Assessment of bioburden on human and animal tissues: Part 1—Results of method development and validation studies

Recovered human and animal tissues are used extensively in surgery for wound repair and reconstruction. In preparation for the validation of chemical disinfection and radiation sterilization processes, studies were performed on the development and validation of quantitative bioburden recovery methods for human bone and soft tissue and also for porcine dermis. The use of a swab-based method was not considered due to the known poor efficiency of recovery for this technique. The “exhaustive extraction” and “inoculated product” approaches to validation of a bioburden recovery efficiency factor have inherent strengths and weaknesses; in this study, tissues were inoculated and also subjected to a series of extractions to determine if/when “exhaustion” occurred. Femoral and tibial shaft rings, iliac crest wedges, sections of Achilles tendon, a soft tissue composite sample, and porcine dermis, were inoculated at several sites with Bacillus atrophaeus spores, and then subjected to either shaking by hand, mechanical shaking, or sonication plus mechanical shaking. Each of these methods of agitation were performed in combination with three rinse (extraction) fluids: phosphate buffer (Butterfield’s buffer), phosphate buffer with 0.2% polysorbate 80 (a surfactant), and water with 1% peptone and 1% polysorbate 80 (Fluid D). The highest recovery efficiencies were observed with sonication plus mechanical shaking; of the three extraction media, Fluid D gave the highest first-rinse recovery efficiency (65%) and Butterfield’s buffer gave the lowest (39%). Each of the three recovery methods, however appeared to reach “exhaustion”, a subsequent rinse giving less than 10% of the recovery found in the first rinse. The results demonstrated the importance of performing bioburden method development and validation studies. The method validation strategy described here, using a combination of tissue inoculation and repetitive extraction, showed the superiority of sonication plus mechanical shaking using Fluid D as the rinse medium. In addition, the use of only the exhaustive extraction approach could have resulted in the development of a methodology that consistently underestimated the bioburden present on/in recovered tissue.     

An improved method for estimating R-phycoerythrin and R-phycocyanin contents from crude aqueous extracts of <Emphasis Type="Italic">Porphyra</Emphasis> (Bangiales,Rhodophyta)

One frequently-cited method for determining phycoerythrin (PE) and phycocyanin (PC) contents from crude aqueous extracts of red seaweeds utilizes peaks and troughs of absorbance spectra. The trough absorbance values are used to establish a linear or logarithmic baseline attributable to background scatter of particulate cellular debris not removed by centrifugation. Pigment contents are calculated by subtracting baseline values from PE and PC absorbance peaks. The baseline correction is intended to make the method independent of centrifugation time and/or speed. However, when crude extracts of Porphyra were analyzed using this protocol, R-PE and R-PC estimates were significantly affected by centrifugation time, suggesting that the method was not reliable for the genus. The present study has shown that with sufficient centrifugation, background scatter in Porphyra extracts can be removed, the remaining spectrum representing the overlapping absorbance peaks of water-soluble pigments in the extract. Using fourth derivative analysis of Porphyra extract absorbance spectra, peaks corresponding to chlorophyll, R-PE, R-PC, and allophycocyanin (APC) were identified. Dilute solutions of purified R-PE, R-PC and chlorophyll were scanned separately to identify spectral overlaps and develop new equations for phycobilin quantification. The new equations were used to estimate R-PE and R-PC contents of Porphyra extracts and purified R-PE, R-PC and chlorophyll solutions were mixed according to concentrations corresponding to the sample estimates. Absorbances and fourth derivative spectra of the sample extract and purified pigment mixtures were compared and found to coincide. The newly derived equations are more accurate for determining R-PE and R-PC of Porphyra than previously published methods.     

Effect of freezing and thawing rates on denaturation of proteins in aqueous solutions

The freeze denaturation of model proteins, LDH, ADH, and catalase, was investigated in absence of cryoprotectants using a microcryostage under well-controlled freezing and thawing rates. Most of the experimental data were obtained from a study using a dilute solution with an enzyme concentration of 0.025 g/l. The dependence of activity recovery of proteins on the freezing and thawing rates showed a reciprocal and independent effect, that is, slow freezing (at a freezing rate about 1 degrees C/min) and fast thawing (at a thawing rate >10 degrees C/min) produced higher activity recovery, whereas fast freezing with slow thawing resulted in more severe damage to proteins. With minimizing the freezing concentration and pH change of buffer solution by using a potassium phosphate buffer, this phenomenon could be ascribed to surface-induced denaturation during freezing and thawing process. Upon the fast freezing (e.g., when the freezing rate >20 degrees C/min), small ice crystals and a relatively large surface area of ice-liquid interface are formed, which increases the exposure of protein molecules to the ice-liquid interface and hence increases the damage to the proteins. During thawing, additional damage to proteins is caused by recrystallization process. Recrystallization exerts additional interfacial tension or shear on the entrapped proteins and hence causes additional damage to the latter. When buffer solutes participated during freezing, the activity recovery of proteins after freezing and thawing decreased due to the change of buffer solution pH during freezing. However, the patterns of the dependence on freezing and thawing rates of activity recovery did not change except for that at extreme low freezing rates (<0.5 degrees C/min). The results exhibited that the freezing damage of protein in aqueous solutions could be reduced by changing the buffer type and composition and by optimizing the freezing-thawing protocol.     

冻融作用对陆地生态系统氮循环关键过程的影响效应及其机制

冻融作用是中、高纬度及高海拔地区土壤普遍存在的一种自然现象,是非生长季陆地生态系统氮循环的重要影响因素.冻融作用主要通过改变土壤的理化性质及生物学性状来影响氮素在土壤中的迁移与转化.目前,冻融作用对陆地生态系统氮循环各个过程影响的研究结果不尽一致,理论机制尚不明晰,研究方法也需进一步地探索与创新,因此有必要对现有成果进行梳理和分析,以更好地把握冻融作用下的氮循环过程.本文结合国内外已有研究成果,论述了冻融作用对陆地生态系统氮循环关键过程（氮矿化、固持、硝化与反硝化过程、氮淋溶及气态损失）的影响效应及其主要机制,对目前研究中存在的不足进行了剖析,并对未来研究中迫切需要关注的重点研究方向进行了探讨与展望.     

PCR and real time PCR for the detection of Cryptosporidium parvum oocyst DNA

Three DNA extraction kits were used, all without preliminary procedures, then DNA extraction was preceded with freeze/thaw cycles in three versions. A lack of desired effect resulted in the application of liquid nitrogen/water bath cycles before the use of the extractions in further experiments. The effectiveness of DNA extraction was measured by PCR signal and C(T) values of real time PCR. A comparison of the efficiency of various Cryptosporidium parvum undiluted oocyst treatments prior to DNA extraction with the use of three kits has shown that the best results were obtained after extraction of DNA with the QIAamp DNA Tissue Mini Kit (T kit), preceded by triple liquid nitrogen/water bath in 100 degrees C for 2 minutes and with overnight proteinase K digestion. After extraction with the T kit, the detection limit was 50 oocysts per 200 microl when effectiveness was evaluated with PCR and 10 oocysts in the case of real time PCR.     

Fluorescence from sensitizing phycobilin chromophores in the blue-green alga Anacystis nidulans.

Regeneration of the pigment system of Anacystis nidulans was studied following nitrate starvation. Three new, distinct fluorescence bands, at 596, 615 and 636 nm attributed to sensitizing phycobilin chromophores were detected. They each possess a separate excitation band at 425, 395 and 410 nm, respectively.     

Comparison of Various Methods for Preparation of Viral Serological Antigens from Infected Cell Cultures

In efforts to prepare more potent and sensitive viral serological antigens, several aspects of the production of antigens from infected cell cultures were studied. Antigens derived from whole, infected culture material and from the cellular and fluid phases were compared. Freezing and thawing, sonication, and alkaline buffer extraction were compared for effectiveness in releasing antigen from host cells. The effect of the multiplicity of infection on titers of viral antigens produced in cell cultures was studied. Generally, higher titered antigens were derived from the infected cells than from the culture fluids, but for certain viruses complement-fixing (CF) antigens derived from the culture fluids gave higher antibody titers than did cell-associated antigens. With each virus-host cell system studied, treatment with alkaline buffers extracted appreciable amounts of CF antigen from the host cells, but in some instances more antigen was released by freezing and thawing or by sonication. Extraction of infected cells with alkaline buffers was not a satisfactory method for preparation of hemagglutinating (HA) antigens for any of the viruses studied. The highest-titered HA antigens were produced from infected cells disrupted by freezing and thawing or sonication. The highest titered CF and HA antigens were produced from cell cultures infected at multiplicities of one or greater. Complement-fixing antigens produced by infecting cells in suspension and then planting had lower titers than antigens produced in parallel by infecting developed monolayers. Optimal methods are summarized for preparation of serological antigens to a variety of viruses of man.     

Mutagenicity studies of ambient airborne particles. II. Comparison of extraction methods

Organic materials were extracted with acetone from airborne particles by shaking, soxhletion and sonication for varying durations. 4-h, 1-h and 1/8-min extractions by shaking, soxhletion and sonication, respectively gave maximum his+ revertants with the Ames Salmonella/microsome assay. In a comparative study of extraction methods, sonication gave the highest and soxhletion the lowest mutagenic response. It appears that sonication with acetone is the best procedure for the extraction of mutagens from airborne particles as shown by Ames assay and Arar assay systems in Salmonella typhimurium.     

Fluorescence from sensitizing phycobilin chromophores in the blue-green alga Anacystis nidulans

Regeneration of the pigment system of Anacystis nidulans was studied following nitrate starvation. Three new, distinct fluorescence bands, at 596, 615 and 636 nm attributed to sensitizing phycobilin chromophores were detected. They each possess a separate excitation band at 425, 395 and 410 nm, respectively.     

EVALUATION OF PIGMENT EXTRACTION METHODS AND A RECOMMENDED PROTOCOL FOR PERIPHYTON CHLOROPHYLL a DETERMINATION AND CHEMOTAXONOMIC ASSESSMENT1

Many methods have been proposed to extract and quantify algal pigments. Comparative studies have found that pigment extraction efficiency varies among solvent and mechanical disruption protocols due to differential cellular resistance, thereby, leading to potential misinterpretation of pigment data. When the type or resistance of algae are unknown, a method is required that efficiently extract pigments from all taxonomic groups. The objective of this study was to develop a simple and efficient one stage periphyton pigment extraction protocol by comparing the extractability of four solvents (acetone, methanol, methanol/acetone, and methanol/acetone/N,N‐dimethylformamide), the effects of grinding, and the effects of freeze‐drying. The best overall extraction was obtained using freeze‐dried samples extracted with methanol/acetone/DMF/water (MAD). Eighty‐six percent more chlorophyll was extracted when the sample was freeze‐dried relative to fresh/frozen samples extracted with 90% acetone. Freeze‐drying greatly improved the extraction of both polar and non‐polar (lipophilic/hydrophobic) pigments while MAD increased the extractability of polar pigments and improved peak resolution of all pigments. Chemotaxonomic assessment differed between samples that were fresh/frozen or freeze‐dried before extraction. The relative abundance of cyanobacteria was greater for freeze‐dried material compared with fresh/frozen due to the improved extractability of cyanobacterial pigments. Based on the results of this study, the traditional approach of 90% acetone as a solvent is not recommended for periphyton samples containing cyanobacteria or when the composition of the mat is unknown. The combination of freeze‐drying and MAD was sufficient for the extraction of pigments from a periphyton mat containing filamentous cyanobacteria, green algae, and diatoms.     

A simple method for the extraction and quantification of photopigments from Symbiodinium spp.

We have developed a simple, mild extraction procedure using methanol which, when coupled with HPLC analysis and diode array detection (DAD), can be used to quantify the major photopigments found in cultured Symbiodinium spp. Extracts were prepared by suspending, fresh or frozen (− 70 °C), wet cell pellets in methanol and sonicating or not sonicating the cell suspensions before soaking the cells for 2 h in an ice bath. To assist the soaking process, cell suspensions were vortex mixed at 30 min intervals. After soaking, 0.5 M ammonium acetate buffer was added (1 part buffer to 9 parts methanol) before suspensions were stored over night at − 20 °C. Greater than 92% the recoverable pigment was obtained in the initial extraction of the four major photopigments, chlorophyll c, peridinin, diadinoxanthin, and chlorophyll a. Neither sonication nor freezing substantially increased the recovery of photopigments extracted with methanol. Extraction by other commonly used solvents such as acetone or acetone:water with or without freezing and sonication were less effective.     

Effects of freezing to −196 °C and thawing on Setaria lutescens seeds

The effects of single and repeated freezing and thawing of Setaria lutescens seeds in liquid nitrogen were investigated. One freeze to ?196 °C followed by a slow thaw, increased seed germination from 40 to 70%, but additional freeze-thaw cycles reduced germination to 30%. Using a scanning electron microscope, evidence was produced that seed coat cracking did not cause either initial increased, or subsequent reduced germination. Observations with a transmission electron microscope revealed that disruption of the integrity of lipid bodies accompanied increased damage from repeated freezing at ?196 °C and thawing. Repeated freezing and thawing of seeds stored in liquid nitrogen should be done with care to avoid loss of the germplasm.     

Studies on excitation energy flow in the photosynthetic pigment system; Structure and energy transfer mechanism

Excitation energy flow in photosynthetic pigment systems is discussed in relation to structure of the system and transfer mechanism for each elementary process. Three typical examples for actual transfer processes are shown for the phycobilin system in cyanobacteria, the antenna system of photosynthetic bacteria and the Chla/c antenna system of brown algae. The main analytical method was the time-resolved fluorescence spectroscopy in the picosecond time range. In general, static optical charactersitics are not the main reason for the transfer efficiency, but the structure of the system is a prerequisite for the transfer process. On the phycobilin system, theoretical investigation was compared with experimental analysis, which leads to the essential understanding of the transfer process in terms of quantum mechanics. Recipient of the Botanical Society Award for Young Scientists, 1989.     

Monitoring of active but non-culturable bacterial cells by flow cytometry

Flow cytometric signatures (i.e., light scatter, red and green fluorescence) were obtained for the active but non-culturable (ABNC) cells of E. coli and a coliform isolate H03N1, in seawater microcosms using BacLight, a live-dead assay kit from Molecular Probes (Eugene/Portland, OR). Previous studies have reported that there are two major adaptations, which cells undergo during the formation of ABNC states: cell wall toughening and DNA condensation. Therefore, we hypothesized that the matured ABNC forms should be more resistant to extreme temperature treatments (i.e., by freezing in liquid nitrogen and thawing at room temperature) than the normal and transition populations. It was shown that the membrane-compromised cells (comprising of normal wild-type and dead cells which are less resistant to rapid freeze thaw) could be differentiated from the matured ABNC using BacLight staining and fluorescence detection by flow cytometry. The population of ABNC cells, which could not be cultured using m-FC media (for the enumeration of fecal coliforms), was resuscitated in phosphate buffer saline followed by growth in Luria broth. Flow cytometry was thus able to detect and differentiate the ABNC cells against a mixed population comprising of culturable cells, transition populations, and dead cells. The results also showed that the formation of ABNC is as early as 2 days in seawater microcosms. By directly comparing the coliform levels enumerated by the BacLight based flow cytometry assays and m-FC technique, it was shown that the presence of coliforms can be undetected by the membrane filtration method.     

A simplified method for screening acetylcholinesterase inhibitors by the flesh fly (Dipt., Sarcophagidae) cell culture system

A simplified economical method for assaying acetylcholinesterase inhibitors was devised. A flesh fly, Sarcophaga peregrina Robineau-Desvoidy, cell line, NIH-SaPe-4, was cultured in 96-well microplates at 25°C. After 2 days culture, the culture media was removed and phosphate buffer was introduced. The cells were disintegrated by freezing–thawing, and a reaction mixture containing substrate, inhibitor, and colour developer was added. The change of absorbance at 405 nm at 25°C was measured with a microplate photometer and the concentration of the test substance required to inhibit the enzyme reaction by 50% (I₅₀) was calculated.     

High-performance liquid chromatographic assay for 3′-amino-3′-deoxythymidine in plasma,with 9-fluorenyl methyl chloroformate as the derivatization agent

We have developed a sensitive high-performance liquid chromatographic assay for the determination of the zidovudine metabolite 3′-amino-3′-deoxythimidine (AMT) using fluorescence detection and sensitivity in the picomolar range. Plasma was diluted with 0.05 M sodium phosphate buffer pH 7.2 and subsequently prepared for analysis using solid-phase extraction. AMT was derivatized with 9-fluorenyl methylchloroformate and chromatographed using a reversed-phase system. The mobile phase consisted of acetonitrile-0.01 M potassium phosphate buffer (pH 7) (32:68, v/v). The fluorescence of the column effluent was monitored at 262 nm (excitation) and 306 nm (emission). Good resolution of AMT from endogenous plasma components was obtained. Within- and between-day variability was less than 10%. The limit of quantitation was 0.9 μg/l. The assay was successfully applied to the determination of AMT in human plasma and plasma of mice treated with zidovudine.     

Ammonium chloride: a novel effective and inexpensive salt solution for phycocyanin extraction from <Emphasis Type="BoldItalic">Arthrospira</Emphasis> (<Emphasis Type="BoldItalic">Spirulina</Emphasis>) <Emphasis Type="BoldItalic">platensis</Emphasis>

Phycocyanin, a blue pigment, is a type of phycobiliproteins. Because of its various potential properties, phycocyanin is applied to various fields, such as nutraceutical, pharmaceutical, medicine, cosmetics, and biotechnological research. The cost and application of phycocyanin are highly dependent on its purity index. In this study, ammonium chloride is presented as a novel, effective, and inexpensive salt for phycocyanin extraction. Compared with sodium phosphate, which is commonly used during phycocyanin extraction process, ammonium chloride solution efficiently extracted phycocyanin with high purity from Arthrospira platensis FACHB-314. In addition, ammonium phosphate solution is also presented as an alternative precipitation agent in phycocyanin purification that may replace the widely used ammonium sulfate. Statistical analysis shows that there is no significant difference in phycocyanin concentration between crude extracts (overall mean of 0.208 and 0.215 for extraction using sodium phosphate and ammonium chloride, respectively). However, the difference in phycocyanin purity ratio (A₆₂₀/A₂₈₀) between these two extractions is significant (overall mean of 0.742 and 1.428 for extraction using sodium phosphate and ammonium chloride, respectively). With ammonium chloride, the purity indexes of phycocyanin are 1.5 and 2.81 after the optimum extraction step, and precipitation used as the primary purification step, respectively. The present study describes a novel purification method to achieve phycocyanin with analytical grade without multiple purification steps.     

Measurement of cytoplasmic pH in Dictyostelium discoideum by using a new method for introducing macromolecules into living cells

We have developed a novel method for introducing exogenous macromolecules from solution into the cytoplasm of living amoebae of the cellular slime mold Dictyostelium discoideum and have used it to measure the cytoplasmic pH of these cells. Amoebae (strain NC-4) were loaded with fluorescein-labelled dextran by sonication in a solution containing 17 mM phosphate buffer, 1 mM CaCl2, and 10 mg/ml of fluorescein-labelled dextran, pH 6.1. The recovery of living cells was approximately 40% after sonication and washing. A significant fraction (10%) of the recovered cells were loaded and contained 10(5) to 10(7) molecules of fluorescein-labelled dextran per cell as assessed by flow cytometry. The cells loaded by sonication appeared both viable and healthy, since they exhibited normal morphology and locomotion, could differentiate to form mature fruiting bodies, could chemotax in a gradient of extracellular cAMP, and could endocytose latex microspheres. The pH of single cells was estimated by using flow cytometry to measure the fluorescence ratio (fluorescein/rhodamine) in cells loaded with a mixture of the two fluorochrome-labelled dextrans. The fluorescence ratios were calibrated in situ with the flow cytometer after treatment of the cells with either weak acid or weak base to clamp the internal pH at known values. The intracellular pH measured in cells loaded with dextran in a simple salt solution was 5.9. The intracellular pH measured in cells loaded with dextran in the same solution supplemented with amino acids and glucose was 6.7. The novel sonication loading technique described may have general utility for loading diverse types of macromolecules into suspensions of living cells.     

Regulation of the distribution of chlorophyll and phycobilin-absorbed excitation energy in cyanobacteria. A structure-based model for the light state transition

The light state transition regulates the distribution of absorbed excitation energy between the two photosystems (PSs) of photosynthesis under varying environmental conditions and/or metabolic demands. In cyanobacteria, there is evidence for the redistribution of energy absorbed by both chlorophyll (Chl) and by phycobilin pigments, and proposed mechanisms differ in the relative involvement of the two pigment types. We assayed changes in the distribution of excitation energy with 77K fluorescence emission spectroscopy determined for excitation of Chl and phycobilin pigments, in both wild-type and state transition-impaired mutant strains of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803. Action spectra for the redistribution of both Chl and phycobilin pigments were very similar in both wild-type cyanobacteria. Both state transition-impaired mutants showed no redistribution of phycobilin-absorbed excitation energy, but retained changes in Chl-absorbed excitation. Action spectra for the Chl-absorbed changes in excitation in the two mutants were similar to each other and to those observed in the two wild types. Our data show that the redistribution of excitation energy absorbed by Chl is independent of the redistribution of excitation energy absorbed by phycobilin pigments and that both changes are triggered by the same environmental light conditions. We present a model for the state transition in cyanobacteria based on the x-ray structures of PSII, PSI, and allophycocyanin consistent with these results.