miREnvironment database: providing a bridge for microRNAs, environmental factors and phenotypes

The interaction between genetic factors and environmental factors has critical roles in determining the phenotype of an organism. In recent years, a number of studies have reported that the dysfunctions on microRNA (miRNAs), environmental factors and their interactions have strong effects on phenotypes and even may result in abnormal phenotypes and diseases, whereas there has been no a database linking miRNAs, environmental factors and phenotypes. Such a resource platform is believed to be of great value in the understanding of miRNAs, environmental factors, especially drugs and diseases. In this study, we constructed the miREnvironment database, which contains a comprehensive collection and curation of experimentally supported interactions among miRNAs, environmental factors and phenotypes. The names of miRNAs, phenotypes, environmental factors, conditions of environmental factors, samples, species, evidence and references were further annotated. miREnvironment represents a biomedical resource for researches on miRNAs, environmental factors and diseases. AVAILABILITY: http://cmbi.bjmu.edu.cn/miren. CONTACT: cuiqinghua@hsc.pku.edu.cn.     

IgE-binding factors from mouse T lymphocytes. I. Formation of IgE-binding factors by stimulation with homologous IgE and interferon

Incubation of normal mouse spleen cells with homologous IgE resulted in the formation of soluble factors that inhibited rosette formation of mouse Fc epsilon R+ cells with IgE-coated ox erythrocytes. The soluble factors could be absorbed with mouse or rat IgE coupled to Sepharose and recovered from the beads by acid elution. However, the factors had no affinity for either human IgE or mouse IgG. The IgE-binding factors were derived from T cells. Production of the factors required Lyt1+ T cells and Fc gamma R+ cells, which suggests that the factors are derived from Fc gamma R+ Lyt 1+ T cells. The molecular size of IgE-binding factors was approximately 15,000 daltons. When IgE-binding factors were formed by BALB/c spleen cells, nearly one-half of the factors had affinity for lentil lectin, and the remaining half of the factors failed to bind to the lectin. The proportion of the two species of IgE-binding factors differed depending on mouse strains. The majority of the factors formed by B6D2F1 spleen cells had affinity for lentil lectin, but those formed by SJL spleen cells failed to bind to the lectin. The IgE-binding factors were also induced by incubation of normal spleen cells with polyinosinic-polycytidylic acid (pI:pC). The nucleotide stimulated splenic adherent cells to form "inducers" of IgE-binding factors, which in turn induced normal lymphocytes to form IgE-binding factors. The inducers of IgE-binding factors were inactivated (or neutralized) by antibodies specific for mouse Type I interferon. It was also found that purified mouse beta interferon could induce the formation of IgE-binding factors. IgE-binding factors induced by pI:pC consisted of two different molecules: one had a m.w. of 15,000 daltons, and another had a m.w. of between 40,000 and 60,000 daltons.     

Multiple growth factors are associated with lesions of atherosclerosis: Specificity or redundancy?

Within the last five years, a number of specific growth factors have been localized in developing lesions of atherosclerosis. This localization of growth factors that is not observed in normal vessels, together with the pleotrophic activities of growth factors, have suggested a role for growth factors in atherosclerotic lesion progression. However, based on in vitro studies, many of the growth factors identified in lesions have overlapping target cells and are derived from the same cellular sources. What is the relative role of the specific growth factors identified? How is the their activity altered by the local conditions in the vessel wall? How do different risk factors for atherosclerosis alter the balance between growth factors and their natural regulators? Evidence for the involvement of specific growth factors in the progression of lesions of atherosclerosis is discussed, as well as the multiple levels at which the activities of these growth factors may be regulated by the vessel wall.     

Neurotrophic factors and their receptors in axonal regeneration and functional recovery after peripheral nerve injury

Over a half a century of research has confirmed that neurotrophic factors promote the survival and process outgrowth of isolated neurons in vitro. The mechanisms by which neurotrophic factors mediate these survival-promoting effects have also been well characterized. In vivo, peripheral neurons are critically dependent on limited amounts of neurotrophic factors during development. After peripheral nerve injury, the adult mammalian peripheral nervous system responds by making neurotrophic factors once again available, either by autocrine or paracrine sources. Three families of neurotrophic factors were compared, the neurotrophins, the GDNF family of neurotrophic factors, and the neuropoetic cytokines. Following a general overview of the mechanisms by which these neurotrophic factors mediate their effects, we reviewed the temporal pattern of expression of the neurotrophic factors and their receptors by axotomized motoneurons as well as in the distal nerve stump after peripheral nerve injury. We discussed recent experiments from our lab and others which have examined the role of neurotrophic factors in peripheral nerve injury. Although our understanding of the mechanisms by which neurotrophic factors mediate their effects in vivo are poorly understood, evidence is beginning to emerge that similar phenomena observed in vitro also apply to nerve regeneration in vivo.     

丹江口水库水滨带植物群落空间分布及环境解释

探讨了环境因素对丹江口水库(南水北调中线水源地)水滨带植物群落空间分布的影响。通过对水滨带植物群落和环境因素的实地调查,用双向指示种分析(TWINSPAN)对201个水滨带植物群落进行分类;结合地形、土壤和水文因素用除趋势典范对应分析法(DCCA)分析环境因素对水滨带植物群落的影响;并对环境因素的解释能力进行定量分离。结果表明:(1)水滨带植物群落包括7种类型,分别是萹蓄群落、苘麻群落、细叶水芹+狗牙根群落、狗牙根群落、响叶杨-狗牙根群落、杜梨-白刺花-狗牙根群落和侧柏-牡荆-三穗苔草群落;(2)海拔和水淹影响对水滨带植物群落空间分布具有主导作用。海拔升高,水淹影响减弱,植物群落呈现由草本植物群落向木本植物群落变化的格局;(3)土壤因素的解释能力大于地形因素,水文因素的解释能力最小。各类环境因素之间存在交互作用,地形、水文和土壤因素三者间的交互作用最大,地形和土壤因素之间的交互作用最小。环境因素共解释水滨带植物群落空间分布的21.99%,未解释部分为78.01%。结果证明环境对植被的解释能力是由植被的复杂程度决定的,植被越复杂,环境的解释能力越低。     

Fitness Factors in Vibrios: a Mini-review

Vibrios are Gram-negative curved bacilli that occur naturally in marine, estuarine, and freshwater systems. Some species include human and animal pathogens, and some vibrios are necessary for natural systems, including the carbon cycle and osmoregulation. Countless in vivo and in vitro studies have examined the interactions between vibrios and their environment, including molecules, cells, whole animals, and abiotic substrates. Many studies have characterized virulence factors, attachment factors, regulatory factors, and antimicrobial resistance factors, and most of these factors impact the organism's fitness regardless of its external environment. This review aims to identify common attributes among factors that increase fitness in various environments, regardless of whether the environment is an oyster, a rabbit, a flask of immortalized mammalian cells, or a planktonic chitin particle. This review aims to summarize findings published thus far to encapsulate some of the basic similarities among the many vibrio fitness factors and how they frame our understanding of vibrio ecology. Factors representing these similarities include hemolysins, capsular polysaccharides, flagella, proteases, attachment factors, type III secretion systems, chitin binding proteins, iron acquisition systems, and colonization factors.     

Site-dependent Life-Cycle Impact Assessment in Sweden (5 pp)

Goal, Scope and Background Although LCA is traditionally a site-independent tool, there is currently a trend towards making LCA more site-dependent if not site-specific. For Europe, site-dependent impact factors have been calculated on a country basis for acidification, terrestrial eutrophication and toxicological impacts. It is, however, an open question whether this is the optimum level for site-dependent factors. The aim of this paper is to develop site-dependent characterisation factors for different parts of Sweden for air emissions of NOx, SOx and particulates regarding ecosystem and human health impacts. Based on experiences from a case-study, the usability of the site-dependent factors for LCA are discussed, as well as the appropriate level of site-dependency for ecosystem and human health impacts. Method logy. The Ecosense model is used for calculating site-dependent factors for some atmospheric pollutants. Characterisation factors are calculated for four different places in Sweden with two different stack heights. Results and Conclusions The characterisation factors for ecosystem impacts show fairly small differences between different parts of Sweden (within a factor of two). For health impacts, the differences between different parts of the country were larger and more significant (up to one order of magnitude). Also the difference between low and high stack heights may be relevant, especially in densely populated areas. These results suggest that for ecosystems, site-dependent characterisation factors for the considered atmospheric pollutants on a country level may be sufficient for most applications. However, for health impacts, site-dependent factors on a country level may be inappropriate. Beside LCA, the calculated factors and the methodology used should also be useful for other environmental system analysis tools, such as Strategic Environmental Assessment, Cost-Benefit Analysis and Environmental Management Systems.     

Properties of cardioinhibitory factors produced in shock.

The widespread occurrence of circulating cardioinhibitory factors in many types of circulatory shock and in a variety of mammalian species is impressive. This review summarizes the properties of the nine best-known factors with regard to their occurrence, chemical properties, sites of origin, biological actions, and pharmacological modification. Cardioinhibitory factors appear to play a significant role in the pathogenesis of circulatory shock. There now are pharmacological means available with which to prevent the formation of such factors. With knowledge on the chemistry of cardioinhibitory factors rapidly accumulating, it is anticipated that specific antagonists to the action of these factors will become available in the near future.     

The role of angiogenic growth factors in organogenesis

Angiogenic growth factors are a class of molecules which exert a fundamental role in the process of blood vessel formation. Besides vasculogenic and angiogenic properties, these compounds mediate a complex series of patterning activities during organogenesis. Angiogenic factors cooperate in the growth and development of embryo tissues in a cross-talk between endothelial cells and tissue cells. It is well established that many tissue-derived factors are involved in blood vessel formation, but there is now emerging evidence that angiogenic factors and endothelial cells themselves represent a crucial source of instructive signals to non-vascular tissue cells during organ development. Thus, angiogenic factors and endothelial cell signalling are currently believed to provide fundamental cues for cell fate specification, embryo patterning, organ differentiation and postnatal tissue remodelling. This review article will summarize some of the recent advances in our understanding of the role of angiogenic factors and endothelial cells as effectors in organ formation.     

Extracellular regulation of fibroblast multiplication: A direct kinetic approach to analysis of role of low molecular weight nutrients and serum growth factors

The principles of enzyme kinetic analysis were applied to quantitate the relationships among serum-derived growth factors, nutrients, and the rate of survival and multiplication of human fibroblasts in culture. The survival or multiplication rate of a population of cells plotted against an increasing concentration of a growth factor or nutrient in the medium exhibited a hyperbolic pattern that is characteristic of a dissociable, saturable interaction between cells and the ligands. Parameters equivalent to the K_m and V_max of enzyme kinetics were assigned to nutrients and growth factors. When all nutrient concentrations were optimized and in steady state, serum factors accelerated the rate of multiplication of a normal cell population. The same set of nutrients that supported a maximal rate of multiplication in the presence of serum factors supported the maintenance of non-proliferating cells in the absence of serum factors. Therefore, under this condition, serum factors are required for cell division and play a purely regulatory iole in multiplication of the cell population. The quantitative requirement for 18 nutrients of 29 that were examined was significantly higher (P < 0.001) for cell multiplication in the presence of serum factors than for cell maintenance in the absence of serum factors. This indicated specific nutrients that may be quantitatively important in cell division processes as well as in cell maintenance. The quantitative requirement for Ca²⁺, Mg²⁺, K⁺, Pi, and 2-oxocarboxylic acid for cell multiplication was modified by serum factors and other purified growth factors. The requirement for over 30 other nutrients could not clearly be related to the level of serum factors in the medium. Serum factors also determined the Ca²⁺, K⁺, and 2-oxocarboxylic acid requirement for maintenance of non-proliferating cells. Therefore, when either Ca²⁺, K⁺, or 2-oxocarboxylic acid concentration was limiting, factors in serum played a role as cell “survival or maintenance” factors in addition to their role in cell division as “growth regulatory” factors. However, with equivalent levels of serum factors in the medium, the requirement for Ca²⁺, K⁺, and 2-oxocarboxylic acids was still much higher for multiplication than for maintenance. Kinetic analysis revealed that the concentrations of individual nutrients modify the quantitative requirement for others for cell multiplication in a specific pattern. Thus, specific quantitative relationships among different nutrients in the medium are important in the control of the multiplication rate of the cell population. When all nutrient concentrations were optimal for multiplication of normal cells, the multiplication response of SV40-virus-transformed cells to serum factors was similar to that of normal cells. When serum factors were held constant, transformed cells required significantly less (P < 0.001) of 12 of the 26 nutrients examined. Therefore, the transformed cells only have a growth advantage when the external concentration of specific nutrients limits the multiplication rate of normal cells. Taken together, the results suggest that the control of cell multiplication is intimately related to external concentrations of nutrients. Specific growth regulatory factors may stimulate cell proliferation by modification of the response of normal cells to nutrients. Transforming agents may confer a selective growth advantage on cells by a constitutive alteration of their response to extracellular nutrients.     

The role of growth factors in the embryogenesis and differentiation of the eye.

The vertebrate eye is composed of a variety of tissues that, embryonically, have their derivation from surface ectoderm, neural ectoderm, neural crest, and mesodermal mesenchyme. During development, these different types of cells are subjected to complex processes of induction and suppressive interactions that bring about their final differentiation and arrangement in the fully formed eye. With the changing concept of ocular development, we present a new perspective on the control of morphogenesis at the cellular and molecular levels by growth factors that include fibroblast growth factors, epidermal growth factor, nerve growth factor, platelet-derived growth factor, transforming growth factors, mesodermal growth factors, transferrin, tumor necrosis factor, neuronotrophic factors, angiogenic factors, and antiangiogenic factors. Growth factors, especially transforming growth factor-beta, have a crucial role in directing the migration and developmental patterns of the cranial neural-crest cells that contribute extensively to the structures of the eye. Some growth factors also exert an effect on the developing ocular tissues by influencing the synthesis and degradation of the extracellular matrix. The mRNAs for the growth factors that are involved in the earliest aspects of the growth and differentiation of the fertilized egg are supplied from maternal sources until embryonic tissues are able to synthesize them. Subsequently, the developing eye tissues are exposed to both endogenous and exogenous growth factors that are derived from nonocular tissues as well as from embryonic fluids and the systemic circulation. The early interaction between the surface head ectoderm and the underlying chordamesoderm confers a lens-forming bias on the ectoderm; later, the optic vesicle elicits the final phase of determination and enhances differentiation by the lens. After the blood-ocular barrier is established, the internal milieu of the eye is controlled by the interactions among the intraocular tissues; only those growth factors that selectively cross the barrier or that are synthesized by the ocular tissues can influence further development and differentiation of the cells. An understanding of the tissue interactions that are regulated by growth factors could clarify the precise mechanism of normal and abnormal ocular development.     

Growth factors, feeding regulation and the nervous system

A variety of growth factors and their receptors are present in the nervous system. Growth factors can modulate specific nervous system functions others than those related to growth, development, and tissue repair. The presence of growth factors in the brain and cerebrospinal fluid is the result of local synthesis (by neuronal, glial, vascular, and mononuclear phagocyte components), and uptake from the peripheral blood through the blood-brain barrier (in specific cases) and circumventricular organs. This paper focuses on the effects of a heterogeneous group of growth factors (acidic and basic fibroblast growth factors, insulin-like growth factors, epidermal growth factor, platelet-derived growth factor, interleukin-1 and others) on the central nervous system (CNS), in particular, on feeding regulation. Recent evidence supporting participation of growth factors in the regulation of feeding by a direct action at the level of the CNS is reviewed. Various growth factors have the ability to suppress short- and long-term food intake (FI), whereas others affect only short-term FI, or do not affect FI. Acute and chronic pathological processes stimulate the synthesis and release of growth factors in various cellular systems, and monitoring of growth factors by the CNS could be part of the regulatory signals that induce FI suppression frequently accompanying acute and chronic disease. Thus, it is proposed that a system regulating FI through growth factor-dependent mechanisms may be operative during specific physiological or pathological conditions.     

Initiation factors that bind mRNA. A comparison of mammalian factors with wheat germ factors

Three mammalian eukaryotic initiation factors (eIF) are required for the ATP-dependent binding of mRNA to the 40 S ribosomal subunit. These three factors, eIF-4A, eIF-4B, and eIF-4F, have also been isolated from wheat germ. Three assays were used to measure the ability of the wheat germ factors to interact with and/or substitute for the mammalian factors. Two assay systems were used to measure partial reactions involving the interaction of the three factors, ATP, and mRNA: 1) RNA-dependent ATP hydrolysis and 2) cross-linking of the factors to the 5' cap of oxidized mRNA. A third assay system was used to measure the ability of the factors to support initiation of protein synthesis. The results of the ATP hydrolysis and cross-linking experiments indicate that the wheat germ factors can interact with or substitute for the mammalian factors. Wheat germ eIF-4A appears to be functionally equivalent to mammalian eIF-4A. Wheat germ eIF-4B and eIF-4F appear to be isozymes possessing functions similar to mammalian eIF-4F. Wheat germ eIF-4B does not appear to be a functional equivalent to the mammalian eIF-4B. In a complete translation system from wheat germ, mammalian factors partially substitute for wheat germ factors, whereas the wheat germ factors are ineffective in the mammalian system.     

Purification of seven protein synthesis initiation factors from Krebs II ascites cells.

Seven protein synthesis initiation factors were isolated from Krebs II ascites cells using the procedures developed for the purification of the corresponding factors from rabbit reticulocytes. The ascites factors display identical characteristics in ion exchange chromatography and sucrose density gradient sedimentation. Based on their profiles in SDS polyacrylamide gels, the ascites factors have polypeptide profiles and molecular weights identical to those of the reticulocyte factors. Most significantly, each ascites factor is competent in replacing its corresponding reticulocyte factor in a reconstituted in vitro protein synthesizing system which is dependent on all seven factors.