Auxology: when auxin meets plant evo-devo

Auxin is implicated throughout plant growth and development. Although the effects of this plant hormone have been recognized for more than a century, it is only in the past two decades that light has been shed on the molecular mechanisms that regulate auxin homeostasis, signaling, transport, crosstalk with other hormonal pathways as well as its roles in plant development. These discoveries established a molecular framework to study the role of auxin in land plant evolution. Here, we review recent advances in auxin biology and their implications in both micro- and macro-evolution of plant morphology. By analogy to the term 'hoxology', which refers to the critical role of HOX genes in metazoan evolution, we propose to introduce the term 'auxology' to take into account the crucial role of auxin in plant evo-devo.     

Arabidopsis epigenetics: when RNA meets chromatin

Recent work in plants and other eukaryotes has uncovered a major role for RNA interference in silent chromatin formation. The heritability of the silent state through multiple cell division cycles and, in some instances, through meiosis is assured by epigenetic marks. In plants, transposable elements and transgenes provide striking examples of the stable inheritance of repressed states, and are characterized by dense DNA methylation and heterochromatin histone modifications. Arabidopsis is a useful higher eukaryotes model with which to explore the crossroads between silent chromatin and RNA interference both during development and in the genome-wide control of repeat elements.     

Extracellular crosstalk: when GDNF meets N-CAM

N-CAM has now been identified as a receptor for glial cell line-derived neurotrophic factor (GDNF). This finding solves a long-standing question regarding RET-independent GDNF signaling, and reveals a novel pathway distinct from both GDNF-RET and N-CAM-N-CAM signaling. Functional assays of Schwann cell migration and axon growth of CNS neurons suggest physiological significance for this GDNF-N-CAM pathway.     

Essential role of caspase-11 in activation-induced cell death of rat astrocytes

We have previously shown that rat astrocytes undergo apoptosis upon inflammatory activation. Nitric oxide (NO) produced by activated astrocytes was the major cytotoxic mediator in this type of autoregulatory apoptosis. However, an inhibitor of nitric oxide synthase did not completely block the apoptosis of activated astrocytes, suggesting the presence of other apoptotic pathways. Here, we present evidence that caspase-11 is an essential molecule in NO-independent apoptotic pathway of activated astrocytes. Inflammatory activation (lipopolysaccharide, interferon-gamma, and tumor necrosis factor-alpha treatment) of rat astrocyte cultures and C6 glioma cells led to the induction of caspase-11 followed by activation of caspases-11, -1, and -3. In contrast, NO donors induced activation of caspase-3 only. Inactivation of caspase-11 by the transfection of dominant negative mutant or treatment with the caspase inhibitors rendered the astrocytes partially resistant to the apoptosis following inflammatory activation, but not NO donor exposure. These results indicate that inflammatory stimuli not only induce the production of cytotoxic NO, but also initiate NO-independent apoptotic pathway through the induction of caspase-11 expression.     

Programmed cell death: Superman meets Dr Death

This year's Cold Spring Harbor meeting on programmed cell death (September 17-21, 2003), organised by Craig Thompson and Junying Yuan, was proof that the 'golden age' of research in this field is far from over. There was a flurry of fascinating insights into the regulation of diverse apoptotic pathways and unexpected non-apoptotic roles for some of the key apoptotic regulators and effectors. In addition to their role in cell death, components of the apoptotic molecular machinery are now known to also function in a variety of essential cellular processes, such as regulating glucose homeostasis, lipid metabolism, cell proliferation and differentiation.     

XIAP: cell death regulation meets copper homeostasis

X-linked inhibitor of apoptosis (XIAP), traditionally known as an anti-apoptotic protein, has recently been shown to be involved in copper homeostasis. XIAP promotes the ubiquitination and degradation of COMMD1, a protein that promotes the efflux of copper from the cell. Through its effects on COMMD1, XIAP can regulate copper export from the cell and potentially represents an additional intracellular sensor for copper levels. XIAP binds copper directly and undergoes a substantial conformational change in the copper-bound state. This in turn destabilizes XIAP, resulting in lowered steady-state levels of the protein. Furthermore, copper-bound XIAP is unable to inhibit caspases and cells that express this form of the protein exhibit increased rates of cell death in response to apoptotic stimuli. These events take place in the setting of excess intracellular copper accumulation as seen in copper toxicosis disorders such as Wilson's disease and establish a new relationship between copper levels and the regulation of cell death via XIAP. These findings raise important questions about the role of XIAP in the development of copper toxicosis disorders and may point to XIAP as a potential therapeutic target in these disease states.     

生物信息学对计算机科学发展的机遇与挑战

生物信息学是一个发展很快的新兴学科,是计算机应用的最重要的领域之一,同时生物信息学的发展又给计算机学科提出了许多新的课题,从而促进计算机学科自身的发展。从数据库技术、海量存储技术、数据挖掘、计算几何、DNA计算、网格计算、机器学习、人工心智、web service等方面,就生物信息学对计算机科学发展的促进作用进行了论述。     

Moving away from nasty encounters enhances cooperation in ecological prisoner's dilemma game

We study the role of migration in the evolution of cooperation. Individuals spatially located on a square lattice play the prisoner's dilemma game. Dissatisfied players, who have been exploited by defectors, tend to terminate interaction with selfish partners by leaving the current habitats, and explore unknown physical niches available surrounding them. The time scale ratio of game interaction to natural selection governs how many game rounds occur before individuals experience strategy updating. Under local migration and strong selection, simulation results demonstrate that cooperation can be stabilized for a wide range of model parameters, and the slower the natural selection, the more favorable for the emergence of cooperation. Besides, how the selection intensity affects cooperators' evolutionary fate is also investigated. We find that increasing it weakens cooperators' viability at different speeds for different time scale ratios. However, cooperation is greatly improved provided that individuals are offered with enough chance to agglomerate, while cooperation can always establish under weak selection but vanishes under very strong selection whenever individuals have less odds to migrate. Whenever the migration range restriction is removed, the parameter area responsible for the emergence of cooperation is, albeit somewhat compressed, still remarkable, validating the effectiveness of collectively migrating in promoting cooperation.     

Eat, kill or die: when amoeba meets bacteria

The core function of the innate immune response, phagocytosis, did not evolve first in metazoans but rather in primitive unicellular eukaryotes. Thus, though amoebae separated from the tree leading to metazoan shortly after the divergence of plants, they share many specific functions with mammalian phagocytic cells. Dictyostelium discoideum is by far the most studied amoeba, and it is proving useful to analyze phagocytosis and intracellular killing of bacteria. Since the basic mechanisms involved appear extremely conserved, Dictyostelium provides novel insights into the function of many new gene products. Bacterial pathogenicity was certainly largely developed to resist predatory amoebae in the environment, and this accounts for the fact that a large number of bacterial virulence traits can be studied using Dictyostelium as a host. This provides a particularly powerful system to analyze the complex interactions between pathogenic bacteria and host cells, where both the Dictyostelium host and the bacteria can be manipulated genetically with relative ease.     

Sclerotome development and morphogenesis: when experimental embryology meets genetics

The vertebra develops from the ventral part of the somite, the sclerotome. Sclerotome progenitors are subject to multiple signaling molecules secreted by the adjacent tissues that control their fate. The aim of this article is to discuss the mechanisms of sclerotome induction, chondrogenesis and morphogenesis. By integrating the results from classical studies and recent molecular advances, this will illustrate how the powerful combination of experimental embryology and genetic approaches has recently illuminated the multiple steps of vertebra formation.     

Treating childhood asthma in Singapore: when West meets East.

Though Western medicines and ideas about asthma have become popular in many Asian nations, local beliefs about treatment prevail. The multiracial society of Singapore shows a variety of beliefs about causes of asthma attacks (for example, the balance of yin and yang) and types of treatment--herbal remedies, inhaled versus eaten medicines, the influence of Ramadan. Many of the cultural practices mentioned are probably preserved among south east Asian minorities residing in the United Kingdom. Eastern treatments typically take a holistic approach to asthma and do not ignore the psychosomatic component of the disorder.     

Salmonella-induced macrophage death: the role of caspase-1 in death and inflammation.

Salmonella typhimurium invades host macrophages and can induce either an almost immediate cell death or establish an intracellular niche within the phagocytic vacuole. Rapid cell death depends on the Salmonella pathogenicity island SPI1 and the host protein caspase-1, a member of the pro-apoptotic caspase family of proteases. Caspase-1-dependent cell death leads to the activation of the potent pro-inflammatory cytokines interleukin (IL)-1beta and IL-18 to produce bioactive cytokines. Animal studies indicate that the activation of these cytokines is necessary for efficient colonization of the mouse gastrointestinal tract. Salmonella that reside in the phagocytic vacuole do not cause this early cell death and can trigger a macrophage death at a much later time point. This late-phase cell death is dependent on SPI2-encoded genes and ompR.     

The S phase checkpoint: when the crowd meets at the fork

Accumulation of unrepaired DNA lesions is the biggest threat to genomic stability. DNA damage checkpoints create windows of time that allow the cell to repair assaults on DNA in each phase of the cell cycle. When DNA lesions arise in S phase, however, the checkpoint machinery must work to coordinate DNA replication and repair processes. In fact some upstream components of the DNA damage checkpoint play parallel roles in maintaining the continuity of DNA replication and signaling to downstream components.