scholarly journals Hyperspectral microscope imaging methods for multiplex detection of Campylobacter

2019 ◽  
Author(s):  
Bosoon Park ◽  
Matthew Eady ◽  
Brian Oakley ◽  
Seung-Chul Yoon ◽  
Kurt Lawrence ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Pathogen Detection ◽  
Shigella Flexneri ◽  
In Situ Hybridisation ◽  
Foodborne Pathogen ◽  
Latex Agglutination ◽  
Molecular Techniques ◽  
Enzyme Linked Immunosorbent Assay ◽  
Fluorescence In Situ Hybridisation ◽  
Microscope Imaging

Campylobacter is an emerging zoonotic bacterial threat in the poultry industry. The current methods for the isolation and detection of Campylobacter are culture-based techniques with several selective agars designed to isolate Campylobacter colonies, which is time-consuming, labour intensive and has low sensitivity. Several immunological and molecular techniques such as enzyme-linked immunosorbent assay (ELISA) and Latex agglutination are commercially available for the detection and identification of Campylobacter. However, these methods demand more advanced instruments as well as specially trained experts. A hyperspectral microscope imaging (HMI) technique with the fluorescence in situ hybridisation (FISH) technique has the potential for multiplex foodborne pathogen detection. Using Alexa488 and Cy3 fluorophores, the HMI (450–800 nm) technique was able to identify Campylobacter jejuni stains with high sensitivity and specificity. In addition, HMI was able to classify six bacteria using scattering intensity from their spectra without a FISH fluorophore. Overall classification accuracy of quadratic discriminant analysis (QDA) method for six bacteria including Bifidobacter longum, Campylobacter jejuni, Clostridium perfringens, Enterobacter cloacae, Lactobacillus salivarius and Shigella flexneri using the HMI technique without fluorescent markers was approximately 88.6 % with pixel-wise classification.

Analysis of nitrifying bacterial communities in aerobic biofilm reactors with different DO conditions using molecular techniques

2008 ◽  
Vol 57 (12) ◽  
pp. 1889-1899 ◽  
Author(s):  
J. J. Park ◽  
I. G. Byun ◽  
J. C. Yu ◽  
S. R. Park ◽  
D. J. Ju ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
In Situ Hybridisation ◽  
Amoa Gene ◽  
Biofilm Reactor ◽  
Molecular Techniques ◽  
Fluorescence In Situ Hybridisation ◽  
Do Concentration ◽  
Pcr Targeting ◽  
The Relationship

In order to assess the relationship between the dissolved oxygen (DO) concentration and the characteristics of nitrifying bacterial communities in an aerobic biofilm reactor, molecular techniques including denaturing gradient gel electrophoresis (DGGE)/cloning based on PCR targeting 16S rRNA and the amoA gene and fluorescence in situ hybridisation (FISH) were conducted. The D-1, D-2, D-3 and D-4 reactors with different DO concentrations (1, 3, 5 and 7 mg/L, respectively) were set up in the thermostat and acclimated. The optimal DO concentration with stable nitrification efficiency was above 5.0 mg/L. As was shown by the results of DGGE and cloning, the community of ammonia-oxidising bacteria (AOB) and the ratio of Nitrosomonas sp. changed only slightly despite their differing nitrification efficiencies. The results of FISH indicated that higher DO concentrations resulted in an increase in AOB and nitrite-oxidising bacteria (NOB), and a reduction in heterotrophic microorganisms. The INT-dehydrogenase activity (DHA) test demonstrated that the activity of AOB decreased with reductions in the DO concentration. This means that the DO concentration does not influence the community of AOB, but rather the activity of AOB. In the relationship between the attached biomass and the nitrification efficiency, only the active biomass affected the nitrification efficiencies.

scholarly journals Microfluidic-Based Approaches for Foodborne Pathogen Detection

2019 ◽  
Vol 7 (10) ◽  
pp. 381 ◽  
Author(s):  
Xihong Zhao ◽  
Mei Li ◽  
Yao Liu
Keyword(s):  
Food Safety ◽  
Foodborne Pathogens ◽  
Pathogen Detection ◽  
Accurate Determination ◽  
Foodborne Pathogen ◽  
Current Status ◽  
Future Research ◽  
Enzyme Linked Immunosorbent Assay ◽  
Human Beings ◽  
Microfluidic Technology

Food safety is of obvious importance, but there are frequent problems caused by foodborne pathogens that threaten the safety and health of human beings worldwide. Although the most classic method for detecting bacteria is the plate counting method, it takes almost three to seven days to get the bacterial results for the detection. Additionally, there are many existing technologies for accurate determination of pathogens, such as polymerase chain reaction (PCR), enzyme linked immunosorbent assay (ELISA), or loop-mediated isothermal amplification (LAMP), but they are not suitable for timely and rapid on-site detection due to time-consuming pretreatment, complex operations and false positive results. Therefore, an urgent goal remains to determine how to quickly and effectively prevent and control the occurrence of foodborne diseases that are harmful to humans. As an alternative, microfluidic devices with miniaturization, portability and low cost have been introduced for pathogen detection. In particular, the use of microfluidic technologies is a promising direction of research for this purpose. Herein, this article systematically reviews the use of microfluidic technology for the rapid and sensitive detection of foodborne pathogens. First, microfluidic technology is introduced, including the basic concepts, background, and the pros and cons of different starting materials for specific applications. Next, the applications and problems of microfluidics for the detection of pathogens are discussed. The current status and different applications of microfluidic-based technologies to distinguish and identify foodborne pathogens are described in detail. Finally, future trends of microfluidics in food safety are discussed to provide the necessary foundation for future research efforts.

Ultrastructure of periplasmic bodies in gram-negative bacteria

1990 ◽  
Vol 48 (3) ◽  
pp. 640-641
Author(s):  
Xie Nianming ◽  
Ding Shaoqing ◽  
Wang Luping ◽  
Yuan Zenglin ◽  
Zhan Guolai ◽  
...  
Keyword(s):  
Electron Microscope ◽  
Campylobacter Jejuni ◽  
Proteus Mirabilis ◽  
Shigella Flexneri ◽  
Morphological Description ◽  
Gram Negative Bacteria ◽  
Periplasmic Space ◽  
Clostridium Tetani ◽  
Gram Negative ◽  
Brucella Canis

Perhaps the data about periplasmic enzymes are obtained through biochemical methods but lack of morphological description. We have proved the existence of periplasmic bodies by electron microscope and described their ultrastructures. We hope this report may draw the attention of biochemists and mrophologists to collaborate on researches in periplasmic enzymes or periplasmic bodies with each other.One or more independent bodies may be seen in the periplasmic space between outer and inner membranes of Gram-negative bacteria, which we called periplasmic bodies. The periplasmic bodies have been found in seven species of bacteria at least, including the Pseudomonas aeroginosa. Shigella flexneri, Echerichia coli. Yersinia pestis, Campylobacter jejuni, Proteus mirabilis, Clostridium tetani. Vibrio cholerae and Brucella canis.

scholarly journals The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicholas M. Negretti ◽  
Christopher R. Gourley ◽  
Prabhat K. Talukdar ◽  
Geremy Clair ◽  
Courtney M. Klappenbach ◽  
...  
Keyword(s):  
Host Cell ◽  
Campylobacter Jejuni ◽  
Foodborne Pathogen ◽  
Small Gtpase ◽  
Host Cells ◽  
Cell Protein ◽  
Host Cell Protein ◽  
Cell Binding ◽  
Actin Reorganization ◽  
Cell Cytosol

AbstractCampylobacter jejuni is a foodborne pathogen that binds to and invades the epithelial cells lining the human intestinal tract. Maximal invasion of host cells by C. jejuni requires cell binding as well as delivery of the Cia proteins (Campylobacter invasion antigens) to the host cell cytosol via the flagellum. Here, we show that CiaD binds to the host cell protein IQGAP1 (a Ras GTPase-activating-like protein), thus displacing RacGAP1 from the IQGAP1 complex. This, in turn, leads to the unconstrained activity of the small GTPase Rac1, which is known to have roles in actin reorganization and internalization of C. jejuni. Our results represent the identification of a host cell protein targeted by a flagellar secreted effector protein and demonstrate that C. jejuni-stimulated Rac signaling is dependent on IQGAP1.

scholarly journals Rapid Multi-Hybridisation FISH Screening for Balanced Porcine Reciprocal Translocations Suggests a Much Higher Abnormality Rate Than Previously Appreciated

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 250
Author(s):  
Rebecca E O’Connor ◽  
Lucas G Kiazim ◽  
Claudia C Rathje ◽  
Rebecca L Jennings ◽  
Darren K Griffin
Keyword(s):  
Semen Analysis ◽  
In Situ Hybridisation ◽  
Economic Loss ◽  
Environmental Damage ◽  
Fluorescence In Situ Hybridisation ◽  
Reciprocal Translocations ◽  
Chromosome Translocations ◽  
Farrowing Rate ◽  
Significant Economic Loss

With demand rising, pigs are the world’s leading source of meat protein; however significant economic loss and environmental damage can be incurred if boars used for artificial insemination (AI) are hypoprolific (sub-fertile). Growing evidence suggests that semen analysis is an unreliable tool for diagnosing hypoprolificacy, with litter size and farrowing rate being more applicable. Once such data are available, however, any affected boar will have been in service for some time, with significant financial and environmental losses incurred. Reciprocal translocations (RTs) are the leading cause of porcine hypoprolificacy, reportedly present in 0.47% of AI boars. Traditional standard karyotyping, however, relies on animal specific expertise and does not detect more subtle (cryptic) translocations. Previously, we reported development of a multiple hybridisation fluorescence in situ hybridisation (FISH) strategy; here, we report on its use in 1641 AI boars. A total of 15 different RTs were identified in 69 boars, with four further animals XX/XY chimeric. Therefore, 4.5% had a chromosome abnormality (4.2% with an RT), a 0.88% incidence. Revisiting cases with both karyotype and FISH information, we reanalysed captured images, asking whether the translocation was detectable by karyotyping alone. The results suggest that chromosome translocations in boars may be significantly under-reported, thereby highlighting the need for pre-emptive screening by this method before a boar enters a breeding programme.

scholarly journals Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Caitlin M. Singleton ◽  
Francesca Petriglieri ◽  
Jannie M. Kristensen ◽  
Rasmus H. Kirkegaard ◽  
Thomas Y. Michaelsen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Wastewater Treatment Plants ◽  
In Situ Hybridisation ◽  
Amplicon Sequencing ◽  
Rrna Genes ◽  
Fluorescence In Situ Hybridisation ◽  
Sequencing Data ◽  
High Quality ◽  
16S Rrna Amplicon Sequencing ◽  
Long Read

AbstractMicroorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

scholarly journals SARS-CoV-2 IgG Antibodies Seroprevalence and Sera Neutralizing Activity in MEXICO: A National Cross-Sectional Study during 2020

2021 ◽  
Vol 9 (4) ◽  
pp. 850
Author(s):  
José Esteban Muñoz-Medina ◽  
Concepción Grajales-Muñiz ◽  
Angel Gustavo Salas-Lais ◽  
Larissa Fernandes-Matano ◽  
Constantino López-Macías ◽  
...  
Keyword(s):  
Immunosorbent Assay ◽  
Neutralizing Antibodies ◽  
Herd Immunity ◽  
Cross Sectional Study ◽  
Molecular Techniques ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Enzyme Linked Immunosorbent Assay ◽  
Cross Sectional ◽  
Neutralizing Activity

Until recently, the incidence of COVID-19 was primarily estimated using molecular diagnostic methods. However, the number of cases is vastly underreported using these methods. Seroprevalence studies estimate cumulative infection incidences and allow monitoring of transmission dynamics, and the presence of neutralizing antibodies in the population. In February 2020, the Mexican Social Security Institute began conducting anonymous unrelated sampling of residual sera from specimens across the country, excluding patients with fever within the previous two weeks and/or patients with an acute respiratory infection. Sampling was carried out weekly and began 17 days before Mexico’s first officially confirmed case. The 24,273 sera obtained were analyzed by chemiluminescent-linked immunosorbent assay (CLIA) IgG S1/S2 and, later, positive cases using this technique were also analyzed to determine the rate of neutralization using the enzyme-linked immunosorbent assay (ELISA). We identified 40 CLIA IgG positive cases before the first official report of SARS-CoV-2 infection in Mexico. The national seroprevalence was 3.5% in February and 33.5% in December. Neutralizing activity among IgG positives patients during overall study period was 86.1%. The extent of the SARS-CoV-2 infection in Mexico is 21 times higher than that reported by molecular techniques. Although the general population is still far from achieving herd immunity, epidemiological indicators should be re-estimated based on serological studies of this type.

scholarly journals Insights into factors sustaining persistence of high malaria transmission in forested areas of sub-Saharan Africa: the case of Mvoua, South Cameroon

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Dominique Mieguim Ngninpogni ◽  
Cyrille Ndo ◽  
Patrick Ntonga Akono ◽  
Anicet Nguemo ◽  
Amine Nguepi ◽  
...  
Keyword(s):  
Anopheles Gambiae ◽  
Malaria Transmission ◽  
Anopheles Funestus ◽  
Mortality Rates ◽  
Molecular Techniques ◽  
Sub Saharan Africa ◽  
World Health ◽  
Enzyme Linked Immunosorbent Assay ◽  
Pyrethroid Insecticides ◽  
Kisumu Strain

Abstract Background In Mvoua, a village situated in a forested area of Cameroon, recent studies have reported high prevalence of Plasmodium falciparum infection among the population. In order to understand factors that can sustain such a high malaria transmission, we investigated the biology of Anopheles vectors and its susceptibility to insecticides, as well as long-lasting insecticidal net (LLIN) coverage, use and bio-efficacy. Methods A longitudinal entomological survey was conducted from July 2018 to April 2019. Adult mosquitoes were collected using the human landing catch (HLC) method and identified using morphological and molecular techniques. Anopheles gambiae (s.l.) larvae were sampled from several stagnant water pools throughout the village and reared to generate F1 adults. The presence of P. falciparum circumsporozoite antigen was detected in the heads and thoraces of mosquitoes collected as adults using an enzyme-linked immunosorbent assay. The insecticide susceptibility status of the local An. gambiae (s.l.) F1 population to the pyrethroid insecticides deltamethrin 0.5% and permethrin 0.75% was determined using World Health Organization-tube bioassays, while the frequency of the knockdown resistance (kdr) mutation was determined by PCR. Coverage, use and physical integrity of LLINs were assessed in households, then cone assays were used to test for their bio-efficacy on both the reference insecticide-susceptible Kisumu strain and on field F1 An. gambiae (s.l.) Results In total, 110 Anopheles mosquitoes were collected, of which 59.1% were identified as Anopheles funestus (s.l.), 38.18% as An. gambiae (s.l.) and 2.72% as An. ziemanii. Anopheles funestus was the most abundant species except in the long rainy season, when An. gambiae (s.l.) predominated (65.8%). In the dry seasons, vectors were principally endophagous (76% of those collected indoors) while they tended to be exophagous (66% of those collected outdoors) in rainy seasons. High Plasmodium infection was observed in An. gambiae (s.l.) and An. funestus, with a circumsporozoitic rate of 14.29 and 10.77%, respectively. Anopheles gambiae (s.l.) was highly resistant to pyrethroid insecticides (mortality rates: 32% for permethrin and 5% for deltamethrin) and harbored the kdr-L1014F mutation at a high frequency (89.74%). Of the 80 households surveyed, only 47.69% had achieved universal coverage with LLNs. Around 70% of the LLINs sampled were in poor physical condition, with a proportionate hole index > 300. Of the ten LLNs tested, eight were effective against the An. gambiae reference insecticide-susceptible Kisumu strain, showing mortality rate of > 80%, while none of these LLINs were efficient against local An. gamabie (s.l.) populations (mortality rates < 11.5%). Conclusion A combination of elevated P. falciparum infection in Anopheles vector populations, insufficient coverage and loss of effectiveness of LLINs due to physical degradation, as well as high resistance to pyrethroid insecticides is responsible for the persistence of high malaria transmission in forested rural area of Mvoua, Cameroon.

Effects of the diploidisation process upon the 5S and 35S rDNA sequences in the allopolyploid species of the Dilatata group of Paspalum (Poaceae, Paniceae)

2019 ◽  
Vol 67 (7) ◽  
pp. 521
Author(s):  
Magdalena Vaio ◽  
Cristina Mazzella ◽  
Marcelo Guerra ◽  
Pablo Speranza
Keyword(s):  
Evolutionary Dynamics ◽  
In Situ Hybridisation ◽  
5S Rdna ◽  
Its Region ◽  
Variable Number ◽  
Rrna Genes ◽  
Fluorescence In Situ Hybridisation ◽  
Rdna Sites ◽  
35S Rdna ◽  
Genome Restructuring

The Dilatata group of Paspalum includes species and biotypes native to temperate South America. Among them, five sexual allotetraploids (x = 10) share the same IIJJ genome formula: P. urvillei Steud, P. dasypleurum Kunze ex Desv., P. dilatatum subsp. flavescens Roseng., B.R. Arrill. &amp; Izag., and two biotypes P. dilatatum Vacaria and P. dilatatum Virasoro. Previous studies suggested P. intermedium Munro ex Morong &amp; Britton and P. juergensii Hack. or related species as their putative progenitors and donors of the I and J genome, respectively, and pointed to a narrow genetic base for their maternal origin. It has not yet been established whether the various members of the Dilatata group are the result of a single or of multiple allopolyploid formations. Here, we aimed to study the evolutionary dynamics of rRNA genes after allopolyploidisation in the Dilatata group of Paspalum and shed some light into the genome restructuring of the tetraploid taxa with the same genome formula. We used double target fluorescence in situ hybridisation of 35S and 5S rDNA probes and sequenced the nrDNA internal transcribed spacer (ITS) region. A variable number of loci at the chromosome ends were observed for the 35S rDNA, from 2 to 6, suggesting gain and loss of sites. For the 5S rDNA, only one centromeric pair of signals was observed, indicating a remarkable loss after polyploidisation. All ITS sequences generated were near identical to the one found for P. intermedium. Although sequences showed a directional homogeneisation towards the putative paternal progenitor in all tetraploid species, the observed differences in the number and loss of rDNA sites suggest independent ongoing diploidisation processes in all taxa and genome restructuring following polyploidy.

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