Meiosis and beyond – understanding the mechanistic and evolutionary processes shaping the germline genome

The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro-evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post-meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge.     

A new rhodopsin R135W mutation induces endoplasmic reticulum stress and apoptosis in retinal pigment epithelial cells

Rhodopsin mutations are associated with the autosomal-dominant form of retinitis pigmentosa (RP). Here we report simultaneous occurrence of RP associated with bilateral nanophthalmos and acute angle-closure glaucoma in patient with a new mutation in rhodopsin (R135W). ARPE-19 cells were transfected with myc-tagged wild-type (WT) and R135W rhodopsin constructs. The half-life of WT and R135W rhodopsin was analyzed via cycloheximide chase analysis. We found that R135W rhodopsin was accumulated in the endoplasmic reticulum (ER) and induced unfolded protein response (UPR) and apoptosis. Moreover, chaperone HSP70 alleviated ER stress and prevented apoptosis induced by R135W rhodopsin by attenuating UPR signaling. These findings reveal the novel pathogenic mechanism of RP and suggest that chaperone HSP70 has potential therapeutic significance for RP.     

iSEE: Interface structure,evolution, and energy-based machine learning predictor of binding affinity changes upon mutations

Quantitative evaluation of binding affinity changes upon mutations is crucial for protein engineering and drug design. Machine learning-based methods are gaining increasing momentum in this field. Due to the limited number of experimental data, using a small number of sensitive predictive features is vital to the generalization and robustness of such machine learning methods. Here we introduce a fast and reliable predictor of binding affinity changes upon single point mutation, based on a random forest approach. Our method, iSEE, uses a limited number of interface Structure, Evolution, and Energy-based features for the prediction. iSEE achieves, using only 31 features, a high prediction performance with a Pearson correlation coefficient (PCC) of 0.80 and a root mean square error of 1.41 kcal/mol on a diverse training dataset consisting of 1102 mutations in 57 protein-protein complexes. It competes with existing state-of-the-art methods on two blind test datasets. Predictions for a new dataset of 487 mutations in 56 protein complexes from the recently published SKEMPI 2.0 database reveals that none of the current methods perform well (PCC < 0.42), although their combination does improve the predictions. Feature analysis for iSEE underlines the significance of evolutionary conservations for quantitative prediction of mutation effects. As an application example, we perform a full mutation scanning of the interface residues in the MDM2–p53 complex.     

花生四烯酸高产菌株的选育

本研究以一株能产生花生四烯酸的被孢霉菌为出发菌株,通过紫外线诱变筛选出一株高产花生四烯酸的突变株Ｍ１０,发酵试验结果表明：突变株Ｍ１０的每升培养液中干菌体得率为３１ｇ,油脂含量为８．３ｇ,而原菌株仅为２０．３ｇ和５．４ｇ,气相色谱分析结果Ｍ１０所产花生四烯酸的量占总脂的１０．０６％（０．８３ｇ／Ｌ培养液）。同时对Ｍ１０菌株的生长和发酵特性及发酵过程中菌丝体形态变化作了一定的探讨。     

Origin and dissemination of the pollen-part mutated SC haplotype which confers self-compatibility in apricot (Prunus armeniaca)

In China, its centre of origin, apricot (Prunus armeniaca) is self-incompatible. However, most European cultivars are self-compatible. In most cases, self-compatibility is a result of a loss-of-function mutation within the pollen gene (SFB) in the SC haplotype. Controlled pollinations performed in this work revealed that the cross 'Ceglédi óriás' (S8S9)x'Ceglédi arany' (SCS9) set well, as expected, but the reciprocal cross did not. Apricot S8, S9 and SC haplotypes were analysed using a multilevel approach including fruit set evaluation, pollen tube growth analysis, RNase activity assays, polymerase chain reaction (PCR) analysis and DNA sequencing of the S-RNase and SFB alleles. SFB8 was revealed to be the first known progenitor allele of a naturally occurring self-compatibility allele in Prunus, and consequently SC=The first intron of SC-RNase is a phase one intron, indicating its more recent evolutionary origin compared with the second intron. Sequence analysis of different cultivars revealed that more single nucleotide polymorphisms accumulated in SC-RNase than in SFBC. New methods were designed to allow high-throughput analysis of S genotypes of apricot cultivars and selections. S-RNase sequence data from various sources helped to elucidate the putative origin and dissemination of self-compatibility in apricot conferred by the SC haplotype.     

新城疫病毒HN和F基因遗传变异相关性的研究

选取国内1999~2005年发生的NDV毒株,经CEF蚀斑纯化和SPF鸡胚增殖,对其融合蛋白(F)和血凝素-神经氨酸酶(HN)基因分别进行克隆测序,结合在GenBank中发表的具有F和HN基因的NDV序列,利用DNAStar软件,对其不同毒株的F或HN基因片段和全长、F和HN基因全长分别进行遗传变异的研究,利用统计学软件SPSS8.0进行同源性相关分析。结果表明:不同NDV毒株F或HN基因片段与其全长之间,核甘酸r≥0.973,氨基酸:0.911≤r≤0.968,遗传变异高度相关,但F与HN基因全长之间核甘酸的遗传变异呈现弱相关(r=0.312)。国内NDV野毒株之间HN核甘酸高度同源(同源率97%以上),而与La Sota同源率仅为79.2%~80.7%,且显示出明显的地域性。