Multiplex PCR for detection and identification of lactococcal bacteriophages

Three genetically distinct groups of Lactococcus lactis phages are encountered in dairy plants worldwide, namely, the 936, c2, and P335 species. The multiplex PCR method was adapted to detect, in a single reaction, the presence of these species in whey samples or in phage lysates. Three sets of primers, one for each species, were designed based on conserved regions of their genomes. The c2-specific primers were constructed using the major capsid protein gene (mcp) as the target. The mcp sequences for three phages (eb1, Q38, and Q44) were determined and compared with the two available in the databases, those for phages c2 and bIL67. An 86.4% identity was found over the five mcp genes. The gene of the only major structural protein (msp) was selected as a target for the detection of 936-related phages. The msp sequences for three phages (p2, Q7, and Q11) were also established and matched with the available data on phages sk1, bIL170, and F4-1. The comparison of the six msp genes revealed an 82. 2% identity. A high genomic diversity was observed among structural proteins of the P335-like phages suggesting that the classification of lactococcal phages within this species should be revised. Nevertheless, we have identified a common genomic region in 10 P335-like phages isolated from six countries. This region corresponded to orfF17-orf18 of phage r1t and orf20-orf21 of Tuc2009 and was sequenced for three additional P335 phages (Q30, P270, and ul40). An identity of 93.4% within a 739-bp region of the five phages was found. The detection limit of the multiplex PCR method in whey was 10(4) to 10(7) PFU/ml and was 10(3) to 10(5) PFU/ml with an additional phage concentration step. The method can also be used to detect phage DNA in whey powders and may also detect prophage or defective phage in the bacterial genome.     

An improved plaque assay for viruses infecting poikilothermic cells; use of ultralow-gelling-temperature agarose

The conventional plaque assay for viruses infecting poikilothermic cells is difficult because the cells are easily damaged at temperatures needed to keep the agarose overlay from solidifying prematurely. A modification of the assay in which these problems were solved by use of a new type of agarose (SeaPrep 15/45) that remains liquid above 15 degrees C, was developed. Use of this agarose made it easy to obtain smooth agar overlays without the risk of thermal damage to the cells.     

Taxonomic differentiation of 101 lactococcal bacteriophages and characterization of bacteriophages with unusually large genomes

Sixty-three virulent bacteriophages of Lactococcus lactis were differentiated by DNA-DNA hybridization. The results, including those of a previous classification of 38 phages of the same bacterial species (P. Relano, M. Mata, M. Bonneau, and P. Ritzenthaler, J. Gen. Microbiol. 133:3053-3063, 1987) show that 48% of the phages analyzed belong to a unique DNA homology group (group III). Phages of this most abundant group had small isometric heads. Group I comprised 29% of the phages analyzed and was characterized by a small phage genome (19 to 22 kilobases) and a particular morphology with a prolate head. Like group III, this group contained representative phages of other classifications. Group II (21%) included virulent and temperate phages with small isometric heads. Two large isometric-headed phages, phi 109 and phi 111, were not related to the three DNA homology groups I, II, and III. The genome of phi 111 was unusually large (134 kilobases) and revealed partial DNA homology with another large isometric phage, 1289, described by Jarvis (type e) (A. W. Jarvis, Appl. Environ. Microbiol. 47:343-349, 1984). The protein compositions of phi 111 and 1289 were similar (three common major proteins of 21, 28, and 32 kilodaltons).     

An improved fluorometric assay for DNA

A modification of the fluorometric assay of Kissane and Robins is described. The modified procedure is very accurate, widely applicable, and reasonably easy to use. A standard cell type instead of a standard DNA solution makes the assay universally reproducible. DNA content is calculated by a simple method from the slope of a DNA concentration series. This can be used to detect technique erros.     

Identification of the receptor-binding protein in 936-species lactococcal bacteriophages

The aim of this work was to identify genes responsible for host recognition in the lactococcal phages sk1 and bIL170 belonging to species 936. These phages have a high level of DNA identity but different host ranges. Bioinformatic analysis indicated that homologous genes, orf18 in sk1 and orf20 in bIL170, could be the receptor-binding protein (RBP) genes, since the resulting proteins were unrelated in the C-terminal part and showed homology to different groups of proteins hypothetically involved in host recognition. Consequently, chimeric bIL170 phages carrying orf18 from sk1 were generated. The recombinant phages were able to form plaques on the sk1 host Lactococcus lactis MG1614, and recombination was verified by PCR analysis directly with the plaques. A polyclonal antiserum raised against the C-terminal part of phage sk1 ORF18 was used in immunogold electron microscopy to demonstrate that ORF18 is located at the tip of the tail. Sequence analysis of corresponding proteins from other lactococcal phages belonging to species 936 showed that the N-terminal parts of the RBPs were very similar, while the C-terminal parts varied, suggesting that the C-terminal part plays a role in receptor binding. The phages investigated could be grouped into sk1-like phages (p2, fd13, jj50, and phi 7) and bIL170-like phages (P008, P113G, P272, and bIL66) on the basis of the homology of their RBPs to the C-terminal part of ORF18 in sk1 and ORF20 in bIL170, respectively. Interestingly, sk1-like phages bind to and infect a defined group of L. lactis subsp. cremoris strains, while bIL170-like phages bind to and infect a defined group of L. lactis subsp. lactis strains.     

Identification of the lower baseplate protein as the antireceptor of the temperate lactococcal bacteriophages TP901-1 and Tuc2009

The first step in the infection process of tailed phages is recognition and binding to the host receptor. This interaction is mediated by the phage antireceptor located in the distal tail structure. The temperate Lactococcus lactis phage TP901-1 belongs to the P335 species of the Siphoviridae family, which also includes the related phage Tuc2009. The distal tail structure of TP901-1 is well characterized and contains a double-disk baseplate and a central tail fiber. The structural tail proteins of TP901-1 and Tuc2009 are highly similar, but the phages have different host ranges and must therefore encode different antireceptors. In order to identify the antireceptors of TP901-1 and Tuc2009, a chimeric phage was generated in which the gene encoding the TP901-1 lower baseplate protein (bppL(TP901-1)) was exchanged with the analogous gene (orf53(2009)) of phage Tuc2009. The chimeric phage (TP901-1C) infected the Tuc2009 host strain efficiently and thus displayed an altered host range compared to TP901-1. Genomic analysis and sequencing verified that TP901-1C is a TP901-1 derivative containing the orf53(2009) gene in exchange for bppL(TP901-1); however, a new sequence in the late promoter region was also discovered. Protein analysis confirmed that TP901-1C contains ORF53(2009) and not the lower baseplate protein BppL(TP901-1), and it was concluded that BppL(TP901-1) and ORF53(2009) constitute antireceptor proteins of TP901-1 and Tuc2009, respectively. Electron micrographs revealed altered baseplate morphology of TP901-1C compared to that of the parental phage.     

An improved glucoseoxidase--peroxidase-coupled assay for -fructofuranosidase activity

An improved glucoseoxidase-peroxidase-coupled assay for the determination of β-fructofuranosidase activity is described. The method makes use of the double effect of Tris (2-amino-2-hydroxymethylpropane-1,3-diol) as an inhibitor of both invertase and contaminating glucosidases. The method is very sensitive and is suitable for routine determinations. The total time needed for a single analysis is less than half an hour.     

Direct detection of lactococcal bacteriophages in cheese whey using DNA probes

Abstract We have designed a new method for the rapid detection of lactococcal phage directly in milk samples. The method was based on a dot blot analysis and did not require a biological assay with sensitive indicator strains. Culture media or whey permeate samples containing phage were spotted directly onto a nylon membrane and the phage were lysed in situ prior to hybridization. For skim milk, whole milk and whey samples, the samples were first treated with 50 mM EDTA, 20% Triton X-100 and heated at 60°C for 5 min, prior to spotting on the membrane. The detection limit was approximately between 10⁵ and 10⁷ pfu/spot. A large number of samples could be processed simultaneously and the results were obtained within 24 h.     

Application of direct plaque assay for detection and enumeration of bacteriophages of Bacteroides fragilis from contaminated-water samples

The direct double-agar-layer plaque assay for the detection and enumeration of specific bacteriophages of Bacteroides fragilis from contaminated-water samples was performed. Several factors that affect the methods, such as conditions of the bacterial culture, composition of the assay medium, addition of divalent cations, and decontamination techniques applied to the sample, were evaluated. The results obtained show that the direct assay technique proved to be more efficient than the most-probable-number technique. A higher recovery of bacteriophages was obtained from 17 of 24 samples with the direct assay. The two methods only showed similar results from samples with a low degree of pollution.     

一种基于胶体微晶纤维素的改良病毒蚀斑测定法的建立与评价北大核心CSCD

胶体微晶纤维素(avicel)是一种由微晶纤维素(microcrystalline cellulose, MCC)和羧甲基纤维素(carboxymethyl cellulose,CMC)制成的混合物,可用于病毒蚀斑测定。常用的avicel由FMC公司生产,其MCC和CMC比例相对固定,无法很好地适应所有类型病毒的蚀斑测定实验。本研究通过对比不同的MCC和CMC配制比例对avicel在病毒蚀斑测定作用的影响,建立了一种操作简便、实用性好和稳定性好的改良avicel病毒蚀斑测定法。为了配制不同浓度MCC和CMC的混合物,本研究制备出12种2×avicel覆盖层,测定其总体黏度及底层黏度,评估其与传统覆盖层相比,使用时的操作难易程度。进一步将12种2×avicel覆盖层制备成avicel-DMEM营养覆盖层,测定96孔板中猪流行性腹泻病毒滴度,比较12种avicel覆盖层及传统覆盖层蚀斑大小、清晰度、稳定性及滴度准确性等的差异,筛选出最佳测定方法。结果显示,12种2×avicel覆盖层中,除4.8%MCC+1.4%CMC和4.8%MCC+1.0%CMC外,其余2×avicel覆盖层在实际使用中均比2×CMC覆盖层更容易吸取和配制营养覆盖层。最后,利用avicel病毒蚀斑测定法测定96孔板中猪流行性腹泻病毒滴度,结果显示CMC浓度越高蚀斑越小,其中终浓度为0.6%MCC+0.7%CMC的avicel覆盖层测定蚀斑染色最清晰,准确度与传统覆盖层相似,但操作较传统覆盖层更简便。综上所述,本研究建立了一种操作简便、实用性好和稳定性好的改良avicel病毒蚀斑测定法,为病毒的病原学、抗病毒药物及疫苗等相关研究的展开提供了良好的实验基础。     

An improved method for the assay of hydroxylysine

An improved method for specific detection of hydroxylysine is presented. The procedure is based on the capability of 0.0015 m periodic acid and periodates to oxidize hydroxylysine without interference of proline. Glycosylated hydroxylysine can be detected in collagen by oxidation of unglycosylated residues before hydrolysis.     

An improved cycling assay for nicotinamide adenine dinucleotide

A new cycling assay for NAD that uses thiazolyl blue as a terminal electron acceptor has been found to offer significant advantages over the more established procedure that employs 2,6-dichlorophenolindophenol. With thiazolyl blue, the cycling assay is linear with NAD at picomole levels, and with time for at least 120 min. In contrast, with 2,6-dichlorophenolindophenol as terminal acceptor, the cycling assay deviates considerably from linearity at picomole levels of NAD, and the reaction rates become linear for shorter periods of time as the level of NAD increases. Data are given which provide a basis for choosing optimal assay conditions using the new thiazolyl blue cycling technique.     

Application of direct plaque assay for detection and enumeration of bacteriophages of Bacteroides fragilis from contaminated-water samples.

The direct double-agar-layer plaque assay for the detection and enumeration of specific bacteriophages of Bacteroides fragilis from contaminated-water samples was performed. Several factors that affect the methods, such as conditions of the bacterial culture, composition of the assay medium, addition of divalent cations, and decontamination techniques applied to the sample, were evaluated. The results obtained show that the direct assay technique proved to be more efficient than the most-probable-number technique. A higher recovery of bacteriophages was obtained from 17 of 24 samples with the direct assay. The two methods only showed similar results from samples with a low degree of pollution.     

An improved radiochemical assay for uridine diphosphoglucose pyrophosphorylase

UDP glucose is an important intermediate in numerous metabolic pathways (1). It is therefore not surprising that the enzyme which catalyses its formation, UDP-glucose pyrophosphorylase is ubiquitous (see (2) for references). The reaction catalysed by UDP-glucose pyrophosphorylase is:

$\text{glucose-1}\text{-P +}\text{UTP ? UDP glucose + PPi}$

and the enzyme has been assayed either in the direction of pyrophosphorolysis of the nucleoside diphosphate sugar or in the direction of UDP-glucose formation.Spectrophotometric assays of UDP-glucose pyrophosphorylase in the direction of pyrophosphorolysis are often nonspecific by virtue of the nature of the coupling enzymes (3), whereas similar assays in the direction of UDPG formation may lack the expected stoichiometry of reaction (3,4). Radioisotopic techniques for the assay of UDP-glucose pyrophosphorylase (5,6) are to be preferred to spectrophotometric assays both for their increased sensitivity and specificity. However, these methods depend upon the specific isolation of the radioactive UDP glucose formed, either by a somewhat tedious adsorption to and elution from charcoal (5) or a hazardous precipitation using mercuric acetate. For routine assay of a large number of samples it would be advantageous to replace these techniques with one involving a safer, more rapid method of radioactive UDP-glucose isolation. The radiochemical assay described in this note utilises the binding of UDP glucose to commercially available, anion-exchange filter-paper discs for this purpose. Although the technique was designed to assay UDP-glucose pyrophosphorylase in cell extracts of the cellular slime mould, Dictyostelium discoideum, it should be applicable to most sources of the enzyme.     

An improved protein binding assay for cyclic AMP

A simplified and inexpensive protein binding assay for cAMP has been developed for the rapid measurement of subpicomole quantities of the nucleotide. Conditions of assay were established in which interferences from salts and nucleotides present in biological samples were eliminated. Sodium chloride was demonstrated to reduce cAMP binding by denaturing the regulatory subunit of the protein kinase.