Real-time polymerase chain reaction as a rapid and efficient alternative to estimation of picornavirus titers by tissue culture infectious dose 50% or plaque forming units

Quantification of viral infectious units is traditionally measured by methods based on forming plaques in semisolid media (PFU) or endpoint dilution of a virus-containing solution (TCID50), methods that are laborious, time-consuming and take on average 3-7 days to carry out. Quantitative real-time PCR is an established method to quantify nucleic acids at high accuracy and reproducibility, routinely used for virus detection and identification. In the present study, a procedure was developed using a two-step real-time PCR and the SYBR Green detection method to study whether there are correlations between TCID50/ml, PFU/ml and Ct values generated by real-time PCR enabling rapid and efficient calculation of titer equivalents when working with viruses in the research laboratory. In addition, an external standard with known concentrations was included using in vitro transcribed viral RNA, thus allowing the calculation of the amount of RNA copies needed for various applications (i.e. per plaque or TCID50).The results show that there is a correlation between the three quantification methods covering a wide range of concentration of viruses. Furthermore, a general regression line between TCID50 and Ct values was obtained for all viruses included in the study, which enabled recording titer equivalents using real-time PCR. Finally, by including an external standard, the amount of RNA genomes generating one TCID50 or PFU for each enterovirus serotype included was determined.

Migratory timing, marine survival and growth of anadromous brown trout Salmo trutta in the River Imsa, Norway

The aim of the paper was to study sea migration, growth and survival of brown trout Salmo trutta of the River Imsa, 1976-2005. The migratory S. trutta were individually tagged and fish leaving or entering the river were monitored daily in traps located near the river mouth. The mean annual duration of the sea sojourn was 6-9 months for first-time migrants moving to sea between January and June. It was 8-18 months for those migrating to sea between July and December. Veteran migrants stayed 12 months or less at sea and most returned to the river in August. Early ascending fish stayed the longest in fresh water because most returned to sea in April to May. The day number of 50% cumulative smolt descent correlated negatively with mean water temperature in February to March and the February North Atlantic Oscillation index (NAOI). Mean annual sea growth during the first 2 years after smolting was higher for S. trutta spending the winter at sea than those wintering in the River Imsa. First year's sea growth was lower for S. trutta descending in spring than autumn. For first-time migrants, it correlated negatively with the February NAOI of the smolt year. Sea survival was higher for spring than autumn descending first-time migratory S. trutta with a maximum in May (14.9%). Number of anadromous S. trutta returning to the river increased linearly with the size of the cohort moving to sea, with no evidence of density-dependent sea mortality. Sea survival of S. trutta smolts moving to sea between January and June correlated positively both with the annual number of Atlantic Salmo salar smolts, the specific growth rate at sea, and time of seaward migration in spring. This is the first study indicating how environmental factors at the time of seaward migration influence the sea survival of S. trutta.

Asymmetric competition drives lake use of coexisting salmonids

To what degree are population differences in resource use caused by competition and the occupation of adjacent positions along environmental gradients evidence of competition? Habitat use may be the result of a competitive lottery, or restricted by competition. We tested to what extent population differences in habitat use of two salmonids, cutthroat trout (Oncorhynchus clarki) and Dolly Varden charr (Salvelinus malma) were influenced by interspecific competition. We hypothesized that the depth distribution of Dolly Varden charr would be affected by competition from the more littoral and surface-oriented cutthroat trout, and that the depth distribution of cutthroat trout would be little affected by competition from Dolly Varden charr. Sympatric populations of cutthroat trout and Dolly Varden charr were created by reciprocal transfers of previously allopatric populations in two experimental lakes. We found evidence of asymmetric competition, as Dolly Varden charr were displaced from littoral habitats when sympatric with cutthroat trout, whereas cutthroat trout remained unaffected by the presence of Dolly Varden charr. Evolved differences between the species, and differences between experimental lakes, also contributed to population differences in habitat use, but asymmetric competition remained as the main driver of different depth distributions in sympatry.

Growth of aflatoxigenic moulds and aflatoxin formation in Brazil nuts

The present study aimed at gaining more knowledge of the growth of aflatoxigenic moulds and aflatoxin production in Brazil nuts in relation to humidity conditions and storage time. For this purpose, the growth of aflatoxigenic moulds and the increase in aflatoxin levels in Brazil nuts was studied in the laboratory at temperature and humidity conditions that are relevant for the Amazon region. Fresh unprocessed Brazil nuts in shell were inoculated with an aflatoxin producing strain of Aspergillus nomius previously isolated from Brazil nuts. The nuts were stored at 27 °C in combination with 97, 90 or 80% surrounding relative humidity in a respirometer for up to 3 months. The General Linear Model (GLM) was used for evaluation of the effect of water activity and time on aflatoxigenic mould levels and on aflatoxin levels, as well as the relationship between mould and aflatoxin levels. During storage at the highest relative humidity (97%) aflatoxin formation occurred rapidly, whereas storage at 90% relative humidity resulted in slower aflatoxin formation. At the lowest relative humidity (80%), aflatoxin formation occurred sporadically during storage. The increase in mould and aflatoxin levels along the production chain is also described, using field data collected in the state of Para, Brazil. The growth of aflatoxigenic moulds and aflatoxin formation increased rapidly between 40-90 days following collection of the nuts, before the nuts reached the final drying stage at the processing plant. In addition, a logistic regression model predicting the probability that the European legislative limit of 4 µg/kg for aflatoxins in nuts will be exceeded in relation to colony counts of either one selected aflatoxigenic mould strain (laboratory experiments) or of a mixture of aflatoxigenic strains (field data) was developed. The probability that total aflatoxin levels will exceed the European legislative limit of 4 µg/kg increased rapidly from approx. 30% to above 80% for both experimental and field samples at mould levels between 2 and 3 log cfu/g.

Thinlip grey mullet Liza ramada (Mugilidae) caught in a

Two individuals of thinlip grey mullet Liza ramada were collected in a southern Norwegian brook (58° 22’ N, 8° 37’ E) on 12th September 2007. The fish were 8.7 and 9.0 cm in total length, 6 and 7 g in total mass, and most probably in their first year of life. The nearest known spawning area of the species is south of the English Channel, meaning that they had probably moved at least 900 km across the North Sea during their first growth season. To our knowledge, this is the first published observation of the catadromous thinlip grey mullet from a Scandinavian freshwater course.

Collection, seminal characteristics and chilled storage of spermatozoa from three species of free-range flying fox (Pteropus spp.)

This study reports observations on the collection and characteristics of semen from free-range populations of flying fox in Brisbane, Australia. Semen was successfully recovered by electroejaculation from 107 of 115 wild flying foxes (Pteropus alecto, Pteropus poliocephalus and Pteropus scapulatus). A proportion of ejaculates collected from all three species contained seminal vesicle secretions, the incidence of which appeared related to breeding season. Ejaculate volume was small (5--160 microL), requiring a specialised collection vessel and immediate extension to avoid desiccation. Sperm morphological abnormalities and characteristics are described for the first time. In two species (P. scapulatus and P. alecto), sperm quality varied with breeding season. Dilution in Tris-citrate-fructose buffer and subsequent incubation (37 degrees C) of Pteropus semen for 2-3h appeared to have a negative impact on sperm motility and the percentage of sperm with intact plasma membranes and acrosomes and represents a concern for the potential development and use of assisted breeding technology in these species. Preliminary attempts to develop a short-term chilled preservation protocol for flying fox semen revealed that sperm viability (percentage motility and percentage live sperm with intact acrosomes) was significantly reduced after 102 h chilled storage at 5 degrees C; nevertheless, approximately 40% of the spermatozoa were still motile and contained intact acrosomes. Glycerol was neither protective nor detrimental to sperm survival during chilled storage. Microbial flora of the prepuce, urethra and semen of all species were isolated and their antibiotic susceptibility tested. Tetracycline, penicillin, ciprofloxacin, and ceftazidime were the most effective antibiotics in preventing growth of all identified bacteria; however, their effects on sperm survival were not investigated.

Predicting noncompliant levels of ochratoxin A in cereal grain from Penicillium verrucosum counts

AIMS

To model the probability of exceeding the European legislative limit of 5 microg ochratoxin A (OTA) per kilogram grain in relation to Penicillium verrucosum levels and storage conditions, and to evaluate the possibilities of using P. verrucosum colony counts for predicting noncompliant OTA levels.

METHODS AND RESULTS

Cereal samples were inoculated with P. verrucosum spores and stored for up to 9 months at temperatures and water activities ranging from 10-25 degrees C and aw 0.77-0.95. A logistic regression analysis showed that the probability of exceeding 5 microg OTA kg(-1) grain was related to colony counts of P. verrucosum and water activity. The sensitivity and specificity of various P. verrucosum count thresholds for predicting noncompliant OTA levels were estimated, using data from the storage trial and natural cereal samples.

CONCLUSION

The risk of exceeding 5 microg OTA kg(-1) grain increased with increasing levels of P. verrucosum, and with increasing water activities. A threshold of 1000 CFU P. verrucosum per gram grain is suggested to predict whether or not the legislative limit is exceeded.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study has provided a tool to evaluate the levels of P. verrucosum in grain in relation to OTA levels. Hence, mycological analyses can be used to identify cereal samples with high risk of containing OTA levels above the legislative limit.

Melanoma and nonmelanoma skin cancer in patients with multiple tumours--evidence for new syndromes in a population-based study

BACKGROUND

The hypotheses that Swedish patients with four or more primary tumours [including at least one cutaneous malignant melanoma (CMM)] harbour an increased number of CDKN2A (formerly p16) germline mutations, and that this group of patients show a predisposition to other tumours, e.g. nonmelanoma skin cancer (NMSC), were studied descriptively. So far the mutation 113insArg explains all CDKN2A-associated CMM in ethnic Swedes.

OBJECTIVES

All patients with four or more primary tumours, of which at least one was a CMM, from the Southern Swedish Regional Tumour Registry, between 1958 and 1999, were included in this study.

METHODS

Forty-four patients were found and subdivided into three groups according to having multiple CMM (group A) or single CMM +/- NMSC (groups B and C). Screening for the presence of the Swedish founder mutation 113insArg in blood or in tissue blocks was performed.

RESULTS

Patients in group A were younger at the time of the first CMM diagnosis than patients in group B and group C. The 113insArg mutation was found in four of 44 patients (9%), three with multiple CMM. In group C (n = 14) no founder mutation was evident, while in group B (n = 15) one mutation carrier was found. Nonmutation carriers with multiple CMM (group A) also had a predilection for meningiomas and neurinomas (four patients) or multiple NMSC (three patients). In group B CMM were especially associated with adenocarcinomas but in group C CMM were associated with multiple NMSC.

CONCLUSION

The association between meningiomas and neurinomas (no acoustic neurinoma was seen) might indicate a new syndrome. Patients in groups B and C may harbour unknown genetic defects, which could interact with different environmental risk factors.

Clinical and histopathological features of malignant melanoma in germline CDKN2A mutation families

Primary cutaneous malignant melanomas (CMMs) from 26 individuals belonging to nine families with an identified mutation were clinically and histopathologically compared with 78 matched CMM controls and with a population-based series of CMMs ( = 667). All tumours were histopathologically re-examined. CDKN2A-associated cases were significantly less invasive compared with the matched controls, with an adjusted odds ratio (adjOR) of 2.9 and a 95% confidence interval (CI) of 1.0-8.1 ( = 0.04). According to the odds ratio (OR) values, CDKN2A-associated cases seemed to have tumours more often located on the head and neck (adjOR 2.9, 95% CI 0.6-13.7), with less inflammation (adjOR 0.7, 95% CI 0.3-1.8) and regression (adjOR 0.6, 95% CI 0.2-1.8) but more frequent histological ulceration (adjOR 1.9, 95% CI 0.6-5.8). In comparison with the population-based material, CDKN2A-associated cases were significantly younger at diagnosis (crude OR 3.5, 95% CI 1.6-7.5, divided at 50 years) and had less regressive reaction in their tumours (crude OR 0.35, 95% CI 0.2-0.8). No significant differences were seen for tumour thickness between the different groups. On multivariate analysis, the overall survival was significantly worse for thicker tumours and older age ( = 0.04 for both). To our knowledge this is the first description of the histopathological features of CMMs from families with mutations in the CDKN2A gene.

Nonrandom karyotypic features in basal cell carcinomas of the skin

Cytogenetic analysis of short-term cultured 44 basal cell carcinomas (BCC) revealed clonal karyotypic abnormalities in 38 tumors. Relatively complex karyotypes (at least four structural and/or numerical changes per clone) with unbalanced structural as well as numerical aberrations were found in eight (approximately 21%) of the BCC, while the remaining BCC (79%) had simple karyotypes (1 to 3 aberrations per clone). Numerical changes only were found in 16 tumors, 15 BCC displayed both numerical and structural aberrations, and the remaining 7 BCC showed only structural aberrations. Extensive intratumoral heterogeneity, in the form of cytogenetically unrelated clones, was found in 21 tumors, whereas related subclones were present in 10 tumors. In order to obtain an overall karyotypic picture in BCC, the findings of our previously published 25 BCC have been reviewed. Our combined data indicate that BCC are characterized by nonrandom karyotypic patterns. A large subset of BCC is characterized by nonrandom numerical changes, notably, +18, +X, +7, and +9. Structural rearrangements often affect chromosomes 1, 4, 2, 3, 9, 7, 16, and 17. A number of chromosomal bands are frequently involved, including 9q22, 1p32, 1p22, 1q11, 1q21, 2q11, 4q21, 4q31, 1p36, 2q37, 3q13, 7q11, 11p15, 16p13, 16q24, 17q21, and 20q13. When the genomic imbalance is assessed, it has been shown that several chromosome segments are repeatedly involved in losses, namely loss of the distal part of 6q, 13q, 4q, 1q, 8q, and 9p. A correlation analysis between the karyotypic patterns and the clinico-histopathologic parameters has been undertaken in the 44 BCC of the present series. The cytogenetic patterns show a significant correlation with tumor status (P=.025), that is, that cytogenetically more complex tumors are also those clinically the most aggressive. Also, the frequency of cytogenetically unrelated clones is significantly higher in recurrent BCC than that in primary lesions (P=.05). No clear-cut association has been found between the karyotypic patterns and histologic subtypes or tumor sites.

Prognostic factors in invasive cutaneous malignant melanoma: a population-based study and review

A population-based study from Sweden identified 711 patients with cutaneous malignant melanoma diagnosed in 1965, 1975, 1985 and 1989. Prognostic factors were evaluated and a review of the literature was performed. On univariate analysis, thick tumours (> 0.8 mm) (odds ratio [OR] 1.8, 95% confidence interval [CI] 1.6-2.1), increasing Clark level (OR 1.8, 95% CI 1.6-2.0), ulceration (OR 1.8, 95% CI 1.6-2.0), nodular melanoma (OR 1.5, 95% CI 1.3-1.6) and increasing age (continuous variable, P < 0.0001) were associated with a shorter survival. Location on extremities (OR 0.8, 95% CI 0.7-0.9), inflammation (OR 0.8, 95% CI 0.7-0.9) and female gender (OR 0.8, 95% CI 0.8-0.9) were associated with improved survival. On multivariate analysis, thick tumours (> 0.8 mm) (OR 1.5, 95% CI 1.2-1.7) and ulceration (OR 1.4, 95% CI 1.2-1.6) were independently related to a poor prognosis, while location on extremities (OR 0.8, 95% CI 0.7-0.9), inflammation (OR 0.8, 95% CI 0.7-0.9) and female gender (OR 0.8, 95% CI 0.8-1.0) were associated with improved survival. No difference in mean tumour thickness was seen over time, but there was a significant increase in the percentage of thin melanomas (< 0.8 mm) in 1985 (P = 0.01) and 1989 (P = 0.002) compared with 1965. The incidence of melanomas with inflammation increased significantly (P = 0.04), as did age at diagnosis (P = 0.005).

Does pretreatment with statins improve clinical outcome after stroke? A pilot case-referent study

BACKGROUND AND PURPOSE

In primary and secondary prevention trials, statins have been shown to reduce the risk of stroke. In addition to lipid lowering, statins have a number of antiatherothrombotic and neuroprotective properties. In a preliminary observational study, we explored whether clinical outcome is improved in patients who are on treatment with statins when stroke occurs.

METHODS

We conducted a population-based case-referent study of 25- to 74-year-old stroke patients with, for each case of a patient who was on statin treatment at the onset of stroke (n=125), 2 referent patients who were not treated with statins but were matched for age, gender, year of onset, and stroke subtype (n=250).

RESULTS

The unadjusted odds ratio for early discharge to home (versus late discharge or death) was 1.41 (95% CI 0.91 to 2.17) when patients on statin treatment were compared with referent stroke patients not on statins. Prognostic factors were, in general, more unfavorable among patients on statins. When this was adjusted for in a logistic regression model, the use of statins was a moderately strong but statistically nonsignificant predictor of discharge to home (multiple-adjusted odds ratio 1.42, 95% CI 0.90 to 2.22).

CONCLUSIONS

The statistical power of this case-referent study was such that only large beneficial effects of statins in acute stroke could be confirmed. However, the observed trend, together with experimental observations, is interesting enough to warrant a more detailed analysis of the relationship between statins and stroke outcome.

Risk of cutaneous malignant melanoma in relation to use of sunbeds: further evidence for UV-A carcinogenicity

In a population-based, matched, case-control study from southern Sweden of 571 patients with a first diagnosis of cutaneous malignant melanoma and 913 healthy controls aged 16-80 years, the association between sunbed use and malignant melanoma was evaluated. A total of 250 (44%) cases and 372 (41%) controls reported ever having used sunbeds. A significantly elevated odds ratio for developing malignant melanoma after regular exposure to sunbeds was found, adjusted for hair colour, raised naevi, skin type and number of sunburns (odds ratio (OR) 1.8, 95% confidence interval (CI) 1.2-2.7). A dose-response relationship between total number of sunbed uses and melanoma risk was only found up to the level of 250 times. The OR was higher in individuals younger than age 36 years (adjusted OR 8.1, 95% CI 1.3-49.5 for regular vs. never use). The association seemed to be true only for subjects with black/dark brown or light brown hair and among females. Lesions of the extremities showed the strongest association of increased risk with sunbed use. An increased risk was related to commercial exposure and to exposure during the winter. The results substantiate the hypothesis that exposure to sunbeds might increase the risk of developing malignant melanoma.

Nonrandom karyotypic features in squamous cell carcinomas of the skin

We report the finding of clonal chromosome abnormalities in 13 short-term cultured squamous cell carcinomas (SCCs) of the skin. Intratumor heterogeneity, in the form of cytogenetically related (subclones) or unrelated clones, was detected in six tumors. Whereas clones with complex karyotypic changes were found in 6 tumors, clones with simple anomalies were observed in 10 tumors, and sometimes these clones coexisted with highly abnormal clones. Rearrangement of chromosome 8, in the form of isochromosome i(8q) or whole arm translocation, was the most common aberration, found predominantly in complex clones. Another recurrent feature, i.e., the centromeric rearrangement of chromosome 1, as isochromosome i(1q) or i(1p), or whole arm translocations, was always part of a complex karyotype. Homogeneously staining regions were found in two cases, one with a highly complex karyotype and the other with a simple karyotype. In order to obtain an overall karyotypic picture in SCC of the skin, the cytogenetic findings in 10 SCCs reported earlier were reviewed. The chromosomes most commonly affected were, in decreasing order, chromosomes 1, 11, 8, 9, 5, 3, and 7. Chromosomal sites most frequently rearranged were almost all pericentromeric: they were 8q10-q11, 1p10-q12, 5p10-q11, 11p15, and 9p10-q10. Recurrent anomalies were i(1q), i(8q), i(5p), i(1p), i(9p), and i(9q). Among them, only i(8q) and i(9q) might be assumed to be early genetic events, considering the fact that they could occasionally be identified in simple clones. The most frequent losses included part of or the entire chromosomes 2, 4, 9, 11, 14, 18, and 21, arm 8p, and chromosomes X, Y, and 13. Overrepresentation most frequently involved 1q, chromosome 7, and 8q. The characteristic karyotypic pattern observed in skin SCC was in line with the experience in several other carcinomas. Genes Chromosomes Cancer 26:295-303, 1999.