DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory

Techniques, procedures, and applications in microbiome analysis

Microbiota is a complex community of microorganisms living in a defined environment. Until the 20th century, knowledge of microbiota was partial, as the techniques available for their characterization were primarily based on bacteriological culture. In the last twenty years, the development of DNA sequencing technologies, multi-omics, and bioinformatics has expanded our understanding of microorganisms. We have moved from mainly considering them isolated disease-causing agents to recognizing the microbiota as an essential component of host biology. These techniques have shown that the microbiome plays essential roles in various host phenotypes, influencing development, physiology, reproduction, and evolution. This chapter provides researchers with a summary of the primary concepts, sample collection, experimental techniques, and bioinformatics analysis commonly used in microbiome research. The main features, applications in microbiome studies, and their advantages and limitations are included in each section.

Rapid Genotyping of Campylobacter coli Strains from Poultry Meat by PFGE, Sau-PCR, and fla-DGGE

The genotyping of Campylobacter coli was done using three methods, pulsed-field gel electrophoresis (PFGE), Sau-polymerase chain reaction (Sau-PCR), and denaturing gradient gel electrophoresis assay of flagellin gene (fla-DGGE) and the characteristics of these assays were compared. The results showed that a total of 53 strains of C. coli were isolated from chicken and duck samples in three markets. All isolates were clustered into 31, 33, and 15 different patterns with Simpson's index of diversity (SID) values of 0.972, 0.974, and 0.919, respectively. Sau-PCR assay was simpler, more rapid, and had higher discriminatory power than PFGE assay. Fla-DGGE assay could detect and illustrate the number of contamination types of C. jejuni and C. coli without cultivation, which saved more time and cost than Sau-PCR and PFGE assays. Therefore, Sau-PCR and fla-DGGE assays are both rapid, economical, and easy to perform, which have the potential to be promising and accessible for primary laboratories in genotyping C. coli strains.

Novel genosensor for probing DNA mismatches and UV-induced DNA damage: Sequence-specific recognition

Human genome is continuously susceptible to changes that may lead to undesirable mutations causing various diseases and cancer. Vast majority of techniques has investigated the discrimination between base-pair mismatched nucleic acid, but many of these techniques are time-consuming, complex, expensive, and limited to the detection of specific type of dsDNA mismatches. In this study, we introduce a simple mix-and-read assay for the sensitive and cost-effective analysis of DNA base mismatches and UV-induced DNA damage using Hoechst genosensor dye (H258). This dye is a minor groove binder that undergoes a drastic conformational change upon binding with mismatch DNA. The difference in binding affinity between perfectly matched and mismatched DNA was studied for sequences at different base mismatch locations and finally, extended for the detection of dsDNA damage by UVC radiation in calf thymus DNA. In addition, a comparative DNA damage kinetic study was performed using H258 (minor groove binder) and EvaGreen (intercalating) dye to get insight on assay selectivity and sensitivity with dye binding mechanism. The result shows good reproducibility making H258 genosensor a cheaper alternative for DNA mismatch and damage studies with possibility of extension for in-vitro detection of hot spots of DNA mutations.

Two novel "release-on-demand" fluorescent biosensors for probing UV-induced DNA damage induced in single stranded and double stranded DNA: Comparative study

Light in the UVC spectral region damages both single-strand (ssDNA) and double-strand DNA (dsDNA), and contributes to the formation of mutagenic photoproducts. In-vivo studies show greater damage for ssDNA compared to dsDNA. However, excited-state spectroscopy shows that dsDNA has longer excited-state lifetime than ssDNA, which increases the probability of damage for dsDNA. However, lack of a direct comparison of in-vitro ssDNA and dsDNA damage rates precludes the development of a model that elucidates the molecular factors responsible for damage. In this work, two novel sensitive "release-on-demand" biosensors are developed for the selective probing of DNA-damage and comparing the rate of DNA damage in ssDNA and dsDNA. The two biosensors involve the use of EvaGreen and Hoechst dyes for the sensitive probing of DNA-damage. The results show that ssDNA is damaged at a faster rate than dsDNA in the presence of UVC light (200-295 nm). Furthermore, we examined the effect of G/C composition on the damage rate for mostly A/T ssDNA and dsDNA oligonucleotides. Our results show that DNA damage rates are highly dependent on the fraction of guanines in the sequence, but that in-vitro dsDNA always exhibits an overall slower rate of damage compared to ssDNA, essentially independent of sequence.

Application of Biotechnology in Specific Spoilage Organisms of Aquatic Products

Aquatic products are delicious and have high nutritive value, however, they are highly perishable during storage due to the growth and metabolism of microorganisms. The spoilage process of aquatic products was demonstrated to be highly related to the composition of microorganisms, in which the specific spoilage organisms (SSOs) are the main factors. In this article, the spoilage indicators of SSOs were systematically described, which could make a comprehensive evaluation of the quality of aquatic products. Quorum sensing (QS) regulates the growth, metabolism and characteristics of SSOs, the common signaling molecules and the QS system in the major SSOs of aquatic products were discussed. Moreover, we compared various technologies for the analysis of SSOs in aquatic products. Besides, quality control techniques based on microbiota regulating of aquatic products, including physical, chemical and biological preservation strategies, were also compared. In conclusion, novel preservation technologies and hurdle techniques are expected to achieve comprehensive inhibition of SSOs.

Metagenomics of the midgut microbiome of Rhipicephalus microplus from China

Background

Ticks, which are ectoparasites of animals, may carry multiple pathogens. The cattle tick Rhipicephalus microplus is an important bovine parasite in China. However, the midgut microbiome of R. microplus from China has not been characterized via metagenomic methods.

Methods

Rhipicephalus microplus were collected from cattle in the city of Changsha in Hunan province, China. The DNA of the midgut contents was extracted from fully engorged adult female R. microplus. A DNA library was constructed and sequenced using an Illumina HiSeq sequencing platform. SOAPdenovo software was used to assemble and analyze the clean data. The latent class analysis algorithm applied to system classification by MEGAN software was used to annotate the information on the species’ sequences. DIAMOND software was used to compare unigenes with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and functional annotation was carried out based on the results of the comparison.

Results

The dominant phyla in the five samples were Firmicutes, Proteobacteria, and Actinobacteria. Streptococcus, Mycobacterium, Anaplasma, Enterococcus, Shigella, Lactobacillus, Brachyspira, Pseudomonas, Enterobacter, Bacillus, and Lactococcus were the dominant genera in the five samples. The endosymbiotic bacterium Wolbachia was also detected in all of the samples. Mycobacterium malmesburyense, Streptococcus pneumoniae, Anaplasma phagocytophilum, Enterococcus faecium, Shigella sonnei, Enterococcus faecalis, Lactobacillus casei, Brachyspira hampsonii, Pseudomonas syringae, Enterobacter cloacae, and Lactococcus garvieae were the dominant species in the five samples. In addition to these bacterial species, we also detected some eukaryotes, such as Rhizophagus irregularis, Enterospora canceri, Smittium culicis, Zancudomyces culisetae, Trachipleistophora hominis, and viruses such as orf virus, human endogenous retrovirus type W, enzootic nasal tumor virus of goats, bovine retrovirus CH15, and galidia endogenous retrovirus in all of the samples at the species level. The results of the annotated KEGG pathway predictions for the gene functions of the midgut microflora of R. microplus indicated genes involved in lipid and amino acid metabolism, infectious diseases (e.g., Streptococcuspneumonia infection, human granulocytic anaplasmosis, Shigellasonnei infection, Salmonella enterica infection, and pathogenic Escherichia coli infection), and cancer.

Conclusions

Our study revealed that the midgut microbiome of R. microplus is not only composed of a large number of bacteria, but that a portion also comprises eukaryotes and viruses. The data presented here enhance our understanding of this tick’s midgut microbiome and provide fundamental information for the control of ticks and tick-borne diseases.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05161-6.

Bioinspired Smart Materials With Externally-Stimulated Switchable Adhesion

Living organisms have evolved, over billions of years, to develop specialized biostructures with switchable adhesion for various purposes including climbing, perching, preying, sensing, and protecting. According to adhesion mechanisms, switchable adhesives can be divided into four categories: mechanically-based adhesion, liquid-mediated adhesion, physically-actuated adhesion and chemically-enhanced adhesion. Mimicking these biostructures could create smart materials with switchable adhesion, appealing for many engineering applications in robotics, sensors, advanced drug-delivery, protein separation, etc. Progress has been made in developing bioinspired materials with switchable adhesion modulated by external stimuli such as electrical signal, magnetic field, light, temperature, pH value, etc. This review will be focused on new advance in biomimetic design and synthesis of the materials and devices with switchable adhesion. The underlying mechanisms, design principles, and future directions are discussed for the development of high-performance smart surfaces with switchable adhesion.

Structured sequences emerge from random pool when replicated by templated ligation

The structure of life emerged from randomness. This is attributed to selection by molecular Darwinian evolution. This study found that random templated ligation led to the simultaneous elongation and sequence selection of oligomers. Product strands showed highly structured sequence motifs which inhibited self-folding and built self-templating reaction networks. By the reduction of the sequence space, the kinetics of duplex formation increased and led to a faster replication through the ligation process. These findings imply that elementary binding properties of nucleotides can lead to an early selection of sequences even before the onset of Darwinian evolution. This suggests that such a simplification of sequence space could result in faster downstream selection for sequence-based function for the origin of life.

The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error threshold to avoid that replicated specific sequences become random because of the incorporated replication errors [M. Eigen, Naturwissenschaften 58 (10), 465–523 (1971)]. Here, we showed that linking short oligomers from a random sequence pool in a templated ligation reaction reduced the sequence space of product strands. We started from 12-mer oligonucleotides with two bases in all possible combinations and triggered enzymatic ligation under temperature cycles. Surprisingly, we found the robust creation of long, highly structured sequences with low entropy. At the ligation site, complementary and alternating sequence patterns developed. However, between the ligation sites, we found either an A-rich or a T-rich sequence within a single oligonucleotide. Our modeling suggests that avoidance of hairpins was the likely cause for these two complementary sequence pools. What emerged was a network of complementary sequences that acted both as templates and substrates of the reaction. This self-selecting ligation reaction could be restarted by only a few majority sequences. The findings showed that replication by random templated ligation from a random sequence input will lead to a highly structured, long, and nonrandom sequence pool. This is a favorable starting point for a subsequent Darwinian evolution searching for higher catalytic functions in an RNA world scenario.

Intraspecific trait variation alters the outcome of competition in freshwater ciliates

Trait variation among heterospecific and conspecific organisms may substantially affect community and food web dynamics. While the relevance of competition and feeding traits have been widely studied for different consumer species, studies on intraspecific differences are more scarce, partly owing to difficulties in distinguishing different clones of the same species. Here, we investigate how intraspecific trait variation affects the competition between the freshwater ciliates Euplotes octocarinatus and Coleps hirtus in a nitrogen-limited chemostat system. The ciliates competed for the microalgae Cryptomonas sp. (Cry) and Navicula pelliculosa (Nav), and the bacteria present in the cultures over a period of 33 days. We used monoclonal Euplotes and three different Coleps clones (Col 1, Col 2, and Col 3) in the experiment that could be distinguished by a newly developed rDNA-based molecular assay based on the internal transcribed spacer (ITS) regions. While Euplotes feeds on Cry and on bacteria, the Coleps clones cannot survive on bacteria alone but feed on both Cry and Nav with clone-specific rates. Experimental treatments comprised two-species mixtures of Euplotes and one or all of the three different Coleps clones, respectively. We found intraspecific variation in the traits "selectivity" and "maximum ingestion rate" for the different algae to significantly affect the competitive outcome between the two ciliate species. As Nav quickly escaped top-down control and likely reached a state of low food quality, ciliate competition was strongly determined by the preference of different Coleps clones for Cry as opposed to feeding on Nav. In addition, the ability of Euplotes to use bacteria as an alternative food source strengthened its persistence once Cry was depleted. Hence, trait variation at both trophic levels codetermined the population dynamics and the outcome of species competition.

Determination of Mutational Spectra Induced by Environmental Toxicants in Complex Human Cell Populations

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in the environment and have potent mutagenic and carcinogenic activities. Studies of mutations induced by these compounds in human cells can help acquire an understanding of their mutagenic pathways. In this chapter, independent cultures of a human cell line expressing cytochrome P450 CYP1A1 (cell line MCL-5) were treated with benzo(a)pyrene (BaP) or dibenzo(a,l)pyrene (DBP), and mutants at the hypoxanthine phosphoribosyltransferase (HPRT) locus were selected en masse by 6-thioguanine resistance (6TG^R). The kinds and positions of the mutations occurring in the third exon of the HPRT gene were analyzed in the mixed HPRT^R mutant cell populations using a combination of polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE). Mutant bands were excised from the gel, amplified using PCR, and sequenced to determine the kinds and positions, or spectrum of mutations.

Tracing insect pests: is there new potential in molecular techniques?

Insects are amongst the greatest pests of agriculture, horticulture and forestry worldwide, inflicting damage and economic costs both directly and by transmitting plant viruses. Many kinds of insects are now resistant or cross-resistant to pesticides. Tracking studies have become very important for combatting insect pests and for better understanding their biology (eg insect population dynamics, movements, feeding behaviour and other ecological interactions). A wide variety of tracing approaches have been used including discriminative, tracer and molecular methods. The perfect technique for insect tracking is the technique that harmonizes with insects' 'normal' biology. Furthermore, the technique should be environmentally safe, cost-effective and easy to use. This paper reviews the current techniques used for insect traceability, documents the advantages and drawbacks of each method, and puts special focus on molecular techniques, including PCR-denaturing gradient gel electrophoresis as a new and promising traceability tool that could provide insects with a unique biological barcode and thus make it possible to trace their movements.

Gut eosinophils and their impact on the mucus-resident microbiota

The gut has the largest commensal bacterial population in the body and its composition can be impacted by host factors such as production of immunoglobulin A (IgA). Eosinophils in the gut have been implicated in the production of antibacterial factors and maintenance of IgA‐secreting plasma cells. We used an eosinophil‐deficient mouse (∆dblGATA‐1^−/−) and littermate controls to investigate the role of eosinophils in the regulation of the microbiota, with particular emphasis on mucus‐resident species in the small and large intestine. We found no differences in IgA production or IgA‐expressing plasma cells between naive littermates in the small or large intestine. However, denaturing gel gradient electrophoresis revealed differences in the bacterial communities of the mucus and stools between wild‐type mice and ∆dblGATA‐1^−/− mice, with the greatest separation between the mucus microbial communities. Mucus‐resident bacteria in ∆dblGATA‐1^−/− mice had reduced diversity in the mucus compared with the stools. A quantitative PCR panel of selected bacteria showed that the most significant differences in the microbiota were between mucus‐resident bacteria and those in stool, such as the abundance of Clostridiales and Bacteroides. Our data implicate eosinophils in the regulation of the microbiota, especially the bacteria most hyperlocal to the gut barrier. Although we see differences between host genotypes in the overall microbial communities, further work is required to establish specifically which bacteria are different between these groups. Most importantly, the data revealed that the mucus and stool microbiota are discrete communities. Stool analysis alone may be insufficient to comprehensively explore and define the role of the gut microbiota in health and disease.

Magnetic nanospheres for convenient and efficient capture and release of hepatitis B virus DNA

Nucleic acid isolation and purification are essential steps in molecular biology. Currently-used isolation methods focus on the extraction of all the nucleic acids from crude samples, yet ignore the specific nucleic acids of interest, which may induce the loss of the specific nucleic acids and hinder their analyses. Herein, a magnetic nanospheres (MNs)-based strategy for efficient capture and release of specific nucleic acids is developed. The DNA sequence of hepatitis B virus (HBV) is taken as a model to validate this method. The MNs are modified with the complementary strand of HBV DNA for specific capture based on hybridization reaction. Then, by melting at high temperature, the captured DNAs are detached from the MNs to achieve release. The capture and release process are performed conveniently with magnetic separation. High capture efficiency (over 80%) and nearly 100% release efficiency for HBV DNA are achieved respectively via 40 min and 5 min interaction. While non-target DNAs are hardly captured, indicative of good selectivity. Moreover, after releasing DNAs, the MNs are directly regenerated and can be reused without degrading performance, which greatly reduces the operation costs. Finally, this method is applied to serum samples without any pretreatment, which exhibits similar capture and release capacity with those in the ideal samples, indicating its great application potential in practice.

Molecular Pathology Techniques: Advances in 2018

Molecular pathology techniques continue to evolve. Although polymerase chain reaction (PCR) remains the cornerstone methodology for nucleic acid amplification, improvements in nucleic acid detection methodologies (i.e. PCR) have increased the detection sensitivity by using fluorescent and bead based array technologies. Single base pair lesions can be detected via sequencing and related techniques to discern point mutations in disease pathogenesis. Novel technologies, such as high- resolution melting analysis, provide fast high throughput post PCR analysis of genetic mutations or variance in nucleic acid sequences. These and other technologies such as hybrid capture, fluorohore and chemiluminescence detections assays allow for rapid diagnosis and prognosis for expeditious and personalized patient management.

Recent Advancements in Intestinal Microbiota Analyses: A Review for Non-Microbiologists

Microbial constituents naturally inhabiting the gastrointestinal tract may influence the homeostasis of the gut environment. The presence or overabundance of some bacterial taxa has been reported to be associated with complex diseases, and the metabolites of certain bacteria may contribute to diverse disorders by influencing signaling pathways. Therefore, the study of gut microbial population has emerged as a crucial field and a new potential area of clinical significance. Advances in the methods of microbiota analysis have shed light upon the details including species diversity, microfloral activities as well as the entire gut microbiota. Nevertheless, comprehensive reviews on this subject are still limited. For elucidating the appropriate selection strategy of the methods to address a particular research question, we comprehensively reviewed the continuously improving technologies, classical to newly developed, and dissected their relative advantages and drawbacks. In addition, aiming at the rapidly advancing next-generation sequencing, we enumerated the improvements in mainstream platforms and made the horizontal and vertical comparison among them. Additionally, we demonstrated the four main -omics methods, which may provide further mechanistic insights into the role of microbiota, to propel phylotyping analysis to functional analysis.

Microbiological comparison of blood culture and amplification of 16S rDNA methods in combination with DGGE for detection of neonatal sepsis in blood samples

It is estimated that 15% of all newborns admitted to the neonatal intensive care unit (NICU) for suspected sepsis receive multiple broad-spectrum antibiotics without pathogen identification. The gold standard for bacterial sepsis detection is blood culture, but the sensitivity of this method is very low. Recently, amplification and analysis of the 16S ribosomal DNA (rDNA) bacterial gene in combination with denaturing gradient gel electrophoresis (DGGE) has proven to be a useful approach for identifying bacteria that are difficult to isolate by standard culture methods. The main goal of this study was to compare two methods used to identify bacteria associated with neonatal sepsis: blood culture and broad range 16S rDNA-DGGE. Twenty-two blood samples were obtained from newborns with (n = 15) or without (n = 7) signs and symptoms of sepsis. Blood samples were screened to identify pathogenic bacteria with two different methods: (1) bacteriological culture and (2) amplification of the variable V3 region of 16S rDNA-DGGE. Blood culture analysis was positive in 40%, whereas 16S rDNA-DGGE was positive in 87% of neonatal sepsis cases. All 16S rDNA-DGGE positive samples were associated with some other signs of neonatal sepsis.

CONCLUSION

Our study shows that the molecular approach with 16S rDNA-DGGE identifies twofold more pathogenic bacteria than bacteriological culture, including complex bacterial communities associated with the development of bacterial sepsis in neonates. What is Known: • Neonatal sepsis affects 2.3% of birth in the NICU with a high mortality risk. • Evidence supports the use of molecular methods as an alternative to blood culture for identification of bacterial associated neonatal sepsis. What is New: • The DGGE gel is a good methodological approach for the identification of bacterial in neonatal blood samples. • This study describes the pattern of electrophoretic mobility obtained by DGGE gels and allows to determine the type of bacteria associated in the development of neonatal sepsis.

Overview of craft brewing specificities and potentially associated microbiota

The brewing process differs slightly in craft breweries as compared to industrial breweries, as there are fewer control points. This affects the microbiota of the final product. Beer contains several antimicrobial properties that protect it from pathogens, such as low pH, low oxygen and high carbon dioxide content, and the addition of hops. However, these hurdles have limited power controlling spoilage organisms. Contamination by these organisms can originate in the raw materials, persist in the environment, and be introduced by using flavoring ingredients later in the process. Spoilage is a prominent issue in brewing, and can cause quality degradation resulting in consumer rejection and product waste. For example, lactic acid bacteria are predominately associated with producing a ropy texture and haze, along with producing diacetyl which gives the beer butter flavor notes. Other microorganisms may not affect flavor or aroma, but can retard fermentation by consuming nutrients needed by fermentation yeast. Quality control in craft breweries today relies on culturing methods to detect specific spoilage organisms. Using media can be beneficial for detecting the most common beer spoilers, such as Lactobacillus and Pediococci. However, these methods are time consuming with long incubation periods. Molecular methods such as community profiling or high throughput sequencing are better used for identifying entire populations of beer. These methods allow for detection, differentiation, and identification of taxa.

A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR-Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches

Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis), to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control. Highlight: We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis) with analytical chemistry approaches to achieve the authentication and quality connotation of the samples.

Sequence-dependent cleavage of mismatched DNA by Ban I restriction endonuclease

Restriction enzymes have previously shown the ability to cleave DNA substrates with mismatched base(s) in recognition sequences; in this study, Ban I endonuclease demonstrated this same ability. Single base substitutions were introduced, and fragments containing various types of unpaired base(s) (heteroduplex fragments) within the Ban I endonuclease recognition sequence, 5'-G|GPyPuCC-3', were generated. Each of the heteroduplex fragments was treated with Ban I endonuclease and analyzed by denaturing gradient gel electrophoresis. Our results showed that heteroduplex fragments containing mismatched bases at either the first or third position of the Ban I recognition sequence or, because of the symmetrical structure of the sequence, the sixth or fourth position on the opposite strand were cleaved by the enzyme. Furthermore, these cleaved fragments contained at least one strand corresponding to the original Ban I recognition sequence. Fragments with mismatches formed by an A (noncanonical, nc) opposite a purine (canonical, ca) or a T (nc) opposite a pyrimidine (ca) were cleaved more efficiently than other types of mismatched bases. These results may help elucidate the mechanisms by which DNA and protein interact during the process of DNA cleavage by Ban I endonuclease.

Contemporary nucleic acid-based molecular techniques for detection, identification, and characterization of Bifidobacterium

Bifidobacteria are one of the most important bacterial groups found in the gastrointestinal tract of humans. Medical and food industry researchers have focused on bifidobacteria because of their health-promoting properties. Researchers have historically relied on classic phenotypic approaches (culture and biochemical tests) for detection and identification of bifidobacteria. Those approaches still have values for the identification and detection of some bifidobacterial species, but they are often labor-intensive and time-consuming and can be problematic in differentiating closely related species. Rapid, accurate, and reliable methods for detection, identification, and characterization of bifidobacteria in a mixed bacterial population have become a major challenge. The advent of nucleic acid-based molecular techniques has significantly advanced isolation and detection of bifidobacteria. Diverse nucleic acid-based molecular techniques have been employed, including hybridization, target amplification, and fingerprinting. Certain techniques enable the detection, characterization, and identification at genus-, species-, and strains-levels, whereas others allow typing of species or strains of bifidobacteria. In this review, an overview of methodological principle, technique complexity, and application of various nucleic acid-based molecular techniques for detection, identification, and characterization of bifidobacteria is presented. Advantages and limitations of each technique are discussed, and significant findings based on particular techniques are also highlighted.

A rapidly-prototyped microfluidic device for size-based nucleic acid fractionation using isotachophoresis

We present a novel microfluidic device for size-based nucleic acid (NA) fractionation using isotachophoresis (ITP) and an ionic spacer.

Novel Bacterial Phylotypes in Endodontic Infections

Although molecular studies have revealed potential oral pathogens among the phyla Spirochaetes and Deferribacteres, their occurrence in endodontic infections has not been consistently investigated. In this study, we devised a nested PCR-DGGE approach to survey samples from infected root canals for the presence of members of these two phyla, and to examine their diversity. The primers used also amplified DNA from Atopobium species. Eight of 10 cases showed bands representative of the target bacterial groups. DGGE profiles revealed a mean number of 6.5 intense and faint bands. No single band occurred in all profiles. Sequences from intense bands excised from the gel showed similarities to species/phylotypes of all target groups— Flexistipes species ( Deferribacteres phylum), uncharacterized spirochetes, and Atopobium species. Analysis of these data indicates that uncultivated Spirochaetes and Deferribacteres phylotypes are frequent members of the endodontic microbiota and may be potential pathogens involved with the etiology of periradicular diseases.

Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics

Bioremediation is generally viewed as a cost effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers. As NGS costs decrease, metagenomics and metatranscriptomics have become increasingly feasible options to rapidly scan sites for specific degradative functions and identify microorganisms important in pollutant degradation. These omic techniques are capable of revolutionizing biological treatment in environmental engineering by allowing highly sensitive characterization of previously uncultured microorganisms. Omics enables the discovery of novel microorganisms for use in bioaugmentation and supports systematic optimization of biostimulation strategies. This review describes the omics journey from roots in biology and medicine to its current status in environmental engineering including potential future directions in commercial application.

An efficient method to genotype the polymorphisms of cholinergic nicotinic receptor subunit genes and their associations with COPD onset risk

BACKGROUND

Single-nucleotide polymorphisms (SNPs) in the cholinergic nicotinic receptor subunit genes on chromosome 15q25.1, including CHRNA3, CHRNB4 and CHRNA5, are well-established biomarkers of chronic obstructive pulmonary disease (COPD) and lung cancer. Thus, there is great demand for a rapid, easy and inexpensive method to detect these variations for purpose of risk prediction in large populations.

AIM OF THE STUDY

The aim of this study was to establish an accurate and efficient method for genotyping CHRN SNPs and testing their association with age at onset of COPD in Chinese population as well as the clinical stage in COPD patients.

MATERIALS AND METHODS

We designed a method to specifically genotype 5 SNPs of CHRN genes based on a modified high-resolution melt (HRM) method and then validated the genotyping results by direct sequencing of 120 samples. We further used the HRM method to genotype these 5 SNPs in 1,013 COPD patients.

RESULTS

Requiring little time, few material costs and only a simplified protocol, the modified HRM method could accurately distinguish the genotypes of CHRN SNPs, demonstrating kappa coefficients >0.96 based on the results from direct sequencing. Furthermore, the data showed that the GG genotype of SNP rs56218866 was associated with a significantly earlier age of COPD onset than A (AA+AG) genotypes (61.0 ± 8.93 vs. 67.8 ± 9.88; P = 0.031), which was not found for the other SNPs. No significant association was observed between the COPD stages and any of the above SNPs.

CONCLUSION

A simple, rapid and efficient HRM method was introduced for CHRN SNP genotyping and a suggestion that the SNP rs56218866A>G is associated with early-onset COPD in a Chinese population was found.

Population Screening of Single-Nucleotide Polymorphisms Exemplified by Analysis of 8000 Alleles

The authors describe a method in which the population frequency of single-nucleotide polymorphisms (SNPs) can be efficiently detected and their allele frequencies accurately measured. Selected SNPs in TNF, IL-4, and CTLA-4 were used to demonstrate the method. Blood from 4000 individuals was pooled, DNA was extracted, and target sequences were PCR amplified and analyzed by denaturant capillary electrophoresis. Alleles were separated into peaks based on melting properties of the double DNA helix. Frequencies of the different alleles were determined by calculating the area under the peaks. Allele frequencies and Hardy-Weinberg equilibrium estimated from the pooled data were verified by analyzing 7.5% of the samples randomly selected from the blood donor series. The method herein is equally suitable for single-samples and/or pooled-samples analysis of SNPs, in which sample treatment is kept to a minimum. The potential throughput of the method is beyond obtainable numbers of samples.

Conformation-Sensitive Gel Electrophoresis as an Ideal High-Throughput Strategy for Accurate Detection of Sequence Variations in DNA: Screening hTomm and hTimm Genes

Conformation-sensitive gel electrophoresis is a heteroduplex-based method that is particularly well suited to high-throughput analyses. Its simplicity makes it amenable to various adaptations and modifications to enhance its applicability to genome-wide mutation scans. Technical aspects that markedly improve the conformation-sensitive gel electrophoresis performance by combining high throughput and high resolution of the bands facilitating the interpretation of the results are described here. The authors report some of the results they have obtained in the screening of the exon 1 of human Timm8A gene as an example of the suitability of the conformation-sensitive gel electrophoresis–based protocol that has been adapted to optimize its throughput, speed, and simplicity in the recognition of both heterozygous and homozygous DNA mutations. The higher throughput is achieved by using 12 batches per gel. The length of the gel is sufficient for an adequate well-to-read distance for each batch that allows a clear distinction and resolution of the conformation-sensitive gel electrophoresis bands. Standardization of the procedure using multichannel pipettes reduces the preparation time of the 96-well PCRs to 10 min and also accelerates the gel loading. The resulting bands give high-quality images, allowing easy detection of known as well as novel mutations.

Efficacy of oral Bifidobacterium bifidum ATCC 29521 on microflora and antioxidant in mice

This study aimed to examine whether Bifidobacterium bifidum ATCC 29521, a species of colonic microflora in humans, is involved in the intestinal tract of mice. This study was also conducted to determine the antioxidant activity of this species by evaluating different microbial populations and reactive oxygen species isolated from feces and intestinal contents for 28 days of oral administration. Microbial diversities were assessed through bacterial culture techniques, PCR–DGGE, and real-time PCR. This study showed that the intake of B. bifidum ATCC 29521 significantly (p < 0.05) improved the ecosystem of the intestinal tract of BALB/c mice by increasing the amount of probiotics (Lactobacillus intestinalis and Lactobacillus crispatus) and by reducing unwanted bacterial populations (Enterobacter, Escherichia coli). Antioxidative activities of incubated cell-free extracts were evaluated through various assays, including the scavenging ability of DPPH radical (64.5% and 67.54% (p < 0.05), respectively, at 21 days in nutrients and 28 days in MRS broth), superoxide anion, and hydroxyl radical (85% and 61.5% (p < 0.05), respectively, at intestinal contents in nutrients and 21 days in MRS broth). Total reducing power (231.5 μmol/L (p < 0.05), 14 days in MRS broth) and mRNA level of genes related to oxidative stress were also determined. Results indicated that B. bifidum ATCC 29521 elicits a beneficial effect on murine gut microbiota and antioxidant activities compared with the control samples. This species can be considered as a potential bioresource antioxidant to promote health. Bifidobacterium bifidum ATCC 29521 may also be used as a promising material in microbiological and food applications.

Development of low-density oligonucleotide microarrays for detecting mutations causing Wilson's disease

Background & objectives:

Wilson's disease (WD) is an autosomal recessive disorder caused by mutations in ATP7B, a copper transporter gene, leading to hepatic and neuropsychiatric manifestations due to copper accumulation. If diagnosed early, WD patients can be managed by medicines reducing morbidity and mortality. Diagnosis of this disease requires a combination of tests and at times is inconclusive due to overlap of the symptoms with other disorders. Genetic testing is the preferred alternative in such cases particularly for individuals with a family history. Use of DNA microarray for detecting mutations in ATP7B gene is gaining popularity because of the advantages it offers in terms of throughput and sensitivity. This study attempts to establish the quality analysis procedures for microarray based diagnosis of Wilson's disease.

Methods:

A home-made microarrayer was used to print oligonucleotide based low-density microarrays for addressing 62 mutations causing Wilson's disease reported from Indian population. Inter- and intra- array comparisons were used to study quality of the arrays. The arrays were validated by using mutant samples generated by site directed mutagenesis.

Results:

The hybridization reaction were found to be consistent across the surface of a given microarray. Our results have shown that 52 °C post-hybridization wash yields better reproducibility across experiments compared to 42 °C. Our arrays have shown > 80 per cent sensitivity in detecting these 62 mutations.

Interpretation & conclusions:

The present results demonstrate the design and evaluation of a low-density microarray for the detection of 62 mutations in ATP7B gene, and show that a microarray based approach can be cost-effective for detecting a large number of mutations simultaneously. This study also provides information on some of the important parameters required for microarray based diagnosis of genetic disorders.

Polymerase specific error rates and profiles identified by single molecule sequencing

DNA polymerases have an innate error rate which is polymerase and DNA context specific. Historically the mutational rate and profiles have been measured using a variety of methods, each with their own technical limitations. Here we used the unique properties of single molecule sequencing to evaluate the mutational rate and profiles of six DNA polymerases at the sequence level. In addition to accurately determining mutations in double strands, single molecule sequencing also captures direction specific transversions and transitions through the analysis of heteroduplexes. Not only did the error rates vary, but also the direction specific transitions differed among polymerases.

Pregastric and caecal fermentation pattern in Syrian hamsters

Few studies have compared the pregastric and caecal digestion of hamsters. Mature Syrian hamsters (

Development of gut inflammation in mice colonized with mucosa-associated bacteria from patients with ulcerative colitis

BACKGROUND

Disturbances in the intestinal microbial community (i.e. dysbiosis) or presence of the microbes with deleterious effects on colonic mucosa has been linked to the pathogenesis of inflammatory bowel diseases. However the role of microbiota in induction and progression of ulcerative colitis (UC) has not yet been fully elucidated.

METHODS

Three lines of human microbiota-associated (HMA) mice were established by gavage of colon biopsy from three patients with active UC. The shift in microbial community during its transferring from humans to mice was analyzed by next-generation sequencing using Illumina MiSeq sequencer. Spontaneous or dextran sulfate sodium (DSS)-induced colitis and microbiota composition profiling in germ-free mice and HMA mice over 3-4 generations were assessed to decipher the features of the distinctive and crucial events occurring during microbial colonization and animal reproduction.

RESULTS

None of the HMA mice developed colitis spontaneously. When treated with DSS, mice in F4 generation of one line of colonized mice (aHMA) developed colitis. Compared to the DSS-resistant earlier generations of aHMA mice, the F4 generation have increased abundance of Clostridium difficile and decrease abundance of C. symbiosum in their cecum contents measured by denaturing gradient gel electrophoresis and DNA sequencing.

CONCLUSION

In our study, mucosa-associated microbes of UC patients were not able to induce spontaneous colitis in gnotobiotic BALB/c mice but they were able to increase the susceptibility to DSS-induced colitis, once the potentially deleterious microbes found a suitable niche.

Bacterial analysis of combined periodontal-endodontic lesions by polymerase chain reaction-denaturing gradient gel electrophoresis

We used denaturing gradient gel electrophoresis (DGGE) to compare bacterial profiles in periodontium and root canals of teeth with combined periodontal-endodontic lesions. Samples of dental plaque and necrotic pulp were collected from thirteen extracted teeth with advanced periodontitis. Genomic DNA was extracted for polymerase chain reaction (PCR) analysis using universal bacterial primers. The PCR products were then loaded onto DGGE gels to obtain fractionated bands. Characteristic DGGE bands were excised and DNA was cloned and sequenced. The number of bands, which indicates the number of bacterial species, was compared between dental plaques and necrotic pulp tissues from the same tooth. Although the difference was statistically significant (P < 0.01), there was no positive correlation; similarity (Dice coefficient) was 13.1% to 62.5%. Some bacteria species were present in both the periodontal pockets and root canals of the same tooth; however, periodontal bacteria did not always invade the root canals, and some bacteria in root canals were not present in periodontal pockets of the same tooth. In some teeth, unique bacteria in root canals had not passed from periodontal pockets. A basic local alignment search tool (BLAST) sequence search in Genbank indicated that new bacteria species were present in periodontal pockets and root canals. Their characteristics must thus be further analyzed.

Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control

Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.

Mutation screening of the TP53 gene by temporal temperature gel electrophoresis (TTGE)

A protocol for detection of mutations in the TP53 gene using temporal temperature gradient electrophoresis (TTGE) is described. TTGE is a mutation detection technique that separates DNA fragments differing by single base pairs according to their melting properties in a denaturing gel. It is based on constant denaturing conditions in the gel combined with a temperature gradient during the electrophoretic run. This method combines some of the advantages of the related techniques, denaturing gradient gel electrophoresis and constant denaturant gel electrophoresis, and eliminates some of the problems. The result is a rapid and sensitive screening technique which is robust and easily set up in smaller laboratory environments.