Positioning Arabidopsis in plant biology. A key step toward unification of plant research

One of the major challenges in biological investigation involves developing a robust predictive framework in which biological outputs can be predicted from input data and knowledge of the state of the system. Currently, genomics-based strategies provide a strong framework for integrating biological knowledge within a species and linking knowledge between diverse organisms, as DNA sequence is a durable, accurate, and complete record of biological information. As such, it provides the best source of information upon which predictive rules can start to be built, tested, and generalized. Generalization is a key component of predictive biology because it defines the extent to which we can accurately predict from one instance to another. In plant science, several important research themes are concerned with generalization, and progress in these areas is reviewed here. The importance of developing a framework for predictive biology that includes a much wider variety of plant species is also emphasized.     

Theory on thermal probe arrays for the distinction between the convective and the perfusive modalities of heat transfer in living tissues

Recent suggestions for an improved model of heat transfer in living tissues emphasize the existence of a convective mode due to flowing blood in addition to, or even instead of, the perfusive mode, as proposed in Pennes' "classic" bioheat equation. In view of these suggestions, it might be beneficial to develop a technique that will enable one to distinguish between these two modes of bioheat transfer. To this end, a concept that utilizes a multiprobe array of thermistors in conjunction with a revised bioheat transfer equation has been derived to distinguish between, and to quantify the perfusive and convective contribution of blood to heat transfer in living tissues. The array consists of two or more temperature sensors one of which also serves to locally insert a short pulse of heat into the tissue prior to the temperature measurements. A theoretical analysis shows that such a concept is feasible. The construction of the system involves the selection of several important design parameters, i.e., the distance between the probes, the heating power, and the pulse duration. The choice of these parameters is based on computer simulations of the actual experiment.     

生物4D打印技术在心血管组织工程中的研究及应用进展

3D生物打印技术是应用包含生物材料与活细胞在内的生物墨水来构造生物医学产品的技术，近年来得到快速发展。3D打印的组织是静态的，而人体的组织则处于实时动态之中，并且随时能够发生形态及性能的变化，要提高体外环境与体内真实环境的吻合度，就需要一种能够模拟这种动态过程的体外组织构建技术。4D打印概念的提出，给实现这种复杂技术提供了一条新的思路。4D打印可理解为“3D打印+时间”，在3D打印基础上，4D打印应用一种或多种对刺激具有响应的智能材料，这种材料可以在相应的刺激下改变它们的形态、性能及功能，以满足多种需求。本文重点关注4D打印技术在心血管系统中的最新研究进展及其潜在应用领域，为该项技术的发展提供一些理论及应用参考价值。     

抑癌基因XEDAR 的研究进展

X-连锁性外胚层发育不良受体(X-linked ectodermal dysplasia receptor,XEDAR)基因位于人类染色体Xq12,编码的蛋白XEDAR作为新近分离出来的肿瘤坏死因子受体家族成员其功能主要涉及细胞增殖、参与细胞分化(胚胎的发育,表皮的分化)、调亡等。XEDAR已在多种肿瘤组织中研究,笔者就其基本概念及在肿瘤研究方面的进展进行综述。     

抑癌基因XEDAR的研究进展

X-连锁性外胚层发育不良受体（X-linked ectodermal dysplasia receptor, XEDAR ）基因位于人类染色体Xq12,编码的蛋白XEDAR作为新近分离出来的肿瘤坏死因子受体家族成员其功能主要涉及细胞增殖、参与细胞分化（胚胎的发育,表皮的分化）、调亡等。XEDAR已在多种肿瘤组织中研究,笔者就其基本概念及在肿瘤研究方面的进展进行综述。     

Meta level concept versus classic reflex concept for the control of posture and movement

Postural reflexes are replaced soon after birth by automatic reactions that allow for volition and cognition. It is still an enigma how this change in postural control is achieved. We suggest that the change involves the formation of a sensory processing level (meta level) that becomes interleaved in between the tight sensor-actuator coupling of the classic reflexes. We assume that the brain applies at this level intersensory interactions to reconstruct the physical stimuli which are causing the physiological stimuli and sensory signals. The thus derived estimates of the physical stimuli are then used as feedback signals in the posture control system. We present this concept on the background of the classic reflex concept and earlier attempts in the literature to overcome it. The earlier attempts were often motivated by the question how the brain prevents voluntary movements from being hampered by reflexive stabilisation of posture (so-called posture-movement problem). We compare our new concept with the classic reflex concept in a theoretical approach, by implementing both concepts into simple postural control models. In simulations of the two models we superimpose external perturbations (the physical stimuli) and a voluntary body lean movement. We show that it is possible to achieve successful stimulus compensation and unperturbed lean movement with both, the model derived from the new concept and the one of the classic reflex concept. With both approaches, the posture-movement problem does not arise. Based on preliminary considerations that include experimental findings from the literature, however, we conclude that the new concept provides more explanatory power than the classic reflex concept.     

PERSPECTIVE: DARWIN,PROGRESS, AND ECONOMIC PRINCIPLES

Darwin's concept of progress was an economic one, with the accumulation of adaptations having a strong analogy to technological innovations. This interpretation makes it easier to understand his differences with Lamarck and others whose views he considered metaphysically objectionable. It also clarifies his relationship to Malthus and such features of his theory as the episodic nature of evolutionary change. His position is consistent with modern theories of biotic invasions and long-term evolutionary trends. It also accords well with current efforts to produce a synthesis between biology and economics.     

Principal/agent theory and decision making in health care

Principal/agent theory, an economics concept that defines an agency relationship as "a contract under which one or more persons engage another person (the agent) to perform some service on their behalf which involves delegating some decision-making authority to the agent," is held to be applicable to the patient/physician relationship, in contrast to the view that this is a fiduciary relationship, not a contractual one. The distinction between fiduciary and contractual relationships is illuminated in the process of evaluating objections to the application of the principal/agent theory to the patient/physician relationship. The ability of the principal/agent theory to reveal important features of advance directives, understood as public documents rather than as confidential instructions from patient to physician, is also examined.     

Animals as sentinels: using comparative medicine to move beyond the laboratory

The comparative medicine approach, as applied to the study of laboratory animals for the betterment of human health, has resulted in important medical and scientific progress. Much of what is known about the human health risks of many toxic and infectious hazards present in the environment derives from experimental studies in animals and observational (epidemiological) studies of exposed human populations. Yet there is a third source of "in vivo" knowledge about host-environment interactions that may be underused and -explored: the study of diseases in naturally occurring animal populations that may signal potential human health threats. Just as canaries warned coal miners of the risk of toxic gases, other nonhuman animals, due to their greater susceptibility, environmental exposure, or shorter life span, may serve as "sentinels" for human environmental health hazards. Traditionally, communication between human and animal health professionals about cross-species sentinel events has been limited, but progress in comparative genomics, animal epidemiology, and bioinformatics can now provide an enhanced forum for such communication. The "One Health" concept involves moving toward a comparative clinical approach that considers "shared risks" between humans and animals and promotes greater cooperation and collaboration between human and animal health professionals to identify and reduce such risks. In doing so, it also creates new opportunities for the field of comparative medicine that can supplement traditional laboratory animal research.     

Thoughts on the cultural evolution of man. Developmental imprinting and transgenerational effect

The biological evolution of man stopped since it has been conveyed to the objects, created by man. This paper introduces the concept of "conveyed evolution". Being part of the cultural evolution, the conveyed evolution is a continuation of the biological one. There are several similarities between the laws of biological and conveyed evolution, albeit the differences are important as well. Some laws of the conveyed evolution are described here. The conveyed evolution has man-made repair mechanisms (medicine, protection of environment) which defend man from harm. Man's fragility limits the progress of conveyed evolution. However, artificial compounds or environmental pollutants which are provoked by the conveyed evolution induce chemical (hormonal) imprinting in the developmental critical periods, which is transmitted to the progeny generations (transgenerational effect). This could cause evolutionary alterations without mutation.     

Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data

MOTIVATION: Modern comparative genomics does not restrict to sequence but involves the comparison of metabolic pathways or protein-protein interactions as well. Central in this approach is the concept of neighbourhood between entities (genes, proteins, chemical compounds). Therefore there is a growing need for new methods aiming at merging the connectivity information from different biological sources in order to infer functional coupling. RESULTS: We present a generic approach to merge the information from two or more graphs representing biological data. The method is based on two concepts. The first one, the correspondence multigraph, precisely defines how correspondence is performed between the primary data-graphs. The second one, the common connected components, defines which property of the multigraph is searched for. Although this problem has already been informally stated in the past few years, we give here a formal and general statement together with an exact algorithm to solve it. AVAILABILITY: The algorithm presented in this paper has been implemented in C. Source code is freely available for download at: http://www.inrialpes.fr/helix/people/viari/cccpart.     

Regulation of IgE antibody production by serum molecules. V. Evidence that coincidental sensitization and imbalance in the normal damping mechanism results in "allergic breakthrough".

Experiments presented in this paper were designed to test a new concept concerning the possible pathogenesis of the allergic phenotype. This concept, termed "allergic breakthrough" considers that one of the avenues toward the allergic phenotype involves coincidental sensitization combined with an imbalance in the normal damping mechanism that serves to limit IgE antibody production. The three predictions of this concept that can be tested experimentally are: 1) manipulations that are effective in heightening or re-establishing the damping mechanism should manifest persistence insofar as IgE antibody synthesis to the relevant allergen is concerned; 2) once allergic breakthrough has occurred, the height of production of IgE antibodies specific for the sensitizing agent should remain elevated at levels characteristic of the allergic phenotype, even after the threshold of damping activity has returned to a normal level; and 3) allergic breakthrough should display specificity in that breakthrough would occur in response to subsequent exposure to the specific antigen to which coincidental sensitization initially occurred, but not for other unrelated antigens. The studies presented herein confirm each one of these predictions, thereby providing substantial support for the validity of this concept as one possible distinguishing feature between individuals manifesting the nonallergic and allergic phenotypes, respectively.     

Molecular mechanisms of self-recognition in Brassica self-incompatibility

Plants have mechanisms to promote outbreeding and thereby to increase their genetic diversity. In species that are self-incompatible, self-pollen is rejected by the stigma. This mechanism has been the subject of intense study for many years and, in the past two years, significant progress has been made in identifying the genes involved in Brassica. Self-recognition involves two genes, one of which determines the male and the other the female specificity. Considerable progress has also been made on the mechanism by which self-recognition leads to pollen rejection, although the delineation of all the genes involved is still not complete.     

Giving addicts their drug of choice: the problem of consent

Researchers working on drug addiction may, for a variety of reasons, want to carry out research which involves giving addicts their drug of choice. In carrying out this research consent needs to be obtained from those addicts recruited to participate in it. Concerns have been raised about whether or not such addicts are able to give this consent. Despite their differences, however, both sides in this debate appear to be agreed that the way to resolve this issue is to determine whether or not addicts have irresistible cravings for drugs – if they do, then they cannot consent to this type of research; if they do not, then they can. This I will argue is a mistake. Determining whether or not addicts can say 'No' to offers of drugs will not help us to make much progress here. Instead we need to look at the various ways in which different types of research may undermine an addict's competence to give consent. What we will find is that the details of the research make a big difference here and that, as such, we need to steer a course between, on the one hand, painting all addicts as being unable to consent to research which involves providing them with drugs, and, on the other, maintaining that there are no problems in obtaining consent from addicts to take part in such research.     

Ecology and genetics of tropical rhizobia species

Biological nitrogen fixation (BNF) technology with special reference to Rhizobium-legume symbiosis is growing very rapidly with the hope of combatting world hunger by producing cheaper protein for animal and human consumption in the Third World. One can see rapid progress made in the biochemistry and molecular biology of symbiotic nitrogen fixation in general; however, less progress has been made on the ecological aspects despite the fact that an enormous amount of literature is available on inoculation problems and on agronomic aspects of symbiotic nitrogen fixation. So far most information on Rhizobium concerns fast-growing rhizobia and their host legume. Although it is essential that food production using BNF technology should be maximized in the Third World, the least work has been done on slow-growing rhizobia, which are generally found in tropical and sub-tropical soils. The majority of the developing countries are in tropical and sub-tropical regions. Except for R. japonicum, a microsymbiont partner of soybean (Glycine max), the majority of the slow-growing rhizobia belong to the cowpea group, and we refer to cowpea rhizobia as tropical rhizobia species. In this review we have tried to consolidate the recent progress made on ecology and genetics of tropical rhizobia. By using recombinant DNA technology techniques it is expected that super strains of rhizobia with desirable characteristics can be produced. One must evaluate the efficiency and effectiveness of these genetically manipulated laboratory strains under field conditions. In conclusion, if one aims at combatting hunger in the Third World using BNF technology, an intensive research programme on fundamental and applied aspects of tropical rhizobia species is suggested. This involves close cooperation between molecular biologists and microbial ecologists.     

Dual conformation of H2H3 domain of prion protein in mammalian cells

The concept of prion is applied to protein modules that share the ability to switch between at least two conformational states and transmit one of these through intermolecular interaction and change of conformation. Although much progress has been achieved through the understanding of prions from organisms such as Saccharomyces cerevisiae, Podospora anserina, or Aplysia californica, the criteria that qualify a protein module as a prion are still unclear. In addition, the functionality of known prion domains fails to provide clues to understand the first identified prion, the mammalian infectious prion protein, PrP. To address these issues, we generated mammalian cellular models of expression of the C-terminal two helices of PrP, H2 and H3, which have been hypothesized, among other models, to hold the replication and conversion properties of the infectious PrP. We found that the H2H3 domain is an independent folding unit that undergoes glycosylations and glycosylphosphatidylinositol anchoring similar to full-length PrP. Surprisingly, in some conditions the normally folded H2H3 was able to systematically go through a conversion process and generate insoluble proteinase K-resistant aggregates. This structural switch involves the assembly of amyloid structures that bind thioflavin S and oligomers that are reactive to A11 antibody, which specifically detects protein oligomers from neurological disorders. Overall, we show that H2H3 is a conformational switch in a cellular context and is thus suggested to be a candidate for the conversion domain of PrP.     

Golgi membranes remain segregated from the endoplasmic reticulum during mitosis in mammalian cells

What happens to organelles during mitosis, and how they are apportioned to each of the daughter cells, is not completely clear. We have devised a procedure to address whether Golgi membranes fuse with the Endoplasmic Reticulum (ER) during mitosis via the detection of interactions between ER and Golgi proteins. This procedure involves coexpressing an FKBP-tagged Golgi enzyme with an ER-retained protein fused to FRAP in COS cells. Since treatment with rapamycin induces a tight association between FKBP and FRAP, one would expect rapamycin to trap the FKBP-fused Golgi protein in the ER if it ever visits the ER during mitosis. However, after the doubly transfected cells progress through mitosis in the presence of rapamycin, we find the Golgi protein in the newly formed Golgi stacks and not in the ER. Based on these results, we conclude that Golgi membranes remain separate from the ER during mitosis in mammalian cells.     

The Complexity and Reversibility of the Timer for the Onset of Aggregation in Dictyostelium

A simple conditional method is used to probe the complexity of the rate limiting pathway, or timer, for the onset of aggregation in the cellular slime mold Dictyostelium discoideum . The method depends upon a difference in the time required for the onset of aggregation under two sets of environmental conditions in which one parameter (ionic strength) is varied, and involves reciprocal shifts between the two sets of conditions at short time intervals. Evidence is presented that the timer for the onset of aggregation is composed of at least two components operating in sequence. In addition, a shift in one direction during the progress of the initial component of the timer causes the timer to be reset to zero. Our results also indicate that resetting the timer delays the acquisition of several aggregation associated changes, including chemotactic responsiveness, cAMP binding sites on the cell surface, and EDTA-resistant agglutination.     

植物DNA甲基化与作物种质资源保存

DNA甲基化是真核生物基因表达调控的重要机制之一。甲基化DNA与甲基特异结合蛋白结合,并作为染色质修饰复合物识别和作用的平台,参与对染色质组织方式的调节,最终影响基因的表达。本文对植物DNA甲基化及其生物学功能、检测分析方法以及作物种质资源保存中存在的甲基化现象进行了综述,旨在为深入了解DNA甲基化修饰对种质资源的影响,更好地开展作物种质资源保护供参考。     

分子进化研究中的一些问题

本文在强调生物系统的层次结构和非线性特征的基础上,就分子进化研究中存在的某些认识上的和方法学上的问题,提出了作者的观点和简要分析。