利用基因诱捕识别哺乳动物发育调控基因

ES细胞是一种来源于胚胎的多潜能细胞,它可在体外培养并进行基因操作,而且通过囊胚注射制作嵌合体的途径,能将外源基因掺入小鼠的基因库中,因此利用ES细胞可筛选出发生基因突变的小概率事件并获得其遗传突变体．利用基因诱捕载体与ES细胞,研究与哺乳动物发育调控有关的未知基因,这一新技术将成为阐明胚胎发育过程中基因表达的时空格式的有效手段．     

Patterns of evolutionary conservation of essential genes correlate with their compensability

Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability—that is, by how easily they can be functionally replaced, for example through increased expression of other genes.     

On the limitations of life cycle assessment and environmental systems analysis tools in general

The potential and limitations of life cycle assessment and environmental systems analysis tools in general are evaluated. More specifically this is done by exploring the limits of what can be shown by LCA and other tools. This is done from several perspectives. First, experiences from current LCAs and methodology discussions are used including a discussion on the type of impacts typically included, quality of inventory data, methodological choices in relation to time aspects, allocation, characterisation and weighting methods and uncertainties in describing the real world. Second, conclusions from the theory of science are practised. It is concluded that it can in general not be shown that one product is environmentally preferable to another one, even if this happens to be the case. This conclusion has important policy implications. If policy changes require that it must be shown that one product is more (or less) environmentally preferable before any action can be taken, then it is likely that no action is ever going to take place. If we want changes to be made, decisions must be taken on a less rigid basis. It is expected that in this decision making process, LCA can be a useful input. Since it is the only tool that can be used for product comparisons over the whole life cycle, it can not be replaced by any other tool and should be used. Increased harmonisation of LCA methodology may increase the acceptability of chosen methods and increase the usefulness of the tool.     

Analysis of Subcellularly Localized mRNAs Using in Situ Hybridization,mRNA Amplification,and Expression Profiling

Targeting of mRNAs to distinct subcellular regions occurs in all polarized cells. The mechanisms by which RNA transport occurs are poorly understood. With the advent of RNA amplification methodologies and expression profiling it is now possible to catalogue the RNAs that are targeted to particular subcellular regions. In particular, neurons are polarized cells in which dendrites receive signals from presynaptic neurons. Upon stimulation (information receipt) the dendrite processes the information such that an immediate dendritic response is generated as well as a longer-term somatic response. The integrated cellular response results in a signal that can be propagated through the axon to the next post-synaptic neuron. Much previous work has shown that mRNAs can be localized in dendrites and that local translation in dendrites can occur. In this chapter the methods for analysis of RNAs that are localized to dendrites are reviewed and a partial list of dendritically localized RNAs is presented. This information may be useful in identifying RNA regulatory regions that are responsible for specifying rate of RNA transport and the dendritic sites at which targeted RNAs dock so that they can be translated.     

Phenotypic variation with respect to fitness: the basis for rank-order selection*

Having argued that phenotypic variation with respect to the component of fitness involved in withstanding density stress is useful for the persistence of populations through time, the sources of such variation are described. Age differences and differences caused by the accidental encounters of dissimilar microenvironments are non-genetic in origin. Genetic bases for phenotypic variation can either be proximate (each individual having a unique genotype) or ultimate. The latter case is one in which the genotypes of individuals are such that the progeny they produce are phenotypically variable. Selection favouring such genotypes can be shown to be Darwinian; group selection is not required. A means for revealing instances of the ultimate genetic control of phenotypic variation is suggested: measures of what should be error variance prove to be larger than those which should, under normal circumstances, include error variance. The last increment of variation that causes what might otherwise be repetitive structures to differ can be ascribed to decisions that are genetically pre-set within developmental programmes.     

What is this stuff called fitness?

This paper considers a variety of attempts to define fitness in such a way as to defend the theory of evolution by natural selection from the criticism that it is a circular argument. Each of the definitions is shown to be inconsistent with the others. The paper argues that the environment in which an animal evolves can be defined only with respect to the properties of the phenotype of the animal and that it is therefore not illuminating to try to explain the phenotypic properties of the animal in terms of adaptation to an environment that is defined by those very properties. Furthermore, since there is no way that the environment can be defined independently of the presence of the animal there is no way that the quality of an animal can be assessed; and there can be no objective criteria by whichany form of selection can be carried out, therefore there can be no criteria by whichnatural selection can be carried out. It is proposed that fitness is nothing more than the production of offspring, that this is a phenotypic property like all the others, and if it is heritable then the offspring of the parents that produce the most offspring will themselves produce the most offspring, and that in principle it is impossible to account for this in terms of the other phenotypic properties of the fittest animals except by circular argument. Differential rates of reproduction are the causes of evolution and the phenotypic causes are strictly inexplicable.     

Structural identification of large systems by reduction to subsystems: VLDL triglycerides

The problem of determining whether or not a particular parameter, or the entire compartmental system, is structural identifiable can be extremely difficult if the number of unknown parameters and the number of compartments is large. However, the problem can be considerably simplified if the system can be decomposed into smaller subsystems in such a way that a parameter is structural identifiable with respect to the large system if and only if it is structural identifiable with respect to the subsystem in which it is contained. The paper offers sufficient conditions under which the desired decomposition can be achieved. The conditions are expressed in terms of the digraph of the system so that they are not difficult to verify. Illustrative examples are provided in terms of application to lipoprotein kinetics.     

Information maximization for exploring neural coding in hippocampus and lateral septum

A central problem in neural coding is to understand what are the features of the stimulus that are encoded by the neural activity. Assuming that neuronal coding is optimized for information transmission, we can use mutual information maximization for extracting the relevant features encoded in certain activity patterns. We show that this algorithm can be successfully applied to the study of different encoding strategies for location and direction of movement in hippocampal and lateral septal cells. Using this approach, we find that in lateral septum, a significant amount of information about location can be encoded in patterns that are not place-fields.     

Restoration of ecosystem services and biodiversity: conflicts and opportunities

Ecological restoration is becoming regarded as a major strategy for increasing the provision of ecosystem services as well as reversing biodiversity losses. Here, we show that restoration projects can be effective in enhancing both, but that conflicts can arise, especially if single services are targeted in isolation. Furthermore, recovery of biodiversity and services can be slow and incomplete. Despite this uncertainty, new methods of ecosystem service valuation are suggesting that the economic benefits of restoration can outweigh costs. Payment for Ecosystem Service schemes could therefore provide incentives for restoration, but require development to ensure biodiversity and multiple services are enhanced and the needs of different stakeholders are met. Such approaches must be implemented widely if new global restoration targets are to be achieved.     

EEG and implanted sources in the brain

Localisation procedures are based on models of the EEG that are relatively simple. The models are based on assumptions and choices of parameters that can be mistaken. Thus, it is crucial to validate the localisation procedures used in EEG. One of the options is to use the data obtained with electrodes that are implanted within the brain of an epileptic patient as part of the pre-surgical evaluation. When one of two neighbouring electrodes is used as a current source and the other as a current sink this can be regarded as a current dipole. The current injected has to be below the threshold for activation of cells. The position of this dipole can be deduced from magnetic resonance or X-ray images. The current dipole gives rise to a potential distribution at the scalp that can be measured by EEG. The measurements can be compared with the potential distribution that is calculated in a forward computation. Another method is to use the measured potential at the scalp to localize the source and to compare the result with the actual position of the dipole. In this paper the measured potential distributions at the scalp due to implanted dipoles were used to evaluate different volume conductor models. Since intracerebral and subdural electrodes were introduced through trephine holes over the fronto-central areas, and the diameter of the holes was rather large, approximately 23 mm, special effort was put into modelling the skull. Two important assumptions could be validated in this study: the electric currents within the head are Ohmic and a dipole can be used to model the induced electric activity of pairs of contacts on subdural electrodes or intra cerebral electrodes.     

Simulation as experiment: a philosophical reassessment for biological modeling

Some scientific modelers suggest that complex simulation models that mimic biological processes should have a limited place in ecological and evolutionary studies. However, complex simulation models can have a role that is different from that of simpler models that are designed to be fit to data. Simulation can be viewed as another kind of experimental system and should be analyzed as such. Here, I argue that current discussions in the philosophy of science and in the physical sciences fields about the use of simulation as an experimental system have important implications for biology, especially complex sciences such as evolution and ecology. Simulation models can be used to mimic complex systems, but unlike nature, can be manipulated in ways that would be impossible, too costly or unethical to do in natural systems. Simulation can add to theory development and testing, can offer hypotheses about the way the world works and can give guidance as to which data are most important to gather experimentally.     

A cell-permeable, activity-based probe for protein and lipid kinases

Protein and lipid kinases are two important classes of biomedically relevant enzymes. The expression and activity of many kinases are known to be dysregulated in a variety of diseases, and proteomic tools that can assess the presence and activity of these enzymes are likely to be useful for their evaluation. Because many of the mechanisms by which protein kinases can become unregulated involve post-translational modifications or changes in protein localization, they can only be detected by examining protein activity, sometimes within the context of the living cell. Wortmannin is a steroid-derived fungal metabolite that covalently inhibits both protein and lipid kinases. Here we describe the synthesis of three wortmannin derivatives, biotin-wortmannin, BODIPY-wortmannin, and tetramethylrhodamine-wortmannin. We demonstrate that these reagents exhibit reactivity similarly as wortmannin and react with members of the phosphatidylinositol 3-kinase and PI3-kinase related kinase families in cellular lysates. Moreover, in some cases these reagents can differentiate between the active and inactive forms of the enzyme, indicating that they are activity-based probes. The reagents also exhibit complementary properties. The biotin-wortmannin reagent is effective in the isolation of labeled proteins; all three can be used for protein labeling, and BODIPY-wortmannin is cell-permeable and can be used to label proteins within cells.     

New magnetic resonance contrast agents as biochemical reporters

Magnetic resonance imaging is a noninvasive, volume rendering diagnostic technique that uses lanthanide complexes to enhance proton relaxation. Magnetic resonance imaging is not limited by light scattering as optical microscopic techniques are, and allows imaging of whole animals. Clinical contrast agents are nonspecific and report solely on anatomy, whereas contrast agents that can be activated can be tailored to report on the physiological status or metabolic activity of biological systems. These new classes of magnetic resonance contrast agents represent a substantial leap in the type of information that can be derived from imaging experiments, and are the focus of this review.     

Potential hazards of biotechnology: the viewpoint from the United Kingdom

(1) There is a danger that our science may be severely restricted in the future if we do not as scientists take action to inform the public. (2) Scientists are agreed that some governmental controls are essential, but there is an urgent need that these should be applied uniformly worldwide. (3) The situation has changed rapidly now that the scientists are poised to demonstrate that genetic engineering has advanced to the stage where it can be applied to the field. Only in that way can we, as scientists, demonstrate that biotechnology can help humanity to overcome the problems of health, disease, and decent living which threaten to get progressively worse.     

Plasma method for processing spent nuclear fuel

Plasma methods for processing spent nuclear fuel are analyzed. It is shown that, by ICR heating in a nonuniform magnetic field, the energy of the heated ash ions can be increased substantially, while nuclear fuel ions can be kept cold. Two methods for extracting heated ash ions from a cold plasma flow are considered, specifically, that by increasing the ion gyroradius and that due to ion drift in a curved magnetic field. It is found that the required degree of separation of ash and fuel ions can be achieved in systems with quite moderate parameters.     

Playing with blocks: some pitfalls of forcing multiple alignments.

Block alignments of multiple amino acid sequences are useful representations of regions thought to share common ancestry and function. Often the block alignments are motivated by the expectation that a protein of interest is similar in function to members of a family of proteins. However, when alignments are forced by using ad hoc methods, it is often difficult to decide whether the proposed relationship is valid. Visual examination can be deceptive, especially when alignments are not carried out in the context of controls subjected to similar procedures. Even computer-aided methods can be misleading when biases are introduced. To illustrate some of the problems that can arise, a few examples from the literature are analyzed. It is concluded that when standard methods fail to find an interesting block alignment unaided by human intervention, then the result should be regarded with caution.     

CEREBRAL ANGIOGRAPHY—Its Use in Acute Head Injuries and Undiagnosed Coma

One of the major factors in treating a patient with acute alteration of consciousness is to determine if progressive intracranial hemorrhage is present. Similar problems are encountered in cases of cerebrovascular disease where increasingly effective medical and surgical methods of treatment are available. Progressive cerebral thrombosis can be arrested by anticoagulants, intracranial hemorrhage can be controlled and atheromatous occlusion of a major artery can be corrected. Intracranial mass lesions can be detected when the history is not available or is misleading.Cerebral angiography is a relatively safe diagnostic test that is certainly preferable to delayed or haphazard treatment when an exact diagnosis is uncertain in an unconscious patient.     

A bias in ML estimates of branch lengths in the presence of multiple signals

Sequence data often have competing signals that are detected by network programs or Lento plots. Such data can be formed by generating sequences on more than one tree, and combining the results, a mixture model. We report that with such mixture models, the estimates of edge (branch) lengths from maximum likelihood (ML) methods that assume a single tree are biased. Based on the observed number of competing signals in real data, such a bias of ML is expected to occur frequently. Because network methods can recover competing signals more accurately, there is a need for ML methods allowing a network. A fundamental problem is that mixture models can have more parameters than can be recovered from the data, so that some mixtures are not, in principle, identifiable. We recommend that network programs be incorporated into best practice analysis, along with ML and Bayesian trees.     

基于模拟退火法由脑磁图推测电流偶极子参数

利用模拟退火（Ｓｉｍｕｌａｔｅｄ Ａｎｎｅａｌｉｎｇ） 算法,由脑磁图（ ＭＥＧ） 数据反演脑内作为磁源的单电流偶极子参数,可以得到理想的结果。在上述工作的基础上,对脑内多电流偶极子参数的反演,则呈现如下状况：即以少于实际源数目的偶极子为源假设反演,目标函数得不到极小优化。反之,目标函数可以得到极小优化, 但出现多余的伪偶极子, 且这些伪偶极子在多次不同条件的反演结果中,处于不稳定状态。若将多次反演结果中处于不稳定状态的偶极子作为伪偶极子的判据而将其排除,则可以得到一种判断磁源偶极子数目的方法