中国和美国原始土壤中非高温泉古菌的发现和鉴定

近年来在非极端环境中已经发现有古菌(Archaea)的存在, 但在中国原始土壤中还未见报道。本研究的目的是调查古菌是否存在于两个分别取自中国新疆和广西的土壤及两个美国亚利桑那州南部地区的土壤中。我们分别构建了这四个原始土壤的古菌16S rDNA文库并对28个克隆的16S rDNA进行了鉴定。所有这些16S rDNA的序列都归类于古菌的泉古菌门(Crenarchaeota)。进化树分析表明, 这些泉古菌的16S rDNA属于非高温陆地环境中的泉古菌种群, 明显区别于海洋和淡水地带的泉古菌种群。这个泉古菌种群又有两个分支, 这两个分支在16S rDNA序列上和G C含量上有明显的区别。本研究在两个中国和两个美国原始土壤中鉴定了非高温泉古菌的存在, 由此证明泉古菌的存在范围不只局限于高温等极端环境。另外, 美国原始土壤中的泉古菌只属于一个进化分支, 这说明非高温泉古菌种群的类型和土壤的地理位置及土壤特性有关。     

Antiglycation Effects of Carnosine and Other Compounds on the Long-Term Survival of Escherichia coli

Glycation, or nonenzymatic glycosylation, is a chemical reaction between reactive carbonyl-containing compounds and biomolecules containing free amino groups. Carbonyl-containing compounds include reducing sugars such as glucose or fructose, carbohydrate-derived compounds such as methylglyoxal and glyoxal, and nonsugars such as polyunsaturated fatty acids. The latter group includes molecules such as proteins, DNA, and amino lipids. Glycation-induced damage to these biomolecules has been shown to be a contributing factor in human disorders such as Alzheimer''s disease, atherosclerosis, and cataracts and in diabetic complications. Glycation also affects Escherichia coli under standard laboratory conditions, leading to a decline in bacterial population density and long-term survival. Here we have shown that as E. coli aged in batch culture, the amount of carboxymethyl lysine, an advanced glycation end product, accumulated over time and that this accumulation was affected by the addition of glucose to the culture medium. The addition of excess glucose or methylglyoxal to the culture medium resulted in a dose-dependent loss of cell viability. We have also demonstrated that glyoxylase enzyme GloA plays a role in cell survival during glycation stress. In addition, we have provided evidence that carnosine, folic acid, and aminoguanidine inhibit glycation in prokaryotes. These agents may also prove to be beneficial to eukaryotes since the chemical processes of glycation are similar in these two domains of life.One factor that may affect the long-term survival of bacterial cells in a population is the level of damage incurred by macromolecules via the nonenzymatic process of glycation, first described by Louis-Camille Maillard (16). The Maillard reaction is responsible for the formation of several compounds identified as advanced glycation end products (AGEs) (9). In vivo this reaction appears to play a role in the aging process, as it leads to slow degradation of molecules. The principal mechanisms of glycation-related damage involve cross-links between proteins and/or DNA, modifying or destroying their functional properties (2, 8, 38). Most studies of glycation have been performed with eukaryotes because of its relationship to aging and disorders such as Alzheimer''s disease and diabetes (6, 21, 30, 42). However, several studies (32, 33) have shown that glycation also takes place in Escherichia coli, affecting protein and DNA of this prokaryote.Many biochemical pathways produce reactive dicarbonyl intermediates, such as glyoxal and methylglyoxal (MG), which can further react with DNA, proteins, or other biomolecules to form AGEs (8, 36). Reaction of glucose with amino groups of proteins and subsequent formation of reactive dicarbonyls via a series of reactions involving Schiff base and Amadori product intermediates have been well documented (40). Methylglyoxal can be formed by spontaneous decomposition of glycolytic triose phosphates such as dihydroxyacetone phosphate (DHAP) (1) or can be produced enzymatically from DHAP by the E. coli enzyme methylglyoxal synthase (MgsA) (12). MG synthesis usually requires an environment low in phosphate and high in DHAP, a situation that occurs most frequently under high-glucose conditions (25, 26). If MG is not degraded, MG accumulation will lead to cell death (12). E. coli maintains pathways for the detoxification of methylglyoxal, including glyoxalase enzymes I and II (encoded by gloA and gloB, respectively), which convert MG to S-lactoyl glutathione and then to d-lactate (12). This system has been proposed to be the predominant MG detoxification system in E. coli (12, 29).Glyoxal is also a toxic dicarbonyl compound capable of damaging cells via AGE formation. One of the AGEs formed in the presence of glyoxal is carboxymethyl lysine (CML), which has been used extensively as a biomarker for aging (11, 20, 31, 39). CML can be formed by different pathways: glucose can be oxidized to glyoxal, which can react with protein to form CML (1, 17); glucose can also react with protein to form fructoselysine (an Amadori product), which can undergo oxidative cleavage to form CML (1). In this study, we investigated CML formation in E. coli growing under standard and glycation-prone laboratory conditions. Since AGE formation may negatively affect cell survival and reproduction during long-term batch culture (35), we hypothesized that CML would accumulate in these cultures as cells progress through stationary phase.One product that may interfere with AGE formation is carnosine (β-alanyl-l-histidine), a naturally occurring dipeptide in many organisms. Although its mechanism of action has not been fully determined, there is evidence that both the free amino group derived from the β-alanine and the imidazole ring of histidine compete with amino groups of proteins in the presence of reactive dicarbonyl compounds (7, 24). In this study we designed assays to determine the effect of carnosine (and other compounds) on survival of cultures of E. coli under a variety of experimental conditions. Additionally, since strains lacking glyoxalase enzymes I and II have a reduced ability to detoxify methylglyoxal, we hypothesized that gloA and/or gloB mutants would require larger amounts of carnosine than would wild-type strains to survive in the presence of this toxic electrophile.     

The Moloney murine leukemia virus repressor binding site represses expression in murine and human hematopoietic stem cells

The Moloney murine leukemia virus (MLV) repressor binding site (RBS) is a major determinant of restricted expression of MLV in undifferentiated mouse embryonic stem (ES) cells and mouse embryonal carcinoma (EC) lines. We show here that the RBS repressed expression when placed outside of its normal MLV genome context in a self-inactivating (SIN) lentiviral vector. In the lentiviral vector genome context, the RBS repressed expression of a modified MLV long terminal repeat (MNDU3) promoter, a simian virus 40 promoter, and three cellular promoters: ubiquitin C, mPGK, and hEF-1a. In addition to repressing expression in undifferentiated ES and EC cell lines, we show that the RBS substantially repressed expression in primary mouse embryonic fibroblasts, primary mouse bone marrow stromal cells, whole mouse bone marrow and its differentiated progeny after bone marrow transplant, and several mouse hematopoietic cell lines. Using an electrophoretic mobility shift assay, we show that binding factor A, the trans-acting factor proposed to convey repression by its interaction with the RBS, is present in the nuclear extracts of all mouse cells we analyzed where expression was repressed by the RBS. In addition, we show that the RBS partially repressed expression in the human hematopoietic cell line DU.528 and primary human CD34(+) CD38(-) hematopoietic cells isolated from umbilical cord blood. These findings suggest that retroviral vectors carrying the RBS are subjected to high rates of repression in murine and human cells and that MLV vectors with primer binding site substitutions that remove the RBS may yield more-effective gene expression.     

Development and optimization of a quantitative cell culture infectivity assay for the microsporidium Encephalitozoon intestinalis and application to ultraviolet light inactivation

Microsporidia are unique parasites recognized as a major cause of intestinal illness among immunocompromised patients and occasionally in otherwise healthy hosts. These organisms have been detected in water and are likely transmitted by the fecal-oral route. The most common human pathogenic microsporidia for which cell culture methods have been established is Encephalitozoon intestinalis. This study describes the development of a quantitative cell culture infectivity assay for E. intestinalis and its application to assess inactivation by ultraviolet (UV) light irradiation. The method described here employs calcofluor white, a fluorescent brightener that targets the chitin spore wall, to visualize groups of developing spores in order to confirm infectivity. Serial dilutions of the spore suspension were seeded into tissue culture well slides containing RK-13 cells. Slides were then rinsed, fixed in methanol and stained with calcofluor white and examined microscopically. Large masses of developing spores were easily visible on infected cell monolayers. Positive and negative wells at each dilution step were used to quantify the number of infectious spores in the original suspension using a most-probable-number (MPN) statistical analysis. This assay was used to evaluate the disinfecting potential of ultraviolet light on E. intestinalis spores in water. The ultraviolet dose required for a 3-log(10) or 99.9% reduction in the number of infective spores was determined to be 8.43 mW s/cm(2).     

Amplification protocols introduce systematic but reproducible errors into gene expression studies

The desire to perform microarray experiments with small starting amounts of RNA has led to the development of a variety of protocols for preparing and amplifying mRNA. This has consequences not only for the standardization of experimental design, but also for reproducibility and comparability between experiments. Here we investigate the differences between the Affymetrix standard and small sample protocols and address the data analysis issues that arise when comparing samples and experiments that have been processed in different ways. We show that data generated on the same platform using different protocols are not directly comparable. Further, protocols introduce systematic biases that can be largely accounted for by using the correct data analysis techniques.     

Lymphatic endothelium: morphological, molecular and functional properties

The lymphatic microvasculature is uniquely adapted for the continuous removal of interstitial fluid and proteins, and is an important point of entry for leukocytes and tumor cells. The traditional view that lymphatic capillaries are passive participants in these tasks is currently being challenged. This overview highlights recent advances in our understanding of the molecular mechanisms underlying the formation and function of lymphatic vessels.     

VEGF is a chemoattractant for FGF-2-stimulated neural progenitors

Migration of undifferentiated neural progenitors is critical for the development and repair of the nervous system. However, the mechanisms and factors that regulate migration are not well understood. Here, we show that vascular endothelial growth factor (VEGF)-A, a major angiogenic factor, guides the directed migration of neural progenitors that do not display antigenic markers for neuron- or glia-restricted precursor cells. We demonstrate that progenitor cells express both VEGF receptor (VEGFR) 1 and VEGFR2, but signaling through VEGFR2 specifically mediates the chemotactic effect of VEGF. The expression of VEGFRs and the chemotaxis of progenitors in response to VEGF require the presence of fibroblast growth factor 2. These results demonstrate that VEGF is an attractive guidance cue for the migration of undifferentiated neural progenitors and offer a mechanistic link between neurogenesis and angiogenesis in the nervous system.     

A label-free optical technique for detecting small molecule interactions

A novel approach for the label-free detection of molecular interactions is presented in which a colorimetric resonant grating is used as a surface binding platform. The grating, when illuminated with white light, is designed to reflect only a single wavelength. When molecules are attached to the surface, the reflected wavelength (color) is shifted due to the change of the optical path of light that is coupled into the grating. By linking receptor molecules to the grating surface, complementary binding molecules can be detected without the use of any kind of fluorescent probe or radioactive label. The detection technique is capable of detecting the addition and removal of small molecules as they interact with receptor molecules on the sensor surface or enzymes in the solution surrounding the sensor. Two assays are presented to exemplify the detection of small molecule interactions with the biosensor. First, an avidin receptor layer is used to detect 244 Da biotin binding. Second, a protease assay is performed in which a 136 Da p-nitroanilide (pNA) moeity is cleaved from an immobilized substrate. Because the sensor structure can be embedded in the plastic surfaces of microtiter plates or the glass surfaces of microarray slides, it is expected that this technology will be most useful in applications where large numbers of biomolecular interactions are measured in parallel, particularly when molecular labels will alter or inhibit the functionality of the molecules under study. Screening of pharmaceutical compound libraries with protein targets, and microarray screening of protein-protein interactions for proteomics are examples of applications that require the sensitivity and throughput afforded by this approach.     

Microscopy: an art?

There can be no doubt that the finest creator of beauty is Mother Nature. And in many ways, science is the exploration of this beauty and of the mechanisms that have created it. Microscopy, as a technique in scientific investigation, has had a key role in uncovering nature's beauty, which has led some to propose that microscopy could be described as an art or even an art form. But is this claim justified?