基因组学: 理解植物入侵性的重要工具

入侵植物基因组学是一个新兴的研究领域, 它利用基因组学方法研究与植物入侵性相关的分子基础和表达调控机制, 甄别入侵性基因型, 进而在基因组水平上揭示外来种入侵性产生和进化的分子机制。本文扼要综述了可用于植物入侵生物学研究的主要基因组学方法, 包括比较基因组学、群体基因组学和表观基因组学等方法; 运用基因组学技术研究入侵植物除草剂抗性和根状茎发育的分子基础已取得了重要进展。然而, 入侵植物基因组学仍处于发展初期, 选择理想的入侵植物模式种, 建立入侵性研究的模式系统, 是当前亟待解决的问题。本文还提出了入侵植物基因组学研究值得关注的几个发展方向, 包括基因组信息的完善、不同环境条件下入侵植物的分子响应机制以及入侵性的系统生物学研究等。     

Estimation of plant litter pools and decomposition-related parameters in a mechanistic model

Modeling the C and N dynamics during decomposition of plant residues depends on robust estimation of the litter pool partitioning (LPP) of residues, i.e. the fraction of their C and N allocated to rapidly and slowly decomposing pools. We searched for ways to estimate LPP by analyzing data on C and N mineralization during decomposition of 60 widely different plant residues, using a simple model with two litter pools and one microbial pool. LPP and relevant global parameters were estimated by model optimization (Levenberg-Marquardt-least-squares algorithm) in one operation. These kinetically-defined LPP values were used in regression analyses against data from stepwise chemical digestion (SCD) and near-infrared reflectance (NIR) analysis of the plant residues. LPP predicted by these regression models resulted in better performance than LPP from measured neutral-detergent-soluble (NDS) C and N when validated on independent data (n?=?15 plant residues). The results demonstrated the potential improvement by simultaneous estimation of residue specific LPP and global parameters, and that kinetically-defined LPP can be equally well predicted by NIR as by total N and NDS-C. Model failure for a minority of the plant-residues could partly be removed by altering the microbial C/N ratio (global optimum 7.1) within the range 5?C15, possibly reflecting a variable dominance of bacteria or fungi.     

Toward a molecular understanding of protein solubility: increased negative surface charge correlates with increased solubility

Protein solubility is a problem for many protein chemists, including structural biologists and developers of protein pharmaceuticals. Knowledge about how intrinsic factors influence solubility is limited due to the difficulty of obtaining quantitative solubility measurements. Solubility measurements in buffer alone are difficult to reproduce, because gels or supersaturated solutions often form, making it impossible to determine solubility values for many proteins. Protein precipitants can be used to obtain comparative solubility measurements and, in some cases, estimations of solubility in buffer alone. Protein precipitants fall into three broad classes: salts, long-chain polymers, and organic solvents. Here, we compare the use of representatives from two classes of precipitants, ammonium sulfate and polyethylene glycol 8000, by measuring the solubility of seven proteins. We find that increased negative surface charge correlates strongly with increased protein solubility and may be due to strong binding of water by the acidic amino acids. We also find that the solubility results obtained for the two different precipitants agree closely with each other, suggesting that the two precipitants probe similar properties that are relevant to solubility in buffer alone.     

Parasitic plant responses to host plant signals: a model for subterranean plant-plant interactions

The ability of plants to fulfill nutritional needs by parasitizing neighboring plants has originated several times in angiosperm evolution. Molecular tools are now being exploited to investigate the evolutionary origins of plant parasitism and to dissect the genetic mechanisms governing parasitic plant-host plant interactions. Investigating the nature of signal exchanges between parasitic plants and their hosts serves as a tractable system for understanding how plants in general communicate in the environment. This work should also lead to the development of novel strategies for minimizing the devastation caused by parasitic weeds in international agriculture.     

Sedimentation equilibrium: a valuable tool to study homologous and heterogeneous interactions of proteins or proteins and nucleic acids

We present a short overview of our experience in analyzing the affinity and stoichiometry of self-associating and heterologous interactions by using the sedimentation equilibrium technique. Data acquisition and the fitting procedure employing the computer programs that we have developed, Polymole and Virial, are utilized for obtaining reliable results under ideal as well as non-ideal conditions. Such data derived from biologically important macromolecules find utility in understanding physiological events such as cell regulation.     

Developing a model of plant hormone interactions

Plant growth and development is influenced by mutual interactions among plant hormones. The five classical plant hormones are auxins, cytokinins, gibberellins, abscisic acid and ethylene. They are small diffusible molecules that easily penetrate between cells. In addition, newer classes of plant hormones have been identified such as brassinosteroids, jasmonic acid, salicylic acid and various small proteins or peptides. These hormones also play important roles in the regulation of plant growth and development. This review begins with a brief summary of the current findings on plant hormones. Based on this knowledge, a conceptual model about interactions among plant hormones is built so as to link and develop an understanding of the diverse functions of different plant hormones as a whole in plants.Key words: abscisic acid, auxin, brassinosteroids, cytokinins, ethylene, gibberellins, jasmonic acid, salicylic acid, plant peptide hormones     

Certificates of confidentiality: a valuable tool for protecting genetic data.

Protecting the confidentiality of genetic research data is an important aspect of genetic research that has been discussed in various forums. Research data must be protected to prevent discrimination and its use in litigation. The certificate of confidentiality was created to protect the subjects of alcohol- and drug-abuse studies, who may be engaging in illegal activities. As revised in 1988, the certificate protects investigators engaging in other kinds of studies from being compelled to reveal information about subjects. Because the certificate protects information that could damage a subject's financial or social standing or employability, it is an appropriate tool to use to maintain the confidentiality of genetic data. The Department of Health and Human Services issues the certificates; the procedure for applying for a certificate of confidentiality is presented.     

Comparative gene mapping: a valuable new tool for mammalian developmental studies

Technological advances in the 1970s encouraged the mapping of homologous gene loci in different mammalian species, including mouse and man. One hundred eighty-five homologous loci have now been mapped in these two species. Conservation of linkage is sufficient to identify substantial segments of the two genomes that have been left intact since their divergence from a common ancestor. The recognition of these conserved segments allows experimental manipulation of mouse chromosomes or chromosomal regions to produce models of human chromosomal anomalies of medical importance. Comparative gene mapping has been extended beyond mouse and man and the genomes of some species, including domestic cattle, appear to be more highly conserved relative to humans than the mouse. Such species may be particularly useful in providing models of human chromosomal anomalies that cannot be duplicated in laboratory mice.     

Biotinylated phosphotyrosine containing peptides: A valuable tool for studies on phosphopeptide interactions with SH2 and PTB domains

A series of biotinylated phosphopeptides has been synthesized and used in the development of an ELISA-based approach to assess SH2/PTB-phosphoprotein interactions in vitro in terms of affinity and specificity.     

Biotinylated phosphotyrosine containing peptides: A valuable tool for studies on phosphopeptide interactions with SH2 and PTB domains

Summary A series of biotinylated phosphopeptides has been synthesized and used in the development of an ELISA-based approach to assess SH2/PTB-phosphoprotein interactions in vitro in terms of affinity and specificity. Abbreviations: BSA, bovine serum albumin; DMSO, dimethylsulfoxie; EGF, epidermal growth factor; ELISA, enzyme-linked immunosorbent assay; HATU,N-[(dimethylamino)1H-1,2,3-triazolo[4,5-b]pyridin-1-ylmethylene]-N-methylmethan-aminium hexafluorophosphateN-oxide; HPLC, high-performance liquid chromatography; GST, glutathione-S-transferase; pY, phosphotyrosine; TFA, trifluoroacetic acid; Tris, tris(hydroxymethyl)aminomethane; TBS-T, Tris buffered saline Tween. The abbreviations used for amino acids follow the recommendations of the IUPAC-IUB Commission of Biochemical Nomenclature [Eur. J. Biochem., 138 (1984) 9].     

嗜热四膜虫——具有发展潜力的功能基因组学研究模型

在真核生物的分子生物学和遗传学研究方面,纤毛类原生动物嗜热四膜虫(Tetrahymenathermophila)已经被证明是一种有价值的生物学模型。通过对它的研究,人们发现并且掌握了核酶的分子机制、RNA的自我拼接、端粒的结构和功能、DNA序列重组等机理。这种原生动物的基因组功能分别由两个细胞核执行,即二倍体的小核与生殖过程有关,而多倍体的大核决定细胞的基因转录,并为转化基因的表达提供了强有力的手段。     

Floquet theory: a useful tool for understanding nonequilibrium dynamics

Many ecological systems experience periodic variability. Theoretical investigation of population and community dynamics in periodic environments has been hampered by the lack of mathematical tools relative to equilibrium systems. Here, I describe one such mathematical tool that has been rarely used in the ecological literature but has widespread use: Floquet theory. Floquet theory is the study of the stability of linear periodic systems in continuous time. Floquet exponents/multipliers are analogous to the eigenvalues of Jacobian matrices of equilibrium points. In this paper, I describe the general theory, then give examples to illustrate some of its uses: it defines fitness of structured populations, it can be used for invasion criteria in models of competition, and it can test the stability of limit cycle solutions. I also provide computer code to calculate Floquet exponents and multipliers. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Endometrial biopsy: a valuable clinical and research tool in bovine reproduction

Studies of postpartum endometrial physiologic and immune mechanisms in cows are compromised by the difficulty in acquiring tissue of suitable quality and in sufficient quantity (Bos taurus). Endometrial biopsy sampling has attracted concern regarding potential animal ill-health and perturbed subsequent fertility. Here, we describe a method of endometrial biopsy that obtains high-quality tissue samples and does not compromise fertility. Using a Hauptner instrument, endometrial biopsies were taken at 15, 30, and 60 d postpartum from 13 mixed-breed beef cows. The effects of repeat biopsy on health (heart rate, respiration rate, color of mucous membranes, rectal temperature), onset of estrous cyclicity, and first service conception rate were monitored. Extensive daily clinical examinations revealed no signs of ill-health. All cows had resumed estrous cyclicity at 60 d postpartum. A conception rate of 77% was achieved after estrus synchronization and artificial insemination. Each biopsy yielded intact endometrial tissue and nucleic acid suitable for extensive histologic and molecular analysis, respectively. We conclude that when carried out appropriately, bovine endometrial biopsy is a safe and reliable technique for assessing postpartum uterine function or health.     

Estimation of parameters for a model of transmitter release at synapses.

We consider models for the release of transmitter in response to nerve impulses, where it is assumed that quanta of transmitter are released from some of n sites, the probability of release from any site being p. It is assumed that the quantal size is either a constant or is distributed as a normal or a gamma variate. Observations on both spontaneous potentials and evoked potentials are used to obtain moment estimated of n and p. Large sample estimates of the standard errors of these estimates are given.     

Isoenzyme patterns: a valuable molecular tool for the differentiation of Zygosaccharomyces species and detection of misidentified isolates

Electrophoretic analysis of esterase, acid phosphatase, lactate dehydrogenase, glucose-6-phosphate dehydrogenase and alcohol dehydrogenase isoenzymes was performed in 39 strains classified into six species of the yeast genus Zygosaccharomyces. The electrophoretic profiles obtained allowed the clear separation of Z. bailii, Z. bisporus, Z. florentinus, Z. lentus, Z. mellis and Z. rouxii, strains of the latter species clustering into two subgroups. Furthermore, this methodology enabled the detection of misidentified strains, as subsequently confirmed by DNA-DNA reassociation and sequencing of the D1/D2 domain of the 26S rRNA gene. Cluster analysis of the global electrophoretic data and those obtained using only two of the isoenzyme systems, esterase and lactate dehydrogenase, yielded similar grouping of the strains examined, indicating that these enzymes are good markers for the differentiation of Zygosaccharomyces species.