Bovine viral diarrhoea virus antigen in foetal calf serum batches and consequences of such contamination for vaccine production.

A protocol to test foetal calf serum (FCS) for contamination with bovine viral diarrhoea virus (BVDV) is described. Following this protocol, which combines cell culture methods and detection of pestivirus RNA, seven batches of FCS were tested. Infectious BVDV was detected in four of those batches. One of the remaining batches contained a relatively high number of non-infectious BVDV particles. A sample of this batch was formulated with aluminium hydroxide and aluminium phosphate as adjuvant into an experimental vaccine preparation. This product was injected twice into BVDV seronegative cattle with a 4 week interval. Blood samples taken 4 weeks after the second application were negative for BVDV specific antibodies. Our data stress that detection of BVDV RNA is not sufficient for a complete risk assessment on FCS. Discrimination between infectious and non-infectious BVDV is essential. This can only be achieved by cell culture methods.     

Resolution of batch variations in pyrolysis mass spectrometry of bacteria by the use of artificial neural network analysis

A simple, but stringent, three group model of bacterial interstrain identity (two cultures of the same strain ofEscherichia coli) and difference (a culture of a serologically distinct strain) was used in multiple serial weekly subcultures for five weeks to demonstrate the effect of both growth-related (phenotypic) and machine-related variation on pyrolysis mass spectra. An aliquot of serum from a single sample was included in each pyrolysis batch to distinguish machine drift from culture drift. Conventional principal component (PC) canonical variate (CV) analysis was successful within each pyrolysis batch but the variations between batches precluded the use of data from more than one batch in successful PCCV analysis. In contrast, artificial neural networks (ANNs) trained with data from one batch could be successfully used to identify groups in data from non-contemporaneous pyrolysis batches. Although the ANN method will require validation in more complex settings than this simple model, it is a promising approach to the problem of batch constraint in pyrolysis mass spectrometry.     

家蚕近交系遗传纯度的RAPD检测

目的分析家蚕近交系IS-c108A的遗传纯度,为家蚕实验动物化的培育工作提供指导。方法应用经过筛选的20条随机引物对家蚕近交系IS-c108A(F10)的3个蛾区各30个个体和该近交系的亲本系统c108、对照实用化品种871各30个个体的基因组DNA进行RAPD扩增,计算个体间和蛾区间的相似系数及遗传距离。结果家蚕近交系IS-c108A(F10)的3个蛾区内的多态性带频率分别为1.807%、1.841%、1.841%,平均为1.830%;起点亲本c108个体间多态性带频率为7.207%,对照品种871个体间的多态性带频率为7.08%;而近交系IS-c108A与c108之间的多态性带频率为49.20%,c108和871品种之间的多态性带频率为58.33%。家蚕近交系IS-c108A10的3个蛾区内个体之间遗传相似系数的平均值分别为0.99581、0.99555、0.99551,总平均为0.99562。结论家蚕近交系IS-c108A(F10)已具有较高的遗传纯合度,家蚕具有易于获得高纯的有利条件。     

The rapid estimation of microbial contamination of raw meat by measurement of adenosine triphosphate (ATP)

Bacteria were separated from raw meat homogenate by a simple three-stage process. Centrifugation (10 s at 2000 g) removed coarse particles; stirring with the cation exchange resin Bio-Rex 70 removed smaller particles and filtration through 0.22 micron membranes removed soluble materials. By this process 70-80% of the microbial populations of meat homogenates were consistently isolated on the filters. A linear relationship was found between log10 microbial ATP and log10 colony count of meat over the range 10(5)-10(9) cfu/g. The value of ATP/cfu for meat samples was within the range previously reported for pure cultures. These data indicated that ATP extracted from the filters originated from bacteria in the meat samples. Several samples can be analysed simultaneously in an elapsed time of 20-25 min. The variability associated with estimates of both colony counts and ATP levels has been determined.     

The rapid estimation of microbial contamination of raw meat by measurement of adenosine triphosphate (ATP)

Bacteria were separated from raw meat homogenate by a simple three-stage process. Centrifugation (10 s at 2000 g) removed coarse particles; stirring with the cation exchange resin Bio-Rex 70 removed smaller particles and filtration through 0.22 μm membranes removed soluble materials. By this process 70—80% of the microbial populations of meat homogenates were consistently isolated on the filters. A linear relationship was found between log₁₀ microbial ATP and log₁₀ colony count of meat over the range 10⁵—10⁹ cfu/g. The value of ATP/cfu for meat samples was within the range previously reported for pure cultures. These data indicated that ATP extracted from the filters originated from bacteria in the meat samples. Several samples can be analysed simultaneously in an elapsed time of 20—25 min. The variability associated with estimates of both colony counts and ATP levels has been determined.     

Comparison of Gelman and Millipore Membrane Filters for Enumerating Fecal Coliform Bacteria

Tests of two leading brands of membrane filters used for enumerating fecal coliform bacteria showed that Gelman GN-6 filters recovered statistically more colonies of bacteria than did Millipore HAWG 047SO filters from pure cultures incubated at either 35 C (the optimal growth temperature) or 44.5 C (the standard temperature for the fecal coliform test). Standard membrane filter procedures with M-FC broth base were used to enumerate the organisms. Densities of colonies incubated on Gelman filters at 44.5 C averaged 2.3 times greater than those on Millipore filters. Plate counts of the bacteria at both temperatures indicated that incubation at 44.5 C did not inhibit propagation of fecal coliform bacteria. For the pour plates, M-FC broth base plus 1.5% agar was used. This modified medium compared favorably to plate count agar for enumerating Escherichia coli. At 35 and 44.5 C, colony counts on Gelman filters agreed closely with plate counts prepared concurrently, but Millipore counts were consistently lower than plate counts, especially at 44.5 C. Comparative analyses of river water for fecal coliform bacteria by the membrane filter technique gave results comparable to those for the pure cultures.     

Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths

High‐throughput sequencing is a powerful tool, but suffers biases and errors that must be accounted for to prevent false biological conclusions. Such errors include batch effects; technical errors only present in subsets of data due to procedural changes within a study. If overlooked and multiple batches of data are combined, spurious biological signals can arise, particularly if batches of data are correlated with biological variables. Batch effects can be minimized through randomization of sample groups across batches. However, in long‐term or multiyear studies where data are added incrementally, full randomization is impossible, and batch effects may be a common feature. Here, we present a case study where false signals of selection were detected due to a batch effect in a multiyear study of Alpine ibex (Capra ibex). The batch effect arose because sequencing read length changed over the course of the project and populations were added incrementally to the study, resulting in nonrandom distributions of populations across read lengths. The differences in read length caused small misalignments in a subset of the data, leading to false variant alleles and thus false SNPs. Pronounced allele frequency differences between populations arose at these SNPs because of the correlation between read length and population. This created highly statistically significant, but biologically spurious, signals of selection and false associations between allele frequencies and the environment. We highlight the risk of batch effects and discuss strategies to reduce the impacts of batch effects in multiyear high‐throughput sequencing studies.     

THE ASSESSMENT OF THE BACTERIOLOGICAL CONDITION OF MILK BOTTLES

SUMMARY: A study of the relative values of a number of bacteriological tests for assessing the condition of milk bottles indicated that the colony count of the bottle rinse solution on yeastrel milk agar incubated for 4 days at 30°, combined with a clot-on-boiling test applied to 1 ml. of rinse in 9 ml. of sterile milk after incubation for 72 hr. at 19–20°, gave the most useful results.
The mean of the ratios of colony counts at 30° to those at 37° was 15·1, while it was as high as 22·9 for rinses with 37° of over 600 for an unsatisfactory bottle should be retained when the test is done at 30°. The thermoduric colony count of rinses of milk bottles, even when laboratory pasteurized in milk, did not provide any additional information to that given by the colony count at 30° made without pasteurization. A high proportion of the organisms in bottle rinses survived laboratory pasteurization in milk, the survival rate being highest in efficiently treated bottles.
The clot-on-boiling test gave results in general agreement with colony counts and served to indicate the potential influence of badly contaminated bottles on the keeping quality of milk placed in them. A substantial proportion of rinses with satisfactory colony counts reduced methylene blue within 48 hr. at 19–20°.
Colony counts at 37° were on the average much lower for bottles treated with steam than for bottles submitted to detergent treatment in various types of bottle washing machines. Treatment of bottles by steam or hypochlorite was more efficiently done on the farms than at the dairies.     

Development and validation of a detection system for wild-type Vibrio cholerae in genetically modified cholera vaccine.

Orochol, a live oral cholera vaccine licensed in Switzerland and in other countries, is based on the genetically modified Vibrio cholerae strain CVD103-HgR. This strain is derived from the wild-type O1 strain Inaba 569B by deletion of a fragment internal to the ctxA gene encoding the A1 subunit of cholera toxin and by replacement of an internal fragment of the hlyA gene with a fragment carrying the mer operon mediating mercury resistance. In this study we describe a polymerase chain reaction (PCR) system for the detection of wild-type Vibrio cholerae and the identification of the vaccine strain for the quality control of production batches. A multiplex PCR system that targets the intact ctxA gene of the wild-type strain and simultaneously the integration site of the mer operon in the hlyA gene (hlyA::mer) of the vaccine strain CVD103-HgR was developed. To evaluate the detection limit of the system, vaccine suspensions were artificially contaminated with wild-type V. cholerae 569B cells and tested by PCR. The detection limit of the system was statistically evaluated and found to be at 11625 wild-type cells per vaccine sachet (95% confidence limit). This number is below the infective dose of wild-type Vibrio cholerae. In Switzerland this test is used in combination with other tests in the official batch-release procedure to assure the safety of each batch of the cholera vaccine Orochol.     

16S-ARDRA, a tool for identification of lactic acid bacteria isolated from grape must and wine

Lactic acid bacteria (LAB) are found in a great variety of habitats, including grape must and wines. There is a close relationship between the species of LAB which develop during fermentation and the eventual quality of the wine. For these reasons analytical techniques allowing fast and reliable identification of wine LAB are needed. In this work a simple and accurate protocol for identifying species of LAB isolated from grape must and wine is presented. This protocol is based on the amplification, directly from colony, of 16S rDNA and later digestion with one of the following restriction enzymes BfaI, MseI and AluI. A sequential use of the three enzymes is proposed to simplify LAB wine identification, first MseI, then BfaI and finally, if necessary, AluI digestion. The technique was able to discriminate 32 of the 36 LAB reference species tested and allowed the identification of 342 isolates from musts and wines. The isolates belonged to the species: Lactobacillus brevis, L. collinoides, L. coryniformis, L. bilgardii, L. mali, L. paracasei, Leuconostoc mesenteroides, Oenococcus oeni, Pediococcus parvulus and P. pentosaceus.     

Relationship between embryo development in vitro and 56-day nonreturn rates of cows inseminated with frozen-thawed semen from dairy bulls

Frozen-thawed bull semen with > 50% post-thaw motility from 40 batches (21 bulls, 2 consecutive ejaculates per batch) was used for fertilization (IVF) and embryo development in vitro to assess the relationship between field and laboratory fertility using a retrospective approach. Each frozen batch was tested in 3 or 4 replicates with 30 oocytes per replicate. Field fertility, quantified as the 56-d nonreturn rate and based on 89 to 441 artificial inseminations per frozen batch, ranged between 46.2 and 74.8%. The cleavage and blastocyst rates after IVF varied from 29.0 to 81.9% and from 1.8 to 32.0%, respectively, with significant differences among frozen batches. Rates of cleavage and blastocyst formation were significantly related to the nonreturn rate (r = 0.59, P < 0.001; r = 0.35, P < 0.05, respectively). The interaction between cleavage and blastocyst rate was 0.69 (P < 0.001). Significant variations (P < 0.05) among frozen semen batches within 15 bulls with >/= 2 different semen batches were found for the nonreturn rate (13.3%) of 2 bulls, for cleavage rates (26.7%) in 4 bulls and for blastocyst rates (20.0%) in 3 bulls. Significant differences (P < 0.05) among replicates within the 40 frozen semen batches were only found in 3 batches (7.5%) for the cleavage rate and in 7 batches (17.5%) for blastocyst rate. Overall, bull and frozen semen batch were the greatest sources of variation in the cleavage rate (30.6 and 29.4%, respectively), while testing date was the greatest source of variation in the blastocyst development rate (21.7%). The results indicated that in vitro fertilization and, to a lesser extent, culture to the blastocyst stage could be useful in estimating the potential fertilizing ability of frozen-thawed semen from dairy bulls.     

Microbiological quality of bottled water sold in retail outlets in Nigeria

M.T. OGAN. 1992. The microbiological quality of four brands of bottled water sold in retail outlets in Nigeria were assessed by routine methods in 90 samples. Samples of two brands were acidic in the pH range 3.5–5.9. Faecal coliforms and streptococci were not recovered from any sample. Heterotrophic plate counts (HPC) numbered 50–800 cfu/ml in two brands, A and B, and 100–87000 cfu/ml in C and D. Component colony types among the HPC bacteria in brands C and D produced water-soluble, fluorescent pigments on colony count and other agar media, and occurred in 11 of 16 batches: their numbers varied from 60 to 82000 cfu/ml. Presumptive antibiotic-resistant proportions of the HPC bacteria were also recovered from brands C and D on agar amended with ampicillin, penicillin or streptomycin. Five isolates from the green pigmented colonies, representing five batches of brands C and D were satisfactorily identified as strains of Pseudomonas aeruginosa. These strains resisted between four and nine of 14 antibiotics tested. Resistance to tetracycline was eliminated in one isolate when it was cured by incubation at 42C for 100 h, but gel electrophoretic resolution of the DNA did not reveal presence of a plasmid. Strains of Bacillus were the second most commonly isolated bacteria; they were the only colony types in most samples with low HPC counts.     

Microbiological quality of bottled water sold in retail outlets in Nigeria.

The microbiological quality of four brands of bottled water sold in retail outlets in Nigeria were assessed by routine methods in 90 samples. Samples of two brands were acidic in the pH range 3.5-5.9. Faecal coliforms and streptococci were not recovered from any sample. Heterotrophic plate counts (HPC) numbered 50-800 cfu/ml in two brands, A and B, and 100-87,000 cfu/ml in C and D. Component colony types among the HPC bacteria in brands C and D produced water-soluble, fluorescent pigments on colony count and other agar media, and occurred in 11 of 16 batches: their numbers varied from 60 to 82,000 cfu/ml. Presumptive antibiotic-resistant proportions of the HPC bacteria were also recovered from brands C and D on agar amended with ampicillin, penicillin or streptomycin. Five isolates from the green pigmented colonies, representing five batches of brands C and D were satisfactorily identified as strains of Pseudomonas aeruginosa. These strains resisted between four and nine of 14 antibiotics tested. Resistance to tetracycline was eliminated in one isolate when it was cured by incubation at 42 degrees C for 100 h, but gel electrophoretic resolution of the DNA did not reveal presence of a plasmid. Strains of Bacillus were the second most commonly isolated bacteria; they were the only colony types in most samples with low HPC counts.     

玫烟色拟青霉适温性及抗多菌灵特性的种内变异

在15 ℃～35 ℃的温度范围内比较测定了玫烟色拟青霉(Paecilomyces fumosoroseus) 6株野生菌的菌落生长、产孢量及孢子活力.结果显示,3个指标均以25 ℃左右最好,但同一温度下菌株间或同一菌株在不同温度下的差异显著, 菌株Pfr116和Pfr6206具有相对稳定优良的生长、产孢及活孢率性状.对不同浓度多菌灵对6株野生菌的菌落生长和单孢菌落形成的影响测定表明,菌株间存在较大差异.不同多菌灵浓度对单孢菌落形成的抑制率观察值可用逻辑斯蒂模型较好地拟合(r²≥0.90).用所获参数估计的最低禁菌浓度MIC值显示,Pfr4205和Pfr116对多菌灵表现为低抗性（MIC≤20.0 μg·ml^-1）;Pfr153、Pfr612和Pfr2175属于低水平中抗,MIC值仅略大于20 μg·ml^-1;而Pfr6206的MIC值高达93.5 μg·ml^-1,接近MIC>100 μg·ml^-1的高抗标准.因此,Pfr6206为适温性和抗多菌灵特性俱佳的菌株,可作为抗多菌灵和适应不同季节或地区的害虫生防菌剂的候选菌株.     

Pooling data for stability studies: testing the equality of batch degradation slopes.

Pharmaceutical products are routinely monitored for their stability over time. Stability studies generally consist of a random sample of dosage units (e.g., tablets, capsules, vials) from a batch or several batches placed in a storage room and periodically assayed for their drug content. The degradation of the drug product is modeled, and according to the Guideline for Submitting Documentation for Stability Studies of Human Drugs and Biologics (Food and Drug Administration, 1987), the shelf-life is calculated as the time point at which the lower 95% confidence limit about the fitted regression line crosses the lowest acceptable limit for drug content (frequently 90% of the labeled amount). When multiple batches are manufactured, preliminary testing for any batch differences (both slope and intercept) should precede pooling stability data from all batches in the analysis. The Guideline recommends a level of significance of .25 for such preliminary testing based on the work described by Bancroft (1964, Biometrics 20, 427-442). Using such a large significance level helps ensure that the power of the test for the batch differences is sufficiently high. This paper presents an approach whereby the power of the test is fixed and the significance level of the test needed to obtain this power is calculated from the data. If the observed significance level does not achieve the calculated significance level, then the data can be pooled. Examples will illustrate the relative performance of the FDA guideline and the proposed procedure.     

Note: Development of an external quality assurance scheme for the detection and enumeration of Pseudomonas aeruginosa from water and comparison of results using modified King's A broth and a commercial agar

Two trials of the isolation and enumeration of a given strain of Pseudomonas aeruginosa from water are reported. In each trial participants received concentrated samples from two batches, one with low and one with high counts, to be diluted to 500 ml in sterile distilled or deionized water and examined for Ps. aeruginosa by membrane filtration. Membranes were incubated at 37°C for 48 h on pads soaked in modified King's A broth (MKAB) and Unipath Pseudomonas Agar plus CFC supplement (PCFC). The first trial involved eight Public Health Laboratories (PHL) and the organizers provided media from single batches. The second trial, involving 50 PHL, examined the feasibility of a large scale external quality assessment (EQA) distribution. Participants were invited to use the same two media and their usual medium if different. Average counts were close to expected and the spread of results was comparable to that observed from the EQA scheme for indicator organisms. From the results of the two trials a better isolation of the strain of Ps. aeruginosa under consideration was noted with PCFC compared with MKAB.     

Adjusting the number of spermatozoa in mini-straws by determination of the operative volume of bovine semen

The importance of the number of sperm per insemination on fertility has been well demonstrated in cattle. This number is usually calculated from the concentration in the extended semen and a theoretical value for the operative volume of semen delivered during insemination. The objective of this experiment was to investigate the usefulness of the measurement of the delivered volume of semen when estimating sperm numbers from frozen-thawed mini-straws, by comparing the results obtained with an analytical balance to the theoretical volume. The density of semen extended with Biociphos Plus and Triladyl was determined to be 1.033 g/ml using the gamma sphere method. This value was used to convert semen weight into operative volume. The effect of semen temperature at the time of weighing (37 degrees C versus 20 degrees C) was investigated on six semen batches, two technicians measuring the operative volume of 50 straws for each combination of temperature and semen batch (a total of 1200 weighings). The temperature effect was found to be insignificant, which allowed warm semen to be weighed before motility was assessed during routine quality control. The operative volume was then measured in straws routinely produced at 17 bovine Al centers (12-105 semen batches per center, mostly three straws from each batch, a total of 1912 measurements). The observed volumes were normally distributed around 198.7 microl, 98% measuring between 180 and 210 microl. The operative volume was significantly different among centers (from 192 to 205 microl, P < 0.0001) and among batches within centers (P < 0.0001). The S.D. among straws within batches was 3.4 microl. Some centers showed high variability in straw volume whereas others were more consistent. Determination of the operative volume of frozen-thawed mini-straws by weighing the delivered contents is an accurate method for estimation of the number of sperm per dose.     

ADVISORY MICROBIOLOGICAL STANDARDS AND TOLERANCES FOR RAW MILK

SUMMARY: To study the value of recent modifications of microbiological tests used for advisory purposes, samples of tuberculin tested milk, taken at weekly intervals over a 5 year period from the Trawscoed Experimental Husbandry Farm and selected at random during a 12 months period from farms in Wales, were examined by a temperature compensated keeping quality test at 22°, colony count on Yeastrel milk agar in 3 days at 30° and coli-aerogenes colony count on violet red bile agar in 20–24 hr at 30°.
The results show that milk produced and handled under hygienic conditions can be expected to have colony counts of less than 2 × 10⁴/ml and coli-aerogenes colony counts less than 10/ml when examined within 18 hr of milking.     

Investigation of vinegar production using a novel shaken repeated batch culture system

Nowadays, bioprocesses are developed or optimized on small scale. Also, vinegar industry is motivated to reinvestigate the established repeated batch fermentation process. As yet, there is no small‐scale culture system for optimizing fermentation conditions for repeated batch bioprocesses. Thus, the aim of this study is to propose a new shaken culture system for parallel repeated batch vinegar fermentation. A new operation mode — the flushing repeated batch — was developed. Parallel repeated batch vinegar production could be established in shaken overflow vessels in a completely automated operation with only one pump per vessel. This flushing repeated batch was first theoretically investigated and then empirically tested. The ethanol concentration was online monitored during repeated batch fermentation by semiconductor gas sensors. It was shown that the switch from one ethanol substrate quality to different ethanol substrate qualities resulted in prolonged lag phases and durations of the first batches. In the subsequent batches the length of the fermentations decreased considerably. This decrease in the respective lag phases indicates an adaptation of the acetic acid bacteria mixed culture to the specific ethanol substrate quality. Consequently, flushing repeated batch fermentations on small scale are valuable for screening fermentation conditions and, thereby, improving industrial‐scale bioprocesses such as vinegar production in terms of process robustness, stability, and productivity. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1158–1168, 2013