An Introduction to the Biosynthesis of Chemicals Used in Plant-Microbe Communication

Abstract Plants accumulate a diverse array of natural products, which can serve either to defend the plant against various microbes in its environment or to attract various microbes, both beneficial and pathogenic. Plants must also attract pollinators, repel or poison herbivores, compete with other plant species, and protect themselves from environmental dangers such as high light intensities. Some compounds have been implicated in playing a role in multiple interactions. Although the structures vary immensely in size and complexity, most are derived from a limited number of core biosynthetic pathways. This review briefly summarizes the biosynthetic origins of phenylpropanoid (including simple phenolics, flavonoids, anthocyanins and isoflavonoids), polyacetate, terpenoid, and alkaloid classes of metabolites. Compounds reported to be important in plant-microbe, plant-animal, and plant-plant interactions will be given as examples of each of these classes. Other aspects of biosynthesis also will be discussed, including the timing or location of biosynthesis, the potential for genetic manipulation of these pathways, and various questions regarding the biosynthesis of these compounds.     

Circulating DNA in the blood and its application in medical diagnosis

Circulating nucleic acids were discovered more than 30 years ago, but did not attract much attention until the past decade. This review summarizes the data on the sources of extracellular DNA circulating in the blood, features of its circulation, and pathways of its removal. The possibility of using circulating DNA in medical diagnosis is discussed.     

Nuclear lipid metabolism in NEST: Nuclear envelope signal transduction

Summary There is increasing evidence that nuclear lipid metabolism in NEST is an important new component in signal transducing networks and as a result, this metabolism is beginning to attract more attention. While agonistinduced nuclear lipid metabolism adds further complexity to the ever increasing array of signal transduction components, it also provides further avenues by which nuclear activities may be regulated. Identification of the coupling mechanisms, regulation, and physiological roles of nuclear lipid metabolism represents a new and exciting area of research which will have a broad impact in our understanding of signal transduction pathways.     

Exploration of small RNAs

For several decades, only a limited number of noncoding RNAs, such as ribosomal and transfer RNA, have been studied in any depth. In recent years, additional species of noncoding RNAs have increasingly been discovered. Of these, small RNA species attract particular interest because of their essential roles in processes such as RNA silencing and modifications. Detailed analyses revealed several pathways associated with the function of small RNAs. Although these pathways show evolutional conservation, there are substantial differences. Advanced technologies to profile RNAs have accelerated the field further resulting in the discovery of an increasing number of novel species, suggesting that we are only just beginning to appreciate the complexity of small RNAs and their functions. Here, we review recent progress in novel small RNA exploration, including discovered small RNA species, their pathways, and devised technologies.     

Differentiation during fig ontogeny suggests opposing selection by mutualists

Dioecy allows separation of female and male functions and therefore facilitates separate co‐evolutionary pathways with pollinators and seed dispersers. In monoecious figs, pollinators' offspring develop inside the syconium by consuming some of the seeds. Flower‐stage syconia must attract pollinators, then ripen and attract seed dispersers. In dioecious figs, male (“gall”) figs produce pollen but not viable seeds, as the pollinators' larvae eat all seeds, while female (“seed”) figs produce mostly viable seeds, as pollinators cannot oviposit in the ovules. Hence, gall and seed figs are under selection to attract pollinators, but only seed figs must attract seed dispersers. We test the hypothesis that seed and gall syconia at the flower stage will be similar, while at the fruiting stage they will differ. Likewise, monoecious syconia will be more similar to seed than gall figs because they must attract both pollinators and seed dispersers. We quantified syconium characteristics for 24 dioecious and 11 monoecious fig species and recorded frugivore visits. We show that seed and gall syconia are similar at the flower stage but differ at the fruit stage; monoecious syconia are more similar to seed syconia than they are to gall syconia; seed and gall syconia differentiate through their ontogeny from flower to fruit stages; and frugivores visit more monoecious and seed syconia than gall syconia. We suggest that similarity at the flower stage likely enhances pollination in both seed and gall figs and that differentiation after pollination likely enhances attractiveness to seed dispersers of syconia containing viable seeds. These ontogenetic differences between monoecious and dioecious species provide evidence of divergent responses to selection by pollinators and seed dispersers.     

The convergent evolution of snake‐like forms by divergent evolutionary pathways in squamate reptiles*

Convergent evolution of phenotypes is considered evidence that evolution is deterministic. Establishing if such convergent phenotypes arose through convergent evolutionary pathways is a stronger test of determinism. We studied the evolution of snake‐like body shapes in six clades of lizards, each containing species ranging from short‐bodied and pentadactyl to long‐bodied and limbless. We tested whether body shapes that evolved in each clade were convergent, and whether clades evolved snake‐like body shapes following convergent evolutionary pathways. Our analyses showed that indeed species with the same numbers of digits in each clade evolved convergent body shapes. We then compared evolutionary pathways among clades by considering patterns of evolutionary integration and shape of relationship among body parts, patterns of vertebral evolution, and models of digit evolution. We found that all clades elongated their bodies through the addition, not elongation, of vertebrae, and had similar patterns of integration. However, patterns of integration, the body parts that were related by a linear or a threshold model, and patterns of digit evolution differed among clades. These results showed that clades followed different evolutionary pathways. This suggests an important role of historical contingency as opposed to determinism in the convergent evolution of snake‐like body shapes.     

Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid–derived hydrocarbons

Fatty acid–derived hydrocarbons attract increasing attention as biofuels due to their immiscibility with water, high‐energy content, low freezing point, and high compatibility with existing refineries and end‐user infrastructures. Yeast Saccharomyces cerevisiae has advantages for production of fatty acid–derived hydrocarbons as its native routes toward fatty acid synthesis involve only a few reactions that allow more efficient conversion of carbon substrates. Here we describe major biosynthetic pathways of fatty acid–derived hydrocarbons in yeast, and summarize key metabolic engineering strategies, including enhancing precursor supply, eliminating competing pathways, and expressing heterologous pathways. With recent advances in yeast production of fatty acid–derived hydrocarbons, our review identifies key research challenges and opportunities for future optimization, and concludes with perspectives and outlooks for further research directions.     

巢居蚂蚁更倾向于在人造光源附近定居繁殖

光污染被认为是“环境陷阱”, 可以聚集周围的昆虫。而昆虫的聚集和光源本身可能会吸引捕食性昆虫在光源附近定居繁殖, 从而改变昆虫群落的结构, 威胁昆虫多样性和生态系统服务功能。蚂蚁(膜翅目)是昆虫中的优势类群, 能提供多种生态系统服务功能, 其中有许多巢居型蚂蚁利用中空的树枝或者竹子筑巢繁殖, 是森林中非常重要的捕食者和分解者。然而, 光污染对巢居蚂蚁群落的影响尚不清楚。本研究以巢居蚂蚁为研究对象, 探究在雨季和干季3种不同生境(原始林、次生林、橡胶林)中发光二极管(LED灯)在空间距离上对巢居蚂蚁筑巢模式以及群落组成的影响。我们在3种生境中共安装了15个LED灯, 并在距离光源0 m、10 m、50 m和100 m处设置不同入口大小的人工竹巢, 7周后回收。竹巢中共发现蚂蚁40种形态种, 隶属于12个属, 其中弓背蚁属(Camponotus)是优势属。接近光源处的竹巢占用率最高, 且在干季最明显; 在远离光源处(10-100 m)占用率较低, 并且在3种不同的生境呈现相同的模式。竹巢入口大小对竹巢占用率没有显著影响。雨季和干季的蚂蚁群落组成差异显著; 干季原始林和次生林、次生林和橡胶林蚂蚁群落组成有弱显著差异; 在3种生境中不同灯距下蚂蚁群落组成没有显著差异。我们的研究表明, 光污染增加了巢居蚂蚁在光源处的筑巢密度, 影响蚂蚁群落组成和空间分布。     

核小体定位的转录调控功能研究进展

核小体是真核生物染色质的基本组成单位,组蛋白八聚体在DNA 双螺旋上精确位置称为核小体定位．核小体定位已被证实在基因转录调控、DNA复制与修复、调控进化等过程中扮演着重要的角色．随着染色质免疫共沉淀-芯片(ChIP-chip)与染色质免疫共沉淀-测序(ChIP-seq)等高通量技术的出现,已测定了多种模式生物全基因组核小体定位图谱,掀起了一股核小体定位及其功能的研究热潮,并取得了一定的成果．本文介绍了核小体定位的概念,总结了核小体在启动子与编码区域内定位的基本模式．在此基础上,综述了核小体定位在转录起始、转录延伸、基因表达模式多样化以及可变剪接等方面的功能研究进展．     

Real-time analysis of the role of Ca(2+) in flagellar movement and motility in single sea urchin sperm

Eggs of many marine and mammalian species attract sperm by releasing chemoattractants that modify the bending properties of flagella to redirect sperm paths toward the egg. This process, called chemotaxis, is dependent on extracellular Ca(2+). We used stroboscopic fluorescence imaging to measure intracellular Ca(2+) concentration ([Ca(2+)]i) in the flagella of swimming sea urchin sperm. Uncaging of cyclic GMP induced Ca(2+) entry via at least two distinct pathways, and we identified a nimodipine-sensitive pathway, compartmentalized in the flagella, as a key regulator of flagellar bending and directed motility changes. We found that, contrary to current models, the degree of flagellar bending does not vary in proportion to the overall [Ca(2+)]i. Instead we propose a new model whereby flagella bending is increased by Ca(2+) flux through the nimodipine-sensitive pathway, and is unaffected by [Ca(2+)]i increases through alternative pathways.     

Effect of solvent conditions upon refolding pathways and intermediates for a simple lattice protein

Folding pathways and intermediates for a two-dimensional lattice protein have been investigated via computer simulation at various denaturant concentrations. The protein is represented as a chain of 8 hydrophobic (H) and 12 polar (P) beads on a square lattice sequenced in such a way that the native state is a compact hydrophobic core surrounded by a shell of polar beads. Two nonbonded H beads are said to attract each other with a potential of mean force of strength ϵ. Increasing |ϵ/kT| mimics decreasing the denaturant concentration in the solution. Dynamic Monte Carlo simulations have been performed in order to investigate the folding transition and the folding pathways. Sharp folding—unfolding transitions are observed and the folding process proceeds along well-defined pathways that are populated by partially folded intermediates. The folding pathways as well as the populations of the intermediates are strongly dependent upon the denaturant concentration. Generally, intermediates containing long open stretches of H beads are more populated at high denaturant concentration, whereas compact intermediates containing a substantial number of hydrophobic contacts are more populated at low denaturant concentrations. The folding process is also observed to be cooperative in nature in that the chain does not start folding until a key fold in the middle section of the chain is formed correctly. © 1997 John Wiley & Sons, Inc. Biopoly 42: 399–409, 1997     

Cuttlefish camouflage: context-dependent body pattern use during motion

It is virtually impossible to camouflage a moving target against a non-uniform background, but strategies have been proposed to reduce detection and targeting of movement. Best known is the idea that high contrast markings produce ‘motion dazzle’, which impairs judgement of speed and trajectory. The ability of the cuttlefish Sepia officinalis to change its visual appearance allows us to compare the animal''s choice of patterns during movement to the predictions of models of motion camouflage. We compare cuttlefish body patterns used during movement with those expressed when static on two background types; one of which promotes low-contrast mottle patterns and the other promotes high-contrast disruptive patterns. We find that the body pattern used during motion is context-specific and that high-contrast body pattern components are significantly reduced during movement. Thus, in our experimental conditions, cuttlefish do not use high contrast motion dazzle. It may be that, in addition to being inherently conspicuous during movement, moving high-contrast patterns will attract attention because moving particles in coastal waters tend to be of small size and of low relative contrast.     

Apport de l’imagerie radioisotopique dans l’artérite inflammatoire des gros vaisseaux

The group of large vessel vasculitis includes giant cell arthritis and Takayasu's disease. If monophotonic nuclear medicine can sometimes show some unusual patterns in these diseases, positron emission tomography with fluorodeoxyglucose seems have a special attract and provide some indications during the monitoring of these patients. However, most of these indications remain to be validated, specially to differentiate weak vascular wall inflammatory activities from physiological and/or atherosclerotic accumulation.     

The social display of the Chilean teal Anas flavirostris flavirostris

Filmed episodes of social display in the Chilean teal were analysed in order to throw light on the function of social display in surface-feeding ducks and the role the female plays in this activity. Four different methods were used to study the associations between different behaviour patterns in several individuals. It appears that the behaviour patterns comprising social display fall into three groups which are described as "attention getting", "close-range" and aggressive. It is proposed that social display allows unpaired males to attract the attention of females in an attempt to establish a pair-bond through the use of the "close-range" behaviour patterns. This forces paired males to compete in "attention-getting" behaviour patterns. Aggression results from this competition and from the threatening presence of unpaired males when the paired males try to strengthen their pair-bonds with the use of the "close-range" behaviour patterns.
Females play an influential role as their behaviour links the "attention-getting" behaviour with the "close-range" and aggressive behaviour. Their "close-range" behaviour suppresses that of other females.     

Dynamics of Notch Activity in a Model of Interacting Signaling Pathways

Networks of interacting signaling pathways are formulated with systems of reaction-diffusion (RD) equations. We show that weak interactions between signaling pathways have negligible effects on formation of spatial patterns of signaling molecules. In particular, a weak interaction between Retinoic Acid (RA) and Notch signaling pathways does not change dynamics of Notch activity in the spatial domain. Conversely, large interactions of signaling pathways can influence effects of each signaling pathway. When the RD system is largely perturbed by RA-Notch interactions, new spatial patterns of Notch activity are obtained. Moreover, analysis of the perturbed Homogeneous System (HS) indicates that the system admits bifurcating periodic orbits near a Hopf bifurcation point. Starting from a neighborhood of the Hopf bifurcation, oscillatory standing waves of Notch activity are numerically observed. This is of particular interest since recent laboratory experiments confirm oscillatory dynamics of Notch activity.     

茶树花挥发物对叶蝉三棒缨小蜂的引诱增强效应

茶树(Camellia sinensis)是我国重要的经济作物。小贯小绿叶蝉(Empoasca onukii)是为害茶树的主要害虫之一。叶蝉三棒缨小蜂(Stethynium empoascae)是小贯小绿叶蝉的主要卵寄生蜂,但茶树花对叶蝉三棒缨小蜂的引诱机制尚不明确。基于析因设计的方差分析结果显示,茶树花可引诱天敌叶蝉...     

Cloning and expression analysis of some genes involved in the phosphoinositide and phospholipid signaling pathways from maize (Zea mays L.)

Previous studies have indicated the phosphoinositide and phospholipid signaling pathways play a key role in plant growth, development and responses to environmental stresses. However, little is known about the phosphoinositide and phospholipid signaling pathways in maize (Zea mays L.). To better understand the function of genes involved in the phosphoinositide and phospholipid signaling pathways in maize, the cDNA sequences of ZmPIS2, ZmPLC2, ZmDGK1, ZmDGK2 and ZmDGK3 were obtained by RACE (rapid amplification of cDNA ends) or in silico cloning combined with PCR. RT-PCR analysis of cDNA from five tissues (roots, stems, leaves, tassels, and ears) indicated that the expression patterns of the five cDNAs we isolated as well as ZmPIS, ZmPLC, ZmPLD varied in different tissues. To determine the effects of different environmental conditions such as cold, drought and various phytohormones (abscisic acid, indole-3-acetic acid and gibberellic acid) on gene expression, we analyzed expression by Real-Time (RT-PCR), and found that the different isoforms of these gene families involved in the phosphoinositide and phospholipid signaling pathways have specific expression patterns. Our results suggested that these genes may be involved in the responses to environmental stresses, but have different functions. The isolation and analysis of expression patterns of genes involved in the phosphoinositide and phospholipid signaling pathways provides a good basis for further research of the phosphoinositide and phospholipid signaling pathways in maize and is a novel supplement to our comprehension of these pathways in plants.     

The neural mechanisms of mate choice: a hypothesis

Scientists have described many physical and behavioral traits in avian and mammalian species that evolved to attract mates. But the brain mechanisms by which conspecifics become attracted to these traits is unknown. This paper maintains that two aspects of mate choice evolved in tandem: 1) traits that evolved in the "display producer" to attract mates and, 2) corresponding neural mechanisms in the "display chooser" that enable them to become attracted to these display traits. Then it discusses our (in-progress) fMRI brain scanning project on human romantic attraction, what we believe is a developed form of "courtship attraction" common to avian and mammalian species as well as the primary neural mechanism underlying avian and mammalian mate choice. The paper hypothesizes that courtship attraction is associated with elevated levels of central dopamine and norepinephrine and decreased levels of central serotonin in reward pathways of the brain. It also proposes that courtship attraction is part of a triune brain system for mating, reproduction and parenting. 1)The sex drive evolved to motivate birds and mammals to court any conspecifics. 2) The attraction system evolved to enable individuals to discriminate among potential mating partners and focus courtship activities on particular individuals, thereby conserving mating time and energy. 3) The neural circuitry for attachment evolved to enable individuals to complete species-specific parental duties.     

Biochemical signaling networks decode temporal patterns of synaptic input

Synapses exhibit a wide repertoire of responses to different temporal patterns of synaptic input. Many of these responses are expressed as short and long-term changes in synaptic strength. Electrical properties of channels and calcium buildup can account for rapid aspects of pattern decoding, but it is not clear how more complex input patterns, especially those lasting over many minutes, could be discriminated. This paper shows that a network of signaling pathways can discriminate between complex input patterns lasting tens of minutes, and can give rise to distinct combinatorial patterns of biochemical signaling activity in pathways involved in synaptic change. Regulatory signaling input can alter and even reverse the strengths of responses to input patterns. Thus the synaptic signaling network may function as a temporal decoder that transforms patterns from the time domain into the domain of chemical signaling. This may underlie different synaptic responses to different stimulus patterns.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1023/A:1019644427655