Sequence-specific endonucleases in strains of Anabaena and Nostoc

The complements of restriction endonucleases of 12 strains of cyanobacteria were determined in cell-free extracts, and were compared with the complements of restriction activities assessed by measuring the relative efficiencies of plating of cyanophages on those cyanobacteria. The hosts which were susceptible to all of the phages contained endo R · AvaI and endo R · AvaII, and in several cases probably endo R · AvaIII, or isoschizomers of these enzymes. Three hosts which were lysed by only a subset (1 or 3) of the phages contained different restriction endonuclease. Anabaena sp. PCC 7120 showed apparent phenotypic restriction of phage An-22 grown in hosts with (isoschizomers of) AvaI, II and III, but no corresponding endonuclease has yet been detected in vitro. Nostoc sp. ATCC 29131 (PCC 6705) was found to contain a restriction enzyme, NspBII, with hitherot unknown specificity, C(A/C)GC(T/G)G.     

Megagametophyte organization in diploid alfalfa meiotic mutants producing 4n pollen and 2n eggs

Megagametogenesis was studied in five diploid alfalfa mutants producing 4n pollen and 2n eggs, using a stain-clearing technique. All mutants produced embryo sacs with a variable number of supernumerary nuclei both at the early (bi- and tetra-nucleate) and at the late (eight-nucleate) stages of development. The presence of supernumerary nuclei is considered to be a consequence of the production of coenocytic megaspores. The production of 2n eggs was confirmed through cytological investigation by means of the diameter of the egg-cell nucleolus. The frequency of 2n eggs was lower than the frequency of binucleated macrospores as previously determined. This discrepancy may be due to environmental effects but also to the fact that binucleated macrospores may degenerate or may, after two mitotic divisions, give rise to eight-nucleated embryo sacs counted as normals.     

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.     

Microarray-based method to evaluate the accuracy of restriction endonucleases HpaII and MspI

A double-strand DNA (ds DNA) microarray was fabricated to analyze the structural perturbations caused by methylation and the different base mismatches in the interaction of the restriction endonucleases HpaII and MspI with DNA. First, a series of synthesized oligonucleotides were arrayed on the aldehyde-coated glass slides. Second, these oligonucleotides were hybridized with target sequences to obtain ds DNA microarray, which includes several types of double strands with the fully methylated, semi-methylated, and unmethylated canonical recognition sequences, semi-methylated and unmethylated base mismatches within the recognition sequences. The cleavage experiments were carried out under normal buffer conditions. The results indicated that MspI could partially cleave methylated and semi-methylated canonical recognition sequences. In contrast, HpaII could not cleave methylated and semi-methylated canonical recognition sequences. HpaII and MspI could both cleave the unmethylated canonical recognition sequence. However, HpaII could partially cleave the sequence containing one GG mismatch and not cleave other base mismatches in the corresponding recognition site. In contrast, MspI could not recognize the base mismatches within the recognition sequence. A good reproducibility was observed in several parallel experiments. The experiment indicates that the microarray technology has great potentials in high-throughput identifying important interactions between protein and DNA.     

我国地方品种萧山鸡白介素2基因的克隆和分子进化分析

鸡白介素细胞2（cIL-2）是新近确定的非哺乳动物类细胞因子。建立了体外诱导鸡IL－2的最佳条件,从ConA激活的脾脏T淋巴细胞中克隆了我国地方品种鸡（浙江萧山鸡）IL－2 cDNA。该基因全长737bp,编码143个氨基酸的前体蛋白质。其编码序列与已公布的3条鸡IL－2仅有1－5个氨基酸的差异,与火鸡的IL－2同源性高达69.4%,与其他哺乳动物IL－2的同源性在21.2%－29.4%之间。二级结构预测表明,N端存在一长22个氨基酸的前导肽,4个关胱氨酸形成两个链内二硫键,并存在类似人IL－2的4个α螺旋,这些结构在维持IL－2生物学活性中起到重要作用。另外D^40、Y^65、E^82、N^108和Q^142等 在酸可能参与鸡IL－2受体的结合。分子系统进货树分析表明,鸡IL－2和哺乳动物IL－2有着共同的祖先;在免疫系统选择性压力下,形成独特的种族特异性。     

农田-荒地边缘地带中蝗虫边缘反应分析

探讨了中华蚱蜢等10种蝗总科昆虫对农田－荒地的边缘反应。研究发现,就同一边缘而言,有些物种的多度在靠近边缘时上升,而有些物种则下降。从科的水平上分析的结果与物种水平上的分析有差异。为了更精确地了解边缘对蝗虫的分布格局的影响,从物种水平上对其进行分析是 很有必要的。     

铁皮石斛2n花粉诱导及其形成的细胞机制研究

以铁皮石斛花蕾为材料,研究不同秋水仙素处理对2n花粉诱导的影响,并探讨2n花粉形成的细胞机制。结果表明:用0.1%秋水仙素微量注射长5.53mm、宽2.3mm左右的花蕾,每天注射1次,共注射3次,诱导2n花粉效果最好,2n花粉诱导率达6.22%,2n花粉粒直径比n花粉粒直径增大49%。减数分裂中期Ⅱ发现纺锤体定位异常,表现为平行纺锤体、三级纺锤体,四分体时期观察到三分体和二分体,故纺锤体定位异常可能是铁皮石斛2n配子形成的细胞学机制之一,其2n花粉在遗传上等同于FDR型。     

衣藻质体分裂相关基因CrFtsZ2的克隆及其进化分析

ＦｔｓＺ(ｆｉｌａｍｅｎｔｉｎｇｔｅｍｐｅｒａｔｕｒｅｓｅｎｓｉｔｉｖｅ)是一类从大肠杆菌温度敏感型突变体中分离到的基因 .该基因与Ｅ .ｃｏｌｉ细胞分裂密切相关 .突变体由于细胞分裂受阻而呈现“长丝状”[1] .此类基因于 1980年首次被克隆[2 ] .随后的研究表明 ,ＦｔｓＺ蛋白在Ｅ .ｃｏｌｉ分裂细胞的凹陷处形成环状多聚体 ,Ｚ环 ,是Ｅ .ｃｏｌｉ细胞分裂的限制因子[3 ] .衣藻属于绿藻 ,在现存的所有单细胞真核藻类中 ,绿藻是与陆生植物亲缘关系最近的一支[4] .由于衣藻为单细胞真核生物 ,并且仅含有一个巨大的叶绿体 ,因而是研究…     

植物2n配子发生及其遗传标记研究进展

文章综述了植物2n配子发生及其遗传标记研究现状,论述涉及有关形态学标记、细胞学标记、同工酶标记乃至DNA标记等遗传标记在2n配子研究中的应用,指出通过花粉形态观察、大小孢子母细胞减数分裂行为观察、杂种后代倍性鉴定以及亲子分子标记相关分析等,对2n配子发生、2n配子遗传类型与杂合性以及2n配子在育种实践中的有效性等进行研究。分子标记技术已经成为2n配子形成相关基因分析等方面的有力工具,利用分子标记等手段,研究2n配子形成的分子机理以及应用于辅助育种等将成为今后的热点,进而推动植物育种尤其是多倍体育种蓬勃发展。     

1998～2008年中国中部H9N2亚型AIV分离毒株HA基因的进化分析

从过去10年由中国中部分离的具有不同致病力的25株H9N2亚型禽流感选出6株(3#、12#、25#、14#、4#、22#)代表性毒株,利用RT-PCR扩增它们的HA基因,并比较分析该基因的序列,旨在探讨HA基因的变异对AIV毒力、抗原性变化的影响。结果表明:6株H9N2 AIV亚型分离株的HA基因在HA1和HA2的氨基酸裂解位点上没有出现高致病性禽流感病毒所特有的R-X-R/K-R模式,它们均为弱毒力毒株。HA上潜在糖基化位点除了3#和12#分离株多出一个之外,其余均为8个。3#和12#所表现出较强的致病性可能与其在HA的头部(HA1)的A抗原位点上多了一个糖基化位点(145~147aa),改变了HA基因空间构型有关,空间构型的改变导致抗HA抗体作用位点的变异或缺失并影响其较近的受体结合位点,从而改变该毒株的抗原性。研究结果提示需要持续跟踪H9N2 AIV在中国鸡群中的传播和进化,以便及时掌握疫情,有效防控禽流感。     

Determination of n+1 Gamete Transmission Rate of Trisomics and Location of Gene Controlling 2n Gamete Formation in Chinese Cabbage (Brassica rapa)

A set of trisomics of Chinese cabbage was used for determining the n+1 gamete transmission rate and locating the gene controlling 2n gamete formation on the corresponding chromosome. The results showed that the transmission rates of extra chromosomes in different trisomica varied from 0% to 15.38% by male gametes and from 0% to 17.39% by female gametes. Of the nine F2 populations derived from the hybridizations between each triaomic and Bp058 (2n gamete material), only Tri-4×Bp058 showed that the segregation ratio of plants without 2n gamete formation to plants with 2n gamete formation was 10.38:1, which fitted the expected segregation ratio of the trisomics (AAa) based on the 7.37% of n+1 gamete transmission through female and 5.88% through male. In other populations the segregation ratios varied from 2.48:1 to 3.72:1, which fitted the expected 3:1 segregation ratio of the bisomice (Aa). These results suggested that the gene controlling 2n gamete formation in Chinese cabbage Bp058 was located on chromosome 4. Further trisomic analysis based on the chromosome segregation and the incomplete stochastic chromatid segregation indicated that the gene locus was tightly linked to the centromere.     

The best of both worlds: Phylogenetic eigenvector regression and mapping

Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998) proposed what they called Phylogenetic Eigenvector Regression (PVR), in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM) was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U) process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses.     

改进的K—mean聚类算法在基因系统发育谱分析中的应用

简要介绍了系统发育谱法的原理,着重阐述了K—mean聚类算法在对基因系统发育谱分析中的改进,并与传统的K—mean聚类算法进行比较。实验结果表明,改进的K—mean聚类算法在运用系统发育谱法进行基因功能注释上是快而有效的,可以快速收敛到近似最优解。     

团头鲂人工同源四倍体、自繁后代、倍间交配后代的染色体组型及形态遗传特征

以2n团头鲂为对照,对诱导产生的同源四倍体、自繁后代(4n-F1)和倍间交配后代(正交3n和反交3n)的染色体组型及形态遗传特征进行比较分析。结果发现:(1)团头鲂四倍体(包括4n和4n-F1)和正反倍间交配三倍体的染色体众数分别为96和72,是2n团头鲂的2倍和1·5倍;在四倍体团头鲂组型排列中,sm1的四条较大的染色体明显可见,可视为标记染色体;(2)9个比例性状的测量结果显示,多倍体的体长/体高、体长/头长比例值显著小于2n团头鲂(P<0·05);而对于背棘长/体长比例值,多倍体则显著大于2n团头鲂(P<0·05);(3)29个参数的主成分分析结果表明,团头鲂同源4n、4n-F1、倍间交配3n及2n团头鲂等5个不同倍性群体的传统形态差别很大部分是由躯干部的形态差异,主要是体长/体高引起的,可作为团头鲂多倍体与二倍体群体鉴别的形态依据;(4)聚类结果显示,正交3n和反交3n相聚类,亲缘关系最近,然后,它们与4n-F1聚类后,再与4n奠基群体聚类,与二倍体群体的聚类关系较远[动物学报51(3):455-461,2005]。     

Tetraploids,triploids, and 2n pollen from diploid interspecific crosses with cassava

Summary Interspecific crosses of five cultivated cassava varieties (2n=36) were made with two related Manihot species, M. epruinosa (2n=36) and M. glaziovii (2n=36). From these diploid interspecific crosses, four spontaneous tetraploids (2n=4x=72) and two triploids (2n=3x=54) were isolated for the first time in cassava. Occurrence of relatively high frequencies (0.1%–35.6%) of 2n pollen and of apomixis seems to be associated with sexual polyploidization. The tetraploids and triploids were very vigorous and one of the tetraploids performed as well as the best variety in uniform yield trials conducted in Nigeria. These spontaneous polypoloids provide greater genetic variation and offer an opportunity to breed radically new cassava varieties. Approaches for isolating and utilizing the polyploid cassava clones for varietal and population improvement are discussed.     

Evidence for the existence of 2n gametes in Lotus tenuis Wald. et Kit. (2n=2x=12): their relevance in evolution and breeding of Lotus corniculatus L. (2n=4x=24)

Summary Crosses between male sterile L. corniculatus (2n=4x=24) and L. tenuis (2n=2x=12) plants were performed in order to verify the presence of 2n gametes in L. tenuis. All but one of the plants from these crosses had 2n=4x=24 and the L. corniculatus phenotype; this plant had 2n=2x=12 and the L. tenuis phenotype. The plants also showed good quantity of pollen at tripping, good pollen fertility and good percentage of seed setting in the backcross to L. corniculatus. On the whole, both cytological and morphological observations, showing that all but one of the plants from L. corniculatus x L. tenuis were normal tetraploids, suggest the existence of diploandrous gametes in L. tenuis. On the other hand, haploid parthenogenesis probably gave origin to the dihaploid plant 2n=2x=12.     

杉科、柏科的系统发生关系研究进展

杉科、柏科是松柏类裸子植物中的重要类群,其系统分类研究一直是裸子植物的研究热点之一.但是杉科与柏科之间及其内部各属之间的系统发生关系却一直存在争议.一般认为杉科、柏科单独成科.近年来的分子系统学及分支系统学研究结果证实:除了金松属以外,杉科和柏科为一单系群,应合并为一个科Cupres-saceae sensu　lato（广义柏科）,其主要分支类群的系统发生关系也已经基本确立,而金松属则单独成立金松科.     

福矛高温大曲中芽孢杆菌16S rDNA-RFLP及系统发育分析

目的:从福建建瓯黄华山酿酒有限公司高温大曲中分离出89株芽孢杆菌,通过初步筛选鉴定并进行微生物多样性研究.方法:对其16S rDNA进行PCR - RFLP分析和系统发育研究.结果:初步筛选得到的18株芽孢杆菌被HhaⅠ和MspⅠ酶切聚类分为四大组.通过系统发育分析样品中有6株Bacillus subtilis,4株Bacillus cereus,2株Bacillus sonorensis,2株Bacillus licheniformis,以及Bacillus pumilus、Bacillus oleronius、Bacillus coagulans和Bacillus thuringiensis各1株.结论:研究显示该高温大曲中可培养芽孢杆菌具有微生物多样性.     

GRK2 interacts with and phosphorylates Nedd4 and Nedd4-2

Epithelial Na(+) channels (ENaC) mediate the transport of sodium (Na) across epithelia in the kidney, gut, and lungs and are required for blood pressure regulation. They are inhibited by ubiquitin protein ligases, such as Nedd4 and Nedd4-2, which bind to proline-rich motifs (PY motifs) present in the C-termini of ENaC subunits. Loss of inhibition leads to hypertension. ENaC channels are maintained in the active state by G-protein-coupled receptor kinase 2 (GRK2), an enzyme implicated in the development of essential hypertension. Here, we report that GRK2 interacts not only with ENaC, but also with both Nedd4 and Nedd4-2. Additionally, GRK2 is capable of phosphorylating both Nedd4 and Nedd4-2 at multiple sites. Of possible significance is the phosphorylation of the threonine at position 466 in Nedd4, which is located in the area of the ww3 domain that binds ENaC. These results support and extend the role of GRK2 in sodium transport regulation.