Genetic diversity and differentiation in Portuguese cattle breeds using microsatellites

Genotype data from 30 microsatellites were used to assess genetic diversity and relationships among 10 native Portuguese cattle breeds, American Charolais and the Brazilian Caracú. Hardy–Weinberg equilibrium was observed for all loci/population combinations except for five loci in Brava de Lide and one locus in Alentejana that exhibited heterozygote deficiency. Estimates of average observed and expected heterozygosities, total number of alleles (TNA) per breed and mean number of alleles (MNA) per locus/population were obtained. A total of 390 alleles were detected. TNA among Iberian cattle ranged from 170 to 237 and MNA ranged from 5.67 to 8.07. The highest observed heterozygosities were found in the Caracú, Maronesa, Garvonesa and Arouquesa and the lowest in Brava de Lide and Mirandesa. Estimation of population subdivision using Wright's F_ST index showed that the average proportion of genetic variation explained by breed differences was 9%. Neighbour‐joining phylogenetic trees based on D_A distances showed that the genetic relationships of present‐day Portuguese native breeds are consistent with historical origins in the Brown Concave (Arouquesa, Mirandesa, Marinhoa) and Red Convex (Mertolenga, Alentejana, Garvonesa, Minhota) evolutionary groups. The Iberian Black Orthoide group, represented by Brava de Lide and Maronesa, and the Barrosã breed appeared to be more closely related to the Brown Concave group but may represent a separate lineage. The Caracú breed was not found to be closely associated with any of the native Portuguese breeds.     

Genetic distance and species formation in evolving populations

Summary We compare the behavior of the genetic distance between individuals in evolving populations for three stochastic models.In the first model reproduction is asexual and the distribution of genetic distances reflects the genealogical tree of the population. This distribution fluctuates greatly in time, even for very large populations.In the second model reproduction is sexual with random mating allowed between any pair of individuals. In this case, the population becomes homogeneous and the genetic distance between pairs of individuals has small fluctuations which vanish in the limit of an infinitely large population.In the third model reproduction is still sexual but instead of random mating, mating only occurs between individuals which are genetically similar to each other. In that case, the population splits spontaneously into species which are in reproductive isolation from one another and one observes a steady state with a continual appearance and extinction of species in the population. We discuss this model in relation to the biological theory of speciation and isolating mechanisms.We also point out similarities between these three models of evolving populations and the theory of disordered systems in physics. Offprint requests to: P.G. Higgs     

进化距离与相对替代率的比较研究

系统树是描述物种、人种甚至基因间亲缘关系和演化的重要工具,必须以进化距离或(相对)替代率作为重要的参数。但以哪一个参数构建的树更能反映真实的系统树呢?事实上迄今并无人对此作过认真的研究。本文以模拟数据并用方差分析法检验两个参数的异同并讨论其包含的生物学意义。研究结果表明,当氨基酸的替代率和核苷酸的替代率分别为0.18和0.13时,它们的进化距离分别为0.199和0.143。经方差分析证实,若检验的氨基酸和核苷酸最大数目均为75只时,不论以替代率或进化距离中那一个作为构树参数,拓扑树事实上几乎只有一个。这就是说,该时拓扑树可靠性很大,而且随着它们替代率的减少,则检验的氨基酸和核苷酸的数目会随之增加。但是一旦氨基酸的替代率和核苷酸的替代率超过上述数字,则两个参数构建的树在拓扑长度上是不等价的。经分析,若进化距离大致上与进化时间成线性关系的话,则应选用进化距离。用进化距离重建的系统树事实上支持中性学说;若进化距离与进化时间显著地不存在线性关系的话,则可选用替代率,该情况表明中性学说不适用,似更倾向于新达尔文主义。     

Photo-induced unfolding and inactivation of bovine carbonic anhydrase in the presence of a photoresponsive surfactant

Photoreversible changes in the conformation and enzymatic activity of bovine carbonic anhydrase have been investigated as a function of photoresponsive surfactant concentration and light conditions. The light-responsive surfactant undergoes a photoisomerization from the relatively hydrophobic trans isomer under visible light to the relatively hydrophilic cis isomer upon UV illumination, providing a means to photoreversibly control enzyme–surfactant interactions. Small-angle neutron scattering and dynamic light scattering measurements, along with fluorescence spectroscopy, indicate that carbonic anhydrase unfolds upon addition of the surfactant under visible light, while only a small degree of unfolding is observed under UV light. Therefore, the enzyme is completely inactivated in the presence of the trans surfactant, while 40% of the native activity is preserved under UV light, providing a photoreversible “on/off switch” of enzyme activity. Small-angle neutron scattering data provide details of the in vitro conformational changes of the enzyme in response to the photosurfactant and light, with the enzyme found to aggregate as a result of photosurfactant-induced unfolding. Fourier transform infrared (FT-IR) spectroscopy further provides information on the secondary structure changes of the protein in the presence of photosurfactant.     

Bilateral similarity function: A novel and universal method for similarity analysis of biological sequences

Bilateral similarity function is designed for analyzing the similarities of biological sequences such as DNA, RNA secondary structure or protein in this paper. The defined function can perform comprehensive comparison between sequences remarkably well, both in terms of the Hamming distance of two compared sequences and the corresponding location difference. Compared with the existing methods for similarity analysis, the examination of similarities/dissimilarities illustrates that the proposed method with the computational complexity of O(N) is effective for these three kinds of biological sequences, and bears the universality for them.     

In silico analysis of expression pattern of a Wnt/β-catenin responsive gene ANLN in gastric cancer

Actin-binding protein anillin (ANLN) is primarily involved in the cytokinesis and known to be dysregulated in many cancers including gastric cancer (GC). However, the regulation and clinical significance of ANLN in GC are far less clear. In the present study, we aimed to investigate the clinical significance and possible regulators of ANLN in GC. We have identified the Wnt/β-catenin associated regulation of ANLN by analyzing the in vitro perturbed β-catenin mRNA expression profiles. Investigating the gastric tumors from publicly available genome-wide mRNA expression profiles, we have identified the over expression of ANLN in gastric tumors. Association between ANLN expression and clinical characteristics of GC showed elevated expression in intestinal type GC. Performing a single sample prediction method across GC mRNA expression profiles, we have identified the over expression of ANLN in proliferative type gastric tumors compared to the invasive and metabolic type gastric tumors. In silico pathway prediction analysis revealed the association between Wnt/β-catenin signaling and ANLN expression in gastric tumors. Our results highlight that expression of a Wnt/β-catenin responsive gene ANLN in GC is a molecular predictor of intestinal and proliferative type gastric tumors.     

Isoenzyme diversity and cryptic speciation in Juniperus excelsa (Cupressaceae) complex in Iran

An isoenzyme analysis was performed on 109 individuals from 11 populations of Juniperus excelsa complex collected from Iran. A total of 61 allozymes from five enzyme systems were scored. The mean numbers of bands per presumed isoenzyme, ranged from 2.07 to 3.23. The value of Euclidean distance ranged from 1.920 to 4.411. The average value of Shannon diversity index (H′) estimated for each population ranged from 0.317 in the population sampled from ‘Fasa’ to 1.053 in the population of ‘Golestan’, and the average H′ value for each enzyme system ranged from 0.031 (SOD-3) to 1.670 (PPO-1). To reveal the relationships among these populations, a cluster analysis based on Euclidean distances was performed. The results of the analysis suggest recognizing three taxa in the complex in Iran: Juniperus polycarpos subsp. polycarpos, Juniperus polycarpos subsp. turcomanica, and one cryptic species not recorded from Iran until now. Moreover, the analysis presented, does not confirm the occurrence of J. excelsa in Iran.     

Effects of brown and turbid water on piscivore–prey fish interactions along a visibility gradient

1. Environmental changes such as eutrophication and increasing inputs of humic matter (brownification) may have strong effects on predator–prey interactions in lakes through a reduction in the visual conditions affecting foraging behaviour of visually oriented predators. 2. In this experiment, we studied the effects of visual range (25–200 cm) in combination with optically deteriorating treatments (algae, clay or brown humic water) on predator–prey interactions between pike (Esox lucius) and roach (Rutilus rutilus). We measured effects on reaction distance and strike distance for pike and escape distance for roach, when pike individuals were exposed to free‐swimming roach as well as to roach held in a glass cylinder. 3. We found that reaction distance decreased with decreasing visual range caused by increasing levels of algae, clay or humic matter. The effect of reaction distance was stronger in turbid water (clay, algae) than in the brown water treatment. 4. Strike distance was neither affected by visual range nor by optical treatment, but we found shorter strike distances when pike attacked roach using visual cues only (roach held in a cylinder) compared to when pike could use multiple senses (free‐swimming roach). Escape distance for roach was longer in turbid than in brown water treatments. 5. Changes in environmental drivers, such as eutrophication and brownification, affecting the optical climate should thus have consequences for the strength of predator–prey interactions through changes in piscivore foraging efficiency and prey escape behaviour. This in turn may affect lake ecosystems through higher‐order interactions.     

口述史方法在风景园林教学中的应用探讨

风景园林专业的教学中,园林历史文化的传承与研习是一个漫长的过程。而高校教育中,除了历史知识、文化内涵的传授、讲解外,如何发挥高等教育及当代“人”在历史与文化中的主动性亦是一个重要课题。“口述史”方法有别于传统历史建构及研究方式,为学习者提供了解、认知、参与风景园林历史脉络的梳理及文化传承中的新可能。因此,以华南农业大学风景园林专业教学中的2项实践“口述工艺”及“广州市城市公园建设与发展研究”为例,探讨口述史在专业教学操作过程中的课程设计方法、应用范围以及与传统历史研习思路的差异。认为“口述史”的教学应用更多地以学生主导、以实践操作为主,推进学生多视角的历史认知、参与风景园林历史脉络的梳理、培养独立思考能力,推动风景园林历史教学改革与职业教育。