天麻3种变型过氧化物酶的同工酶研究

采用聚丙烯酰胺凝胶电泳（PAGE）对天麻3种变型的过氧化物酶（POD）的同工酶进行了研究。结果表明,天麻3种变型的过氧化物酶的同工酶活性不同,酶谱条带数在5～7条之间,且具有特征谱带。其中乌天麻和红天麻的酶谱条带数相同,两者的酶谱条带数均多于绿天麻;绿天麻、乌天麻和红天麻的酶谱条数依次分别为5条、7条和7条;其中基本酶带有5条,Rf值分别为0．06、0．24、0．83,0．89、0．98;乌天麻与红天麻的相似度指数为0．86,说明这两个种亲缘关系近;乌天麻与绿天麻的相似度指数为0．71,反映它们之间的亲缘关系相对较远。     

A general law for animal locomotion?

The propulsion system of animals that fly or swim are quite different from each other in their morphology and function, yet the propulsive efficiency could be maximized by a surprising similarity in the fine tuning of flapping frequency, amplitude and forward speed, according to a new study by Taylor et al. This conclusion was based on an analysis of the Strouhal number, which is a dynamic similarity index relevant to propulsion that relies on vortex shedding for thrust generation. Such fine-tuning of the propulsive system suggests possible consequences for physiological and ecological adaptations related to, for example muscle operating frequency and optimal speed of muscle contraction.     

Response of saprotrophic microfungi degrading the fulvic fraction of soil organic matter to different N fertilization intensities,different plant species cover and elevated atmospheric CO<Subscript>2</Subscript> concentration

The response of the cenosis composition of soil saprotrophic microfungi able to utilize the fulvic fraction of soil organic matter to increased concentration of atmospheric carbon dioxide, plant species cover quality and different levels of nitrogen fertilization was determined under field conditions in a free-air carbon dioxide enrichment experiment. Twenty-nine species of microfungi were isolated from the tested soil. The effects of CO₂ enrichment and plant species cover were not significant. Nitrogen fertilization was identified as the only significant factor inducing changes in the abundance of soil microorganisms. This was reflected in a relatively low value of quantitative Sørensen similarity index on comparing fertilized and unfertilized treatments and in 2-way ANOVA of total CFU counts. Some differences were observed in species diversity between the two variants of all treatments. No association between microfungi and the factors under study was found by using the Monte Carlo Permutation test in redundancy analysis.     

Spouse-to-Spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untranslated Region of Hepatitis C Virus Analyzed by Next-Generation Sequencing

Hepatitis C virus (HCV) transmission between spouses remains poorly characterized, largely due to the limited availability of samples from the early stage of infection, as well as methodological constraints. A fifty-eight year-old male developed acute hepatitis C infection and his 53-year old spouse has been HCV-positive for over 10 years. Serum samples were collected from both at the time of acute hepatitis C diagnosis in male (baseline) and then at 9 and 13 months. Hypervariable region 1 (HVR1) and 5’ untranslated region (5’UTR) sequences were amplified and subjected to next generation sequencing (NGS) using a pyrosequencing platform. Genetic variants were inferred by Shorah reconstruction method and compared by phylogenetic and sequence diversity analysis. As the sequencing error of the procedure was previously determined to be ≤ 1.5%, the analysis was conducted with and without the 1.5% cut-off with regard to the frequency of variants. No identical HVR1 variants were identified in spouses at baseline and follow-up samples regardless whether the cut-off was applied or not. However, there was high similarity (98.3%) between a minor baseline donor variant (1.7% frequency) and the most abundant baseline recipient variant (62.5% frequency). Furthermore, donor and recipient strains clustered together when compared to 10 control subjects from the same area and infected with the same HCV subtype. There was an increase in HVR1 complexity (number of genetic variants) over time in both spouses. In contrast, the 5''UTR region was stable and of low complexity throughout the study. In conclusion, intrafamilial HCV transmission may be established by a very minor variant and investigation of this phenomenon requires high-sensitivity assays, such as NGS.     

剑尾鱼近交系遗传纯度的RAPD分析

目的　分析近交系剑尾鱼 (Xiphophorushelleri)的遗传纯度 ,以指导剑尾鱼实验动物化的培育工作。方法　应用经过筛选的 2 9条随机引物对剑尾鱼的第 19代近交系 12尾剑尾鱼个体基因组DNA进行RAPD扩增 ,计算近交系个体间的相似系数及遗传距离。结果　筛选的 2 9条引物共扩增出 30 6条带 ,扩增片段的大小在 0 2 - 3kb之间。其中多态性带 2 9条 ,多态性带频率在 0～ 5 0 0 0 %之间 ,平均为 9 48%。近交系剑尾鱼不同个体拥有相同条带的比率较高。计算得到近交系的平均相似系数 (S)为 0 9839(0 973～ 0 997) ,平均等位基因频率 ( q)为 0 8731,最低平均杂合率 ( H)为 0 12 6 9。 结论　剑尾鱼第 19代近交系有较高的遗传纯合度。     

Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants

Effective and precise grouping of highly similar sequences remains a major bottleneck in the evaluation of high-throughput sequencing datasets. Amplicon sequence variants (ASVs) offer a promising alternative that may supersede the widely used operational taxonomic units (OTUs) in environmental sequencing studies. We compared the performance of a recently developed pipeline based on the algorithm DADA2 for obtaining ASVs against a pipeline based on the algorithm SWARM for obtaining OTUs. Illumina-sequencing of 29 individual ciliate species resulted in up to 11 ASVs per species, while SWARM produced up to 19 OTUs per species. To improve the congruency between species diversity and molecular diversity, we applied sequence similarity networks (SSNs) for second-level sequence grouping into network sequence clusters (NSCs). At 100% sequence similarity in SWARM-SSNs, NSC numbers decreased from 7.9-fold overestimation without abundance filter, to 4.5-fold overestimation when an abundance filter was applied. For the DADA2-SSN approach, NSC numbers decreased from 3.5-fold to 3-fold overestimation. Rand index cluster analyses predicted best binning results between 97% and 94% sequence similarity for both DADA2-SSNs and SWARM-SSNs. Depending on the ecological questions addressed in an environmental sequencing study with protists we recommend ASVs as replacement for OTUs, best in combination with SSNs.     

Charge Variants of an Avastin Biosimilar Isolation,Characterization, In Vitro Properties and Pharmacokinetics in Rat

The similarity between a proposed biosimilar product and the reference product can be affected by many factors. This study is designed to examine whether any subtle difference in the distribution of the charge variants of an Avastin biosimilar can affect its in vitro potency and in vivo PK. Here, the acidic, basic and main peak fractions of a biosimilar product were isolated using high-performance cation-exchange chromatography and were subjected to various studies to compare their in vitro properties and in vivo PK profile. A serial of analytical methods, including size exclusion chromatography (SEC), imaged capillary isoelectric focusing (icIEF) capillary zone electrophoresis (CZE) and cation-exchange chromatography (CEX-HPLC) were also used to characterize the isolated charge variants. The kinetics constant was measured using a Biacore X100 system. The study indicates the biosimilar product has a high similarity with avastin in physicochemical properties. The potency in vitro and PK profile in rat of charge variants and biosimilar product are consistent with avastin.     

Germline alterations of the RNASEL gene, a candidate HPC1 gene at 1q25, in patients and families with prostate cancer

The RNASEL gene (2',5'-oligoisoadenylate-synthetase dependent) encodes a ribonuclease that mediates the antiviral and apoptotic activities of interferons. The RNASEL gene maps to the hereditary-prostate-cancer (HPC)-predisposition locus at 1q24-q25 (HPC1) and was recently shown to harbor truncating mutations in two families with linkage to HPC1. Here, we screened for RNASEL germline mutations in 66 Finnish patients with HPC, and we determined the frequency of the changes in the index patients from 116 families with HPC, in 492 patients with unselected prostate cancer (PRCA), in 223 patients with benign prostatic hyperplasia (BPH), and in 566 controls. A truncating mutation, E265X, was found in 5 (4.3%) of the 116 patients from families with HPC. This was significantly higher (odds ratio [OR] =4.56; P=.04) than the frequency of E265X in controls (1.8%). The highest mutation frequency (9.5%) was found in patients from families with four or more affected members. Possible segregation was detected only in a single family. However, the median age at disease onset for E265X carriers was 11 years less than that for noncarriers in the same families. In addition, of the four missense variants found, R462Q showed an association with HPC (OR=1.96; P=.07). None of the variants showed any differences between controls and either patients with BPH or patients with PRCA. We conclude that, although RNASEL mutations do not explain disease segregation in Finnish families with HPC, the variants are enriched in families with HPC that include more than two affected members and may also be associated with the age at disease onset. This suggests a possible modifying role in cancer predisposition. The impact that the RNASEL sequence variants have on PRCA burden at the population level seems small but deserves further study.     

城市河流改造工程对河流生态系统野生维管植物的影响

随着城市化的发展,许多城市对流经市区的河流进行了大规模工程改造,在获得了多种效益的同时,也引起了诸如生物多样性破坏和物种组成改变等一系列生态问题,因此对城市河流改造工程的生态影响进行研究非常重要,将有助于在未来城市河流改造中更有效地保护河流生态系统。该文以汾河太原段的河道改造工程为研究对象,用Shannon-Weiner 多样性指数、Sørensen群落相似性指数和单因素方差分析方法,研究了河流改造工程对河流生态系统中的野生维管植物物种多样性、频度和群落物种组成相似性的影响。结果表明:太原汾河段改造后比改造前的野生维管植物物种数和Shannon-Weiner 多样性指数显著降低;低频度的物种数明显增加而高频度的物种数明显减少;河流改造前后的群落相似性明显降低。由此可见,城市河流改造工程对河流生态系统中的野生维管植物物种多样性、频度和群落相似性有明显影响。     

Distribution of albumin variants in Indians and non-Indians of Mexico

The distribution of albumin variants amongst several Mexican Indian and non-Indian (Mestizo) groups was studied. Of the former, a total of 1606 individuals belonging to 11 different tribes were examined with an overall frequency of 1.5% of Albumin Mexico fairly uniformly distributed in all four main linguistic groups. The 2548 Mestizos studied belong in six groups, two from Mexico City and four from elsewhere in the country. The first of the Mexico City groups consisted of 1313 individuals randomly chosen from the outpatient clinic of the Instituto Nacional de la Nutrición, while the rest included healthy individuals. The overall frequency was 1.9%, also fairly evenly distributed, with no difference between the hospital population and the others. No anomalous albumin, other than Albumin Mexico was encountered in the whole study. It is concluded that the similarity between Indians and Mestizos is due to the high Indian component of the latter and that the presence of albumin Mexico is a good anthropological marker for this region of the world.     

白腹管鼻蝠两个冬眠群不同个体的随机扩增多态DNA分析

用随机扩增多态ＤＮＡ方法研究了白腹管鼻蝠冬眠群群内与群间个体之间的亲缘关系。结果显示：所研究的两个蝙蝠群内个体的遗传相似性平均为０．８６和０．８９,两群之间的遗传相似性平均为０．８４,群内与群间个体之间在遗传相似性方面有一定差别（Ｐ〈０．０５）。因此认为：在同一个洞中冬眠的白腹管鼻蝠可能亲缘关系很近,冬眠群的构成在亲缘关系方面存在着一定关系,即亲缘关系有可能影响冬眠群构成。     

Functional Properties of Rare Missense Variants of Human CDH13 Found in Adult Attention Deficit/Hyperactivity Disorder (ADHD) Patients

The CDH13 gene codes for T-cadherin, a GPI-anchored protein with cell adhesion properties that is highly expressed in the brain and cardiovascular system. Previous studies have suggested that CDH13 may be a promising candidate gene for Attention Deficit/Hyperactivity Disorder (ADHD). The aims of this study were to identify, functionally characterize, and estimate the frequency of coding CDH13 variants in adult ADHD patients and controls. We performed sequencing of the CDH13 gene in 169 Norwegian adult ADHD patients and 63 controls and genotyping of the identified variants in 641 patients and 668 controls. Native and green fluorescent protein tagged wild type and variant CDH13 proteins were expressed and studied in CHO and HEK293 cells, respectively. Sequencing identified seven rare missense CDH13 variants, one of which was novel. By genotyping, we found a cumulative frequency of these rare variants of 2.9% in controls and 3.2% in ADHD patients, implying that much larger samples are needed to obtain adequate power to study the genetic association between ADHD and rare CDH13 variants. Protein expression and localization studies in CHO cells and HEK293 cells showed that the wild type and mutant proteins were processed according to the canonical processing of GPI-anchored proteins. Although some of the mutations were predicted to severely affect protein secondary structure and stability, no significant differences were observed between the expression levels and distribution of the wild type and mutant proteins in either HEK293 or CHO cells. This is the first study where the frequency of coding CDH13 variants in patients and controls is reported and also where the functional properties of these variants are examined. Further investigations are needed to conclude whether CDH13 is involved in the pathogenesis of ADHD or other conditions.     

Distribution of single‐nucleotide variants on protein–protein interaction sites and its relationship with minor allele frequency

Recent advances in DNA sequencing techniques have identified rare single‐nucleotide variants with less than 1% minor allele frequency. Despite the growing interest and physiological importance of rare variants in genome sciences, less attention has been paid to the allele frequency of variants in protein sciences. To elucidate the characteristics of genetic variants on protein interaction sites, from the viewpoints of the allele frequency and the structural position of variants, we mapped about 20,000 human SNVs onto protein complexes. We found that variants are less abundant in protein interfaces, and specifically the core regions of interfaces. The tendency to “avoid” the interfacial core is stronger among common variants than rare variants. As amino acid substitutions, the trend of mutating amino acids among rare variants is consistent in different interfacial regions, reflecting the fact that rare variants result from random mutations in DNA sequences, whereas amino acid changes of common variants vary between the interfacial core and rim regions, possibly due to functional constraints on proteins. This study illustrated how the allele frequency of variants relates to the protein structural regions and the functional sites in general and will lead to deeper understanding of the potential deleteriousness of rare variants at the structural level. Exceptional cases of the observed trends will shed light on the limitations of structural approaches to evaluate the functional impacts of variants.     

Effects of introduced species on floristic similarity: Comparing two US states

This study aims to examine the effects of introduced species on increasing (homogenizing) or decreasing (differentiating) floristic similarity of plant composition. We calculated the Jaccard index for each pair of counties within two states of USA, California and Florida. We computed the Jaccard index separately for all (native plus exotic) species, for native species, and for exotic species. We further calculated a homogenization index between all species and native species for each pair of counties by subtracting similarity index for native species from that for all species. We correlated the Jaccard and homogenization indices to geographic distance, latitude separation, and longitude separation between pairs of counties and to average human population density and average land area of the two counties. We find a very strong pattern of differentiation for introduced species among nearly all Florida counties. In California, introduced species have a differentiating effect in about half the comparisons. We also find that introduced species tend to have a more homogenizing (or less differentiating) effect with increasing distances between counties. Our results do not show a clear relationship between human population density and the homogenization index.     

Allele variants of Borrelia afzelii found by sequencing of the chromosome gene p66

Sequencing of gene p66 fragments of 246-337 p.b. was performed in 45 isolates of Aorrelia afzelii isolated from different transmitting agents and reservoir hosts within the habitation area of the spirochaeta. At least seven allele variants of the pathogenic agent were found indifferent natural foci of the disease. The extent of similarity between the nucleotide sequences of the isolates of the same allele variant was 99.9-100%; the extent of similarity between different allele variants was 98.9-99.7%. It was found that the majority of genovariants of A. afzelii (with respect to 5S-23S) incorporated several different allele variants of gene p66, all allele variants being found in the two genogroups (VS461 and NT28) of the pathogenic agent.     

A New Quantitative Technique for Categorizing Whistles Using Simulated Signals and Whistles from Captive Bottlenose Dolphins (Delphinidae,Tursiops truncatus)

A widespread problem in the study of animal vocalizations is evaluating the acoustic similarity of signals both between individuals of a social group and between social groups. This problem becomes especially salient when classifying the narrow-band frequency-modulated signals, such as whistles, found in many avian and mammalian species. Whistles are usually characterized by their relative change in frequency over time, known as whistle ‘contour’. Measuring such a characteristic is difficult as it is not a single measurement, such as the mean frequency or duration of a signal, but several associated measurements of frequency across time. This paper reports on a new quantitative technique for determining whistle types based on whistle contour similarity and an application of this technique to the whistles of bottlenose dolphins to demonstrate its utility. This ‘contour similarity’ technique (CS technique) uses cluster analysis to group the correlation coefficients of frequency measurements from a data set of signals. To demonstrate the efficacy of this CS technique, three data sets were analysed, two using computer-generated signals and a third using adult bottlenose dolphin whistles, to (1) examine the efficacy of correlation coefficients for grouping signals by their similarity in whistle contour and (2) determine the viability of this technique for categorizing bottlenose dolphin whistles. Measured actual frequencies and correlation matrices from the four simulated signal types and a correlation matrix from the whistles of five captive adult bottlenose dolphins were each subjected to K-means cluster analysis and the resulting signal types were evaluated. Results indicated that the technique grouped actual frequencies according to the amount of shared actual frequencies and grouped correlation coefficients successfully according to signal contour. This result endured even if contours differed in overall duration or actual frequency or were expanded or compressed with respect to frequency or time. The results suggest that this approach is a viable method for assigning whistle contours to categories in bottlenose dolphins or any other species with narrow-band, frequency-modulated signals.     

SNP identification, linkage disequilibrium, and haplotype analysis for a 200-kb genomic region in a Korean population

Understanding patterns of linkage disequilibrium (LD) across genomes may facilitate association mapping studies to localize genetic variants influencing complex diseases, a recognition that led to the International Haplotype Mapping Project (HapMap). Divergent patterns of haplotype frequency and LD across global populations require that the HapMap database be supplemented with haplotype and LD data from additional populations. We conducted a pilot study of the LD and haplotype structure of a genomic region in a Korean population. A total of 165 SNPs were identified in a 200-kb region of 22q13.2 by direct sequencing. Unphased genotype data were generated for 76 SNPs in 90 unrelated Korean individuals. LD, haplotype diversity, and recombination rates were assessed in this region and compared with the HapMap database. The pattern of LD and haplotype frequencies of Korean samples showed a high degree of similarity with Japanese data. There was a strong correlation between high LD and low recombination frequency in this region. We found considerable similarities in local LD patterns between three Asian populations (Han Chinese, Japanese, and Korean) and the CEPH population. Haplotype frequencies were, however, significantly different between them. Our results should further the understanding of distinctive Korean genomic features and assist in designing appropriate association studies.     

Measuring beta‐diversity from taxonomic similarity

Question: The utility of beta (β‐) diversity measures that incorporate information about the degree of taxonomic (dis)similarity between species plots is becoming increasingly recognized. In this framework, the question for this study is: can we define an ecologically meaningful index of β‐diversity that, besides indicating simple species turnover, is able to account for taxonomic similarity amongst species in plots? Methods: First, the properties of existing measures of taxonomic similarity measures are briefly reviewed. Next, a new measure of plot‐to‐plot taxonomic similarity is presented that is based on the maximal common subgraph of two taxonomic trees. The proposed measure is computed from species presences and absences and include information about the degree of higher‐level taxonomic similarity between species plots. The performance of the proposed measure with respect to existing coefficients of taxonomic similarity and the coefficient of Jaccard is discussed using a small data set of heath plant communities. Finally, a method to quantify β‐diversity from taxonomic dissimilarities is discussed. Results: The proposed measure of taxonomic β‐diversity incorporates not only species richness, but also information about the degree of higher‐order taxonomic structure between species plots. In this view, it comes closer to a modern notion of biological diversity than more traditional measures of β‐di‐versity. From regression analysis between the new coefficient and existing measures of taxonomic similarity it is shown that there is an evident nonlinearity between the coefficients. This nonlinearity demonstrates that the new coefficient measures similarity in a conceptually different way from previous indices. Also, in good agreement with the findings of previous authors, the regression between the new index and the Jaccard coefficient of similarity shows that more than 80% of the variance of the former is explained by the community structure at the species level, while only the residual variance is explained by differences in the higher‐order taxonomic structure of the species plots. This means that a genuine taxonomic approach to the quantification of plot‐to‐plot similarity is only needed if we are interested in the residual system's variation that is related to the higher‐order taxonomic structure of a pair of species plots.     

喀斯特石漠生态系统不同自然演替阶段中苔藓植物多样性特征分析

以“空间代替时间”方法研究了贵州喀斯特石漠地区植被自然恢复演替过程中各演替阶段苔藓植物的群落特征及苔藓植物物种α和β多样性指数。研究结果表明：该区共有苔藓植物群落21种,并以美灰藓（Eurohypnum leptothallum）为优势物种。苔藓植物α多样性指数随演替阶段的发展,表现出先下降、再反弹（藤刺灌丛阶段）、最后再次降低的变化趋势。苔藓植物Pielou均匀度指数的大小表现为：苔藓群落阶段（0.9392）〉 乔灌丛阶段（0.8675）〉 藤刺灌丛阶段（0.8651）〉 草灌丛阶段（0.7677）〉 草丛阶段（0.7676）。β多样性指数（Sorenson多样性指数）分析表明,苔藓植物群落随着演替阶段的发展,相同种类的数目随之减少,群落间相似性系数也逐渐降低。虽然苔藓植物群落在草丛阶段和藤刺灌丛阶段的相似性高于草丛阶段和草灌丛阶段之间的相似性系数,但总的相似性系数却呈现下降趋势。该研究结果可为喀斯特石漠生态系统演替的研究提供依据。     

Hosts as habitats: faunal similarity of phytophagous insects between host plants

1. Published lists on the phytophages recorded on 86 cabbage plant species (Brassicaceae) and 30 thistle species (Cynaroideae) were used to investigate patterns in the faunal similarity of phytophages. This was done by calculating the Jaccard index and a standardised index of similarity between pairs of host species using presence/absence data. 2. The faunal similarity measured as Jaccard indices indicated that pairs of cabbage hosts share on average 36% of phytophagous species whereas pairs of thistle hosts share only 10%. 3. The faunal similarity between two host species increased with the taxonomic affinity of hosts. This increase was more pronounced in thistles than in cabbage plants. 4. Irrespective of the taxonomic affinity of hosts, in the cabbage plants the faunal similarity of endophages was lower than in ectophages. In contrast, in the thistles faunal similarity differed only between endophages and ectophages for hosts of the same genera. 5. Differences in the patterns of faunal similarity between the two host taxa may be due to idiosyncratic characteristics of the plant taxa, e.g. the unique chemical properties of the cabbage plants and the resource‐rich flower heads of thistles.