Mapping the Fitness Landscape of Gene Expression Uncovers the Cause of Antagonism and Sign Epistasis between Adaptive Mutations

How do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once? Here we combined independently-arising beneficial mutations that altered enzyme levels in the central metabolism of Methylobacterium extorquens to uncover the fitness landscape defined by gene expression levels. We found strong antagonism and sign epistasis between these beneficial mutations. Mutations with the largest individual benefit interacted the most antagonistically with other mutations, a trend we also uncovered through analyses of datasets from other model systems. However, these beneficial mutations interacted multiplicatively (i.e., no epistasis) at the level of enzyme expression. By generating a model that predicts fitness from enzyme levels we could explain the observed sign epistasis as a result of overshooting the optimum defined by a balance between enzyme catalysis benefits and fitness costs. Knowledge of the phenotypic landscape also illuminated that, although the fitness peak was phenotypically far from the ancestral state, it was not genetically distant. Single beneficial mutations jumped straight toward the global optimum rather than being constrained to change the expression phenotypes in the correlated fashion expected by the genetic architecture. Given that adaptation in nature often results from optimizing gene expression, these conclusions can be widely applicable to other organisms and selective conditions. Poor interactions between individually beneficial alleles affecting gene expression may thus compromise the benefit of sex during adaptation and promote genetic differentiation.     

Effects of ACTH and 3′,5′-cyclic purine nucleotides on the morphology and metabolism of normal adult human adrenocortical cells in primary tissue culture

Summary Stereological studies showed that treatment of normal adult human adrenocortical cells in primary culture with ACTH or cyclic-AMP for 2 days results in similar increases in the volume of cells, of the mitochondrial and membrane space compartments and of the surface area of the smooth endoplasmic reticulum and mitochondrial cristae, and decrease in the lipid content of the cells. These changes were more marked after 8 days of treatment. Treatment for 2 days with cyclic-GMP had no striking effects on cell ultrastructure, whereas an 8-day treatment led to ultrastructural changes similar to those obtained after 2 days of ACTH-or cyclic-AMP-treatment. A discrete population of untreated cortical cells maintained a slow proliferation that was not effected by exposure to cyclic-GMP, but was significantly increased in cultures treated with ACTH or cyclic-AMP. Radioimmunological studies showed that untreated cortical cells kept secreting progesterone and cortisol and that ACTH, but neither cyclic nucleotide, increased the secretion rate per cell of both hormones. These results assign a major role to cyclic-AMP and a minor one to cyclic-GMP in the mediation of the differentiation-promoting and trophic effects, but not in the steroidogenic effects of ACTH on the human adrenal cortex.The authors wish to thank Miss A. Coi and Mr. G. Gottardo for their technical assistance. These investigations were partly supported by a contract with CNR-Italy (CT 74.00226/115.3439)     

Neonatal rat hepatocytes in primary tissue culture free from density-dependent regulation of growth

Summary Studies employing [³H]thymidine and radioautography as well as colchicine and Feulgen staining of DNA showed that up to 19-fold increases in the degree of cell crowding in vitro, i.e. from 1.45 to 27.55×10⁴ cells per specimen, did not change the rates of entry into DNA synthesis and mitosis of cultivated primary neonatal rat hepatocytes.     

Effects of purine cyclic nucleotides on the growth of neonatal rat hepatocytes in primary tissue culture

cGMP and db-cGMP administered for 20–24 h to neonatal rat hepatocytes in primary culture stimulated their DNA synthesis and proliferation only at concentrations higher than the physiological one, whereas at concentrations equal to or lower than the physiological concentration they were ineffective or inhibitory for both activities. Induction of DNA synthesis to be effected by cGMP required 15 h of treatment, preceded, however, by inhibition of the same process between the 6th and the 14th hour of exposure. In contrast, cAMP and db-cAMP stimulated the flow of cultivated hepatocytes into the S and M stages of their mitotic cycle when administered at very wide concentration range, including the physiological for cAMP and the sub-physiological for db-cAMP. cAMP was effective after 12–14 h of treatment. Equimolar mixtures of cGMP with cAMP and of db-cGMP with db-cAMP also stimulated the proliferative activity of primary hepatocytes, but only at very low doses, which induced a first peak of DNA synthesis between the 2nd and the 6th hour of treatment and a second peak at about the 18th hour. These actions of the cyclic compounds, employed singly or in equimolar combination, were shown to be specific, since they could not be reproduced by their main metabolites. The present results strengthen the view that cAMP plays a pre-eminent role in the positive regulation of hepatocyte proliferation. Contrary to the postulate of the dualistic doctrine, cGMP by itself is not proliferogenic in the physiological range; in fact, cGMP acts as an ancillary, possibly dispensable, compound whose physiological role may be to help, in cooperation with cAMP, liver cells to cross the G1/S boundary of their growth-division cycle.     

Structural dynamics of myoglobin: ligand migration among protein cavities studied by Fourier transform infrared/temperature derivative spectroscopy.

Fourier transform infrared (FTIR) spectroscopy in the CO stretch bands combined with temperature derivative spectroscopy (TDS) was used to characterize intermediate states obtained by photolysis of two sperm whale mutant myoglobins, YQR (L29(B10)Y, H64(E7)Q, T67(E10)R) and YQRF (with an additional I107(G8)F replacement). Both mutants assume two different bound-state conformations, A(0) and A(3), which can be distinguished by their different CO bands near 1965 and 1933 cm(-1). They most likely originate from different conformations of the Gln-64 side chain. Within each A substate, a number of photoproduct states have been characterized on the basis of the temperature dependence of recombination in TDS experiments. Different locations and orientations of the ligand within the protein can be distinguished by the infrared spectra of the photolyzed CO. Recombination from the primary docking site, B, near the heme dominates below 50 K. Above 60 K, ligand rebinding occurs predominantly from a secondary docking site, C', in which the CO is trapped in the Xe4 cavity on the distal side, as shown by crystallography of photolyzed YQR and L29W myoglobin CO. Another kinetic state (C") has been identified from which rebinding occurs around 130 K. Moreover, a population appearing above the solvent glass transition at approximately 180 K (D state) is assigned to rebinding from the Xe1 cavity, as suggested by the photoproduct structure of the L29W sperm whale myoglobin mutant. For both the YQR and YQRF mutants, rebinding from the B sites near the heme differs for the two A substates, supporting the view that the return of the ligand from the C', C", and D states is not governed by the recombination barrier at the heme iron but rather by migration to the active site. Comparison of YQR and YQRF shows that access to the Xe4 site (C') is severely restricted by introduction of the bulky Phe side chain at position 107.     

重金属Hg2+离子作用于PSII 23 kD外周蛋白的光谱学研究

23 kD蛋白是光系统II(PSII)的外周蛋白,具有增加Ca2 和C l-的结合以维持放氧活性的作用。本文借助内源荧光光谱和紫外吸收差谱考察了23 kD蛋白与Hg2 的相互作用。所得结果表明:低浓度的Hg2 离子(<10μM)引起23 kD蛋白的荧光淬灭,淬灭程度与Hg2 离子浓度相关;进一步分析显示,Hg2 离子对23 kD蛋白色氨酸荧光的淬灭属于静态淬灭。紫外吸收差谱可以检测到明显的配体向金属进行电荷转移的谱带(LMCT band)。随着Hg2 浓度的增加,LMCT带的强度逐渐增强。分析显示23 kD蛋白只存在一类Hg2 离子结合位点。     

江苏近海北部海域春季鱼类群落结构的年间变化

根据2009—2014年在江苏近海北部海域(34.00°—35.13°N,119.40°—121.50°E)的底拖网调查数据,结合综合性指标和多元统计分析等方法研究了该海域的鱼类群落结构随时间的变化.结果表明: 江苏近海海域共有鱼类68种,相对资源量波动较大,站位平均渔获质量的变化范围为0.75～1.62 kg·h^-1,站位平均渔获尾数显著下降,变化范围为203～370 ind·h^-1. 2009—2014年江苏近海的鱼类群落平均营养级指数在3.58～3.72,2009—2010年相对较低,2011—2014年在3.70以上波动.2009—2014年鱼类群落的平均个体大小在2.93～11.18 g之间波动上升,变化趋势与平均营养级基本一致.聚类分析和非度量多维标度排序分析表明,研究期间大致分为2009—2010和2011—2014年两个年份组.组间分歧种主要有尖海龙、小头栉孔虾虎鱼和玉筋鱼等.对前后两个年份组的分析表明,中上层、浮游生物食性鱼类优势度增加,冷温种和本地种优势度下降.表明江苏近海海域鱼类群落结构发生了较为明显的演替.针对演替规律提出了渔业管理的建议,为渔业资源的合理利用提供理论参考.     

A metabolomic approach to characterize the acid-tolerance response in <Emphasis Type="Italic">Sinorhizobium meliloti</Emphasis>

Introduction

Sinorhizobium meliloti establishes a symbiosis with Medicago species where the bacterium fixes atmospheric nitrogen for plant nutrition. To achieve a successful symbiosis, however, both partners need to withstand biotic and abiotic stresses within the soil, especially that of excess acid, to which the Medicago-Sinorhizobium symbiotic system is widely recognized as being highly sensitive.

Objective

To cope with low pH, S. meliloti can undergo an acid-tolerance response (ATR(+)) that not only enables a better survival but also constitutes a more competitive phenotype for Medicago sativa nodulation under acid and neutral conditions. To characterize this phenotype, we employed metabolomics to investigate the biochemical changes operating in ATR(+) cells.

Methods

A gas chromatography/mass spectrometry approach was used on S. meliloti 2011 cultures showing ATR(+) and ATR(?) phenotypes. After an univariate and multivariate statistical analysis, enzymatic activities and/or reserve carbohydrates characterizing ATR(+) phenotypes were determined.

Results

Two distinctive populations were clearly defined in cultures grown in acid and neutral pH based on the metabolites present. A shift occurred in the carbon-catabolic pathways, potentially supplying NAD(P)H equivalents for use in other metabolic reactions and/or for maintaining intracellular-pH homeostasis. Furthermore, among the mechanisms related to acid resistance, the ATR(+) phenotype was also characterized by lactate production, envelope modification, and carbon-overflow metabolism.

Conclusions

Acid-challenged S. meliloti exhibited several changes in different metabolic pathways that, in specific instances, could be identified and related to responses observed in other bacteria under various abiotic stresses. Some of the observed changes included modifications in the pentose-phosphate pathway (PPP), the exopolysaccharide biosynthesis, and in the myo-inositol degradation intermediates. Such modifications are part of a metabolic adaptation in the rhizobia that, as previously reported, is associated to improved phenotypes of acid tolerance and nodulation competitiveness.

     

冠心病合并代谢综合征患者的冠状动脉病变特点及与 代谢综合征组分的相关性研究

目的:探讨冠心病合并代谢综合征(metabolic syndrome,MS)患者的冠脉病变特点及冠心病与MS各组分的相关性。方法:选取540例冠心病患者为研究对象,其中合并MS患者164例,非合并MS患者376例,并将所有患者根据MS的组分个数进行分组,比较冠心病合并MS的病变特点、MS组分个数对冠状动脉病变程度的影响及冠状动脉病变程度与代谢综合症各组分的相关性;结果:①冠心病合并MS组BMI、FBG、TG、LDL-C、TC、UA、FIB、高血压分级等指标较非MS组高,差异有统计学意义(P<0.01),HDL-C、LVEF较非MS组低,差异有显著性(P<0.01);②MS组冠脉Gensini积分较高,三支病变、主干病变发生率高,差异有显著性(P<0.01);③随着合并MS组分个数的增加,冠脉Gensini积分也逐渐增加,各组间比较有显著性差异(P<0.01);④冠脉Gensini积分与MS组分BMI、高血压分级、TG、TC、LDL-C、UA等指标存在正相关(P<0.05),与性别、HDL-C存在负相关(p<0.01);调整传统危险因素后,Gensini积分与MS的组分数显著相关(r=0.739、P<0.01)。结论:冠心病患者有较高的MS患病率,冠心病合并MS患者冠脉病变程度更重,且以多支病变、主干病变为主;随着合并MS组分个数的增加,冠脉病变程度也呈加重趋势;MS的各个组分均与冠状动脉病变程度显著相关,可以作为冠心病严重程度的预测指标。     

血浆蛋白质组学的研究进展

血浆蛋白质组学是研究血浆蛋白质的功能和变化的一门科学。血浆中蕴藏着生命机体的所有信息,因此只有彻底了解血浆中存在哪些蛋白质,才能知道如何利用血浆来预测人体对疾病的易感性并监控疾病的进程,以期达到对疾病进行早诊断早治疗。由于血浆蛋白质组动态范围大,给研究带来了很大的困难。尤其是高丰度蛋白质的存在影响了低丰度蛋白质的检测率。而低丰度蛋白质都是有意义的具有临床诊断价值的蛋白质。因此去除高丰度蛋白质的干扰成了血浆蛋白质组学研究的关键。近年来,血浆蛋白质组学相关研究技术也得到了长足进展,为深入研究血浆蛋白质做出了重要贡献。血浆蛋白质组学作为一种无创性的研究方法,值得我们去探讨。本文就血浆蛋白质组学研究进展情况做一简要综述。