An alternative nonradioactive method for labeling DNA using biotin

An alternative nonradioactive labeling method and a highly sensitive technique for detecting specific DNA sequences are described. The labeling method requires the "Klenow" fragment of DNA polymerase I and random hexanucleotides (synthesized or naturally extracted) as a primer for the production of highly sensitive DNA probes. The system has three main steps: (i) labeling of DNA with biotinylated 11-dUTP; (ii) detection of biotinylated DNA by a one-step procedure with streptavidin-alkaline phosphatase complex; (iii) blocking of background with Tween 20. Twenty attograms (2 X 10(-17) g) of pBR322 plasmid DNA was detected by dot-blot hybridization. Upon Southern blot hybridization, 7.4 fg (7.4 X 10(-15) g) of pBR322 HindIII DNA was detected using the biotinylated pBR322 plasmid DNA probe; 40.8 ag and 7.4 fg of lambda HindIII DNA were detected with the biotinylated whole lambda DNA probe by dot and Southern blot hybridization, respectively. Specific bands were also detected with the biotinylated argininosuccinolyase probe upon Northern blotting of mouse poly(A+) RNA. Further applications for in situ hybridization are also described.     

An alternative method for the culture of Diplostomum spathaceum (Trematoda) in chick embryos

Metacercariae of Diplostomum spathaceum were maintained in the allantoic cavities of chick embryos for 15 days. Some embryos had 0.2 ml chicken serum added to the allantoic cavity each day. Although the level of development varied considerably, worms from embryos with added serum developed hind bodies that were substantially larger than those of parasites maintained without added serum. There was no evidence that any worm ingested blood, and only 1 individual, from the serum-augmented group, became ovigerous.     

An alternative sputum processing method using chitin for the isolation of Mycobacterium tuberculosis

An alternative bio-friendly sputum processing method is the need of the hour to augment the rate of detection of TB cases and to improve the sensitivity of rapid growth based diagnostic methods. Chitin, mucolytic in nature and present ubiquitously in animal kingdom, was found to have decontaminating activity when used for processing sputum specimens. The aim of the present study is to develop an alternative bio friendly sputum processing method using chitin. Smear microscopy was done on direct sputum samples and on the deposits obtained after processing with modified Petroff’s method as well as Chitin method. Two direct smears were made from each of the sputum samples and stained by Ziehl Neelsen and Auramine phenol (AP) method. The samples were divided in to two aliquots and processed by chitin and modified Petroff’s method. Smears were made from each of the deposits and stained by both methods. The deposits were inoculated on to two Lowenstein Jensen slopes. AP method showed a sensitivity of 95% in direct smear. Samples processed by chitin and the deposit smears stained by AP method showed a sensitivity of 80% and a specificity of 89% compared to that of modified Petroff’s method. The sensitivity of chitin culture is 87% and the specificity is 85%. Chitin–H₂So₄ solution took less time compared to 4% NaOH to homogenize the mucopurulent sputum specimens. Chitin–H₂So₄ can be used as an alternative method of sputum processing for the detection of M. tuberculosis.     

An alternative method for irones quantification in iris rhizomes using headspace solid-phase microextraction

Introduction – The essential oil obtained from iris rhizomes is one of the most precious raw materials for the perfume industry. Its fragrance is due to irones that are gradually formed by oxidative degradation of iridals during rhizome ageing. Objective – The development of an alternative method allowing irone quantification in iris rhizomes using HS‐SPME‐GC. Methodology – The development of the method using HS‐SPME‐GC was achieved using the results obtained from a conventional method, i.e. a solid–liquid extraction (SLE) followed by irone quantification by CG. Results – Among several calibration methods tested, internal calibration gave the best results and was the least sensitive to the matrix effect. The proposed method using HS‐SPME‐GC is as accurate and reproducible as the conventional one using SLE. These two methods were used to monitor and compare irone concentrations in iris rhizomes that had been stored for 6 months to 9 years. Conclusion – Irone quantification in iris rhizome can be achieved using HS‐SPME‐GC. This method can thus be used for the quality control of the iris rhizomes. It offers the advantage of combining extraction and analysis with an automated device and thus allows a large number of rhizome batches to be analysed and compared in a limited amount of time. Copyright © 2010 John Wiley & Sons, Ltd.     

Fin-spines attachment,a novel external attachment method for the ultrasonic transmitters on hard fin-spines fish (Sparidae)

The purpose of this study was to develop a novel method for the external attachment of ultrasonic transmitters on hard fin-spines fish (Sparidae). Acanthopagrus latus, one of the main stocking Sparidae fishes in the northern South China Sea, was employed to conduct the 40-day tank experiment by using dummy ultrasonic transmitters. The experiment consisted of 3 treatment groups, i.e., drilling on dorsal fin-spine (DD) group, drilling on anal fin-spine (DA) group, and control (C) group, with each group having 3 replicates and 30 fish per replicate. The feasibilities of DD and DA for the external attachment of ultrasonic transmitters were tested and evaluated using parameters: the specific growth rate, survival rate, and tag retention rate of each group. And the tagging procedures for the external attachment of hard fin-spines fish were also proposed. The results showed that there were no significant differences in the specific growth rate of fish between groups. Both the survival rates of DD group (96.67%) and DA group (94.44%) were less (but not significant) than C group (97.78%), while the tag retention rate of DA group (100%) was higher (but not significant) than DD group (98.89%). These results demonstrate that drilling on dorsal or anal fin-spines is feasible as an external attachment method of ultrasonic transmitters on Sparidae fishes. In addition, considering the friction between the tagged transmitters and rocks at the bottom of natural waters, which possibly affect the fish behaviors such as swimming, feeding, etc., or lead to tag loss, so drilling on the dorsal fin-spine is preferred for rocky-bottom Sparidae fishes like A. latus as small as 14 cm body length.     

An alternative method of endotracheal intubation of common marmosets (Callithrix jacchus)

Endotracheal intubation was carried out in 11 common marmosets (Callithrix jacchus). A commercially available tilting stand and a Miller laryngoscope blade were used to visualize the larynx. Anaesthesia was induced with alphaxalone (10.6 ± 1.6 mg/kg intramuscularly, followed by 3.2 ± 1.2 mg/kg intravenously). The diameter of the proximal trachea easily fitted an endotracheal tube made from readily available material (a 12 G 'over the needle' catheter). Once the tip of the endotracheal tube was at the level of the vocal folds, the tube had to be gently rotated through a 180° angle in order to pass through the larynx into the trachea. Assessment of the dimensions of the larynx and trachea, and comparison with external anatomical features of the animals (n = 10) showed that the length of the trachea could be predicted by multiplying the craniosacral length of the marmoset by a factor of 0.42.     

Novel BOD (biological oxygen demand) sensor using mediator-less microbial fuel cell

A microbial fuel cell type of biosensor was used to determine the biochemical oxygen demand (BOD) of wastewater. The biosensor gave a good correlation between the BOD value and the coulomb produced. The BOD sensor has been operated for over 5 years in a stable manner without any servicing. This is much longer that that of previously reported BOD biosensors.     

An extraction method for nematodes in decomposition studies using the minicontainer-method

The minicontainer-method is a new method developed to study biological processes related to soil litter decomposition. An adaptation of the classical Baermann-funnel technique is described which can be used, in association with the minicontainer method, to investigate the role of Nematoda in litter decomposition. The use of the extraction method is illustrated in a study of the effects of different tillage systems on the decomposition of rye straw and on the nematode density in minicontainers with different mesh sizes of 20 µm, 500 µm and 2 mm. Three tilled plots (conventional deep plough, cultivator and two-layer plough) and an untilled control were compared after periods of 4 weeks and 38 weeks. On both sample dates there were significant main effects of treatment and mesh size on the nematode density, and additionally, after 38 weeks significant treatment x soil depth interactions. After 4 weeks, there were significant main effects of treatment and soil depth on the decomposition, but no mesh size effects, whereas after 38 weeks, all experimental factors had a significant effect on the decomposition of the straw. Due to the small volume of litter substrate used in the minicontainer method, the efficiency of nematode extraction is high and the lack of oxygen in the minicontainers presents no serious problem during the extraction process. The method also allows the simultaneous extraction of a large number of samples within a short period of time. Our results indicate that the method is suitable to study the microdistribution of nematode activity within the soil profile and improves the possible applications of the minicontainer-method.     

Identification and characterization of the T lymphocyte adhesion receptor for an alternative cell attachment domain (CS-1) in plasma fibronectin

Using mAb technology (Wayner, E. A., W. G. Carter, R. Piotrowicz, and T. J. Kunicki. 1988. J. Cell Biol. 107:1881-1891), we have identified a new fibronectin receptor that is identical to the integrin receptor alpha 4 beta 1. mAbs P3E3, P4C2, and P4G9 recognized epitopes on the alpha 4 subunit and completely inhibited the adhesion of peripheral blood and cultured T lymphocytes to a 38-kD tryptic fragment of plasma fibronectin containing the carboxy-terminal Heparin II domain and part of the type III connecting segment (IIICS). The ligand in IIICS for alpha 4 beta 1 was the CS-1 region previously defined as an adhesion site for melanoma cells. The functionally defined mAbs to alpha 4 partially inhibited T lymphocyte adhesion to intact plasma fibronectin and had no effect on their attachment to an 80-kD tryptic fragment containing the RGD (arg-gly-asp) adhesion sequence. mAbs (P1D6 and P1F8) to the previously described fibronectin receptor, alpha 5 beta 1, completely inhibited T lymphocyte adhesion to the 80-kD fragment but had no effect on their attachment to the 38-kD fragment or to CS-1. Both alpha 4 beta 1 and alpha 5 beta 1 localized to focal adhesions when fibroblasts that express these receptors were grown on fibronectin-coated surfaces. These findings demonstrated a specific interaction of both receptors with fibronectin at focal contacts. In conclusion, these findings show clearly that cultured T lymphocytes use two independent receptors during attachment to fibronectin and that (a) alpha 5 beta 1 is the receptor for the RGD containing cell adhesion domain, and (b) alpha 4 beta 1 is the receptor for a carboxy-terminal cell adhesion region containing the Heparin II and IIICS domains. Furthermore, these data also show that T lymphocytes express a clear preference for a region of molecular heterogeneity in IIICS (CS-1) generated by alternative splicing of fibronectin pre-mRNA and that alpha 4 beta 1 is the receptor for this adhesion site.     

Potential of partial rootzone drying as an alternative irrigation technique for potatoes (Solanum tuberosum)

The increasing demands on limited water supplies worldwide require the adoption of more efficient irrigation techniques for sustainable production in agriculture. Partial rootzone drying (PRD) is one of the techniques that offer potential saving of irrigation water. This technique involves alternate irrigation to two sides of a plant root system. The studies reported here investigated PRD irrigation regimes and the optimum time of starting PRD in potatoes grown in a protected environment. In the first experiment, plants of the potato cv. Estima were exposed to five different irrigation treatments and a fully watered control at tuber initiation. The treatment that performed most similar to the control was alternate PRD to field capacity (APRD₁₀₀). This treatment produced similar total leaf area, haulm fresh and dry weights, plant water status and no significant yield reduction compared with the control plants. The APRD₁₀₀ treatment utilised 29% less water and increased water use efficiency (WUE) by 19%. In the second experiment, the APRD₁₀₀ irrigation was started at 2, 4, 6, 8 and 10 weeks after plant emergence. Vegetative growth and yield increased with the delay of the APRD₁₀₀. APRD₁₀₀ started at 6 weeks after emergence did not significantly reduce fresh tuber yield but received 21% less total water with a 19% increase in WUE. The results indicate that PRD may have potential use in the potato crop for conserving irrigation water with minimal loss of yield.     

An improved cell recovery method for iron oxidizing bacterial (IOB) enrichments

Two cell recovery methods for IOB enrichments were evaluated for DNA extraction and further PCR-based 16S rRNA gene clone library creation. One was a published method consisting of heating plus oxalic acid treatment and the other one was a new method based on enzymatic agarose digestion (using beta-agarase I). The results indicated that the enzymatic method was much gentler on IOB cells and yielded an approximately 5000-fold higher DNA mass than the published method. The 16S rRNA gene clone library developed from the beta-agarase I treated IOB enrichments indicated a high IOB community diversity with sequences in alpha-, beta-, gamma-, delta-, epsilon-Proteobacteria, unclassified Proteobacteria, unclassified Bacteroidetes and unclassified Bacteria. In contrast, the published method resulted in mainly gamma-Proteobacterial clone sequences. In addition, only the cells recovered by agarase treatment were amenable to direct fluorescence in situ hybridization (FISH). Therefore, we propose that the agarase method is a better IOB cell recovery method, because it is simpler, faster, and retains more genetic diversity.     

An alternative Candida spp. cell wall disruption method using a basic sorbitol lysis buffer and glass beads

This report describes a modified, cost-effective method of cell wall disruption for the yeast Candida spp., which employs the use of glass beads in a simple sorbitol lysis buffer. This method can be used in conjunction with a commercial RNA or genomic DNA isolation method to obtain high-quality RNA or DNA.     

An alternative Candida spp. cell wall disruption method using a basic sorbitol lysis buffer and glass beads

This report describes a modified, cost-effective method of cell wall disruption for the yeast Candida spp., which employs the use of glass beads in a simple sorbitol lysis buffer. This method can be used in conjunction with a commercial RNA or genomic DNA isolation method to obtain high-quality RNA or DNA.     

An alternative quantitative acoustical and electrical method for detection of cell adhesion process in real-time

Sauerbrey [(1956), Z Phys 55:206-222] showed that the shift in resonance frequency of thickness shear mode (TSM) of a quartz crystal sensor is proportional to the mass, which is deposited on it. However, new powerful electrical circuits were developed that are capable of operating TSM quartz crystal sensors in fluids which enabled this method to be introduced into electrochemical and biological applications. These applications include the detection of virus capsids, bacteria, mammalian cells, the interaction of DNA and RNA with complementary strands, specific recognition of protein ligands by immobilized receptors, and last but not least the study of complete immunosensors. Piezoelectric quartz transducers allow a label-free identification of molecules; they are more than mass sensors since the biosensor response is also influenced by the surface charge of adsorbed proteins, interfacial phenomena, surface roughness and viscoelastic properties of the adhered biomaterial. These new characteristics have recently been used to investigate cell, liposome, and protein adhesion onto surfaces, thus permitting the rapid determination of morphological cell changes as a response to pharmacological substances, and changes in the water content of biopolymers avoiding of time-consuming methods. We validated an alternative quantitative acoustical engineering for cell adhesion process monitored by the TSM. Shear acoustical results (motional resistance) are further correlated to cell counting procedures and are sensitive of adhesion processes in real-time.     

A method for microbial cell surface fingerprinting based on surface plasmon resonance

A method for microbial cell surface fingerprinting using surface plasmon resonance (SPR) is suggested. Four different Escherichia coli mutants have been used as model cells. Cell surface fingerprints were generated by registration of the interaction between the cell mutants and four different surfaces, with different physical and chemical properties, when a cell suspension was flown over the surface. Significant differences in fingerprint pattern between some of the mutants were observed. At the same time, the physical properties of the cell surfaces were determined using microelectrophoresis, contact angle measurements and aqueous two-phase partitioning and compared to the SPR fingerprints. The generated cell surface fingerprints and the physical property data were evaluated with multivariate data analysis that showed that the cells were separated into individual groups in a similar way using principal component analysis plots (PCA).     

A method for microbial cell surface fingerprinting based on surface plasmon resonance

A method for microbial cell surface fingerprinting using surface plasmon resonance (SPR) is suggested. Four different Escherichia coli mutants have been used as model cells. Cell surface fingerprints were generated by registration of the interaction between the cell mutants and four different surfaces, with different physical and chemical properties, when a cell suspension was flown over the surface. Significant differences in fingerprint pattern between some of the mutants were observed. At the same time, the physical properties of the cell surfaces were determined using microelectrophoresis, contact angle measurements and aqueous two-phase partitioning and compared to the SPR fingerprints. The generated cell surface fingerprints and the physical property data were evaluated with multivariate data analysis that showed that the cells were separated into individual groups in a similar way using principal component analysis plots (PCA).     

The use of psyllium (isubgol) as an alternative gelling agent for microbial culture media

Psyllium (Isubgol), the mucilage husk of Plantago ovata, was successfully used as an alternative gelling agent (5% w/v as ground husk for pouring medium and 4% w/v as ground husk in combination with 0.5% w/v agar for slant) for microbial culture. Most of the undesirable features of psyllium-gelled media (slant as well as pouring) were removed by adding the u.v.-treated (20min) or oven-sterilized (120^°C for 1h) psyllium as ground husk to autoclaved medium at 50–60^°C under aseptic condition just before pouring.     

Perfusion method for assaying microbial activities in sediments: applicability to studies of n(2) fixation by c(2)h(2) reduction

A perfusion method for assaying nitrogenase activity (acetylene reduction) in marine sediments was developed. The method was used to assay sediment cores from Spartina alterniflora (salt marsh), Zostera marina (sea grass), and Thalassia testudinum (sea grass) communities, and the results were compared with those of conventional sealed-flask assays. Rates of ethylene production increased progressively with time in the perfusion assays, reaching plateau values of 2 to 3 nmol . g of dry sediment . h by 10 to 20 h. Depletion of interstitial NH(4) was implicated in this stimulation of nitrogenase activity. Initial acetylene reduction rates determined by the perfusion assay of cores from the Spartina community ranged from 0.15 to 0.60 nmol of C(2)H(4) . g of dry sediment . h. These rates were similar to those for sediments assayed in sealed flasks without seawater when determined over linear periods of C(2)H(4) production. Initial values obtained by using the perfusion method were 0.66 nmol of C(2)H(4) . g of dry sediment . h for sediments from Zostera communities and 0.70 nmol of C(2)H(4) . g of dry sediment . h for sediments from Thalassia communities. In all cases, rates determined by simultaneous slurry assays were lower than those determined by the perfusion method.     

An alternative, less invasive blood sample collection technique for serologic studies utilizing triatomine bugs (Heteroptera; Insecta)

The collection of blood samples for serological studies is often stressful for the focus animal. Recently, the use of bloodsucking bugs, such as Dipetalogaster maximus or Triatoma infestans (Reduviidae; Triatominae; Heteroptera), has been suggested as a new and less invasive method for blood collection. To evaluate this technique, we collected paired blood samples from 20 domestic rabbits (Oryctolagus cuniculus) during a study of rabbit hemorrhagic disease virus (RHDV). For each rabbit, blood samples were collected by the conventional method (needle and syringe from the vena auricularis) and through feeding by D. maximus. Samples were tested for RHDV antibodies using standard test kits at three different dilutions. Antibody titers were identical for 56 paired samples and differed in only four cases. The simple matching indices were 1 for the 1:10 dilution and 0.9 for the 1:100 and 1:1000 dilutions. The major advantages of the new technique are 1) the possibility to obtain blood from animals where veins are inaccessible and 2) the fact that anesthesia of focus animals may not be necessary.