellales dominated during early spring, with L. ochracea becoming more abundant for the remainder of the year. Analysis of tagged pyrosequencing reads of the small subunit ribosomal RNA gene (SSU rRNA) collected during seasonal progression supported a clear Gallionellales to L. ochracea transition, and community structure grouped according to observed dominant FeOB forms. Axis of redundancy analysis of physicochemical parameters collected from iron mats during the season, plotted with FeOB abundance, corroborated several field and microscopy-based observations and uncovered several unanticipated relationships. On the basis of these relationships, we conclude that the ecological niche of the stalk-forming Gallionellales is in waters with low organic carbon and steep redoxclines, and the sheath-forming L. ochracea is abundant in waters that contain high concentrations of complex organic carbon, high Fe and Mn content and gentle redoxclines. Finally, these findings identify a largely unexplored relationship between FeOB and organic carbon.     

The robustness of a network of ecological networks to habitat loss

There have been considerable advances in our understanding of the tolerance of species interaction networks to sequential extinctions of plants and animals. However, communities of species exist in a mosaic of habitats, and the vulnerability of habitats to anthropogenic change varies. Here, we model the cascading effects of habitat loss, driven by plant extinctions, on the robustness of multiple animal groups. Our network is constructed from empirical observations of 11 animal groups in 12 habitats on farmland. We simulated sequential habitat removal scenarios: randomly; according to prior information; and with a genetic algorithm to identify best‐ and worst‐case permutations of habitat loss. We identified two semi‐natural habitats (waste ground and hedgerows together comprising < 5% of the total area of the farm) as disproportionately important to the integrity of the overall network. Our approach provides a new tool for network ecologists and for directing the management and restoration of multiple‐habitat sites.