Correlation of microbial mass with ATP and DNA concentrations in acidogenesis of whey permeate

In this paper, we examine variations in the contents of ATP and DNA per unit microbial mass in an acidogenesis of whey permeate. We also introduce a novel approach to estimate microbial mass by measuring ATP and DNA when the ratios of ATP and DNA to microbial mass vary. Acidogenic experiments were performed at 35°C and pH 6.0 in batch mode. The amounts of ATP and DNA per unit microbial mass were not consistent during the incubation except during the post-decay phase. Especially within the exponential phase, each showed a 10-fold difference between maximal and minimal values. In this case, the conventional method which converts ATP or DNA concentration into microbial mass using a fixed conversion factor can give inaccurate results. While the constant ratios of 0.74 mg ATP/g VSS and 1.96 mg DNA/g VSS were determined for the post-decay phase, the ATP and DNA concentrations showed strong linear relationships with the microbial mass (r ² = 0.99) within the ranges of 0.039–1.078 mg ATP/l and 0.075–2.080 mg DNA/l, respectively. The linear regression equations are as follows: (1) microbial mass concentration (mg/l) = 478.5 × ATP concentration (mg/l) + 293.5, (2) microbial mass concentration (mg/l) = 257.2 × DNA concentration (mg/l) + 250.4. Therefore, changes in the mass of the acidogenic population should be monitored by the combined use of the regression equations obtained in the exponential phase and the constant ratios determined in the post-decay phase. This procedure should be widely applicable to the acidogenesis of dairy processing wastewaters, especially of a highly suspended organic wastewater such as whey.     

Determination of urinary thiocyanate and nitrate using fast ion-interaction chromatography

A simple and rapid chromatographic method for determination of nitrite, nitrate and thiocyanate is reported, and applied to the analysis of non-, medium and heavy smokers' urine samples. Ion-interaction liquid chromatography was carried out on a short 30 mm x 4.6 mm C18 column (3 microm particle size) with a mobile phase of 10 mM tetrabutylammonium phosphate in 20% MeOH. The chromatography was performed at an elevated temperature of 45 degrees C, at a flow-rate of 1 ml/min. Detection was by direct UV absorption at 230 nm. Sample preparation involved centrifugation and dilution, followed by sample clean-up on a C18 solid-phase extraction cartridge. The developed method proved both precise (% RSD <2%) and sensitive (standard detection limits <0.1 mg/l), and yielded total run times of under 10 min when applied to urine analysis of smokers and non-smokers, with thiocyanate eluting in under 5 min.     

Simultaneous determination of cyanide and thiocyanate in blood by ion chromatography with fluorescence and ultraviolet detection

An ion chromatographic method for the simultaneous determination of cyanide and thiocyanate in blood has been developed. After extraction by adding water and methanol to blood, cyanide was derivatized with 2,3-naphthalenedialdehyde and taurine to give a fluorescent product of 1-cyanobenz[f]isoindole. This compound was detected with high sensitivity by fluorometry and the underivatized thiocyanate was detected by ultraviolet absorption. The detection limits were 3.8 pmol ml⁻¹ for cyanide and 86 pmol ml⁻¹ for thiocyanate, and the recoveries from blood were ca. 83% and ca. 100%, respectively. The proposed method was successfully applied to the analysis of both anions in blood from smokers, non-smokers and fire victims.     

The Discovery of Error-prone DNA Polymerase V and Its Unique Regulation by RecA and ATP

My career pathway has taken a circuitous route, beginning with a Ph.D. degree in electrical engineering from The Johns Hopkins University, followed by five postdoctoral years in biology at Hopkins and culminating in a faculty position in biological sciences at the University of Southern California. My startup package in 1973 consisted of $2,500, not to be spent all at once, plus an ancient Packard scintillation counter that had a series of rapidly flashing light bulbs to indicate a radioactive readout in counts/minute. My research pathway has been similarly circuitous. The discovery of Escherichia coli DNA polymerase V (pol V) began with an attempt to identify the mutagenic DNA polymerase responsible for copying damaged DNA as part of the well known SOS regulon. Although we succeeded in identifying a DNA polymerase, one that was induced as part of the SOS response, we actually rediscovered DNA polymerase II, albeit in a new role. A decade later, we discovered a new polymerase, pol V, whose activity turned out to be regulated by bound molecules of RecA protein and ATP. This Reflections article describes our research trajectory, includes a review of key features of DNA damage-induced SOS mutagenesis leading us to pol V, and reflects on some of the principal researchers who have made indispensable contributions to our efforts.     

Identification of the microbial community responsible for thiocyanate and thiosulfate degradation in an activated sludge process

An activated sludge reactor fed with thiocyanate and/or thiosulfate was operated to examine the characteristics of its microbial community. Terminal-restriction fragment length polymorphism analyses were conducted to detect shifts in the microbial community structure corresponding to influent conditions. Then, clone library analyses and RNA-based stable-isotope probing were conducted to identify sulfur-oxidizing bacteria (SOB) responsible for the degradation of each substrate. The results suggested that there were two types of SOB: thiocyanate-degrading bacteria (that can utilize both thocyanate and thiosulfate) and thiosulfate-specific bacteria (that cannot utilize thiocyanate). Thiocyanate-degrading SOB, however, were outcompeted by thiosulfate-specific SOB when the influent contained only thiosulfate. Of the sequenced clones, Marinicella-related (with 98.7% identity) and Methylobacter-related (with 91.3% identity) bacteria were identified as thiocyanate-degrading SOB, whereas Thiomicrospira thermophila-related (with 100% identity over 903 bp) bacteria were identified as thiosulfate-specific SOB.     

Comparisons of direct extraction methods of microbial DNA from different paddy soils

Molecular analyses for the study of soil microbial communities often depend on the direct extraction of DNA from soils. The present work compares the effectiveness of three different methods of extracting microbial DNA from seven different paddy soils. Comparison among different DNA extraction methods against different paddy soil samples revealed a marked variation in DNA yields from 3.18–20.17 μg DNA/g of dry soil. However, irrespective of the soil samples and extraction methods the DNA fragment size was >10 kb. Among the methods evaluated, method-C (chemical–enzymatic–mechanical) had better cell lysis efficiency and DNA yield. After purification of crude DNA by Purification Kit, A₂₆₀/A₂₃₀ and A₂₆₀/A₂₈₀ ratios of the DNA obtained by method-C reached up to 2.27 and 1.89, respectively, sustaining the efficacy of this technique in removing humic acid, protein and other contaminants. Results of the comprehensive evaluation of DNA extraction methods suggest that method-C is superior to other two methods (chemical–enzymatic and chemical–mechanical), and was the best choice for extraction of total DNA from soil samples. Since soil type and microbial community characteristics influence DNA recovery, this study provides guidance for choosing appropriate extraction and purification methods according to experimental goals.     

Synergistic Activation of DNA Synthesis in Astrocytes by Fibroblast Growth Factors and Extracellular ATP

Abstract: The effects of extracellular ATP and polypeptide growth factors on DNA synthesis in primary cultures of rat astrocytes have been examined. It was found that ATP acts synergistically with either acidic or basic fibroblast growth factor to stimulate DNA synthesis. The specificity of this effect was demonstrated by the inability of ATP to potentiate DNA synthesis induced by platelet-derived growth factor or epidermal growth factor. ATP appears to act via P₂ purinergic receptors, because (a) it was more effective than adenosine and (b) the synergistic effect was observed with the hydrolysis-resistant P₂ agonists, ADPβS and ATPγS. The evidence suggests that extracellular ATP may be an important factor in regulating the extent of gliosis and, as such, may be involved in mechanisms of neural injury and repair.     

基于ATP生物发光法的微生物数量快速检测技术的研究进展

微生物数量的快速检测一直是工业生产与食品行业需要解决的问题,腺嘌呤核苷三磷酸(adenosine triphosphate,ATP)生物发光法具有操作简便、检测周期短等优点,可满足一般微生物检测的需求。然而,ATP生物发光法的准确性也受到不同因素的影响,如微生物的ATP检测限值较高、微生物自身及其他因素(如非微生物ATP、提取剂种类、荧光素酶活性等)均对微生物数量的检测产生影响。本文简述了不同微生物数量检测方法的优缺点,介绍了ATP生物发光法的发展历程及原理,综述了非微生物ATP与游离ATP、微生物量、ATP提取剂、荧光素酶等因素对ATP生物发光法灵敏度与稳定性的影响,归纳总结了ATP生物发光法及检测设备在食品、医疗、污水处理等领域的应用现状,并就ATP生物发光法体系的优化及ATP在线检测的应用等方面进行了展望,以期为ATP生物发光法的高效应用提供新的思路。     

DNA指纹图技术分析微生物肥料菌种组成稳定性

目的 分析2种市售微生物肥料在不同生产批次中微生物菌种组成的稳定性。方法 利用ERIC-PCR基因组DNA指纹图技术和16S rDNA V3扩增一温度梯度凝胶电泳（PCR-TGGE）指纹图技术。结果 这2种微生物肥料在同一个生产批次不同包装之间的2种DNA指纹图谱相似性较高,分别在78%～95%和96%～100%,表明同一个批次内的菌种组成比较一致,但其在不同的生产批次之间菌种组成差异存在显著性,反映在2种DNA指纹图谱上,不同生产批次样品间ERIC-PCR指纹图相似性最低只有10%,PCR-TGGE指纹图相似性最低为46%。结论 通过ERIC-PCR和PCR-TGGE DNA指纹图技术可以对微生物肥料中菌种组成的稳定性进行快速、准确的分析,如何保持菌种组成在批次之间的稳定一致,是复合菌种微生物肥料质量控制中面临的难题。     

Electricity generation and microbial community changes in microbial fuel cells packed with different anodic materials

Four materials, carbon felt cube (CFC), granular graphite (GG), granular activated carbon (GAC) and granular semicoke (GS) were tested as packed anodic materials to seek a potentially practical material for microbial fuel cells (MFCs). The microbial community and its correlation with the electricity generation performance of MFCs were explored. The maximum power density was found in GAC, followed by CFC, GG and GS. In GAC and CFC packed MFCs, Geobacter was the dominating genus, while Azospira was the most populous group in GG. Results further indicated that GAC was the most favorable for Geobacter adherence and growth, and the maximum power densities had positive correlation with the total biomass and the relative abundance of Geobacter, but without apparent correlation with the microbial diversity. Due to the low content of Geobacter in GS, power generated in this system may be attributed to other microorganisms such as Synergistes, Bacteroidetes and Castellaniella.     

DNA extraction method affects microbial community profiles from soils and sediment

To evaluate whether different deoxyribonucleic acid (DNA) extraction procedures can affect estimates of bacterial community composition, based on the 16S ribosomal ribonucleic acid gene denaturing gradient gel electrophoresis (DGGE) profiles, we compared four in situ lysis procedures using three soils and one marine sediment. Analysis of DGGE profiles, generated by polymerase chain reaction of purified DNA extracts, demonstrated that the choice of DNA extraction method significantly influenced the bacterial community profiles generated. This was reflected both in the number of bands or ribotypes detected from each sample and in subsequent principle coordinate analysis and unweighted-pair group method using arithmetic average analyses. The methods also differed significantly in their robustness, i.e. reproducibility across multiple analyses. Two methods, both based on bead beating, were demonstrated to be suitable for comparative studies of a range of soil and sediment types. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

ATP Binding, ATP Hydrolysis, and Protein Dimerization Are Required for RecF to Catalyze an Early Step in the Processing and Recovery of Replication Forks Disrupted by DNA Damage

In Escherichia coli, the recovery of replication following disruption by UV-induced DNA damage requires the RecF protein and occurs through a process that involves stabilization of replication fork DNA, resection of nascent DNA to allow the offending lesion to be repaired, and reestablishment of a productive replisome on the DNA. RecF forms a homodimer and contains an ATP binding cassette ATPase domain that is conserved among eukaryotic SMC (structural maintenance of chromosome) proteins, including cohesin, condensin, and Rad50. Here, we investigated the functions of RecF dimerization, ATP binding, and ATP hydrolysis in the progressive steps involved in recovering DNA synthesis following disruption by DNA damage. RecF point mutations with altered biochemical properties were constructed in the chromosome. We observed that protein dimerization, ATP binding, and ATP hydrolysis were essential for maintaining and processing the arrested replication fork, as well as for restoring DNA synthesis. In contrast, stabilization of the RecF protein dimer partially protected the DNA at the arrested fork from degradation, although overall processing and recovery remained severely impaired.     

Analysis of proteins showing differential changes during ATP oscillations in chondrogenesis

Prechondrogenic condensation is a critical step for skeletal pattern formation. Our previous study showed that ATP oscillations play an essential role in prechondrogenic condensation because they induce oscillatory secretion. However, the molecular mechanisms that underlie ATP oscillations remain poorly understood. We examined how differential changes in proteins are implicated in ATP oscillations during chondrogenesis by using liquid chromatography/mass spectrometry. Our analysis showed that a number of proteins involved in ATP synthesis/consumption, catabolic/anabolic processes, actin dynamics, cell migration and adhesion were detected at either the peak or the trough of ATP oscillations, which implies that these proteins have oscillatory expression patterns that are coupled to ATP oscillations. On the basis of the results, we suggest that (1) the oscillatory expression of proteins involved in ATP synthesis/consumption and catabolic/anabolic processes can contribute to the generation or maintenance of ATP oscillations and that (2) the oscillatory expression of proteins involved in actin dynamics, cell migration and adhesion plays key roles in prechondrogenic condensation by inducing collective adhesion and migration in cooperation with ATP oscillations. Copyright © 2014 John Wiley & Sons, Ltd.     

ATP调控策略及其在微生物代谢产物合成中的应用

辅因子工程是代谢工程的一个新兴分支领域,主要通过直接调控细胞内关键酶的辅因子,如ATP/ADP、NADH/NAD+、NADPH/NADP+等的浓度和形式来实现代谢流的最大化,快速地将物质流导向目标代谢物。ATP作为一种重要辅因子参与微生物细胞内大量的酶催化反应,将物质代谢途径串联或并联成复杂的网络体系,最终使得物质代谢流的分配受到牵制。因此ATP调控策略有望成为微生物菌株改造的有利工具,用于提高目标代谢物的浓度和生产能力,强化微生物对于环境的耐受以及促进底物利用等。文中将重点论述目前常用的有效ATP调控策略以及ATP调控对于细胞代谢的影响,以期为微生物细胞工厂的高效构建提供参考。     

Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study

Based on the comparative study of the DNA extracts from two soil samples obtained by three commercial DNA extraction kits, we evaluated the influence of the DNA quantity and purity indices (the absorbance ratios A260/280 and A260/230, as well as the absorbance value A320 indicating the amount of humic substances) on polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) and a functional gene microarray used in the study of microbial communities. Numbers and intensities of the DGGE bands are more affected by the A260/280 and A320 values than by the ratio A260/230 and conditionally affected by the DNA yield. Moreover, we demonstrated that the DGGE band pattern was also affected by the preferential extraction due to chemical agents applied in the extraction. Unlike DGGE, microarray is more affected by the A260/230 and A320 values. Until now, the successful PCR performance is the mostly used criterion for soil DNA purity. However, since PCR was more influenced by the A260/280 ratio than by A260/230, it is not accurate enough any more for microbial community assessed by non-PCR-based methods such as microarray. This study provides some useful hints on how to choose effective DNA extraction method for the subsequent assessment of microbial community.     

Analysis of biological wastewater treatment processes using multicomponent gas phase mass balancing.

A reactor system using off-gas analysis was developed for analyzing wastewater treatment process reactions. Using a mass spectrometer for the gas analysis provides the ability to simultaneously measure several gas components (such as oxygen, nitrogen, carbon dioxide, and argon). One of the benefits of the reactor design was the precise control of the dissolved oxygen concentration, uncoupled from the system turbulence, which was controlled via a gas recycle loop. This feature allowed control of the turbulence within the reactor without any need for mechanical stirring. Using oxygen as the test gas, the reactor was shown to perform well in the measurement of oxygen uptake rate of nitrifying activated sludge. The oxygen uptake rate calculations were made using a simple calibration method developed for the reactor system. The reactor was able to provide precise and accurate results for this test case. Furthermore, the system was capable of measuring under dynamic process conditions, as well as when the process rates were constant (steady state).     

Measurement of free and bound fractions of extracellular ATP in biological solutions using bioluminescence.

Measurement of extracellular ATP in biological solutions is complicated by protein-binding and rapid enzymatic degradation. We hypothesized that the concentration of extracellular ATP could be determined luminometrically by limiting degradation and measuring the free and protein-bound fractions. ATP was added (a) at constant concentration to solutions containing varying albumin concentrations; (b) at varying concentrations to a physiological albumin solution (4 gm/dL); (c) at varying concentrations to plasma. After centrifugation, a fraction of each supernatant was heated. ATP in heated and unheated samples was measured luminometrically. Blood was drawn into saline or an ATP-stabilizing solution and endogenous plasma ATP measured. ATP-albumin binding was a linear function of albumin concentration (3.5% ATP bound at 100 micromol/L to 33.2% ATP bound at 1000 micromol/L) but independent of ATP concentration (29.3%, 10-1000 nmol/L ATP in 602 micromol/L albumin). Heating released the majority of bound ATP from albumin-containing solutions (94.8 +/- 1.7%) and plasma (97.6 +/- 5.1%). Total endogenous plasma ATP comprised 93 +/- 27 nmol/L (free) and 150 +/- 40 nmol/L (total fraction). Without stabilizing solution, degradation of free endogenous plasma ATP occurred. Within a physiological range (10-1000 nmol/L), ATP binds albumin independently of ATP concentration. Heating releases bound ATP, enabling accurate luminometric measurement of total extracellular ATP (free and bound) in biological samples.     

Analysis of microbial diversity in oligotrophic microbial fuel cells using 16S rDNA sequences

Molecular ecological techniques were applied to analyze the bacterial diversity of two oligotrophic microbial fuel cells (MFCs) enriched using river water or artificial wastewater (AWW) as fuel. Denaturing gradient gel electrophoresis (DGGE) of the PCR amplified 16S rDNA showed that different microbial communities were present in the two MFCs and these were different from the river sediment used to initiate the enrichment. Nearly complete 16S rDNA was amplified and sequenced. Over 80% of the clones were Proteobacteria. Betaproteobacteria were the dominant clones (46.2%) in MFCs fed with river water, and about 64.4% of the clones in MFCs fed with AWW were Alphaproteobacteria. Actinobacteria were found only in the MFC fed with AWW, and Deltaproteobacteria, Acidobacteria, Chloroflexi and Verrucomicrobia in the MFC fed with river water. Many clones were related to uncultured bacteria, some with homology less than 95%, indicating that many novel bacteria were enriched in the oligotrophic MFCs.