A process-orientated design and performance assessment methodology for passive mine water treatment systems

The aim of this paper is the development of a methodology for assessing the iron removal efficiency of passive mine water treatment settling lagoons and reed beds. Previous work in the design and sizing of coal mine drainage lagoons and wetlands has focussed on the use of standard hydraulic residence times or using the 10 g m⁻² d⁻¹ metric, these criteria have been applied without regard to the fundamental physical and chemical processes controlling iron removal in the system, namely the pH dependent rates of Fe(II) oxidation and physical settling of the particulate Fe(III). In this study field water quality data have been collected from lagoons and reed beds. These data are examined alongside data from the UK Coal Authority database and combined with simple mathematical formulations to provide a framework through which to understand passive treatment schemes from a process-orientated perspective. It is demonstrated that for the sites studied reed beds are more efficient for iron removal. This paper recommends that judgements of iron removal performance should be based on a derived treatment efficiency index (?) and that the modelling approach espoused in this paper should be used when designing passive mine water treatment schemes.     

Protein function annotation by homology-based inference

With many genomes now sequenced, computational annotation methods to characterize genes and proteins from their sequence are increasingly important. The BioSapiens Network has developed tools to address all stages of this process, and here we review progress in the automated prediction of protein function based on protein sequence and structure.     

Organ culture as a model for investigating the effects of antimetabolites and nucleoside transport inhibitors on rodent colonic mucosa

Summary The in-vitro effects of hydroxyurea 5-FU and 5-FUdR have been extensively studied in experimental systems employing cell-line techniques. In this study we investigated the effects of these drugs on the levels of incorporation of labeled nucleosides into DNA in explants of intact rat colonic mucosa maintained in organ culture. The effects of the nucleoside transport inhibitors nitrobenzylthioinosine (NBMPR) and dipyridamole—which are modulators of antimetabolite cytotoxicity—on the incorporation of tritiated thymidine [(³H]TdR) into DNA were also studied. The incorporation of tritiated TdR into DNA was reduced by hydroxyurea but was not altered by either 5-FU or 5-FUdR. The levels of tritiated deoxyuridine were reduced by 5-FU and 5-FUdR in separate experiments; this is in keeping with thymidylate synthase inhibition. NBMPR and dipyridamole also reduced 3H-TdR incorporation into DNA. These results can be explained in terms of the known mechanisms of action of these drugs. This experimental model is therefore useful in assessing the effects of antimetabolites and nucleoside transport inhibitors in intact colonic mucosa.     

A blood sampling technique for prehatched chicks

ABSTRACT Collecting blood from neonatal or prehatched chicks is sometimes necessary, requiring specialized blood collection techniques and skills. However, such sampling can be difficult and could potentially have adverse effects. I developed a method for collecting blood from chicks still in an egg. The technique involves enlarging the pipping hole, removing the chick's head to take blood from a jugular vein, and returning the chick into its original position in the egg to complete hatching back in the nest. I used this technique on Crested Tern (Thalasseus bergii) chicks (N= 13), with no apparent adverse effects to growth or short‐term survival. The amount of blood extracted (0.1–0.15 ml) was sufficient for a blood smear, hematocrit, and total white blood cell count. This method should be useful for eggs as small as 40 mm in length; eggs smaller than this would likely not be good candidates for this technique because eggshells may be too thin to safely handle. This technique may be useful for investigators studying the immunological and endocrinological transition between embryos and hatchlings.     

Clinical report: Recovery of a degenerating 14-day embryo in the uterine flush of a mare 7 days after ovulation

A 15-mm diameter degenerating embryonic vesicle and a normal, 200-u early blastocyst were recovered in a uterine flush of a mare 7 d after ovulation. From its size, the degenerating vesicle appeared to be 13 to 14 d of age. The mare had been bred during a previous cycle and then treated with prostaglandin 9 days after ovulation. The advanced vesicle that was recovered suggests that a conceptus from the previous cycle continued to grow for about 5 d after prostaglandin administration, and remained in the uterus during estrus, when plasma progesterone concentrations were below 1 ng/ml. From the estimated age of the conceptus, its development stopped at about the time the mare was inseminated. Had this conceptus survived through estrus and insemination, superfetation would have occurred.     

Subpopulation analysis of drug-induced cell-cycle delay in human tumor cells using 90 degrees light scatter

A mitotic cell subset has been identified with nuclear light scatter. Colcemid-treated T-47D human breast cancer cells were permeabilised, stained with ethidium bromide, and analysed by flow cytometry. Cells with G2M DNA content exhibited a unimodal distribution for DNA fluorescence and forward scatter, but two peaks were discernible with 90 degrees light scatter. A discrete low-scattering cell cluster could be distinguished from the G2 cell subset on two-dimensional contour plots of 90 degrees light scatter vs. DNA fluorescence; this cluster was reproduced by mitotic shake-off experiments and varied quantitatively with mitotic indices determined either by microscopy or by stathmokinetic cell-cycle analysis of DNA fluorescence. Cell sorting confirmed that the low-scattering cell cluster comprised predominantly metaphase and anaphase cells. Identification of mitotic cells with this one-step technique enables rapid analysis of drug-induced cell-cycle delay in cell populations with different rates of cell-cycle traverse. Hence, vincristine-induced cytostasis is shown to arise in part because of premitotic G2 arrest, whereas etoposide is shown to affect cycling cells with equal sensitivity in quiescent and activated cell populations. The use of light scatter to discriminate mitotic cells in this way facilitates analysis of drug-induced cell-cycle delay and supplements the information obtainable by conventional cell-cycle analysis.     

Comparative evaluation of fresh, fixed, and cryopreserved solid tumor cells for reliable flow cytometry of DNA and tumor associated antigen.

Five different protocols for the short-term preservation of cells used for multiparameter flow cytometric assay of tumour associated antigens (TAA) and DNA were assessed in cell suspensions prepared by mechanical disaggregation of 15 gynecological tumors. The protocols at 4 degrees C were 1) storage in buffer, 2) storage in 50% methanol, and 3) storage in buffer after formalin fixation. Tissues were also cryopreserved as cell suspensions and tissue blocks. When the TAA expression and DNA histograms of the preserved cells were compared with those in fresh cell suspensions, cryopreservation was found to be the best method: TAA expression was well preserved and there was a good correlation between TAA expression and the quality of the DNA histograms, respectively, in fresh and cryopreserved cells (RS: 0.82-0.91, P less than 0.001 for all TAAs). The cell suspensions preserved at 4 degrees C all showed a significant increase in background fluorescence (P less than 0.05) and a reduction in the TAA specific fluorescence (P less than 0.011). Methanol fixation was better than buffered formalin for the proteins studied, though both gave significantly worse results than cryopreservation. The quality of these cell suspensions and the correlation with TAA measurements in fresh cell suspensions deteriorated progressively with time, particularly if they were stored more than a week.     

Convenient and Efficient Syntheses of Oligodeoxyribonucleotides Containing O 6-(Carboxymethyl)Guanine and O 6-(4-Oxo-4-(3-Pyridyl)Butyl)Guanine

O ⁶-(carboxymethyl)guanine (O ⁶-CMG) and O ⁶-(4-oxo-4-(3-pyridyl)butyl)guanine (O ⁶-pobG) are toxic lesions formed in DNA following exposure to alkylating agents. O ⁶-CMG results from exposure to nitrosated glycine or nitrosated bile acid conjugates and may be associated with diets rich in red meat. O ⁶-pobG lesions are derived from alkylating agents found in tobacco smoke. Efficient syntheses of oligodeoxyribonucleotides (ODNs) containing O ⁶-CMG and O ⁶-pobG are described that involve nucleophilic displacement by the appropriate alcohol on a common synthetic ODN containing the reactive base 2-amino-6-methylsulfonylpurine. ODNs containing O ⁶-pobG and O ⁶-CMG were found to be good substrates for the S. pombe alkyltransferase-like protein Atl1.

[Supplemental materials are available for this article. Go to the publisher's online edition of Nucleosides, Nucleotides & Nucleic Acids to view the free supplemental file.]