高寒退化草地星毛委陵菜根系分叉数和连接长度的关系

根系分叉数和连接长度影响着植物根系的空间分布和资源获取,二者的权衡关系有助于深层次的理解植物根系构型的生态适应性。在祁连山北坡高寒退化草地,设置未退化(T_1)、轻度退化(T_2)、中度退化(T_3)和重度退化(T_4)4个退化梯度样地,采用全根挖掘和Win-RHIZO根系分析仪相结合的方法,研究了星毛委陵菜(Potentilla acaulis)根系分叉数和连接长度之间的关系。结果表明:随着天然草地退化程度的加剧,草地群落的密度、高度、盖度、地上生物量和土壤含水量逐渐减小,土壤紧实度不断增大,星毛委陵菜种群的密度、高度、盖度、地上和地下生物量、根冠比和根系连接长度逐渐增大,分叉数呈相反的变化趋势;不同退化草地星毛委陵菜根系分叉数与连接长度之间的相关性存在差异(P0.05),在未退化(T_1)和重度退化(T_4)草地星毛委陵菜根系分叉数和连接长度之间存在极显著的负相关关系(P0.01),在轻度退化(T_2)和中度退化(T_3)草地二者之间存在显著的负相关关系(P0.05)。随着天然草地的退化,星毛委陵菜选择减小根系分叉数和增大根系连接长度的构型构建模式,反映了植物不同功能性状间生物量分配的权衡机制。     

Selection-by-function: efficient enrichment of cathepsin E inhibitors from a DNA library

A method for efficient enrichment of protease inhibitors out of a DNA library was developed by introducing SF-link technology. A two-step selection strategy was designed consisting of the initial enrichment of aptamers based on binding function while the second enrichment step was based on the inhibitory activity to a protease, cathepsin E (CE). The latter was constructed by covalently linking of a biotinylated peptide substrate to each of the ssDNA molecule contained in the preliminarily selected DNA library, generating 'SF-link'. Gradual enrichment of inhibitory DNAs was attained in the course of selection. One molecule, SFR-6-3, showed an IC(50) of around 30 nM, a K(d) of around 15 nM and high selectivity for CE. Sequence and structure analysis revealed a C-rich sequence without any guanine and possibly an i-motif structure, which must be novel to be found in in vitro-selected aptamers. SF-link technology, which is novel as the screening technology, provided a remarkable enrichment of specific protease inhibitors and has a potential to be further developed.     

Cartilage link protein 1 (Crtl1), an extracellular matrix component playing an important role in heart development

To expand our insight into cardiac development, a comparative DNA microarray analysis was performed using tissues from the atrioventricular junction (AVJ) and ventricular chambers of mouse hearts at embryonic day (ED) 10.5-11.0. This comparison revealed differential expression of approximately 200 genes, including cartilage link protein 1 (Crtl1). Crtl1 stabilizes the interaction between hyaluronan (HA) and versican, two extracellular matrix components essential for cardiac development. Immunohistochemical studies showed that, initially, Crtl1, versican, and HA are co-expressed in the endocardial lining of the heart, and in the endocardially derived mesenchyme of the AVJ and outflow tract (OFT). At later stages, this co-expression becomes restricted to discrete populations of endocardially derived mesenchyme. Histological analysis of the Crtl1-deficient mouse revealed a spectrum of cardiac malformations, including AV septal and myocardial defects, while expression studies showed a significant reduction in versican levels. Subsequent analysis of the hdf mouse, which carries an insertional mutation in the versican gene (CSPG2), demonstrated that haploinsufficient versican mice display septal defects resembling those seen in Crtl1(-/-) embryos, suggesting that reduced versican expression may contribute to a subset of the cardiac abnormalities observed in the Crtl1(-/-) mouse. Combined, these findings establish an important role for Crtl1 in heart development.     

Molecular characterisation of TNF,AIF, dermatopontin and VAMP genes of the flat oyster Ostrea edulis and analysis of their modulation by diseases

Bonamiosis and disseminated neoplasia (DN) are the most important diseases affecting cultured flat oysters (Ostrea edulis) in Galicia (NW Spain). Previous research of the response of O. edulis against bonamiosis by suppression subtractive hybridisation yielded a partial expressed sequence tag of tumour necrosis factor (TNF) and allograft inflammatory factor (AIF), as well as the whole open reading frame for dermatopontin and vesicle-associated membrane (VAMP). Herein, the complete open reading frames of TNF and AIF genes were determined by the rapid amplification of cDNA, and the deduced amino acid sequences of the four genes were characterised. Phylogenetic relationships for each gene were studied using maximum likelihood parameters. Quantitative-PCR assays were also performed in order to analyse the modulation of the expression of these genes by bonamiosis and disseminated neoplasia. Gene expression profiles were studied in haemolymph cells and in various organs (gill, gonad, mantle and digestive gland) of oysters affected by bonamiosis, DN, and both diseases with regard to non-affected oysters (control). TNF expression in haemolymph cells was up-regulated at heavy stage of bonamiosis but its expression was not affected by DN. AIF expression was up-regulated at heavy stage of bonamiosis in haemolymph cells and mantle, which is associated with heavy inflammatory response, and in haemolymph cells of oysters affected by DN. AIF expression was, however, down-regulated in other organs as gills and gonads. Dermatopontin expression was down-regulated in haemolymph cells and digestive gland of oysters affected by bonamiosis, but DN had no significant effect on its expression. Gills and gonads showed up-regulation of dermatopontin expression associated with bonamiosis. There were significant differences in the expression of TNF and VAMP depending on the bonamiosis intensity stage whereas no significant differences were detected between light and heavy severity degrees of DN for the studied genes. VAMP expression showed also differences among haemolymph cells and the organs studied. The occurrence of both diseases in oysters involved haemolymph cell gene expression patterns different from those associated to each disease separately: no significant effect was observed in TNF expression, dermatopontin was up-regulated and marked up-regulation of AIF and VAMP was recorded, which suggests a multiplier effect of the combination of both diseases for the latter two genes.     

Widespread occurrence of power-law distributions in inter-repeat distances shaped by genome dynamics

Repetitive DNA sequences derived from transposable elements (TE) are distributed in a non-random way, co-clustering with other classes of repeat elements, genes and other genomic components. In a previous work we reported power-law-like size distributions (linearity in log-log scale) in the spatial arrangement of Alu and LINE1 elements in the human genome. Here we investigate the large-scale features of the spatial arrangement of all principal classes of TEs in 14 genomes from phylogenetically distant organisms by studying the size distribution of inter-repeat distances. Power-law-like size distributions are found to be widespread, extending up to several orders of magnitude. In order to understand the emergence of this distributional pattern, we introduce an evolutionary scenario, which includes (i) Insertions of DNA segments (e.g., more recent repeats) into the considered sequence and (ii) Eliminations of members of the studied TE family. In the proposed model we also incorporate the potential for transposition events (characteristic of the DNA transposons' life-cycle) and segmental duplications. Simulations reproduce the main features of the observed size distributions. Furthermore, we investigate the effects of various genomic features on the presence and extent of power-law size distributions including TE class and age, mode of parental TE transmission, GC content, deletion and recombination rates in the studied genomic region, etc. Our observations corroborate the hypothesis that insertions of genomic material and eliminations of repeats are at the basis of power-laws in inter-repeat distances. The existence of these power-laws could facilitate the formation of the recently proposed "fractal globule" for the confined chromatin organization.     

不同坡向甘肃臭草根系分叉数和连接长度的权衡关系

根系分叉数和连接长度影响植物根系分布格局, 二者的权衡关系对理解植物根系构型的生态适应策略有重要意义。利用ArcGIS建立研究区域的数字高程模型, 并提取坡向数据, 采用全根挖掘和Win-RHIZO根系分析仪相结合的方法, 研究了祁连山北坡高寒退化草地不同坡向甘肃臭草(Melica przewalskyi)根系分叉数与连接长度间的关系。结果表明: 随着坡向由北坡向东坡、西坡、南坡转变, 草地群落的密度、高度、地上生物量和土壤含水量逐渐减小, 甘肃臭草种群的密度、高度以及根系连接长度呈逐渐增大的趋势、分叉数逐渐减小; 不同坡向甘肃臭草根系分叉数与连接长度间的相关性存在差异(p < 0.05), 在南坡和北坡甘肃臭草根系分叉数和连接长度之间存在极显著的负相关关系(p < 0.01), 在东坡和西坡二者之间存在显著的负相关关系(p < 0.05), 甘肃臭草分配给根系分叉数与连接长度的资源间存在着“此消彼长”的权衡关系。不同坡向甘肃臭草根系分叉数和连接长度的资源配置模式反映了植物根系功能性状对环境的响应和适应, 以及根系构型构建的投资权衡机制。     

Crosslinking of Cys142 of Methyltransferase SsoII with DNA Duplexes Containing a Single Internucleotide Phosphoryldisulfide Link

DNA duplexes containing a single phosphoryldisulfide link in place of the natural internucleotide phosphodiester bond were employed in affinity modification of Cys142 in cytosine-C5 DNA methyltransferase SsoII (M.SsoII). The possibility of duplex–M.SsoII conjugation as a result of disulfide exchange was demonstrated. The crosslinking efficiency proved to depend on the DNA primary structure, modification position, and the presence of S-adenosyl-L-homocysteine, a nonreactive analog of the methylation cofactor. The SH group of M.SsoII Cys142 was assumed to be close to the DNA sugar-phosphate backbone in the DNA–enzyme complex.     

Scale‐Dependent Spatial Match between Fruits and Fruit‐eating Birds during the Breeding Season in Yungas Andean Forests

The multi‐scale spatial match between bird and food abundances is a main driver of the structure of fruit‐eating bird assemblages. We explored how the activity of fruit‐eating birds was influenced by the abundance of fruits at the local and landscape scales in Andean mountain forests during the breeding season, when most birds forage close to their nest. We measured: (1) the spatial scale of variation in the abundance of fruits, (2) the spatial scale of variation in the activity of fruit‐eating birds, and (3) the spatial match between both variables. The sampling design consisted of eleven 1.2‐ha sites, each subdivided into 30 cells of 20 × 20 m, where we sampled fruits and fruit‐eating birds. We found that fruit consumption, and to a lesser extent bird abundance, were associated with local spatial variation in abundance of selected fruit species. However, fruit‐eating birds did not modify their spatial distribution in the landscape following changes in availability of these fruits. Our study shows that fruit‐eating birds detect local spatial variation in fruit availability in their home breeding ranges, and exploit patches with large clusters of selected fruits. However, it may be unprofitable for breeding birds to stray too far from their nests to exploit fruit‐rich patches, accounting for the absence of fruit tracking at larger spatial scales.     

Possible recognition of the GnRH receptor by an antiserum against a peptide encoded by nucleotide sequence complementary to mRNA of a GnRH precursor peptide

Two peptides, rHRnG and hproHRnG, which were encoded by the nucleotide sequences complementary to mRNA of rat hypothalamic gonadotropin-releasing hormone (GnRH) and human placental proGnRH(−3–13), respectively, were synthesized. A remarkable hydropathic anti-complementarity was observed in the N-terminal region between hproHRnG and human proGnRH(−3–13). Neither hproHRnG nor rHRnG bound GnRH in ELISA unless exremely high concentrations of peptides were used. ¹²⁵I-GnRH failed to bind with either rHRnG or hproHRnG previously coated polypropylene tubes. Antisera against these peptides were generated in rabbits. All the rabbits produced antibodies with high titer as tested by ELISA. One rabbit immunized with hproHRnG showed markedly reduced serum testosterone levels as compared with those of other rabbits. Intravenous administration of 1 ml serum from this rabbit, antiserum R281, into ovariectomized rats significantly decreased plasma LH. Using antiserum R281, about 10% of female rat pituitary cells were stained by immunohistochemistry. The staining was specific to hproHRnG since it was abolished by preabsorption of the antiserum with hproHRnG, but not with rHRnG, GnRH, LH nor any other peptide tested. This particular antiserum may have recognized the GnRH receptor, and thereby interfered with the action of endogenous GnRH. These results appear to be in agreement with the view that there is a structural similarity between the receptor for a peptide and the so-called complementary peptide.