Pneumocystis Pneumonia After Allogeneic Hematopoietic Cell Transplantation: A Case-Control Study on Epidemiology and Risk Factors on Behalf of the Infectious Diseases Working Party of the European Society for Blood and Marrow Transplantation

Pneumocystis pneumonia (PCP) is a life-threatening complication after allogeneic hematopoietic cell transplantation (allo-HCT). However, allo-HCT procedures have evolved toward older patients, unrelated donors, and reduced-intensity conditioning, possibly modifying the risks. Polymerase chain reaction (PCR), widely used nowadays, is more sensitive than microscopy diagnostic methods. This study aimed to assess the factors associated with PCP in allo-HCT recipients within 2 years of HCT and managed according to current procedures. This multicenter, nested case-control study included PCP cases diagnosed by PCR, cytology, or immunofluorescence on bronchoalveolar lavage fluid between 2016 and 2018. Two controls per case were selected from the ProMISe registry and matched for the center, transplant date, and underlying disease. Fifty-two cases and 104 controls were included among the 5452 patients who underwent allo-HCT in the participating centers. PCP occurred at a median of 11.5 months after transplantation. The mortality rate was 24% on day 30 after the PCP diagnosis and 37% on day 90. The clinical presentation and mortality rates of the 24 patients diagnosed using only PCR were not different from those diagnosed with microscopy methods. Our study demonstrates a substantial incidence of, and mortality from, PCP, after allogeneic HCT despite well-established prophylactic approaches. In our experience, PCP nowadays occurs later after transplant than previously reported, justifying the prolongation of prophylaxis after six months in many cases. Allo-HCT recipients diagnosed with PCR as the only PCP marker should benefit from specific treatment as for other patients.

Urine exosome mRNA-based test for monitoring kidney allograft rejection: Effects of sample transportation and storage, and interference substances

BACKGROUND

Exosomes are 30-150 nm nanovesicles with sophisticated nucleic acids cargo, actively secreted by all cells within human body, and found in abundance in all body fluids, including urine. These extracellular vesicles have tremendous potential for next generation diagnostics, theoretically enabling noninvasive assessment of organ and tissue function via liquid biopsy analysis.

AIM

Recently, feasibility of an exosomal molecular test was demonstrated for post-organ transplant monitoring: Analysis of urine-derived exosomal mRNA cargo allowed early detection of kidney allograft rejection. Here, we further studied urine-derived exosomes and their mRNA content as a highly promising diagnostic modality. This included stability studies of urine samples and exosomal mRNA upon transportation from the point of collection to a centralized testing facility, short-term storage of urine at different conditions upon receipt till the point molecular assay is performed, and effects of various potentially interfering substances on the downstream quantitative polymerase chain reaction (qPCR) assay.

METHODS

The urine specimens were stored at various conditions and pre-processed in different ways. Next, samples were passed through the columns to capture all extracellular vesicles, the vesicles were lysed to release their content and the exosomal RNA was purified on the mini-columns, reverse transcription was performed, next pre-amplification, followed by a qPCR analysis for a panel of mRNA markers.

RESULTS

To ensure exosomal RNA integrity, the harvested urine specimens should be shipped refrigerated, by overnight delivery. Urine can next be stored at the test site for up to 1 wk at 4 °C, and long term should be frozen at -80 °C. Urine specimens must be centrifuge at low G-force to deplete cells and debris, to ensure consistent top results in downstream molecular assays. All commonly used medications (tacrolimus, cyclosporin A, mycophenolic acid, everolimus, sirolimus, ascomycin, teriflunomide) were tested and confirmed that they do not cause assay interference.

CONCLUSION

mRNA from urine-derived exosomes was shown to be stable across a broad range of conditions and produced accurate results when analyzed via qPCR assay for detection of kidney allograft rejection. We identified the most optimal conditions for every step of the process, ensuring pre-analytical sample integrity and robust qPCR results.

Developing diagnostic tools for canine periodontitis: combining molecular techniques and machine learning models

BACKGROUND

Dental plaque microbes play a key role in the development of periodontal disease. Numerous high-throughput sequencing studies have generated understanding of the bacterial species associated with both canine periodontal health and disease. Opportunities therefore exist to utilise these bacterial biomarkers to improve disease diagnosis in conscious-based veterinary oral health checks. Here, we demonstrate that molecular techniques, specifically quantitative polymerase chain reaction (qPCR) can be utilised for the detection of microbial biomarkers associated with canine periodontal health and disease.

RESULTS

Over 40 qPCR assays targeting single microbial species associated with canine periodontal health, gingivitis and early periodontitis were developed and validated. These were used to quantify levels of the respective taxa in canine subgingival plaque samples collected across periodontal health (PD0), gingivitis (PD1) and early periodontitis (PD2). When qPCR outputs were compared to the corresponding high-throughput sequencing data there were strong correlations, including a periodontal health associated taxa, Capnocytophaga sp. COT-339 (rs =0.805), and two periodontal disease associated taxa, Peptostreptococcaceae XI [G-4] sp. COT-019 (rs=0.902) and Clostridiales sp. COT-028 (rs=0.802). The best performing models, from five machine learning approaches applied to the qPCR data for these taxa, estimated 85.7% sensitivity and 27.5% specificity for Capnocytophaga sp. COT-339, 74.3% sensitivity and 67.5% specificity for Peptostreptococcaceae XI [G-4] sp. COT-019, and 60.0% sensitivity and 80.0% specificity for Clostridiales sp. COT-028.

CONCLUSIONS

A qPCR-based approach is an accurate, sensitive, and cost-effective method for detection of microbial biomarkers associated with periodontal health and disease. Taken together, the correlation between qPCR and high-throughput sequencing outputs, and early accuracy insights, indicate the strategy offers a prospective route to the development of diagnostic tools for canine periodontal disease.

Diagnostic models to predict nuclear DNA and mitochondrial DNA recovery from incinerated teeth

Teeth are frequently used for human identification from burnt remains, as the structure of a tooth is resilient against heat exposure. The intricate composition of hydroxyapatite (HA) mineral and collagen in teeth favours DNA preservation compared to soft tissues. Regardless of the durability, the integrity of the DNA structure in teeth can still be disrupted when exposed to heat. Poor DNA quality can negatively affect the success of DNA analysis towards human identification. The process of isolating DNA from biological samples is arduous and costly. Thus, an informative pre-screening method that could aid in selecting samples that can potentially yield amplifiable DNA would be of excellent value. A multiple linear regression model to predict the DNA content in incinerated pig teeth was developed based on the colourimetry, HA crystallite size and quantified nuclear and mitochondrial DNA. The chromaticity a* was found to be a significant predictor of the regression model. This study outlines a method to predict the viability of extracting nuclear and mitochondrial DNA from pig teeth that were exposed to a wide range of temperatures (27 to 1000 °C) with high accuracy (99.5-99.7%).

Quantitation of oxidized nuclear and mitochondrial DNA in plasma samples of patients with abdominal aortic aneurysm

There is accumulating evidence that pro-inflammatory features are inherent to mitochondrial DNA and oxidized DNA species. 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) is the most frequently studied oxidatively generated lesion. Modified DNA reaches the circulation upon cell apoptosis, necrosis or neutrophil extracellular trap (NET) formation. Standard chromatography-based techniques for the assessment of 8-oxodGuo imply degradation of DNA to a single base level, thus precluding the attribution to a nuclear or mitochondrial origin. We therefore aimed to establish a protocol for the concomitant assessment of oxidized mitochondrial and nuclear DNA from human plasma samples. We applied immunoprecipitation (IP) for 8-oxodGuo to separate oxidized from non-oxidized DNA species and subsequent quantitative polymerase chain reaction (qPCR) to assign them to their subcellular source. The IP procedure failed when applied directly to plasma samples, i.e. isotype control precipitated similar amounts of DNA as the specific 8-oxodGuo antibody. In contrast, DNA isolation from plasma prior to the IP process provided assay specificity with little impact on DNA oxidation status. We further optimized sensitivity and efficiency of qPCR analysis by reducing amplicon length and targeting repetitive nuclear DNA elements. When the established protocol was applied to plasma samples of abdominal aortic aneurysm (AAA) patients and control subjects, the AAA cohort displayed significantly elevated circulating non-oxidized and total nuclear DNA and a trend for increased levels of oxidized mitochondrial DNA. An enrichment of mitochondrial versus nuclear DNA within the oxidized DNA fraction was seen for AAA patients. Regarding the potential source of circulating DNA, we observed a significant correlation of markers of neutrophil activation and NET formation with nuclear DNA, independent of oxidation status. Thus, the established method provides a tool to detect and distinguish the release of oxidized nuclear and mitochondrial DNA in human plasma and offers a refined biomarker to monitor disease conditions of pro-inflammatory cell and tissue destruction.

Design, Development, and Validation of a Culture-Independent Nucleic Acid Diagnostics Method for the Rapid Detection and Quantification of the Burkholderia cepacia Complex in Water with an Equivalence to ISO/TS 12869:2019

In the wake of a series of outbreaks of finished pharmaceutical product-related Burkholderia cepacia complex (Bcc) human infections worldwide, the United States Food and Drug Administration (FDA) in 2017, and subsequently in 2021, issued advisory notifications to the pharmaceutical industry for stringent Bcc testing requirements for pharmaceutical manufacturing processes and for finished pharmaceutical products prior to release to the marketplace. The advisory notifications highlight non-sterile aqueous finished pharmaceutical products as being a major culprit associated with many of these human infection events. As such, there has been a significant number of Bcc-contaminated finished product recalls resulting in company revenue losses, delayed finished product release, finished product shortages for patients, and manufacturing plant shutdowns coupled with company reputational damage. With many of the finished product recall events, pharmaceutical grade water and/or manufacturing facility water distribution systems were identified as the primary origin source of Bcc contamination. Testing and monitoring regimes currently employed to identify Bcc contamination of water associated with pharmaceutical manufacturing are often limited by costly, laborious, lengthy, and nonspecific traditional microbial culture-based methodologies. Presently FDA approved, European Conformity (CE) marked, and International Organization for Standardization (ISO) standard microbial culture-independent rapid, quantitative, specific, and sensitive nucleic acid diagnostics (NAD) methodologies are now gaining greater widespread acceptance in their routine usage in testing laboratories. Here we present the development of a rapid (<4 hours from sample in to result out) single test culture-independent Bcc NAD method, incorporating a quantitative real-time polymerase chain reaction (qPCR) assay. This method can be used for the detection and simultaneous identification of all 24 Bcc species currently assigned, directly from water samples. This culture-independent Bcc NAD method is validated to the testing method equivalent of the ISO/TS 12869:2019 standard, which is a widely used rapid culture-independent NAD method for detecting Gram-negative Legionella species in water.

Epidemiology of soil-transmitted helminths using quantitative PCR and risk factors for hookworm and Necator americanus infection in school children in Dak Lak province, Vietnam

BACKGROUND

Soil-transmitted helminth (STH) infection is driven by a complex interaction of demographic, socioeconomic and behavioural factors, including those related to water, sanitation and hygiene (WASH). Epidemiological studies that measure both infection and potential risk factors associated with infection help to understand the drivers of transmission in a population and therefore can provide information to optimise STH control programmes.

METHODS

During October and November 2019, we conducted a cross-sectional survey of the prevalence and intensity of STH infection and associated risk factors among 7710 primary-school-age children from 64 primary schools across 13 districts in Dak Lak province, Vietnam. Quantitative PCR (qPCR) was used to detect and quantify STH infections.

RESULTS

The predominant STH species was the hookworm Necator americanus (overall cluster-adjusted prevalence of 13.7%), and its prevalence was heterogeneously distributed across surveyed schools (0% to 56.3%). All other STH species had a prevalence of less than 1%. Using mixed-effects logistic regression, we found that the adjusted odds ratio (aOR) was significantly higher for both infection and moderate-to-heavy-intensity infection with N. americanus among children from multiple ethnic minority groups, compared to children from the majority group (Kinh). Adjusted odds of infection with N. americanus were also higher in children who reported practising open defecation at school (aOR 1.42, 95% CI 1.05, 1.93, P = 0.02) and in those who had an unimproved household water supply (aOR 1.28, 95% CI 1.04, 1.57, P = 0.02). Conversely, children with a flushing household toilet had a reduced risk of infection (aOR 0.58, 95% CI 0.47, 0.70, P < 0.01), as did those whose primary female carer attended secondary (aOR 0.65, 95% CI 0.51, 0.84, P < 0.01) or tertiary education (aOR 0.39, 95% CI 0.24, 0.63, P < 0.01).

CONCLUSIONS

This study is the largest reported prevalence survey of STH infections conducted using qPCR as a diagnostic technique. The findings of higher adjusted odds of infection amongst ethnic minority children highlight that STH control programmes may not be reaching certain population groups and that additional culturally appropriate approaches may be required. Additionally, the associations between specific WASH factors and infection indicate potential programmatic targets to complement preventive chemotherapy programmes.

Rapid detection and diagnosis of herpetic keratitis using quantitative microfluidic polymerase chain reaction system for herpes simplex and varicella-zoster virus DNA: a case series

BACKGROUND

A microfluidic real-time polymerase chain reaction (PCR) system can rapidly detect the viral DNA in specimens. Detection of herpes simplex virus (HSV) and varicella-zoster virus (VZV) DNA in tears is a useful diagnostic tool for herpes simplex virus keratitis (HSK) and herpes zoster ophthalmicus (HZO).

METHODS

In total, 20 patients were included in this cross-sectional study. Among them, 8 patients with infectious epithelial HSK and 12 patients with HZO were included in HSK and HZO groups, respectively. In addition, 8 patients with non-herpetic keratitis and 4 healthy individuals without keratitis were included in the control group. Numbers of HSV and VZV DNA copies in tears of all patients and individuals were evaluated using a microfluidic real-time PCR system. Regarding HSV/VZV DNA test, tear specimens were collected by filter paper method using Schirmer's test paper, and subsequently, DNA was extracted from the filter paper using an automated nucleic acid extractor. Afterward, quantitative PCR was performed using a microfluidic real-time PCR system.

RESULTS

From tear collection to real-time PCR result determination, the HSV/VZV DNA test took approximately 40 min. In the HSK group, the sensitivity and specificity of the HSV DNA tests were 100% each. The median value (range) of number of HSV DNA copies for affected eyes was 3.4 × 10⁵ copies/μL (under a lower detection limit of 7.6). In the HZO group, the sensitivity and specificity of the VZV DNA tests were 100% each. The median value (range) of number of VZV DNA copies for affected eyes was 5.3 × 10⁵ copies/μL (under a lower detection limit of 5.6 × 10^-2).

CONCLUSION

In conclusion, quantitative PCR for HSV and VZV DNA in tears using a microfluidic real-time PCR system is useful for diagnosing and monitoring HSK and HZO.

Parvicapsula pseudobranchicola in the northeast Pacific Ocean is rare in farmed Atlantic salmon Salmo salar despite widespread occurrence and pathology in wild Pacific salmon Oncorhynchus spp

BACKGROUND

Infection with the myxozoan parasite Parvicapsula pseudobranchicola causes disease in wild and farmed salmonids in Norway. In the northeast Pacific Ocean, the parasite has been reported in Pacific salmon Oncorhynchus spp. without evidence of disease. The objectives of the present study were to confirm the identity of P. pseudobranchicola in the Pacific, document its host and geographic ranges, and describe associated pathological changes.

METHODS

Ocean-entry year wild pink salmon Oncorhynchus gorbuscha, chum salmon O. keta, Chinook salmon O. tshawytscha, coho salmon O. kisutch and sockeye salmon O. nerka were collected in summer and autumn surveys near Vancouver Island (VI) and from a winter survey in the Gulf of Alaska. Samples were also obtained from farmed Atlantic salmon Salmo salar and Chinook salmon near VI. Samples were analysed by qPCR and histology using conventional staining or in situ hybridisation. Parasite sequence was obtained from small subunit ribosomal RNA gene (SSU rDNA).

RESULTS

Identical 1525 base-pair SSU rDNA sequences from infected pink salmon, chum salmon and Chinook salmon shared 99.93% identity with a P. pseudobranchicola sequence from Norwegian Atlantic salmon. In autumn surveys, the prevalence was greatest in chum salmon (91.8%) and pink salmon (85.9%) and less so in Chinook salmon (68.8%) and sockeye salmon (8.3%). In farmed salmon, the prevalence was zero in Atlantic salmon (n = 967) and 41% in Chinook salmon (n = 118). Infections were preferentially sited in pseudobranch and visualised by in situ hybridisation. Heavy parasite burdens in all species of Pacific salmon were inconsistently associated with focal granulomatous pseudobranchitis.

CONCLUSIONS

In the northeast Pacific, widespread occurrence of P. pseudobranchicola in Pacific salmon together with its absence or sporadic occurrence in farmed Atlantic salmon differs from its epidemiology in Norway, despite similar pathological development in the pseudobranch. Consequences of the infections to the health of wild Pacific salmon, identity of the invertebrate host and the distribution and abundance of infective actinospores are unknown and remain high priorities for research.

Yeast diversity during the spontaneous fermentation of wine with only the microbiota on grapes cultivated in Japan

Making wine via spontaneous fermentation without sulfur dioxide and commercial yeast (spontaneous winemaking) is increasing in recent year, but there is scant research regarding microbial communities present in Japan during spontaneous winemaking using culture-independent molecular methods. We analyzed fungal communities and populations during laboratory-scale spontaneous winemaking using sterilized labware to avoid winery-resident microbes. In the spontaneous fermentation of four grape varieties (Pinot Noir, Riesling, Koshu, and Koshusanjaku) grown in the same Japanese vineyard, our analysis of yeast and other fungal species by next-generation sequencing based on the ITS1 region demonstrated that Saccharomyces cerevisiae was eventually dominant in seven of 12 fermentation batches (three replications for each grape variety), whereas non-Saccharomyces species (e.g., Schizosaccharomyces japonicus, Lachancea dasiensis, and Hanseniaspora valbyensis) became dominant in four batches at the end of fermentation. In another batch, lactic acid bacteria (LAB) became dominant and the fermentation remained incomplete. Diverse microbes were involved in the spontaneous fermentation (particularly in Koshusanjaku), indicating that residual sugar remained and lactic and acetic acid largely increased. Compared to the control wine made with SO₂ and commercial yeast, the concentration of lactic acid was 47-fold higher in the must dominated by L. dasiensis, and the concentrations of acetic acid and lactic acid were 10-fold and 20-fold higher in the must dominated by LAB, respectively. Even when indigenous S. cerevisiae became dominant, the finished wines obtained high sensory-analysis scores for complexity but low scores for varietal typicality, indicating the risk of fermentation with unselected wild yeast on the grapes grown in Japan.

Evaluation of nitrogen removal, functional gene abundance and microbial community structure in a stormwater detention basin

Stormwater control measures such as detention basins are used to mitigate the negative effects of urban stormwater resulting from watershed development. In this study, the performance of a detention basin in mitigating nitrogen pollution was examined and the abundance of N-cycling genes (amoA, nirK, nosZ, hzsB and Ntsp-amoA) present in the soil media of the basin was measured using quantitative PCR. Results showed a net export of nitrogen from the basin, however, differences between in- and outflow concentrations were not significant. Furthermore, the quantitative PCR showed that nirK (denitrification gene) was more abundant in the winter season, whereas amoA (nitrification gene) was more abundant in the summer season. The abundance of nirK, Ntsp-amoA and hzsB genes also varied with the sampling depth of soil and based on 16S rRNA gene sequencing of soil samples, Actinobacteria and Proteobacteria were the most dominant phyla. Species diversity appeared higher in summer, while the top and bottom layer of soil clustered separately based on the bacterial community structure. These results underline the importance of understanding nitrogen dynamics and microbial processes within stormwater control measures to enhance their design and performance.

Detection of Streptococcus mutans and Streptococcus sobrinus and Their Association with Oral Microbiome Stressors in 6-18-month-old Infants

Aim

To determine the presence of Streptococcus mutans (S. mutans) and Streptococcus sobrinus (S. sobrinus) and their association with extrinsic and intrinsic variables in 6-18-month-old infants.

Methods

This was an analytical, cross-sectional study of 65 6-18-month-old infants who visited the Centers for Early Childhood in Buenos Aires City. Three groups were established according to the presence of teeth-group I (GI)-edentulous infants, group II (GII)-infants with 1-8 teeth, and group III (GIII)-infants with 9-16 teeth. Data on the variables, diet, use of artificial teats, and oral hygiene were gathered using a self-administered questionnaire. An oral examination was performed according to the International Caries Detection and Assessment System (ICDAS II) criterion. A saliva sample was taken by aspiration with a sterile plastic syringe. Cariogenic Streptococci (CS) were counted using the adherence test in modified gold broth (AT-MGB). Molecular detection and quantification were performed by quantitative polymerase chain reaction (qPCR) (gtfB, gtfT, and tuf).

Results

A total of 12% of infants received oral hygiene, 38% used bottles, 30% used pacifiers, and 55% had sugar intake. S. sobrinus and S. mutans were detected in 57.1 and 28.6% of the children with caries, respectively. Groups I, II, and III had CS counts of log 2, 3.4, and 3.7, respectively. S. sobrinus was detected in 26.7% of GI, 52.9% of GII, and 85.7% of GIII, while S. mutans was detected in 13.3%, 35.3%, and 57.7%, respectively.

Conclusion

The prevalence of S. sobrinus was higher than S. mutans in all groups. The presence of CS was significantly associated with sugar intake. No association was found between S. mutans and S. sobrinus and the presence of caries, hygiene habits, or use of artificial teats.

Clinical Significance

This study supports the role of diet in developing a cariogenic biofilm in children under 2 years of age.

How to cite this article

Cornejo CF, Soken LJ, Salgado PA, et al. Detection of Streptococcus mutans and Streptococcus sobrinus and Their Association with Oral Microbiome Stressors in 6-18-month-old Infants. Int J Clin Pediatr Dent 2023;16(1):68-73.

A new real-time quantitative polymerase chain reaction method using locked nucleic acids to detect Neisseria gonorrhoeae infection and point mutation on gyrA associated with quinolone susceptibility

In Neisseria gonorrhoeae, fluoroquinolone resistance is caused by mutations on various genes, especially on gyrA. Locked nucleic acid DNA sequence was added to the forward primer for gyrA and subjected to real-time quantitative polymerase chain reaction, enabling simultaneous detection of N. gonorrhoeae and mutations associated with antimicrobial resistance.

Developmental and Hepatic Gene Expression Changes in Chicken Embryos Exposed to p-Tert-Butylphenyl Diphenyl Phosphate and Isopropylphenyl Phosphate via Egg Injection

Organophosphate flame retardants (OPFRs) are used in a variety of products such as clear coats, resins, and plastics; however, research into their toxicological effects is limited. p-Tert-butylphenyl diphenyl phosphate (BPDP) and isopropylphenyl phosphate (IPPP) are two OPFRs that were prioritized for whole-animal toxicological studies based on observed effects in cultured avian hepatocytes in a previous study. The present study investigates the toxicity of BPDP and IPPP in chicken embryos at different developmental stages by evaluating morphological and gene expression endpoints. Chicken eggs were exposed via air cell injection to 0-250 μg/g (nominal) of either compound and then artificially incubated. At day 11 (midincubation), liver samples were collected for mRNA expression analysis; and at day 20 (1 day prehatch), morphological measurements and liver samples for transcriptomic evaluation were collected. At 250 μg/g, gallbladder size was significantly reduced for both compounds, head/bill length and tarsus length were significantly decreased, and liver somatic index was significantly increased following IPPP exposure only. No effects on mortality were observed up to the highest administered concentration for either chemical. Using a ToxChip polymerase chain reaction array, we report significant differences in hepatic gene expression for both compounds and time points; the most pronounced transcriptomic effects occurred at midincubation. Genes related to xenobiotic metabolism, bile acid/cholesterol regulation, and oxidative stress were significantly dysregulated. Given these changes observed throughout avian embryonic development, further research into the long-term effects of BPDP and IPPP are warranted, especially as they pertain to liver cholestasis. Environ Toxicol Chem 2022;41:739-747. © 2021 Her Majesty the Queen in Right of Canada. Environmental Toxicology and Chemistry © 2021 SETAC. Reproduced with the permission of the Minister of Environment and Climate Change Canada.

Measurement of Cytosolic Mitochondrial DNA After NLRP3 Inflammasome Activation

The NLRP3 inflammasome, a key component of the innate immune system that mediates caspase-1 activation, which in turn induces cleavage of the pyroptosis executioner gasdermin D and the proinflammatory cytokines IL-1β and IL-18, requires two signals to be activated. First, inflammasome priming is achieved after activation of Toll-like receptors, which leads to NF-κB signaling and transcriptional activation of the genes for NLRP3 and IL-1β. Next, the inflammasome complex is activated by a second signal that induces extrusion of mitochondrial DNA to the cytosol of the cell, which leads to its oligomerization by a not fully understood mechanism. Here we describe a simple method that employs quantitative polymerase chain reaction (qPCR) using SYBR green to measure the presence of mitochondrial DNA (mtDNA) in the cytosol, which can be used to measure cytosolic mtDNA levels after inflammasome activation.

Analysis of telomere length variation and Shelterin complex subunit gene expression changes in ethanol-exposed human embryonic stem cells

Telomeres protect chromosome ends from degradation. Telomere length (TL) can be altered by aging and environmental stress. Shortened TL has been observed in peripheral blood leukocytes of alcohol dependent subjects and ethanol-exposed somatic cells. To understand the impact of ethanol on telomeres in pluripotent stem cells, we investigated the influence of ethanol on TL and the expression of six Shelterin complex subunit or telomere-regulating genes (POT1, RAP1, TIN2, TPP1, TRF1, and TRF2) in human embryonic stem cells (hESCs), which were exposed to 0, 25, 50, or 100 mM of ethanol for 3, 7, or 14 days. Ethanol-induced TL and Shelterin complex subunit gene expression changes were examined by quantitative polymerase chain reactions. Two-way ANOVA tests indicated that TL variation and expression changes of four associated Shelterin complex subunit genes (POT1, TPP1, TIN2, and TRF2) were mainly dependent on the length of ethanol exposure, while TRF1 and RAP1expression was influenced by ethanol concentration, exposure time, and the interaction of ethanol concentration and exposure time. Tukey's multiple comparison tests showed that TL and the expression of POT1, RAP1, TIN2, TPP1, and TRF1 were decreased after a 7-day (versus a 3-day) ethanol exposure. However, the decreased expression of all six Shelterin complex subunit genes was recovered and TL was not further shortened after a 14-day (versus a 7-day) ethanol exposure, likely due to the adaptation of hESCs to ethanol-induced stress. Our study provided further evidence that TL is regulated and maintained by telomere-regulating genes in stem cells under ethanol stress.

Use of a new multiplex quantitative polymerase chain reaction based assay for simultaneous detection of Neisseria meningitidis, Escherichia coli K1 , Streptococcus agalactiae, and Streptococcus pneumoniae

Background and Objectives

Neisseria meningitidis, Escherichia coli K₁, Streptococcus agalactiae, and Streptococcus pneumoniae cause 90% of bacterial meningitis. Almost all infected people die or have irreversible neurological complications. Therefore, it is essential to have a diagnostic kit with the ability to quickly detect these fatal infections.

Materials and Methods

The project involved 212 patients from whom cerebrospinal fluid samples were obtained. After total genome extraction and performing multiplex quantitative polymerase chain reaction (qPCR), the presence or absence of each infectious factor was determined by comparing with standard strains.

Results

The specificity, sensitivity, positive predictive value, and negative predictive value calculated were 100%, 92.9%, 50%, and 100%, respectively. So, due to the high specificity and sensitivity of the designed primers, they can be used instead of bacterial culture that takes at least 24 to 48 hours.

Conclusion

The remarkable benefit of this method is associated with the speed (up to 3 hours) at which the procedure could be completed. It is also worth noting that this method can reduce the personnel unintentional errors which may occur in the laboratory. On the other hand, as this method simultaneously identifies four common factors that cause bacterial meningitis, it could be used as an auxiliary method diagnostic technique in laboratories particularly in cases of emergency medicine.

Freeze-drying improves DNA yield from teeth

The common method of preparing teeth prior to DNA extraction involves cleaning, decontamination, drying and pulverisation. Moisture in post-mortem teeth can promote bacterial growth and hydrolytic damage that could contribute to DNA degradation, whilst also possibly reducing the efficiency of sample pulverisation and DNA release. Here we compared DNA extraction from pig teeth, with- and without freeze-drying, to examine the impact of removing moisture on DNA yield. Quantitative real-time polymerase chain reaction (qPCR) was used to quantify an 83 bp mitochondrial DNA fragment and two nuclear DNA fragments of 82 bp and 150 bp. The comparative results showed that sample preparation with freeze-drying resulted in a higher DNA yield without compromising the DNA quality. This study highlights the advantage of incorporating a freeze-drying to improve the DNA yield and minimising the loss of DNA during sample preparation of teeth.

Application of ddPCR for detection of Enterococcus spp. in coastal water quality monitoring

Droplet digital polymerase chain reaction (ddPCR) was evaluated for the detection of fecal indicator bacteria (FIB), Enterococcus spp., in San Diego County beach water samples collected under diverse conditions, from multiple pollution sources, as part of regulatory monitoring activities over 20 months. Two US EPA-approved methods, qPCR (EPA 1609.1) and Enterolert (SM9230D), were used as reference comparator methods. A total of 361 samples were assayed by both ddPCR and qPCR and yielded an acceptable Index of Agreement (IA) of 0.89, based on EPA Site-Specific analysis guidelines. A Pearson's correlation coefficient of r = 0.87 (p < 0.001), further indicated a strong relationship between the methods results. From the 361 samples, 185 split samples with ddPCR and Enterolert values within the limits of quantification, were used as a 'training' data set to derive an intrinsic copy number equation (ICE) for scaling ddPCR gene copy number to Enterolert most probable number (MPN). Of the 1993 samples that comprised the complete 'test' data set assayed by ddPCR and Enterolert, 1086 generated results that fell within the limits of quantification for Enterolert and yielded an overall IA of 0.64. Re-analysis using median as a measure of central tendency to account for significant skewing of Enterolert data yielded an IA of 0.72. Beach grouping-specific IA values ranged from 0.63 to 0.93. Pearson's correlation coefficient, r, ranged from 0.13 to 0.94 within beach groupings and generated a combined value of 0.60 for all groupings. Using the ICE, a ddPCR advisory threshold of 1413 DNA copy number/100 mL was empirically determined to be the equivalent to the California Enterolert beach action threshold of 104 MPN/100 mL, based on comparison with all 1993 paired ddPCR and Enterolert results. Using the 1413 DNA copy number/100 mL as a beach action threshold for ddPCR resulted in a 90.4% agreement with Enterolert (6.0% false negative and 3.7% false positive). Together these findings support the conclusion that ddPCR readouts align closely with Enterolert MPN for identifying FIB exceedance levels of Enterococcus spp. in coastal waters of San Diego, CA.

Investigation of relationships between fecal contamination, cattle grazing, human recreation, and microbial source tracking markers in a mixed-land-use rangeland watershed

The United States National Forests are mixed-use lands that support human recreation and cattle grazing. Overuse by humans or cattle, however, can lead to the fecal contamination of local waterways. Until recently, the source of these contaminants was a subject of conjecture; however, microbial source tracking tools have become widely used and are proving to be a valid methodology to identify the contamination source. This study aims to analyze and model the quantity and sources of fecal contamination in the Mink Creek watershed in southeastern Idaho. The U.S. Forest Service Caribou-Targhee National Forest (USFS) manages this watershed. Previous research has indicated that some localities within the watershed exceed US EPA standards for coliform bacteria. In 2019, water samples were collected before livestock began grazing and throughout the spring, summer, and fall after livestock grazing had ended. Fourteen sites were sampled seven times during the field season, allowing the water to be analyzed for total coliforms and E. coli bacteria. Microbial source tracking techniques using Bacteroides bacteria, which are known to live in specific digestive tracks, were used to identify the source of E. coli at each sampling location. The analysis indicated that E. coli counts exceeded state regulatory limits 35% of the time. These exceedances were associated with DNA source tracking markers for humans (58.8%), cattle (5.9%), or both cattle and humans (5.9%). Unknown sources were responsible for the Bacteroides bacteria 29.4% of the time. A statistical model was developed to estimate E. coli using the datasets of microbial source tracking measures, the presence or absence of humans, cattle, the proximity of the sampling date to a holiday, and other seasonal factors. The resulting model showed good performance indices at all the 14 sites based on a K-fold cross-validation scheme (R² = 0.83 and NSE = 0.69). The results demonstrated that E. coli exceedances have a close association with human recreation and unknown sources and negatively influenced by dissolved oxygen.

A real-time quantitative polymerase chain reaction for the specific detection of Hammondia hammondi and its differentiation from Toxoplasma gondii

Introduction

Hammondia hammondi and Toxoplasma gondii are closely related protozoan parasites, but only T. gondii is zoonotic. Both species use felids as definitive hosts and cannot be differentiated by oocyst morphology. In T. gondii, a 529-base pair (bp) repetitive element (TgREP-529) is of utmost diagnostic importance for polymerase chain reaction (PCR) diagnostic tests. We identified a similar repetitive region in the H. hammondi genome (HhamREP-529).

Methods

Based on reported sequences, primers and probes were selected in silico and optimal primer probe combinations were explored, also by including previously published primers. The analytical sensitivity was tested using serial dilutions of oocyst DNA. For testing analytical specificity, DNA isolated from several related species was used as controls. The newly established TaqMan PCR (Hham-qPCR1) was applied to tissues collected from H. hammondi-infected gamma-interferon gene knockout (GKO) mice at varying time points post-infection.

Results

Ten forward and six reverse primers were tested in varying combinations. Four potentially suitable dual-labelled probes were selected. One set based on the primer pair (Hham275F, Hham81R) and the probe (Hham222P) yielded optimal results. In addition to excellent analytic specificity, the assay revealed an analytical sensitivity of genome equivalents of less than one oocyst. Investigation of the tissue distribution in GKO mice revealed the presence of parasite DNA in all examined organs, but to a varying extent, suggesting 100- to 10,000-fold differences in parasitic loads between tissues in the chronic state of infection, 42 days post-infection.

Discussion

The use of the 529-bp repeat of H. hammondi is suitable for establishing a quantitative real-time PCR assay, because this repeat probably exists about 200 times in the genome of a single organism, like its counterpart in T. gondii. Although there were enough sequence data available, only a few of the primers predicted in silico revealed sufficient amplification; the identification of a suitable probe was also difficult. This is in accord with our previous observations on considerable variability in the 529-bp repetitive element of H. hammondi.

Conclusions

The H. hammondi real-time PCR represents an important novel diagnostic tool for epidemiological and cell biological studies on H. hammondi and related parasites.

Template length, concentration and guanidine and cytosine content influence on multiple displacement amplification efficiency

Detection of low abundance human health pathogens in environmental samples is a challenge for water monitoring. This limitation can be overcome by the introduction of multiple displacement amplification (MDA) where a minute amount of genetic material can be amplified using a phi-29 DNA polymerase. However, the genetic makeup and the concentration of the polynucleotides might influence the amplification process due to inherent assay bias. Herein, a series of experiments were designed to demonstrate the effect of genome length, guanidine and cytosine content, and template concentration on the efficiency of MDA. Quantitative polymerase chain reaction (qPCR) was performed to quantify pre- and post-MDA concentrations of selected genes. Linear regression between pre- and post-MDA log gene copies L^-1 of both environmental and lab-grown samples showed a positive correlation (F = 77.59, P < 0.001, R² = 0.7, slope = 1.01). Correlation between relative polynucleotide increase after MDA and target organism length and gene target guanidine and cytosine (G + C) content (F = 4.3, P = 0.02) shows that lower G + C and higher genome length is favored in the MDA process. The MDA process was shown to favor a longer genome over a shorter genome (1.19 and 1.04 change in log gene copy L^-1, respectively) and a lower G + C content over a higher G + C content (1.11 and 0.61 change in log gene copy L^-1, respectively). There was no MDA bias observed when polynucleotides had the same G + C and genome length but different initial concentrations. This study highlights the need for increased caution when interpreting relative abundance of organisms amplified by MDA such as in next generation sequencing.

Signaling in TNFSF15-mediated Suppression of VEGF Production in Endothelial Cells

Vascular endothelial growth factor (VEGF) plays a pivotal role in promoting neovascularization. Tumor necrosis factor superfamily 15 (TNFSF15) is an antiangiogenic cytokine prominently produced by endothelial cells in a normal vasculature. In this study, Western blot, quantitative polymerase chain reaction (qPCR), and dual luciferase reporter gene assay were used to validate the mechanisms of TNFSF15-mediated suppression of VEGF production in endothelial cells. We report that TNFSF15 inhibits VEGF production via microRNA-29b (miR-29b) targeting the 3'-UTR of VEGF transcript in mouse endothelial cell line bEnd.3. Neutralizing antibody against TNFSF15, 4-3H, inhibits the level of miR-29b and reinvigorates VEGF. In addition, TNFSF15 activates the JNK signaling pathway as well as the transcription factor GATA3, resulting in enhanced miR-29b production. SP600125, an inhibitor of JNK, eradicates TNFSF15-induced GATA3 expression. Moreover, GATA3 siRNA suppressed TNFSF15-induced miR-29b expression. Together, this study provides evidence and method of activation of the JNK-GATA3 signaling pathway by TNFSF15 that suppresses VEGF gene expression, which gives rise to upregulation of miR-29b.

All-fiber all-optical quantitative polymerase chain reaction (qPCR)

Quantitative polymerase chain reaction (qPCR), the real-time amplification and measurement of a targeted DNA molecule, has revolutionized the biological sciences and is routinely applied in areas such as medical diagnostics, forensics, and agriculture. Despite widescale use of qPCR technology in the lab, the availability of low-cost and high-speed portable systems remains one of the barriers to routine in-field implementation. Here we propose and demonstrate a potential solution using a photonics-based qPCR system. By using an all-optical approach, we achieve ultra-fast temperature response with real-time temperature feedback using nanoliter scale reaction volumes. The system uses a microcavity to act as a nanoliter scale reaction vessel with a laser-driven and optically monitored temperature cycling system for ultrafast thermal cycling and incorporates an all-fiber fluorescence excitation/detection system to achieve real-time, high sensitivity fluorescence monitoring of the qPCR process. Further, we demonstrate the potential of the system to operate as a label-free qPCR system through direct optical measurement of the sample refractive index. Due to advantages in portability and fabrication simplicity, we anticipate that this platform technology will offer a new strategy for fundamental techniques in biochemistry applications, such as point-of-care and remote diagnostics.

Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata

Quantitative polymerase chain reaction (qPCR) has been used as a standard molecular detection tool in many scientific fields. Unfortunately, there is no standard method for managing published qPCR data, and those currently used generally focus on only managing raw fluorescence data. However, associated with qPCR experiments are extensive sample and assay metadata, often under-examined and under-reported. Here, we present the Molecular Detection Mapping and Analysis Platform for R (MDMAPR), an open-source and fully scalable informatics tool for researchers to merge raw qPCR fluorescence data with associated metadata into a standard format, while geospatially visualizing the distribution of the data and relative intensity of the qPCR results. The advance of this approach is in the ability to use MDMAPR to store varied qPCR data. This includes pathogen and environmental qPCR species detection studies ideally suited to geographical visualization. However, it also goes beyond these and can be utilized with other qPCR data including gene expression studies, quantification studies used in identifying health dangers associated with food and water bacteria, and the identification of unknown samples. In addition, MDMAPR’s novel centralized management and geospatial visualization of qPCR data can further enable cross-discipline large-scale qPCR data standardization and accessibility to support research spanning multiple fields of science and qPCR applications.

Total bacterial load, inflammation, and structural lung disease in paediatric cystic fibrosis

BACKGROUND

Cystic fibrosis (CF) is characterised by reduced airway clearance, microbial accumulation, inflammation, and lung function decline. Certain bacterial species may contribute disproportionately to worsening lung disease. However, the relative importance of these microorganisms compared to the absolute abundance of all bacteria is uncertain. We aimed to identify the characteristics of lower airway microbiology that best reflect CF airway inflammation and disease in children.

METHODS

Analysis was performed on bronchoalveolar lavage (BAL) fluid from 78 participants of the Australasian CF Bronchoalveolar Lavage (ACFBAL) clinical trial, aged 4.5-5.5 years. Universal bacterial quantitative PCR (qPCR), species-specific qPCR, and 16S rRNA gene sequencing were performed on DNA extracts to determine total bacterial load, species-specific load and taxa relative abundance. Quantification of pre-specified pathogens was performed by culture-based methods. Bacteriological data were related to neutrophil counts, interleukin-8, lung function, and two computed-tomography based measures, CF-CT (as the primary measure) and PRAGMA.

RESULTS

Of all bacteriological measures assessed, total bacterial load determined by qPCR correlated most strongly with structural disease (CF-CT total score, r_s=0.30, P=0.0095). Specifically, total bacterial load correlated with bronchiectasis, airway wall thickening, mucus plugging and parenchymal disease sub-scores. In contrast, culture-based quantification, microbiota-derived measures, and pathogen-specific qPCR-based quantification were weakly associated with total CF-CT. Regression analyses supported correlation findings, with total bacterial load explaining the greatest variance in total CF-CT (R²=0.097, P=0.0061). Correlations with PRAGMA score were comparable to CF-CT total score.

CONCLUSIONS

Within the ACFBAL trial, culture-independent quantification of total bacteria provided the most clinically-informative bacteriological measure in 5-year-old CF patients.

Exosomal miR-182 regulates the effect of RECK on gallbladder cancer

BACKGROUND

As the most common biliary malignancy, gallbladder cancer (GC) is an elderly-biased disease. Although extensive studies have elucidated the molecular mechanism of microRNA 182 (miR-182) and reversion-inducing-cysteine-rich protein with kazal motifs (RECK) in various cancers, the specific role of exosomal miR-182 and RECK in GC remains poorly understood.

AIM

To explore the relationship between exosomal miR-182/RECK and metastasis of GC.

METHODS

Paired GC and adjacent normal tissues were collected from 78 patients. Quantitative polymerase chain reaction was employed to detect miR-182 and exosomal miR-182 expression, and Western blotting was conducted to determine RECK expression. In addition, the effects of exosomal miR-182/RECK on the biological function of human GC cells were observed. Moreover, the double luciferase reporter gene assay was applied to validate the targeting relationship between miR-182 and RECK.

RESULTS

Compared with normal gallbladder epithelial cells, miR-182 was highly expressed in GC cells, while RECK had low expression. Exosomal miR-182 could be absorbed and transferred by cells. Exosomal miR-182 inhibited RECK expression and promoted the migration and invasion of GC cells.

CONCLUSION

Exosomal miR-182 can significantly promote the migration and invasion of GC cells by inhibiting RECK; thus miR-182 can be used as a therapeutic target for GC.

Mouse Models for Use in Cryptosporidium Infection Studies and Quantification of Parasite Burden Using Flow Cytometry, qPCR, and Histopathology

Cryptosporidiosis threatens life of young children in developing countries and newborn calves around the world. No vaccine or therapy can prevent or cure this diarrhea-inducing enteric disease caused by Cryptosporidium spp. protozoan parasites. There is an essential need to discover new therapeutic drugs efficient in reducing parasite burden in infected individuals. Research therefore relies on reliable small animal models of cryptosporidiosis. Here, we present excellent mouse models which can efficiently mimic pathogenesis of human and bovine cryptosporidiosis. We also describe methods to purify C. parvum oocysts from stool and intestine of infected mice to facilitate oocyst quantification. Moreover, we present protocols using flow cytometry, quantitative polymerase chain reaction, and histopathology to accurately quantify parasite burden in stool or intestine samples.

Strong association of Torque teno virus/Torque teno-like minivirus to Kikuchi-Fujimoto lymphadenitis (histiocytic necrotizing lymphadenitis) on quantitative analysis

INTRODUCTION

Kikuchi-Fujimoto disease (KFD) is a rare benign lymphadenitis that mainly involves cervical lymph nodes of young Asian women with unknown etiology. Recently, we experienced a case of KFD found with Torque teno virus/Torque teno-like mini virus (TTV/TTMV) from a 26-year-old woman. TTV/TTMV is a genus of Circoviridae that causes necrotizing lymphadenitis in pigs, which shares the key histologic finding of KFD. The purpose of this study is to investigate the pathogenic role of TTV/TTMV in KFD by quantitative polymerase chain reaction (qPCR) analysis.

METHOD

We performed two-step qPCR specific to TTV/TTMV with formalin-fixed paraffin-embedded tissue of sequentially selected 100 KFD patients and 50 randomly selected, matched normal controls. Consequent direct sequencing was done for confirmation with PCR products.

RESULTS

PCR amplification of TTV and TTMV was found in a significantly higher proportion in KFDs than normal controls (TTV, 85% vs. 18%, p < 0.000; TTMV, 91% vs. 24%, p < 0.000). After the sequencing, KFD samples showed more sequence matching than control samples for TTMV (94% vs. 30%, p < 0.000).

CONCLUSION

This finding strongly suggests the possible implication of TTV/TTMV in the pathogenesis of KFD. Animal or in vivo experimental design should be followed in the future.Key Points• Kikuchi-Fujimoto disease (KFD) is rare and its etiology is still unclear.• Torque teno/Torque teno-like minivirus (TTV/TTMV) is a recently introduced virus in the Circoviridae family that causes necrotizing lymphadenitis in pigs, histologically similar to KFD.• We discovered the significantly increased TTV/TTMV viral loads in the KFD patients than normal controls, which implicates TTV/TTMV in the pathogenesis of KFD.

Rapid start-up of partial nitritation in aerobic granular sludge bioreactor and the analysis of bacterial community dynamics

The rapid start-up of the partial nitritation process in a laboratory-scale aerobic granular sludge-sequencing batch reactor was successful by controlling low dissolved oxygen and gradually increasing the influent ammonia levels. The microbial community dynamics were analyzed by high-throughput sequencing and quantitative polymerase chain reaction. The microbial communities were significantly affected by the different influent NH₄⁺-N concentrations (77.84, 119.42, 170.31, and 252.21 mg/L) in Phases I, II, III, and IV. The sludge Shannon index in Phases I, II, III, and IV was 3.9, 4.39, 3.47, and 2.13, respectively, which was higher than that of the inoculated sludge (1.62). The dominant class transformed from Alphaproteobacteria and Gammaproteobacteria in Phase I to Betaproteobacteria in Phase IV. Furthermore, Sphingobacteria and Clostridia were the dominant bacteria in Phases III and IV. The quantitative polymerase chain reaction (qPCR) results suggested that Nitrosomonadaceae_uncultured belonging to ammonia-oxidizing bacterium was the dominant species, but the relative abundance of nitrite-oxidizing bacteria (mainly Nitrospira and Nitrobacter) was extremely rare in Phase IV. Furthermore, Thauera, Denitratisoma, and Planctomycetacia were the dominant functional nitrogen removal microbes in Phases III and IV. Some nitrogen removal pathways such as partial nitritation, denitrification, and anaerobic ammonium oxidation co-existed in the partial nitritation process.

Clinical significance and role of up-regulation of SERPINA3 expression in endometrial cancer

BACKGROUND

Serpin peptidase inhibitor, clade A member 3 (SERPINA3) belongs to the serpin family with an inhibitory activity against proteases. Its aberrant expression has been observed in a wide range of tumor cells. However, its clinical significance and biological function in endometrial cancer have been rarely studied. We designed a study to determine the levels of SERPINA3 and its significance in patients with endometrial cancer.

AIM

To investigate the clinical significance and role of SERPINA3 expression in endometrial cancer cells.

METHODS

Eighty endometrial tissue samples collected from patients with endometrial cancer were included in an observation group and 80 paraffin-embedded tissues samples collected from patients with normal endometrial tissues undergoing myomectomy were employed as a control group between January 2014 and December 2018. The expression of SERPINA3 mRNA was detected by quantitative polymerase chain reaction (PCR) for all endometrial tissues included in the study.

RESULTS

The positive expression rate of SERPINA3 protein in endometrial cancer cells was 71.25% in the observation group, which was significantly higher than that in the control group (31.25%; P < 0.05). There was no correlation between SERPINA3 protein in endometrial cancer cells and the age range at which women experienced menopause (P > 0.05). However, it was associated with pathological grade, clinical stage, vascular invasion, and lymph node metastasis (P < 0.05). Pathological grade, clinical stage, vascular invasion, and lymph node metastasis were independent prognostic factors for endometrial cancer.

CONCLUSION

The follow-up study of SERPINA3 can be used as a prognostic biomarker for endometrial cancer and as one of the targets for bio-targeted therapy for endometrial cancer.

Identification of plasma microRNA expression changes in multiple system atrophy and Parkinson's disease

MicroRNAs (miRNAs) are endogenous small (18–25 nt), single-stranded, non-coding RNAs that play key roles in post-transcriptional gene expression regulation. The expression profiles of miRNAs in biofluids and tissues change in various diseases. Multiple system atrophy (MSA) and Parkinson’s disease (PD) are both categorized as α-synucleinopathies and often present with similar clinical manifestations. This study aimed to identify miRNAs that are differently expressed in plasma samples of PD patients, MSA patients, and healthy controls. We used microarray analysis to screen for miRNAs that are up- and down-regulated in these patients and analyzed the relative-quantitative expression levels of the identified miRNAs by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Hsa-miR-671-5p, hsa-miR-19b-3p, and hsa-miR-24-3p showed significantly different expression levels among patients with MSA-C, MSA-P, or PD, and healthy controls. Hsa-miR-671-5p levels were lower in the MSA-P and PD than the MSA-C and control groups, hsa-miR-19b-3p levels were higher in the PD than the other groups, and hsa-miR-24-3p levels were higher in the PD than the MSA-C group. Hsa-miR-671-5p was the first miRNA shown to be expressed differently between MSA-C and MSA-P in plasma. Interestingly, the expression levels of hsa-miR-19b-3p and hsa-miR-24-3p were positively correlated, indicating that these miRNAs may be involved in the same processes in PD pathogenesis. Our findings suggest that hsa-miR-671-5p, hsa-miR-19b-3p, and hsa-miR-24-3p may reflect the pathophysiology or symptoms of PD and MSA.

IgG4:IgG RNA ratio differentiates active disease from remission in granulomatosis with polyangiitis: a new disease activity marker? A cross-sectional and longitudinal study

OBJECTIVES

An important limitation in granulomatosis with polyangiitis (GPA) is the lack of disease activity markers. Immunoglobulin G4-positive (IgG4+) B cells and plasma cells are implicated in the pathogenesis of GPA. We hypothesized that the presence of these cells in peripheral blood could serve as disease activity parameter in GPA.

METHODS

We included 35 proteinase 3-antineutrophil cytoplasmic antibodies-positive patients with GPA in a cross-sectional study. Active disease was defined as Birmingham Vasculitis Activity Score (BVAS) ≥ 3 (n = 15), remission as BVAS of 0 (n = 17), and low disease activity (LDA) as BVAS of 1-2 and clinical remission (n = 3). Healthy subjects (n = 10), patients with systemic lupus erythematosus (n = 24), and patients with rheumatoid arthritis (n = 19) functioned as control subjects. An additional longitudinal study was performed in ten patients with GPA. Using a validated qPCR test, we measured the IgG4:IgG RNA ratio in all groups and compared the results with known biomarkers.

RESULTS

The median qPCR score was higher in active GPA (21.4; IQR 12.1-29.6) than in remission/LDA (3.3; IQR 1.6-5.6) (Mann-Whitney U test, p < 0.0001) and outperformed other known disease activity parameters in detecting activity. A cutoff qPCR score of 11.2% differentiated active disease from remission/LDA accurately (AUC 0.993). The qPCR test correlated well with the BVAS (Spearman r = 0.77, p < 0.0001). In the longitudinal study, a decrease in BVAS correlated with qPCR score reduction (paired t test, p < 0.05).

CONCLUSIONS

The IgG4:IgG RNA ratio in GPA accurately distinguishes active disease from remission and correlates well with disease activity in these single-center studies. If these results are confirmed in larger longitudinal studies, this test might help to steer treatment decisions in patients with GPA.

Selective effect and elimination of antibiotics in membrane bioreactor of urban wastewater treatment plant

Analyzing the temporal dynamics of antibiotics, antibiotic resistance genes (ARGs) and the functional community could contribute to the regulation and optimization of wastewater treatment plant (WWTP) operation to achieve better antibiotics and ARGs removal performances during different seasons. However, there is little research in this area. Therefore, in this study, samples were collected from the influent, activated sludge (AS), and permeate of the membrane bioreactor (MBR) in a WWTP located in Beijing, China, biweekly over 13 months, and then analyzed systematically. The removal efficiency for all detected antibiotics through biodegradation and adsorption was 59.25 ± 2.79%, with the highest rate of 64.79 ± 4.68% observed in summer, indicating that the higher temperature in summer may promote biodegradation in MBR. In contrast, the elimination of antibiotics through microfiltration was negligible and unfavorable, with negative overall removal rates. However, a positive rejection rate of 9.48 ± 8.92% was only observed in winter, indicating that a colder temperature might lead to better, but still limited, antibiotics rejection. Sulfonamides (SAs) were more likely to impose a selective pressure on their corresponding ARGs. However, due to the degradability of tetracyclines (TCs) and potential selection of ARGs in wastewater before entering WWTP, there were still TC resistances with non-detectable TCs. Significantly negative relationships were observed between the relative abundance of nitrifying bacteria (Nitrosomonas and Nitrospira) and the concentrations of certain antibiotic classes, indicating that nitrifying bacteria could be involved in the co-metabolic biodegradation of certain antibiotics through enzyme catalyzation during nitrification.

Liquid Biopsy and Lung Cancer

The identification of non-small cell lung cancer (NSCLC) patients potentially responsive to targeted therapies relies on a number of relevant biomarkers, including EGFR, ALK, ROS-1, and PD-L1. Biomarker identification is most commonly based on surgical sample collection. However, when tissues are difficult to reach or when multiple analyses are necessary to monitor tumor progression and treatment response, liquid biopsy is a valid noninvasive alternative. This analysis, which is preferentially performed on circulating tumor DNA (ctDNA) extracted from plasma samples, has the major advantage of reducing the inherent risks and discomfort of tissue biopsy. However, a major disadvantage is that it yields only a low number of ctDNA targets. Thus, to avoid false-positive and false-negative results, it is important to adopt and validate technologies with high sensitivity and specificity in the pre-analytical phase of sampling. This review succinctly addresses the principal methodologies for analyzing plasma-derived ctDNA in NSCLC patients.

Quantitative analysis of biofilm bacteria according to different stages of early childhood caries

OBJECTIVE

Monitoring selected key species related to health or disease may facilitate caries risk assessment and discovery of novel ecological preventive and therapeutic approaches. This study aimed at quantifying Actinomyces naeslundii, Bifidobacterium spp., Lactobacillus acidophilus, Lactobacillus casei group, Streptococcus gordonii, Mitis group and Streptococcus mutans by quantitative polymerase chain reaction (qPCR) in dental biofilm from Brazilian children with different stages of early childhood caries (ECC).

DESIGN

Seventy-five preschool children were clinically evaluated by ICDAS criteria and divided into groups: caries-free (CF; n = 20), enamel caries lesions (ECL; n = 17) and dentine caries lesions (DCL; n = 38). Plaque samples from all children were collected for detection and quantification of the selected bacteria.

RESULTS

L. acidophilus and L. casei group were absent in almost all plaque samples. No differences in relative proportions of A. naeslundii, Mitis group and S. gordonii were observed in any stage of caries. However, S. mutans and Bifidobacterium spp. were present at higher concentrations in the biofilm of children with DCL (p < 0.001). Multivariate analysis showed that S. mutans and Bifidobacterium spp. were strongly associated with biofilm in children with DCL.

CONCLUSION

Differences were observed in the proportion of acidogenic and aciduric bacteria with dental caries progression. The data indicate that S. mutans and Bifidobacterium spp. in dental biofilm may be involved in some progression processes for ECC.

Comparison of tests for detecting Helicobacter pylori in gastric biopsy

AIM

To figure out a method to detect Helicobacter pylori (H. pylori) infection that is of high sensitivity and specificity as well as clinically easy-handling by comparing four common H. pylori detection methods.

METHODS

Four hundred and ninety gastric mucosa biopsies were tested separately by the rapid urease test (RUT), fluorescence quantitative polymerase chain reaction (qPCR), methylene blue staining, and immunohis-tochemistry (IHC). Positive rates obtained by the different methods were analyzed by the χ² test.

RESULTS

The positive rates of H. pylori obtained by RUT, qPCR, methylene blue staining, and IHC were 18.98%, 63.88%, 32.04%, and 38.16%, respectively, which were statistically different (P < 0.005).

CONCLUSION

IHC provides a visual scene for observers, and there is a sharp contrast for IHC images between H. pylori infected and surrounding areas. This feature can facilitate researchers to obtain morphological information with potential clinical value. Furthermore, IHC protocols are friendly to instruments and operators. Hence, we recommend that IHC be used to detect H. pylori in gastric biopsies for diagnosing H. pylori infection and determining H. pylori treatment.

An integrated cell absorption process and quantitative PCR assay for the detection of the infectious virus in water

Here we developed an integrated cell absorption process and quantitative (reverse transcription) polymerase chain reaction (ICAP-q(RT)PCR) assay to detect infectious viruses, which based on the detection of the viral nucleic acid (RNA or DNA) in the early stage of viral attachment and entry towards cells. The results showed that the poliovirus or adenovirus whose concentration was as low as 0.2 TCID₅₀/mL could be detected by ICAP-q(RT)PCR after 4 h incubation. The ICAP-q(RT)PCR exhibited much higher sensitivity than the plaque assay. In parallel, it took shorter time to detect the viruses towards field samples compared with the integrated cell culture (ICC)-qPCR, but could still get the consistent detecting results with ICC-qPCR. This method is verified by detecting four different kinds of viruses including poliovirus, adenovirus, rotavirus, and astrovirus, which existed in the actual water samples. Among all the 24 Jinhe river samples, 50% (12/24) of river water samples were positive for poliovirus when detected by ICAP-q(RT)PCR, which was in accordance with the results detected by ICC-qPCR. However, 21% (5/24) and 68% (18/24) of the samples were detected to be positive for poliovirus by the plaque counting and the direct qPCR method, respectively. Compared with ICAP-q(PT)PCR and ICC-qPCR, the detecting results of qPCR or plaque assay displayed a marked expansion or decline, respectively, which lead to the evident deviations in the accuracy. The results demonstrated that our developed ICAP-q(RT)PCR method could dramatically reduce the test duration and quite improve the sensitivity towards infectious viruses. Therefore, the ICAP-q(RT)PCR method could be an effective and quantitative tool for detecting infectious viruses in water environments.

A minimally parametrized branching process explaining plateau phase of qPCR amplification

Quantitative polymerase chain reaction (qPCR) is a commonly used molecular biology technique for measuring the concentration of a target nucleic acid sequence in a sample. The whole qPCR amplification process usually consists of an exponential, a linear and a plateau phase. In qPCR experiments, amplification curves of samples with different template concentrations often, even though not always, have the same plateau height. The biological theory for this phenomenon is that the plateau height is determined by reaction kinetics. Does it mean that the target concentration has no effect on the final plateau height? We proposed a branching process based on Michaelis-Menten kinetics. Our model can describe all phases of qPCR amplification despite its simplicity (it depends on only one parameter). We theoretically showed, through almost sure convergence, that amplification curves will eventually plateau at finite values in any experiment, under any condition. We conclude that the plateau height is largely determined by reaction kinetics but could also be affected by the template concentration. This is in accordance with the current biological theory.

Proceedings of the 2017 Viral Clearance Symposium, Session 4: Submission Strategies

Appropriate performance of virus validation studies and testing of unprocessed bulk harvests for retrovirus particle count are procedures in the demonstration of an acceptable level of viral safety for cell-derived biotechnology products. Product-specific validation studies on virus reduction with two model viruses [usually murine leukemia virus (MuLV) and a parvovirus] performed in duplicate runs are standard for clinical trial applications. For the retroviral safety margin, a 6 log reduction is normally expected. Retroviral particle counts are measured traditionally by transmission electron microscopy (TEM) and are commonly performed at contract laboratories. These procedures are quite time-consuming and can be associated with significant costs. In particular, the time factor is a hurdle for companies that want to quickly bring their new products to the clinic. In this session, several strategies on how to lower time, cost, and workload in the evaluation of viral safety for early clinical trial applications, while still ensuring sufficient level of viral safety of the product, were presented. In addition, virus reduction strategies for molecules that do not have the standard antibody structure are presented. Also presented in this session is the feasibility of the use of retrovirus-like particle (RVLP) in the prevalidation of virus removal and the use of quantitative polymerase chain reaction (qPCR) as an alternative to infectivity assays in virus validation studies as well as its use as an alternative to quantitative TEM analysis for determining RVLP count in the bulk harvest of a perfusion bioreactor.LAY ABSTRACT: In this session, several strategies on how to lower time, cost, and workload in the evaluation of viral safety for early clinical trial applications of cell-derived biotechnology products, while still ensuring sufficient level of viral safety of the product, were presented. In addition, virus reduction strategies for molecules that do not have the standard antibody structure are presented. Also presented in this session is the feasibility of the use of retrovirus-like particle (RVLP) in the prevalidation of virus removal and the use of quantitative polymerase chain reaction (qPCR) as an alternative to infectivity assays in virus validation studies as well as its use as an alternative to quantitative TEM analysis for determining RVLP count in the bulk harvest of a perfusion bioreactor.

Epidemiology of respiratory pathogen carriage in the homeless population within two shelters in Marseille, France, 2015-2017: cross sectional 1-day surveys

Objectives

To assess risk factors for respiratory tract infection symptoms and signs in sheltered homeless people in Marseille during the winter season, including pathogen carriage.

Methods

Data on 479 male participants within two shelters who completed questionnaires and a total of 950 nasal and pharyngeal samples were collected during the winters of 2015–2017. Respiratory pathogen carriage including seven viruses and four bacteria was assessed by quantitative PCR.

Results

The homeless population was characterized by a majority of individuals of North African origin (300/479, 62.6%) with a relatively high prevalence of chronic homelessness (175/465, 37.6%). We found a high prevalence of respiratory symptoms and signs (168/476, 35.3%), a very high prevalence of bacterial carriage (313/477, 65.6%), especially Haemophilus influenzae (280/477, 58.7%), and a lower prevalence of virus carriage (51/473, 10.8%) with human rhinovirus being the most frequent (25/473, 5.3%). Differences were observed between the microbial communities of the nose and throat. Duration of homelessness (odds ratio (OR) 1.77, p 0.017), chronic respiratory diseases (OR 5.27, p <0.0001) and visiting countries of origin for migrants (OR 1.68, p 0.035) were identified as independent risk factors for respiratory symptoms and signs. A strong association between virus (OR 2.40, p 0.012) or Streptococcus pneumoniae (OR 2.32, p 0.014) carriage and respiratory symptoms and signs was also found.

Conclusions

These findings allowed identification of the individuals at higher risk for contracting respiratory tract infections to better target preventive measures aimed at limiting the transmission of these diseases in this setting.

Expression of aryl hydrocarbon receptor-regulated genes and superoxide dismutase in the Antarctic eelpout Pachycara brachycephalum exposed to benzo[a]pyrene

The aryl hydrocarbon receptor (AhR) pathway mediates many, if not all, responses of fish to dioxin-like compounds. The Southern Ocean is progressively exposed to increasing concentrations of anthropogenic pollutants. Antarctic fish are known to accumulate those pollutants, yet nothing is known about their capability to induce chemical biotransformation via the AhR pathway. The objective of the present study was to investigate whether Antarctic eelpout, Pachycara brachycephalum, respond to anthropogenic pollutants by activation of the AhR and its target gene cytochrome P4501A (CYP1A), and of superoxide dismutase (SOD), which served as a representative for oxidative stress. We exposed P. brachycephalum to 10 and 100 mg benzo[a]pyrene (BaP)/kg body weight for 10 d and measured the expression of AhR, CYP1A, and SOD in liver tissue via quantitative polymerase chain reaction. We identified two distinct AhR isoforms in the liver of P. brachycephalum. Antarctic eelpout responded to both BaP exposures by an up-regulation of AhR and SOD, and by a particularly strong induction of CYP1A expression, which remained high until day 10 of the exposure time. Our data suggest that P. brachycephalum possesses the potential to up-regulate xenobiotic biotransformation pathways, at least at the gene expression level. The time course of the AhR and CYP1A response points to an efficient but slow xenobiotics metabolism. Moreover, BaP exposure could include adverse effects such as oxidative stress. Environ Toxicol Chem 2018;37:1487-1495. © 2018 SETAC.

Comparison of microscopic and molecular enumeration methods for insect viruses: Cryptophlebia leucotreta granulovirus as a case study

Enumeration techniques were compared for quantification of the South African isolate of Cryptophlebia leucotreta granulovirus (CrleGV-SA), used as a biopesticide to control false codling moth (Thaumatotibia leucotreta), an insect pest of various fruits and nuts, including citrus. The routine enumeration method for CrleGV-SA virus particles in experimentation and production of CrleGV-SA biopesticides is dark field microscopy. This method was compared with spectrophotometry, scanning electron microscopy (SEM) and real time quantitative polymerase chain reaction (qPCR). The purpose was to develop an accurate and reliable routine enumeration method for CrleGV-SA occlusion bodies (OBs) and to validate the use of dark field microscopy. Purified and semi-purified CrleGV-SA viral stocks were used. Spectrophotometry was not a suitable or accurate enumeration method. Dark field microscopy and SEM were accurate and statistically comparable (p = 0.064), validating the use of dark field microscopy as an enumeration method for granulovirus (GV). However, SEM has superior resolution and the advantage of easily distinguishing virus particles from debris in semi-purified viral stock preparations. A quantitative PCR technique has been developed based on use of specific oligonucleotide primers for the granulin gene. This has the advantage of not being affected by contamination with non-biological debris or biological material, which impact on the other methods.

Growth and Neurotrophic Factors in Embryonic Stem Cells

In this chapter we illustrate protocols to investigate growth and neurotrophic factors in human and rodent (rat and mouse)-derived embryonic stem cells. The conventional two-dimensional cell monolayer system to grow embryonic stem cells is presented, focusing on the coating strategies also using extracellular matrix components. Then, different approaches for three-dimensional stem cell culture are presented, using hydrogels and scaffolds. Quantitative polymerase chain reaction, immunocytochemistry, immunoenzymatic ELISA assay, and multiparametric assays to quantify growth and neurotrophic factor production are presented.

Diagnosis of Acute Q Fever by Detection of Coxiella burnetii DNA using Real-Time PCR, Employing a Commercial Genesig Easy Kit

INTRODUCTION

Query (Q) fever is an important zoonosis and a cause of concern for humans, due to the potential bioterrorism threat posed by the causative agent, Coxiella burnetii. Because of the danger of contracting the illness, isolation attempts are seldom made. Serological and molecular diagnostic tests are the main option.

AIM

To study the prevalence of acute Q fever in Puducherry and surrounding districts of Tamil Nadu, India, employing a new commercial Real-Time Polymerase Chain Reaction (RT-PCR) kit and confirming it by the gold standard Immunofluorescence Assay (IFA).

MATERIALS AND METHODS

Acute phase blood samples from 72 consecutive febrile patients and 24 healthy individuals were included in this prospective study. DNA was extracted from the buffy coats and preserved at -80°C. Detection of C. burnetii was carried out employing a commercial Real-Time PCR kit. Serum samples were tested for IgM (Phase I+II) and IgG (Phase I+II) by QM-120 and QG-120, Coxiella burnetii IFA Fuller Laboratories, California, USA. Sensitivity, Specificity, Positive Predictive Value (PPV) and Negative Predictive Value (NPV) were calculated keeping IFA as the reference.

RESULTS

Presumptive diagnosis of acute Q fever was made in two febrile patients by the Genesig Easy kit (2.78%). In addition to these two PCR positive cases, one more patient was positive for both Phase II IgM and Phase II IgG antibodies by the gold standard IFA. All 24 healthy controls were negative for Q fever by both PCR and IFA. The sensitivity, specificity, NPV and PPV for Genesig Easy kit PCR were: 66.67%, 100%, 100% and 98.57 % respectively against IFA as the reference.

CONCLUSION

The true prevalence of Q fever in India and other developing countries is poorly understood, owing to the difficulties in the diagnosis of this infection. Since molecular diagnostic tests have good specificity and are mandated for confirmation of single acute samples, validation of commercial Q fever PCR kits is the need of the hour. Genesig Easy kit in our hands was found to be reliable with the moderate sensitivity and high specificity. Performing both PCR (with acute specimens) and IFA (with paired sera) would be ideal for Q fever diagnosis.

Can germ cell neoplasia in situ be diagnosed by measuring serum levels of microRNA371a-3p?

Purpose

Diagnosing germ cell neoplasia in situ (GCNis) can detect germ cell tumours (GCTs) at the pre-invasive stage. To date, testicular biopsy with the potential of surgical complications is the only way of safely diagnosing GCNis. Recently, microRNAs (miRs) 371-3, and miR 367 were shown to be valuable serum biomarkers of GCTs. We explored the usefulness of these candidate miRs as a marker for GCNis.

Methods

27 patients with GCNis and no concomitant GCT were enrolled. All patients underwent measuring serum levels of miR-371a-3p and miR-367-3p before treatment, 11 had repeat measurement after treatment, 2 also had testicular vein blood examinations. Serum levels were measured by quantitative PCR. In addition, four orchiectomy specimens of patients with GCT were examined immunohistochemically and by in situ hybridization (ISH) with a probe specific for miR-371a-3p to look for the presence of this miR in GCNis cells.

Results

The median serum level of miR-371a-3p was significantly higher in patients with GCNis than in controls, miR-367 levels were not elevated. Overall, 14 patients (51.9%) had elevated serum levels of miR-371a-3p. The highest levels were found in patients with bilateral GCNis. Levels in testicular vein serum were elevated in both of the cases. After treatment, all elevated levels dropped to normal. In two orchiectomy specimens, miR-371a-3p was detected by ISH in GCNis cells.

Conclusions

Measuring miR-371a-3p serum levels can replace control biopsies after treatment of GCNis. In addition, the test can guide clinical decision making regarding the need of testicular biopsy in cases suspicious of GCNis.

Quantitative assessment of salivary oral bacteria according to the severity of dental caries in childhood

This study aimed to assess differences in selected oral bacteria in children according to the severity of dental caries. One hundred and thirty-six children, 36-60 months old were divided into three groups according to caries status: caries-free (CF) (n=47), early childhood caries (ECC) (n=40) and severe-early childhood caries (S-ECC) (n=49). Saliva was collected for detection and quantification of selected oral streptococci, Actinomyces naeslundii, Lactobacillus spp., Bifidobacterium spp., and Scardovia wiggsiae by quantitative-polymerase chain reaction. The results showed that the detection and quantitative levels of S. mutans, S. sobrinus, Bifidobacterium spp. and S. wiggsiae were significantly higher in S-ECC children compared to CF and ECC children, while for S. salivarius were significantly higher in CF compared to ECC and S-ECC children. There was no statistical difference among the clinical groups for S. mitis, S. oralis, A. naeslundii and Lactobacillus spp. levels and detection. S-ECC children had a lower monthly family income, started tooth brushing later and were breastfeed for a longer duration compared to CF children. S. mutans levels were positively correlated with S. wiggsiae and Bifidobacterium spp. levels, lower mother's education and child bottle-feeding before sleeping and negatively correlated with S. salivarius. It was concluded that in addition to S. mutans, other bacterial species, including bifidobacteria, Scardovia wiggsiae and S. sobrinus, are associated with severity of early childhood caries, although their role in the progress of dental caries remains unclear.

Necessity of purification during bacterial DNA extraction with environmental soils

Complexity and heterogeneity of soil samples have often implied the inclusion of purification steps in conventional DNA extraction for polymerase chain reaction (PCR) assays. Unfortunately the purification steps are also time and labor intensive. Therefore the necessity of DNA purification was re-visited and investigated for a variety of environmental soil samples that contained various amounts of PCR inhibitors. Bead beating and centrifugation was used as the baseline (without purification) method for DNA extraction. Its performance was compared with that of conventional DNA extraction kit (with purification). The necessity criteria for DNA purification were established with environmental soil samples. Using lysis conditions at 3000 rpm for 3 minutes with 0.1 mm glass beads, centrifugation time of 10 minutes and 1:10 dilution ratio, the baseline method outperformed conventional DNA extraction on cell seeded sand samples. Further investigation with PCR inhibitors (i.e., humic acids, clay, and magnesium [Mg]) showed that sand samples containing less than 10 μg/g humic acids and 70% clay may not require purifications. Interestingly, the inhibition pattern of Mg ion was different from other inhibitors due to the complexation interaction of Mg ion with DNA fragments. It was concluded that DNA extraction method without purification is suitable for soil samples that have less than 10 μg/g of humic acids, less than 70% clay content and less than 0.01% Mg ion content.

Quantification of metastatic load in a syngeneic murine model of metastasis

Bioluminescence imaging (BLI) is an established method for evaluating metastatic load in preclinical cancer models; however, BLI can produce observational error due to differences in substrate concentration and signal depth. In our syngeneic murine model of metastasis (VM-M3), we used a quantitative polymerase chain reaction (qPCR) method of DNA quantification to bypass these limitations. Liver, spleen, and brain from VM/Dk (VM) mice bearing VM-M3 tumor cells were first imaged ex vivo with BLI. qPCR quantification of tumor cell DNA was then performed on DNA extracted from these organs. Linear regression indicated that qPCR data predicted BLI data in solid tissue. Furthermore, the tumor cell detection limit was lower for qPCR analysis than for BLI analysis. In order to validate qPCR for use in detecting blood metastases, qPCR quantification was performed on whole blood collected from mice whose global organ metastatic load (summation of liver, spleen, kidneys, lungs, and brain) was quantified through BLI. Linear regression indicated that qPCR data in blood predicted BLI data in solid tissue. The results demonstrate that qPCR is an accurate and sensitive method of metastatic quantification in syngeneic murine models.

Is polymeric substrate in influent an indirect impetus for the nitrification process in an activated sludge system?

Different from monomeric substrate, polymeric substrate (PS) needs to undergo slow hydrolysis process before becoming available for consumption by bacteria. Hydrolysis products will be available for the heterotrophs in low concentration, which will reduce competitive advantages of heterotrophs to nitrifiers in mixed culture. Therefore, some links between PS and nitrification process can be expected. In this study, three lab-scale sequencing batch reactors with different PS/total substrate (TS) ratio (0, 0.5 or 1) in influent were performed in parallel to investigate the influence of PS on nitrification process in activated sludge system. The results showed that with the increase of PS/TS ratio, apparent sludge yields decreased, while NO₃^--N concentration in effluent increased. The change of PS/TS ratio in influent also altered the cycle behaviors of activated sludge. With the increase of PS/TS ratio from 0 to 0.5 and 1, the ammonium and nitrite utilization rate increased ∼2 and 3 times, respectively. The q-PCR results showed that the abundance of nitrifiers in activated sludge for PS/TS ratio of 0.5 and 1 were 0.7-0.8 and 1.4-1.5 orders of magnitude higher than that for PS/TS ratio of 0. However, the abundance of total bacteria decreased about 0.5 orders of magnitude from the former two to the latter. The FISH observation confirmed that the nitrifiers' microcolony became bigger and more robust with the increase of PS/TS ratio. This paper paves a path to understand the role of PS/TS in affecting the nitrification process in biological wastewater treatment systems.