Anaerobic Production of Thiobacillus denitrificans for the Enzyme Rhodanese

A method for the anaerobic growth of Thiobacillus denitrificans in a 140-liter (total capacity) stainless-steel culture vessel is described. As a result of controlling the pH value of cultures, and of ensuring that certain essential nutrients were in excess, cell yields approaching 700 mg (dry weight) per liter were obtained. These were over threefold higher than the best yields hitherto reported. The average rhodanese content of the cells from four cultures was 176,000 units per gram (dry weight). Adenosine-5′-phosphosulfate reductase (average content, 238 units per gram dry weight) and adenylate kinase (average content, 15,300 units per gram, dry weight) were also present.     

Specific Dot-Immunobinding Assay for Detection and Enumeration of Thiobacillus ferrooxidans

A specific and very sensitive dot-immunobinding assay for the detection and enumeration of the bioleaching microorganism Thiobacillus ferrooxidans was developed. Nitrocellulose spotted with samples was incubated with polyclonal antisera against whole T. ferrooxidans cells and then in ¹²⁵I-labeled protein A or ¹²⁵I-labeled goat antirabbit immunoglobulin G; incubation was followed by autoradiography. Since a minimum of 10³ cells per dot could be detected, the method offers the possibility of simultaneous processing of numerous samples in a short time to monitor the levels of T. ferrooxidans in bioleaching operations.     

Rhodanese from Thiobacillus A2: catalysis of reactions of thiosulphate with dihydrolipoate and dihydrolipoamide.

Rhodanese (thiosulphate:cyanide sulphurtransferase EC.2.8.1.1) was purified 25- to 30-fold from thiosulphate-grown Thiobacillus A2. It exhibited a pH optimum between pH 10-2 and 10-4 and apparent Km values of 0-36 mM-Na2S2O3 and 17 mM-KCN. Ultraviolet spectrophotometry and thin-layer chromatography showed that the enzyme catalysed the reaction of S2O3(2-) with dihydrolipoic acid or dihydrolipoamide, producing alpha-lipoate or lipoamide, with the intermediate production of the persulphides of dihydrolipoate and dihydrolipoamide, which were demonstrated chromatographically. This is the first demonstration of catalysis by a thiobacillus rhodanese of reactions which are likely to be physiologically important in the oxidative dissimilation of thiosulphate by a central energy-conserving pathway.     

Improved Assay Method for Phospholipase C

A lecithin sol dispersed with deoxycholate was found to be attacked by phospholipase C in the presence of calcium ion more rapidly than were any other lecithin sols. The inorganic phosphate could be released quantitatively from the acid soluble phosphate liberated from lecithin by an excess amount of alkaline phosphatase present in phospholipase C reaction mixture. A simple and accurate assay method for phospholipase C was developed with the sol and the alkaline phosphatase.     

Improved Method of Assay for Choline

A modified assay for choline is described which is shorter, yields more consistent responses, and requires considerably less time, space, and equipment than the existing assays.     

Rhodanese in higher plants

Rhodanese activity was detected in crude leaf extracts of 12 randomly selected plant species consisting of 9 non-cyanophoric and 3 cyanophoric species. In each case, the enzyme exhibited high activity at pH 10·4 and 55°. There appeared to be no correlation between rhodanese activity and the cyanophoric nature of the plant.     

Improved Medium for Isolation of Azospirillum spp

Colonies of Azospirillum spp. could be readily distinguished from colonies of other diazotrophs by scarlet coloration in culture media in which Congo red was included.     

Improved cloning vectors for Bifidobacterium spp.

The recombinant plasmids pDLI41, pDGA7 and pDCO7 were constructed by cloning in pDG7, a vector based on Bifidobacterium longum replicon pMB1, the following heterologous genes: Pseudomonas fluorescens lipase, Bacillus licheniformis α-amylase and Streptomyces sp. cholesterol oxidase. The hybrid plasmids efficiently transformed Bifidobacterium belonging to five different species. A novel Escherichia coli-Bifidobacterium set of shuttle vectors based on the replicon pMB1 (pLF5, pCLJ15, pSPEC1) featuring chloramphenicol, erythromycin and spectinomycin resistance genetic determinants as selection marker for bifidobacteria, was developed. The plasmid pTRE3, a derivative of pLF5, was the smallest (2·8 kb) Bifidobacterium vector, possessed a convenient multicloning site and presented high structural and segregational stability.     

Improved Methods for Capture,Extraction, and Quantitative Assay of Environmental DNA from Asian Bigheaded Carp (Hypophthalmichthys spp.)

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.     

Improved Hemagglutination Inhibition Assay for Mammary Tumor Virus Antigen

It is our experience that the use of sheep red blood cells pretreated with formaldehyde and pyruvaldehyde before sensitizing with viral antigen yields results that are comparable to that obtained by using the tannic acid method. The double aldehyde method provides the added advantage of being useful for assaying the viral antigen content in substances which contain high levels of interfering substances which would preclude the use of other assay methods.     

Growth Kinetics of Hyphomicrobium and Thiobacillus spp. in Mixed Cultures Degrading Dimethyl Sulfide and Methanol

The growth kinetics of Hyphomicrobium spp. and Thiobacillus spp. on dimethyl sulfide (DMS) and methanol (in the case of Hyphomicrobium spp.) in an enrichment culture created from a biofilter cotreating DMS and methanol were studied. Specific growth rates of 0.099 h⁻¹ and 0.11 h⁻¹ were determined for Hyphomicrobium spp. and Thiobacillus spp., respectively, growing on DMS at pH 7. These specific growth rates are double the highest maximum specific growth rate for bacterial growth on DMS reported to date in the literature. When the pH of the medium was decreased from pH 7 to pH 5, the specific growth rate of Hyphomicrobium spp. decreased by 85%, with a near 100-fold decline in the yield of Hyphomicrobium 16S rRNA gene copies in the mixed culture. Through the same pH shift, the specific growth rate and 16S rRNA gene yield of Thiobacillus spp. remained similar. When methanol was used as a substrate, the specific growth rate of Hyphomicrobium spp. declined much less over the same pH range (up to 30%) while the yield of 16S rRNA gene copies declined by only 50%. Switching from an NH₄⁺-N-based source to a NO₃⁻-N-based source resulted in the same trends for the specific growth rate of these microorganisms with respect to pH. This suggests that pH has far more impact on the growth kinetics of these microorganisms than the nitrogen source. The results of these mixed-culture batch experiments indicate that the increased DMS removal rates observed in previous studies of biofilters cotreating DMS and methanol are due to the proliferation of DMS-degrading Hyphomicrobium spp. on methanol at pH levels not conducive to high growth rates on DMS alone.Dimethyl sulfide (DMS) is a reduced sulfur compound that is emitted from both natural and anthropogenic sources. Natural DMS emissions are largely the result of the cleavage of dimethylsulfoniopropionate (9), the breakdown of the sulfur-containing amino acids methionine and cysteine (9, 11), and the degradation of methoxylated aromatic compounds (3, 9). Anthropogenic DMS emissions tend to be the result of high-temperature industrial processes and are problematic due to the foul smell of DMS and its low odor threshold (34). Industries that are sources of anthropogenic DMS emissions include wastewater treatment (14), aerobic composting (40), animal rendering (23), and kraft pulping (35).In the environment, microbial degradation can be a significant sink for DMS. In seawater, approximately 90% of the DMS produced is removed biologically before it reaches the atmosphere (21). Removal of DMS in the environment can be carried out by a variety of pathways. Aerobic bacteria, such as Hyphomicrobium spp. (7, 27, 36, 45), Thiobacillus spp. (6, 19, 42), or Methylophaga spp. (10), convert DMS to oxidized inorganic sulfur products such as sulfate and thiosulfate. There are also a wide variety of microorganisms, such as Pseudomonas spp. (46), capable of oxidizing DMS to dimethyl sulfoxide (DMSO) (11, 18). Finally, DMS can be eliminated through several anaerobic pathways, with a variety of methanogens (13, 22), sulfate-reducing bacteria (39), phototrophic bacteria (41, 44), and denitrifiers (42) capable of growth on DMS being reported in the literature.The prevalence of bacteria in the environment capable of growth on DMS has created interest in developing low-cost biotechnological methods to remove DMS from industrial waste gas streams. One possible technology is biofiltration which involves passing waste air through a packed bed of microorganisms. Removal of DMS in these systems, however, has proved to be difficult. This is believed to be due to the acidification of the biofilter bed brought about by the conversion of DMS to sulfate (32).Previous research by our group investigated the effect of the presence of methanol on DMS removal rates in inorganic biofilters treating DMS inoculated with sludge since industrial biofilters often treat mixtures of waste gases with biofilms composed of mixed microbial communities. It was demonstrated that the DMS degradation rate in biofilters where the pH of the biofilter bed was allowed to acidify naturally over time to pH 5 before the pH was neutralized back to pH 7 could be increased by up to 11-fold with methanol cotreatment (47). The increase in the DMS removal rates was shown to be the result of an order of magnitude increase in the concentration of Hyphomicrobium spp., which were also capable of growth on methanol (16). Methanol addition also resulted in a decrease in the full conversion of DMS to sulfate (increase in S⁰) and nitrification in biofilters cotreating DMS and methanol compared to the biofilter treating DMS alone, resulting in a decrease in the rate of acidification in these biofilters (48). Finally, it was shown that the DMS removal rate in these biofilters could be optimized by adopting step-feeding (49) and pulse-feeding (50) strategies.This paper focuses on the mechanism behind increased DMS removal rates in biofilters cotreating DMS and methanol. The behavior of an enrichment culture created from a biofilter cotreating DMS and methanol under different conditions relevant to biofilter operations as reported previously was investigated. Batch studies coupled with quantitative PCR (qPCR) methods were conducted to determine the effect of pH and nitrogen source on the kinetics of Hyphomicrobium spp., Thiobacillus spp., and a group of bacteria closely related to Chitinophaga spp. present in the enrichment culture grown on DMS and methanol.     

Improved PCR-BSP Assay for Multiplex Methylation Pattern Analysis in Minimal Amount of DNA

Cell-specific DNA methylation pattern detection is of great importance for the tumorigenesis and differentiation studies. Comparatively, large amounts of DNA were needed for traditional methods of DNA methylation pattern detection, and therefore, more sensitive method for high throughput analysis with a limited amount of DNA is needed. With Mouse 3T3 cells, we developed new multiplex-nested PCR technologies for bisulfite-assisted genomic sequencing PCR (BSP) methylation pattern detection method. Primers step add-in method and templates precipitation methods efficiently increase the throughput of the assay, and the nested PCR method also increased the sensitivity. The optimized assay could successfully detect 15 sequences of methylation pattern with a minimal amount of DNA (500–1,000 cells of genome DNA).     

Cytochrome b Gene-Based Assay for Monitoring the Resistance of Colletotrichum spp. to Pyraclostrobin

Resistance to pyraclostrobin due to a single nucleotide polymorphism at 143rd amino acid position on the cytochrome b gene has been a major source of concern in red pepper field infected by anthracnose in Korea. Therefore, this study investigated the response of 24 isolates of C. acutatum and C. gloeosporioides isolated from anthracnose infected red pepper fruits using agar dilution method and other molecular techniques such as cytochrome b gene sequencing, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and allele-specific polymerase chain reaction (PCR). The result showed that four isolates were resistant to pyraclostrobin on agar dilution method and possessed GCT (alanine) codon at 143rd amino acid position, whereas the sensitive isolates possessed GGT (glycine). Furthermore, this study illustrated the difference in the cytochrome b gene structure of C. acutatum and C. gloeosporioides. The use of cDNA in this study suggested that the primer Cacytb-P2 can amplify the cytochrome b gene of both C. acutatum and C. gloeosporioides despite the presence of various introns in the cytochrome b gene structure of C. gloeosporioides. The use of allele-specific PCR and PCR-RFLP provided clear difference between the resistant and sensitive isolates. The application of molecular technique in the evaluation of the resistance status of anthracnose pathogen in red pepper provided rapid, reliable, and accurate results that can be helpful in the early adoption of fungicide-resistant management strategies for the strobilurins in the field.     

Improved DNA‐FISH for cytometric detection of Candida spp

Aims: We developed improved methods for DNA‐based fluorescence in situ hybridization (FISH) for rapid detection of Candida spp. and Candida albicans via flow cytometry. Methods and Results: Two previously reported C. albicans‐targeted DNA probes were evaluated against whole cells of C. albicans and related Candida species using a rapid, high‐temperature hybridization protocol. One probe (CalB2208) was shown for the first time to be suitable as a FISH probe. Although cell labelling for both probes was relatively bright, we were able to substantially improve our results by altering fixation and hybridization conditions. For fixation, a 60 : 40 mixture of 10% buffered formalin and ethanol was most effective. Probe intensity was improved as much as ten‐fold through the use of unlabelled helper probes, and buffer containing 0·9 mol l^?1 NaCl plus 10% formamide yielded the best hybridizations for both probe/helper cocktails. Although optimal labelling occurred with longer hybridizations, we found that C. albicans could be completely differentiated from the nontarget yeast Rhodotorula glutinis after only 15 min using the brightest probe (Calb‐1249) and that a formal washing step was not required. Specificities of probe/helper cocktails under optimal conditions were determined using a panel of target and nontarget cell types, including four strains of Candida dubliniensis. Calb‐1249 cross‐reacted slightly with Candida parapsilosis and strongly with both Candida tropicalis and C. dubliniensis. In contrast, we found that CalB2208 was exclusive for C. albicans. The molecular basis of this specificity was confirmed by DNA sequencing. Conclusions: We describe DNA probe‐based approaches for rapid and bright labelling of Candida spp. and for specific labelling of C. albicans without cross‐reaction with C. dubliniensis. Our work improves upon previously described methods. Significance and Impact of the Study: The methods described here for rapid FISH‐based detection of Candida spp. may have applications in both clinical and food microbiology.     

An Improved Method for Enumeration of X-C Cell Assay for Murine Leukemia Virus

A modification for the enumeration of X-C syncytia is described wherein the projected image of the entire infected culture is observed. This method is rapid, reliable, and reproducible.     

Rhodanese functions as sulfur supplier for key enzymes in sulfur energy metabolism

How microorganisms obtain energy is a challenging topic, and there have been numerous studies on the mechanisms involved. Here, we focus on the energy substrate traffic in the hyperthermophilic bacterium Aquifex aeolicus. This bacterium can use insoluble sulfur as an energy substrate and has an intricate sulfur energy metabolism involving several sulfur-reducing and -oxidizing supercomplexes and enzymes. We demonstrate that the cytoplasmic rhodanese SbdP participates in this sulfur energy metabolism. Rhodaneses are a widespread family of proteins known to transfer sulfur atoms. We show that SbdP has also some unusual characteristics compared with other rhodaneses; it can load a long sulfur chain, and it can interact with more than one partner. Its partners (sulfur reductase and sulfur oxygenase reductase) are key enzymes of the sulfur energy metabolism of A. aeolicus and share the capacity to use long sulfur chains as substrate. We demonstrate a positive effect of SbdP, once loaded with sulfur chains, on sulfur reductase activity, most likely by optimizing substrate uptake. Taken together, these results lead us to propose a physiological role for SbdP as a carrier and sulfur chain donor to these key enzymes, therefore enabling channeling of sulfur substrate in the cell as well as greater efficiency of the sulfur energy metabolism of A. aeolicus.     

用磷酸二酯酶定量检测植物钙调素方法的改进

从磷酸二酯酶(PDE)提取方法、钙调素(CaM)到定反应时间、测定体系中的Ca^2 和cAMP浓度、样品处理及活性计算等方面对叶正华等测定钙调素的PDE法作了改进。实验表明,改进后的方法使PDE的提取比较较简便快捷,CaM检测过程中的误差减小,结果的准确性、重复性和可比性都更好,可用于多个样品的同时测定。