Genome size and recombination in angiosperms: a second look

Despite dramatic differences in genome size--and thus space for recombination to occur--previous workers found no correlation between recombination rate and genome size in flowering plants. Here I re-investigate these claims using phylogenetic comparative methods to test a large data set of recombination data in angiosperms. I show that genome size is significantly correlated with recombination rate across a wide sampling of species and that change in genome size explains a meaningful proportion ( approximately 20%) of variation in recombination rate. I show that the strength of this correlation is comparable with that of several characters previously linked to evolutionary change in recombination rate, but argue that consideration of processes of genome size change likely make the observed correlation a conservative estimate. And finally, although I find that recombination rate increases less than proportionally to change in genome size, several mechanistic and theoretical arguments suggest that this result is not unexpected.     

Construction of two recombination yeast two-hybrid vectors by in vitro recombination

Recombination-based restrictionless, ligation-independent cloning has been proven to be advantageous over restriction digestion and ligation cloning. To utilize the recombination cloning and previously constructed two-hybrid cDNA libraries, a new Gateway yeast two-hybrid bait vector, pEZY202, and a new prey vector, pEZY45, were constructed. The two-hybrid vectors were generated by in vitro recombination using a protocol that can be easily adapted for the conversion of other existing vectors. The new vectors were used to assay the interaction between the WW domain of PQBP1 (PQBPww) and the WW domain binding protein WBP11. Both PQBPww and WBP11 were cloned into a Gateway donor vector by in vitro recombination. They were then subcloned into pEZY45 and pEZY202, respectively, by in vitro recombination. The binding between PQBPww and WBP11 was reported in a two-hybrid experiment using the new vectors. The results of testing the new vectors in combination with the original vectors indicated that the new bait vector could be used to screen cDNA libraries that are constructed using the original prey vectors.     

基于蛋白质结构预测的胰岛素样生长因子-1的制备及活性分析北大核心CSCD

为了更经济高效地制备胰岛素样生长因子-1 (insulin-like growth factor-1, IGF-1),本研究采用计算机模拟技术对3种IGF-1融合蛋白进行蛋白质结构预测与分子对接,筛选出酶切最适配的IGF-1融合蛋白表达形式。利用基因工程技术构建并鉴定了IGF-1融合蛋白原核表达载体,并转化大肠杆菌Origami B(DE3)菌株,获得重组子;经异丙基-β-D-硫代吡喃半乳糖苷(isopropyl-β-D-1-thiogalactopyranoside, IPTG)诱导表达后,对菌体的破菌上清进行亲和层析、脱盐、凝血酶酶切及酶切产物亲和层析纯化得到目的蛋白;通过3T3细胞增殖法建立活性评价体系并对获得的IGF-1进行活性测定。结果显示,构建的IGF-1融合蛋白原核表达载体序列正确,获得的重组子在25℃、0.05 mmol/L IPTG诱导16 h时融合蛋白为可溶性表达,经初步纯化、凝血酶酶切、再次纯化后可获得纯度大于90%的IGF-1目的蛋白,在建立的活性评价体系下测得制备的IGF-1比活为2.47×10^(5)U/mg,与市售标准品接近。本研究建立了一条用于制备IGF-1的完整工艺路线,为IGF-1药物的研制及工业化生产奠定基础。     

Population structure promotes the evolution of costly sex in artificial gene networks

We build on previous observations that Hill–Robertson interference generates an advantage of sex that, in structured populations, can be large enough to explain the evolutionary maintenance of costly sex. We employed a gene network model that explicitly incorporates interactions between genes. Mutations in the gene networks have variable effects that depend on the genetic background in which they appear. Consequently, our simulations include two costs of sex—recombination and migration loads—that were missing from previous studies of the evolution of costly sex. Our results suggest a critical role for population structure that lies in its ability to align the long‐ and short‐term advantages of sex. We show that the addition of population structure favored the evolution of sex by disproportionately decreasing the equilibrium mean fitness of asexual populations, primarily by increasing the strength of Muller's Ratchet. Population structure also increased the ability of the short‐term advantage of sex to counter the primary limit to the evolution of sex in the gene network model—recombination load. On the other hand, highly structured populations experienced migration load in the form of Dobzhansky–Muller incompatibilities, decreasing the effective rate of migration between demes and, consequently, accelerating the accumulation of drift load in the sexual populations.     

抑制植物减数分裂重组的分子机理

减数分裂重组不仅保证了真核生物有性生殖过程中染色体数量的稳定,还通过父母亲本间遗传物质的互换在后代中产生遗传变异。因此,减数分裂重组是遗传多样性形成的重要途径,也是生物多样性和物种进化的主要动力。在绝大多数真核生物中,不管染色体数目的多少或基因组的大小,减数分裂重组的形成都受到严格的调控,但抑制减数分裂重组的分子机理目前仍不清楚。近年来,通过正向遗传学筛选鉴定出多个减数分裂重组抑制基因,揭示了抑制基因的功能和调控途径。本文基于拟南芥中减数分裂重组抑制基因的研究现状,综述了植物减数分裂重组抑制基因研究取得的突破性进展,并结合基因功能与其调控网络阐述了抑制植物减数分裂重组的分子机理。     

PARP inhibitors in ovarian cancer: Sensitivity prediction and resistance mechanisms

Poly (ADP‐ribose) polymerase (PARP) inhibitors have provided great clinical benefits to ovarian cancer patients. To date, three PARP inhibitors, namely, olaparib, rucaparib and niraparib have been approved for the treatment of ovarian cancer in the United States. Homologous recombination deficiency (HRD) and platinum sensitivity are prospective biomarkers for predicting the response to PARP inhibitors in ovarian cancers. Preclinical data have focused on identifying the gene aberrations that might generate HRD and induce sensitivity to PARP inhibitors in vitro in cancer cell lines or in vivo in patient‐derived xenografts. Clinical trials have focused on genomic scar analysis to identify biomarkers for predicting the response to PARP inhibitors. Additionally, researchers have aimed to investigate mechanisms of resistance to PARP inhibitors and strategies to overcome this resistance. Combining PARP inhibitors with HR pathway inhibitors to extend the utility of PARP inhibitors to BRCA‐proficient tumours is increasingly foreseeable. Identifying the population of patients with the greatest potential benefit from PARP inhibitor therapy and the circumstances under which patients are no longer suited for PARP inhibitor therapy are important. Further studies are required in order to propose better strategies for overcoming resistance to PARP inhibitor therapy in ovarian cancers.     

Interface‐Modification‐Induced Gradient Energy Band for Highly Efficient CsPbIBr2 Perovskite Solar Cells

Inorganic cesium lead halide perovskite solar cells (PSCs) have received enormous attention due to their excellent stability compared with that of their organic–inorganic counterparts. However, the lack of optimization strategies leads the inorganic PSCs to suffer from low efficiency arising from significant recombination. To overcome this dilemma, a surface modification of the electron transport layer (ETL)/perovskite interface is undertaken by using SmBr₃ to improve the crystallization and morphology of the perovskite layer for enhanced ETL/perovskite interface interaction. Encouragingly, a gradient energy band is created at the interface with an outstanding hole blocking effect. As a result, both the charge recombination occurring at the interface and the nonradiative recombination inside the perovskite are suppressed, and, simultaneously, the charge extraction is improved successfully. Therefore, the power conversion efficiency of the CsPbIBr₂ PSCs is increased to as high as 10.88% under one sun illumination, which is 30% higher than its counterparts without the modification. It is logically inferred that this valuable optimization strategy can be extended to other analogous structures and materials.     

Aging Effect of a Cu(In,Ga)(S,Se)2 Absorber on the Photovoltaic Performance of Its Cd‐Free Solar Cell Fabricated by an All‐Dry Process: Its Carrier Recombination Analysis

Cd‐free Cu(In,Ga)(S,Se)₂ (CIGSSe) solar cells are fabricated by an all‐dry process (a Cd‐free and all‐dry process CIGSSe solar cell) with aged CIGSSe thin film absorbers. The aged CIGSSe thin films are kept in a desiccator cabinet under partial pressure of oxygen of ≈200 Pa for aging time up to 10 months. It is reported for the first time that aged CIGSSe thin film with increased aging time results in significant enhancement of photovoltaic performance of Cd‐free and all‐dry process CIGSSe solar cells, regardless of the alkali treatment. Based on carrier recombination analysis, carrier recombination rates at the interface and in the depletion region of the Cd‐free and all‐dry process CIGSSe solar cells are reduced owing to avoidance of sputtering damage on CIGSSe absorber surface, which is consistent with the strong electron beam‐induced current signal near CIGSSe surface after the increased aging time. It is implied that the interface and near‐surface qualities are clearly improved through the increased aging time, which is attributable to the self‐forming of In_x(O,S)_y near CIGSSe surface, which acts as a buffer layer. Ultimately, the 22.0%‐efficient Cd‐free CIGSSe solar cell fabricated by all‐dry process is achieved with the aged Cs‐treated CIGSSe absorber with the aging time of 10 months.     

LDJump: Estimating variable recombination rates from population genetic data

As recombination plays an important role in evolution, its estimation and the identification of hotspot positions is of considerable interest. We propose a novel approach for estimating population recombination rates based on genotyping or sequence data that involves a sequential multiscale change point estimator. Our method also permits demography to be taken into account. It uses several summary statistics within a regression model fitted on suitable scenarios. Our proposed method is accurate, computationally fast, and provides a parsimonious solution by ensuring a type I error control against too many changes in the recombination rate. An application to human genome data suggests a good congruence between our estimated and experimentally identified hotspots. Our method is implemented in the R ‐package LDJump, which is freely available at https://github.com/PhHermann/LDJump .     

The role of recombination,niche‐specific gene pools and flexible genomes in the ecological speciation of bacteria

Bacteria diversify into genetic clusters analogous to those observed in sexual eukaryotes, but the definition of bacterial species is an ongoing problem. Recent work has focused on adaptation to distinct ecological niches as the main driver of clustering, but there remains debate about the role of recombination in that process. One view is that homologous recombination occurs too rarely for gene flow to constrain divergent selection. Another view is that homologous recombination is frequent enough in many bacterial populations that barriers to gene flow are needed to permit divergence. Niche‐specific gene pools have been proposed as a general mechanism to limit gene flow. We use theoretical models to evaluate additional hypotheses that evolving genetic architecture, specifically the effect sizes of genes and gene gain and loss, can limit gene flow between diverging populations. Our model predicts that (a) in the presence of gene flow and recombination, ecological divergence is concentrated in few loci of large effect and (b) high rates of gene flow plus recombination promote gene loss and favor the evolution of niche‐specific genes. The results show that changing genetic architecture and gene loss can facilitate ecological divergence, even without niche‐specific gene pools. We discuss these results in the context of recent studies of sympatric divergence in microbes.