A quantitative fluorescence-based microplate assay for the determination of double-stranded DNA using SYBR Green I and a standard ultraviolet transilluminator gel imaging system

PicoGreen assay for nucleic acid quantification - Applications, challenges, and solutions

Various analytical methods and reagents have been employed for nucleic acid analysis in cells, biological fluids, and formulations. Standard techniques like gel electrophoresis and qRT-PCR are widely used for qualitative and quantitative nucleic acid analysis. However, these methods can be time-consuming and labor-intensive, with limitations such as inapplicability to small RNA at low concentrations and high costs associated with qRT-PCR reagents and instruments. As an alternative, PicoGreen (PG) has emerged as a valuable method for the quantitative analysis of nucleic acids. PG, a fluorescent dye, enables the quantitation of double-stranded DNA (dsDNA) or double-stranded RNA, including miRNA mimic and siRNA, in solution. It is also applicable to DNA and RNA analysis within cells using techniques like FACS and fluorescence microscopy. Despite its advantages, PG's fluorescence intensity is affected by various experimental conditions, such as pH, salts, and chemical reagents. This review explores the recent applications of PG as a rapid, cost-effective, robust, and accurate assay tool for nucleic acid quantification. We also address the limitations of PG and discuss approaches to overcome these challenges, recognizing the expanding range of its applications.

Biodegradable and switchable near-infrared fluorescent probes for hypoxia detection

Aims: Among solid tumors, hypoxia is a common characteristic and responsible for chemotherapeutic resistance. Hypoxia-sensitive imaging probes are therefore essential for early tumor detection, growth monitoring and drug-response evaluation. Despite significant efforts, detecting hypoxic oxygen levels remains challenging. Materials & methods: This paper demonstrates the use of an amine-rich carbon dot probe functionalized with an imidazole group that exhibits reversible fluorescence switching in normoxic and hypoxic environments. Results & conclusion: We demonstrate the ability to emit near-infrared light only under hypoxic conditions. The probes are found to be biodegradable in the presence of human digestive enzymes such as lipase. Ex vivo tissue imaging experiments revealed promising near-infrared signals even at a depth of 5 mm for the probe under ex vivo imaging conditions.

Detecting Microbiology in the Upper Atmosphere: Relative-Velocity Filtered Sampling

The purpose of this article is to reopen from a practical perspective the question of the extent in altitude of Earth's biosphere. We make a number of different suggestions for how searches for biological material could be conducted in the mesosphere and lower thermosphere, colloquially referred to as the "ignore-osphere" because it has been generally ignored in the meteorological community compared to other regions. Relatively recent technological advances such as CubeSats in very low Earth orbit or more standard approaches such as the rocket-borne MAGIC meteoric smoke particle sampler are shown as potentially viable for sampling biological material in the ignore-osphere. The issue of contamination is discussed, and a potential solution to the problem is proposed by means of a new detector design that filters for particles based on their size and relative velocity to the detector.

A label-free fluorescent aptamer sensor for testosterone based on SYBR Green I

Testosterone is a steroid hormone that plays an indispensable role in the normal metabolism of organisms. However, exogenous testosterone, even as low as nmol L^-1, will harm the human body due to accumulation. In this study, we developed an unlabeled fluorescent sensor for testosterone based on SYBR Green I. SYBR Green I is a fluorescent dye that can be embedded into the G-quadruplex of the testosterone aptamer T5. The fluorescence quenching effect is utilized to achieve quantitative detection, which occurs by the competition between testosterone and SYBR Green I for the T5 aptamer binding sites. In this work, we optimized the detection conditions to make the fluorescent sensor more sensitive and verify the specificity, linear range, and detection ability in the buffer and real water samples. The sensor's LOD and LOQ values were 0.27 nmol L^-1 and 0.91 nmol L^-1, respectively, while the detection range was linear from 0.91 nmol L^-1 to 2000 nmol L^-1. According to the results, the sensor shows high specificity and good performance even in real sample detection such as tap water and river water, providing an alternative method for the quantitative detection of testosterone in the environment, which is more convenient and efficient.

Biostimulation of tomato growth and biocontrol of Fusarium wilt disease using certain endophytic fungi

BACKGROUND

Tomato plant (Solanum lycopersicum L.) suffers from numerous fungal pathogens that cause damage to yeild production qualitatively and quantitatively. One of the most destructive disease of tomato is Fusarium wilt that caused by soil borne fungus called F. oxysporum.

METHODS

In this study, the anti-Fusarium capabilities of the foliar application of fungal endophytes extracts have been investigated on tomato under Fusarium challenges. Antifungal assay, inhibition of conidial germination, disease severity, photosynthetic pigments, osmolytes, secondary metabolites, oxidative stress, peroxidase (POD) and polyphenol oxidases (PPO) isozymes were tested for potential resistance of tomato growing under Fusarium infection.

RESULTS

Ethyl acetate extracts of A. flavus MZ045563, A. fumigatus MZ045562 and A. nidulans MZ045561 exhibited antifungal activity toward F. oxysporum where inhibition zone diameters were 15, 12 and 20 mm, respectively. Moreover, extracts of all fungal isolates at concentration 7.5 mg/mL reduced conidia germination from 94.4 to 100%. Fusarium infection caused a destructive effects on tomato plant, high severity desiese index 84.37%, reduction in growth parameters, photosynthetic pigments, and soluble protein. However, contents of proline, total phenol, malondialdehyde (MDA), hydrogen peroxide (H₂O₂) and antioxidant enzymes activity were increased in tomato plants grown under Fusarium wilt. Treatment of healthy or infected tomato plants by ethyl acetate fungal extracts showed improvements in morphological traits, photosynthetic pigments, osmolytes, total phenol and antioxidant enzymes activity. Besides, the harmful impacts of Fusarium wilt disease on tomato plants have also been reduced by lowering MDA and H₂O₂ levels. Also, treated tomato plants showed different responses in number and density of POD and PPO isozymes.

CONCLUSION

It could be suggested that application of ethyl acetate extracts of tested fungal endophytes especially combination of A. flavus, A. nidulans and A. fumigatus could be commercially used as safe biostimulation of tomato plants as well as biofungicide against tomato Fusarium wilt disease.

Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application

Small-molecule contaminants, such as antibiotics, pesticides, and plasticizers, have emerged as one of the substances most detrimental to human health and the environment. Therefore, it is crucial to develop low-cost, user-friendly, and portable biosensors capable of rapidly detecting these contaminants. Antibodies have traditionally been used as biorecognition elements. However, aptamers have recently been applied as biorecognition elements in aptamer-based biosensors, also known as aptasensors. The systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro technique used to generate aptamers that bind their targets with high affinity and specificity. Over the past decade, a modified SELEX method known as Capture-SELEX has been widely used to generate DNA or RNA aptamers that bind small molecules. In this review, we summarize the recent strategies used for Capture-SELEX, describe the methods commonly used for detecting and characterizing small-molecule-aptamer interactions, and discuss the development of aptamer-based biosensors for various applications. We also discuss the challenges of the Capture-SELEX platform and biosensor development and the possibilities for their future application.

Preparation of bioplastic consisting of salmon milt DNA

The microplastic that pollutes the ocean is a serious problem around the world. The bioplastic consisting of biopolymers which is degraded in nature, is one of the strategies to solve this problem. Although the bioplastics consisting of protein, polysaccharide, polylactic acid, etc., have been reported, which consist of DNA, one of the most important materials in the genetic process, have not been reported to the best of our knowledge. In addition, a large amount of DNA-containing materials, such as salmon milts, is discarded as industrial waste around the world. Therefore, we demonstrated the preparation of a bioplastic consisting of salmon milt DNA. The DNA plastic was prepared by the immersion of a DNA pellet in a formaldehyde (HCHO) solution and heating. As a result, the water-stable DNA plastics were obtained at the HCHO concentration of 20% or more. Particularly, the DNA plastic with a 25% HCHO treatment showed water-insoluble, thermally stable, and highly mechanical properties. These are due to the formation of a three-dimensional network via the crosslinking reaction between the DNA chains. In addition, since DNA in plastic possesses the double-stranded structure, these plastics effectively accumulated the DNA intercalator, such as ethidium bromide. Furthermore, the DNA plastics indicated a biodegradable property in a nuclease-containing aqueous solution and the biodegradable stability was able to be controlled by the HCHO concentration. Therefore, salmon milt DNA has shown the potential to be a biodegradable plastic.

Recent advances in bioprobes and biolabels based on cyanine dyes

As a functional dye, cyanine dye promotes the widespread application of bioprobes in the fields of medicine, genetics and environment, owing to its advantages of good photophysical properties, excellent biocompatibility and low toxicity to biological systems. Nowadays, it is mainly used in the fields of life sciences such as fluorescent labeling of biological macromolecules, disease diagnosis, immunoassay and DNA detection, all of which lie at the core of this review. First, we briefly introduced the characteristics and principles of the cyanine dye bioprobe. Afterward, we paid attention to the recent progress of cyanine dye bioprobes widely used in the 10 years from 2010 to 2020. The application of cyanine dyes as bioprobes with different identification elements, including enzymes, organelles, immunity and DNAs, was mainly summarized. Finally, this review gave an outlook on the future development trend of cyanine dye bioprobes. This facilitates the construction of a new type of multifunctional fluorescent probe and promotes its clinical application.

Dimethyl Sulfoxide-Free and Water-Soluble Fluorescent Probe for Detection of Bovine Serum Albumin Prepared by Ionic Co-assembly of Amphiphiles

Detection of bovine serum albumin (BSA) is an important issue in the sense of medical applications and enzymatic reactions; however, the recently developed fluorescent probes require the involvement of dimethyl sulfoxide (DMSO), which may be detrimental to proteins. In this study, we demonstrated a DMSO-free and water-soluble fluorescent probe prepared by ionic co-assembly of amphiphiles. The cationic amphiphile is a newly designed molecule (denoted by DPP-12) bearing a conjugated diketopyrrolopyrrole (DPP) and two tetraphenylethylene groups. It turns out that the fluorescence emission of DPP-12 depends on the amount of anionic amphiphilic sodium dodecyl benzene sulfonate (SDBS). The fluorescence intensity first increases and then decreases with the concentration of SDBS, and each branch presents a linear relationship. BSA consumes SDBS by the formation of complexes, thus leading to an increase of fluorescence intensity of the mixed solution of DPP-12 and SDBS. Therefore, the mixed solution of DPP-12 and SDBS was applied as a fluorescent probe to detect the low concentration of BSA by back-titration. This fluorescent probe does not require DMSO and has good tolerance to metal ions in blood and good photostability. The limit of detection is as low as 940 nM, almost 3 orders of magnitude lower than the content in organisms.

Progress and challenges in the use of fluorescence-based flow cytometric assays for anti-malarial drug susceptibility tests

Drug-resistant Plasmodium is a frequent global threat in malaria eradication programmes, highlighting the need for new anti-malarial drugs and efficient detection of treatment failure. Plasmodium falciparum culture is essential in drug discovery and resistance surveillance. Microscopy of Giemsa-stained erythrocytes is common for determining anti-malarial effects on the intraerythrocytic development of cultured Plasmodium parasites. Giemsa-based microscopy use is conventional but laborious, and its accuracy depends largely on examiner skill. Given the availability of nucleic acid-binding fluorescent dyes and advances in flow cytometry, the use of various fluorochromes has been frequently attempted for the enumeration of parasitaemia and discrimination of P. falciparum growth in drug susceptibility assays. However, fluorochromes do not meet the requirements of being fast, simple, reliable and sensitive. Thus, this review revisits the utility of fluorochromes, notes previously reported hindrances, and highlights the challenges and opportunities for using fluorochromes in flow cytometer-based drug susceptibility tests. It aims to improve drug discovery and support a resistance surveillance system, an essential feature in combatting malaria.

Fluorescence Sensing of Nucleic Acid by Curcumin Encapsulated Poly(Ethylene Oxide)-Block-Poly(Propylene Oxide)-Block-Poly(Ethylene Oxide) Based Nanocapsules

In a novel approach, curcumin has been encapsulated inside Poly(Ethylene Oxide)-Block-Poly(Propylene Oxide)-Block-Poly(Ethylene Oxide) (F108) nanocapsules. FTIR spectra have indicated a type of hydrogen bonding and dipole interaction between curcumin and F108. Fluorescence and UV-visible absorption profiles of curcumin in nanocapsules have indicated location of curcumin in more hydrophobic microenvironment. The relative fluorescence yield has increased by 6 times in the nanocapsules, which renders them as more sensitive probes to be used later on in sensing study. Therefore, based on the functionality of curcumin as a fluorescent transducer, encapsulated curcumin is used in biomedical application as DNA and RNA sensing. Detection limits are detected as 50 μM and 60 μM for DNA and RNA respectively. Linear dynamic concentration range obtained in this proposed method is much higher than reported in literature. The interaction between the nanocapsules and targeted DNA/RNA molecules is further approved by zeta potential studies. Furthermore, the real interaction of DNA with the encapsulated curcumin is confirmed by the interaction of the adenine and cytosine nucleotides. This has been verified through zeta potential measurements. Moreover, our prepared nanocapsules has presented a high percentage recovery of DNA and RNA (96-101%). Finally, stability results have illustrated a high photostability of encapsulated curcumin, indicating that proposed nanocapsules can be considered as a stable sensor during measurement time.

High-Fidelity Single Molecule Quantification in a Flow Cytometer Using Multiparametric Optical Analysis

Microfluidic techniques are widely used for high-throughput quantification and discrete analysis of micron-scale objects but are difficult to apply to molecular-scale targets. Instead, single-molecule methods primarily rely on low-throughput microscopic imaging of immobilized molecules. Here we report that commercial-grade flow cytometers can detect single nucleic acid targets following enzymatic extension and dense labeling with multiple distinct fluorophores. We focus on microRNAs, short nucleic acids that can be extended by rolling circle amplification (RCA). We labeled RCA-extended microRNAs with multicolor fluorophores to generate repetitive nucleic acid products with submicron sizes and tunable multispectral profiles. By cross-correlating the multiparametric optical features, signal-to-background ratios were amplified 1600-fold to allow single-molecule detection across 4 orders of magnitude of concentration. The limit of detection was measured to be 47 fM, which is 100-fold better than gold-standard methods based on polymerase chain reaction. Furthermore, multiparametric analysis allowed discrimination of different microRNA sequences in the same solution using distinguishable optical barcodes. Barcodes can apply both ratiometric and colorimetric signatures, which could facilitate high-dimensional multiplexing. Because of the wide availability of flow cytometers, we anticipate that this technology can provide immediate access to high-throughput multiparametric single-molecule measurements and can further be adapted to the diverse range of molecular amplification methods that are continually emerging.

Development of multi-ARMS-qPCR method for detection of hookworms from cats and dogs

Hookworms are blood-sucking nematodes that infect dogs, cats, and humans, causing iron-deficiency anemia, abdominal pain, diarrhea, and skin inflammation. Amplification refractory mutation system (ARMS) is a modified technology based on allele-specific PCR, which is widely used in mutation detection and genotyping. However, no data about ARMS application in hookworm detection. This study aims to establish a multi-ARMS-qPCR method for the detection of three hookworm species from dogs and cats. A universal forward primer and three specific primers (ARMS-Cey, ARMS-Can, and ARMS-Tub) were designed based on the three ITS SNPs (ITS250, ITS78 and ITS153) of Ancylostoma ceylanicum, A. caninum, and A. tubaeforme, respectively. The results showed that the three designed ARMS primers generated specific melting curves for the three hookworms' standard plasmids. The melting temperature (T_m) values were 88.40 °C (A. ceylanicum), 83.15 °C (A. caninum), and 85.65 °C (A. tubaeforme), with good reproducibility of intra- and inter-assay. No amplification was observed with other intestinal parasites. The limit of detection using the established technique was 1, 2, and 104 egg per gram feces (EPG) for A. caninum, A. tubaeforme and A. ceylanicum, respectively. Using multi-ARMS-qPCR assay, 17 out of 50 fecal samples were positive for hookworms, including ten single and seven mixed infections, and single infections were quantified. In conclusion, the used multi-ARMS-qPCR method has the advantages of high efficiency, sensitivity, specificity, and quantitative analysis and can be used for the clinical detection, epidemiological investigation, and zoonotic risk assessment of canine and feline hookworms.

The staining efficiency of cyanine dyes for single-stranded DNA is enormously dependent on nucleotide composition

The staining of nucleic acids with fluorescent dyes is one of the most fundamental technologies in relevant areas of science. For reliable and quantitative analysis, the staining efficiency of the dyes should not be very dependent on the sequences of the specimens. However, this assumption has not necessarily been confirmed by experimental results, especially in the staining of ssDNA (and RNA). In this study, we found that both SYBR Green II and SYBR Gold did not stain either homopyrimidines or ssDNA composed of only adenine (A) and cytosine (C). However, these two dyes emit strong fluorescence when the ssDNA contains both guanine (G) and C (and/or both A and thymine (T)) and form potential Watson-Crick base pairs. Interestingly, SYBR Gold, but not SYBR Green II, strongly stains ssDNA consisting of G and A (or G and T). Additionally, we found that the secondary structure of ssDNA may play an important role in DNA staining. To obtain reliable results for practical applications, sufficient care must be paid to the composition and sequence of ssDNA.

Comparing methods to normalize insulin secretion shows the process may not be needed

Glucose-stimulated insulin secretion (GSIS) is a well-accepted method to investigate the physiological and pathophysiological function of islets. However, there is little consensus about which method is best for normalizing and presenting GSIS data. In this study, we evaluated the sufficiency of islet area, total protein, total DNA, and total insulin content as parameters to normalize GSIS data. First, we tested if there is a linear correlation between each parameter and the number of islets (10, 20, 30, and 40 islets). Islet area, total protein, and insulin content produced excellent linear correlations with islet number (R2 >0.9 for each) from the same islet material. Insulin secretion in 11mM glucose also correlated reasonably well for islet area (R2=0.69), protein (R2=0.49), and insulin content (R2=0.58). DNA content was difficult to reliably measure and was excluded from additional comparisons. We next measured GSIS for 18 replicates of 20 islets each, measuring 3mM and 11mM glucose to calculate the stimulation index and to compare each normalization parameter. Using these similar islet masses for each replicate, none of the parameters produced linear correlations with GSIS (R2<0.05), suggesting that inherent differences in GSIS dominate small differences in islet mass. We conclude that when comparing GSIS for islets of reasonably similar size (<50% variance), normalization does not improve the representation of GSIS data. Normalization may be beneficial when substantial differences in islet mass are involved. In such situations, we suggest that using islet cross-sectional area is superior to other commonly used techniques for normalizing GSIS data.

A label-free aptasensor for the detection of tetracycline based on the luminescence of SYBR Green I

A novel fluorescent method based on tetracycline-binding aptamers and the luminescence of SYBR Green I (SGI) was established for the sensitive and selective detection of tetracycline. Under natural conditions, the aptamers of tetracycline show the G-quadruplex spatial structures while SGI is nearly nonfluorescent in aqueous solution. After mixture with the G-quadruplex structured aptamers, SGI can recognize and intercalate into the aptamers, resulting in a strong fluorescence emission. When the target tetracycline was added into the solution, the specific recognition and high-affinity binding of aptamers with tetracycline will induce the conformational changes of aptamers from G-quadruplex structures to hairpin structures. Thereafter, SGI will be released from the aptamer molecules, leading to the fluorescence decline. The quantitative detection of tetracycline can be achieved by measuring the fluorescence change of the system. Under the optimum conditions, the linear range of tetracycline in the milk was from 5 to 25 μg/mL, and the detection limit was as low as 0.10 μg/mL. The recoveries of the spiked milk samples were in the range of 98.98%-104.67% with the relative standard deviations (RSDs) of 0.16%-0.67%, and the results were in agreement with those from HPLC. Therefore, the biosensor based on the specific recognition of aptamers and the fluorescence properties of SGI can detect the tetracycline in milk accurately, rapidly and specifically.

Circulating tumor DNA and liquid biopsy: opportunities, challenges, and recent advances in detection technologies

Cell-free DNA (cfDNA) refers to short fragments of acellular nucleic acids detectable in almost all body fluids, including blood, and is involved in various physiological and pathological phenomena such as immunity, coagulation, aging, and cancer. In cancer patients, a fraction of hematogenous cfDNA originates from tumors, termed circulating tumor DNA (ctDNA), and may carry the same mutations and genetic alterations as those of a primary tumor. Thus, ctDNA potentially provides an opportunity for noninvasive assessment of cancer. Recent advances in ctDNA analysis methods will potentially lead to the development of a liquid biopsy tool for the diagnosis, prognosis, therapy response monitoring, and tracking the rise of new mutant sub-clones in cancer patients. Over the past few decades, cancer-specific mutations in ctDNA have been detected using a variety of untargeted methods such as digital karyotyping, personalized analysis of rearranged ends (PARE), whole-genome sequencing of ctDNA, and targeted approaches such as conventional and digital PCR-based methods and deep sequencing-based technologies. More recently, several chip-based electrochemical sensors have been developed for the analysis of ctDNA in patient samples. This paper aims to comprehensively review the diagnostic, prognostic, and predictive potential of ctDNA as a minimally invasive liquid biopsy for cancer patients. We also present an overview of current advances in the analytical sensitivity and accuracy of ctDNA analysis methods as well as biological and technical challenges, which need to be resolved for the integration of ctDNA analysis into routine clinical practice.

The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons

In this study, the effect of different DNA extraction procedures and primer sets on pyrosequencing results regarding the composition of bacterial communities in the ileum of piglets was investigated. Ileal chyme from piglets fed a diet containing different amounts of zinc oxide was used to evaluate a pyrosequencing study with barcoded 16S rRNA PCR products. Two DNA extraction methods (bead beating versus silica gel columns) and two primer sets targeting variable regions of bacterial 16S rRNA genes (8f-534r versus 968f-1401r) were considered. The SEED viewer software of the MG-RAST server was used for automated sequence analysis. A total of 5.2 × 10(5) sequences were used for analysis after processing for read length (150 bp), minimum sequence occurrence (5), and exclusion of eukaryotic and unclassified/uncultured sequences. DNA extraction procedures and primer sets differed significantly in total sequence yield. The distribution of bacterial order and main bacterial genera was influenced significantly by both parameters. However, this study has shown that the results of pyrosequencing studies using barcoded PCR amplicons of bacterial 16S rRNA genes depend on DNA extraction and primer choice, as well as on the manner of downstream sequence analysis.

Nucleic acid-based biomarkers in body fluids of patients with urologic malignancies

This review focuses on the promising potential of nucleic acids in body fluids such as blood and urine as diagnostic, prognostic, predictive and monitoring biomarkers in urologic malignancies. The tremendous progress in the basic knowledge of molecular processes in cancer, as shown in the companion review on nucleic acid-based biomarkers in tissue of urologic tumors, provides a strong rationale for using these molecular changes as non-invasive markers in body fluids. The changes observed in body fluids are an integrative result, reflecting both tissue changes and processes occurring in the body fluids. The availability of sensitive methods has only recently made possible detailed studies of DNA- and RNA-based markers in body fluids. In addition to these biological aspects, methodological aspects of the determination of nucleic acids in body fluids, i.e. pre-analytical, analytical and post-analytical issues, are particularly emphasized. The characteristic changes of RNA (differential mRNA and miRNA expression) and DNA (concentrations, integrity index, mutations, microsatellite and methylation alterations) in serum/plasma and urine samples of patients suffering from the essential urologic cancers of the prostate, bladder, kidney and testis are summarized and critically discussed below. To translate the promising results into clinical practice, laboratory scientists and clinicians have to collaborate to resolve the challenges of harmonized and feasible pre-analytical and analytical conditions for the selected markers and to validate these markers in well-designed and sufficiently powered multi-center studies.

Label-free fluorescent sensor for lead ion detection based on lead(II)-stabilized G-quadruplex formation

A label-free fluorescent DNA sensor for the detection of lead ions (Pb(2+)) based on lead(II)-stabilized G-quadruplex formation is proposed in this article. A guanine (G)-rich oligonucleotide, T30695, was used as a recognition probe, and a DNA intercalator, SYBR Green I (SG), was used as a signal reporter. In the absence of Pb(2+), the SG intercalated with the single-stranded random-coil T30695 and emitted strong fluorescence. While in the presence of Pb(2+), the random-coil T30695 would fold into a G-quadruplex structure and the SG could barely show weak fluorescence, and the fluorescence intensity was inversely proportional to the involving amount of Pb(2+). Based on this, a selective lead ion sensor with a limit of detection of 3.79 ppb (parts per billion) and a detection range from 0 to 600 ppb was constructed. Because detection for real samples was also demonstrated to be reliable, this simple, low-cost, sensitive, and selective sensor holds good potential for Pb(2+) detection in real environmental samples.

Expression profiling by real-time quantitative polymerase chain reaction (RT-qPCR)

Real-time quantitative PCR is a variation of the standard PCR technique that is commonly used to quantify nucleic acid. However, in this technique the amount of amplified specific sequence can be quantified at each stage of the PCR cycle. If investigated sequence is present in large number of copies in particular sample, amplification product is detected already in earlier cycles; if the sequence is rare, amplification is observed in later cycles. Quantification of amplified product is acquired using fluorescent probes or fluorescent DNA-binding dyes. Accumulation of fluorescent signal can be measured by real-time PCR instruments during each of 35-45 cycwwles of the PCR reaction, which simplify the procedure by eliminating the visualization of the amplified products using gel electrophoresis. Real-time-PCR allows quantifying the amount of product already during the PCR reaction as soon as it is detectable. Correctly performed, this method may be used for precise gene expression analysis in life science, medicine, and diagnostics and has become the standard method of choice for the quantification of mRNA. However in the past few years it became obvious that real-time PCR is complex and variability of RNA templates, assay designs, inappropriate data normalization, and data interpretation may cause diverse analytical problems.

Novel strategy combining SYBR Green I with carbon nanotubes for highly sensitive detection of Salmonella typhimurium DNA

A simple, selective, sensitive and label-free fluorescent method for detecting trpS-harboring Salmonella typhimurium was developed in this study. This assay used the non-covalent interaction of single-stranded DNA (ssDNA) probes with SWNTs, since SWNTs can quench fluorescence. Fluorescence recovery (78% with 1.8 nM target DNA) was detected in the presence of target DNA as ssDNA probes detached from SWNTs hybridized with target DNA, and the resulting double-stranded DNA (dsDNA) intercalated with SYBR Green I (SG) dyes. The increasing fluorescence intensity reached 4.54-fold. In contrast, mismatched oligonucleotides (1- or 3-nt difference to the target DNA) did not contribute to significant fluorescent recovery, which demonstrated the specificity of the assay. The increasing fluorescence intensity increased 3.15-fold when purified PCR products containing complementary sequences of trpS gene were detected. These results confirmed the ability to use this assay for detecting real samples.

Highly sensitive and selective detection of silver(I) in aqueous solution with silver(I)-specific DNA and Sybr Green I

We report a label-free fluorescence turn-on approach for the sensitive and selective sensing of silver ion Ag(+) based on Ag(+) induced conformational change of cytosine-rich single-stranded DNA. A silver specific oligonucleotide (SSO) undergoes a structural transition from single-stranded DNA (ssDNA) to a C-Ag(+)-C mediated hairpin structure, which can be recognized by a double-stranded DNA (dsDNA) intercalator Sybr Green I (SG). The linear response range for Ag(+) detection was from 1 nM to 100 nM. The method presented here is highly sensitive and a limit of detection of 1 nM was obtained. More importantly, this optical method was successfully used to identify complex sample mixtures.

Biological nutrient removal with limited organic matter using a novel anaerobic-anoxic/oxic multi-phased activated sludge process

An anaerobic-anoxic/oxic (A2/O) multi-phased biological process called "phased isolation tank step feed technology (PITSF)" was developed to force the oscillation of organic and nutrient concentrations in process reactors. PITSF can be operated safely with a limited carbon source in terms of low carbon requirements and aeration costs whereas NAR was achieved over 95% in the last aerobic zone through a combination of short HRT and low DO levels. PCR assay was used for XAB quantification to correlate XAB numbers with nutrient removal. PCR assays showed, high NAR was achieved at XAB population 5.2 × 10(8) cells/g MLVSS in response to complete and partial nitrification process. It was exhibited that low DO with short HRT promoted XAB growth. Simultaneous nitrification and denitrification (SND) via nitrate were observed obviously, SND rate was between 69-72%, at a low DO level of 0.5 mg/l in the first aerobic tank during main phases and the removal efficiency of TN, [Formula: see text], COD, TP was 84.7 .97, 88.3 and 96% respectively. The removal efficiencies of TN, [Formula: see text], and TP at low C/N ratio and DO level were 84.2, 98.5 and 96.9% respectively which were approximately equal to the complete nitrification-denitrification with the addition of external carbon sources at a normal DO level of (1.5-2.5 mg/l).

Prognostic and predictive roles for circulating biomarkers in gastrointestinal cancer

Circulating tumor cells (CTCs) and circulating free DNA (cfDNA) have been studied as promising prognostic and predictive tumor-derived biomarkers in the bloodstream of patients with gastrointestinal malignancies because they may be an alternative noninvasive tool to tumor tissue biopsies. Quantification and molecular characterization of CTCs and cfDNA may provide additional insights into cancer biology, potentially revealing novel targets to individualize cancer care. The present article aims to review the biology and current methods to assess CTCs and cfDNA, and the efforts to establish both tumor-derived biomarkers as prognostic and predictive factors in esophageal, gastric and colorectal cancer.

Flow cytometric enumeration of Plasmodium berghei-infected red blood cells stained with SYBR Green I

High-throughput methods for evaluation of in vivo efficacy of candidate compounds against Plasmodium parasites are necessary during the antimalarial drug development process. It is essential that enumeration of parasitemia in the infected blood from experimental host animals is accurate and reliable. Flow cytometric enumeration of parasitized cells stained with fluorescent dye is a rapid alternative method to conventional microscopic counting. In this study, a protocol for flow cytometric enumeration of rodent malaria parasite Plasmodium berghei-infected red blood cells (RBC) stained with SYBR Green I was developed. The optimal concentration of SYBR Green I used to stain infected RBC was 4× for 30 min. This SYBR Green I staining protocol in combination with the bi-dimensional FL-1(530)/FL-3(620) detection method accurately detects parasitemia above 0.02%. The dye is stable during the prolonged incubation period necessary for accurate enumeration of parasitemia, with no loss of fluorescent signal over a period of hours. This protocol was validated in an antimalarial assay and the result was comparable to that obtained from conventional microscopic counting. The SYBR Green I flow cytometric protocol is thus a rapid and precise tool for high-throughput in vivo antimalarial drug screening.

Widespread atypical mitochondrial DNA structure in isopods (Crustacea, Peracarida) related to a constitutive heteroplasmy in terrestrial species

Metazoan mitochondrial DNA (mtDNA) is generally composed of circular monomeric molecules. However, a few exceptions do exist and among them two terrestrial isopods Armadillidium vulgare and Porcellionides pruinosus have an atypical mtDNA composed of linear monomers associated with circular "head-to-head" dimers: a very unusual structure for animal mtDNA genome. To assess the distribution of this atypical mtDNA among isopods, we performed RFLP and Southern blot analyses on mtDNA of 16 terrestrial (Oniscidea family) and two aquatic isopod species: the marine Sphaeroma serratum (suborder Flabellifera, sister group of Oniscidea) and the freshwater Asellus aquaticus (Asellota, early derived taxon of isopod). The atypical mtDNA structure was observed in 15 terrestrial isopod species and A. aquaticus, suggesting a wide distribution of atypical mtDNA among isopods. However, a typical metazoan mtDNA structure was detected in the marine isopod S. serratum and the Oniscidea Ligia oceanica . Our results suggest two possible scenarios: an early origin of the atypical mtDNA in isopods followed by reversion to the typical ancestral mtDNA structure for several species, or a convergent appearance of the atypical mtDNA structure in two isopod suborders. We compare this distribution of the atypical mtDNA structure with the presence of a heteroplasmy also observed in the mtDNA of several terrestrial isopod species. We discuss if this transmitted heteroplasmy is vectored by the atypical mtDNA and its impact on the maintenance of the atypical mtDNA in isopods.

Label-free fluorescent assay for real-time monitoring site-specific DNA cleavage by EcoRI endonuclease

DNA cleavage reaction catalyzed by nucleases is essential in many important biological processes and medicinal chemistry. Therefore, it is important to develop reliable and facile methods to assay nuclease activity. With this goal in mind, we report a fluorescent assay for label-free, facile, and real-time monitoring of DNA cleavage by EcoRI endonuclease using SYBR Green I (SGI) as a signal probe. The fluorescence of SGI dramatically increased when the free SGI was mixed with double-stranded DNA (dsDNA) substrate. Upon interacting with EcoRI, which cleaves the dsDNA into small fragments, the weakened interaction between SGI and the shortened DNA fragments caused a decrease in fluorescence of SGI. EcoRI-DNA interaction was real-time studied by monitoring fluorescence change with the prolonging of interaction time. The important kinetic parameters, including Michaelis-Menten constant (K(M)) and maximum initial velocity (V(max)), were accurately calculated, which is consistent with previously reported studies. Site-specific DNA cleavage by EcoRI endonuclease has also been verified by gel electrophoresis analysis, which indicated that this method is a simple and effective approach to assay DNA cleavage reaction. Specificity investigation demonstrated that EcoRI-DNA interactions can be studied with high selectivity. Compared with previously reported methods, this approach is selective, simple, convenient and cost-efficient without any labeling of the probe or of the target.

Abundance and diversity of Sphingomonas in Shenfu petroleum-wastewater irrigation zone, China

INTRODUCTION

Members of the genus Sphingomonas have raised increasing attention due to their ability for polycyclic aromatic hydrocarbon (PAH) degradation and their ubiquity in the environment. However, few studies have revealed the ecological information on the abundance and diversity of Sphingomonas in the environment.

MATERIALS AND METHODS

A primer set targeting the Sphingomonas 16S rRNA gene was designed. The specificity was tested with four petroleum-contaminated soils by construction of clone libraries and further restriction fragment length polymorphism analysis. Subsequently, real time PCR and denaturing gradient gel electrophoresis (DGGE) assays were used to evaluate the abundance and diversity of Sphingomonas in the Shenfu irrigation zone, China.

RESULTS

A genus-specific primer set SA/429f-933r was developed, and 90% of the sequences retrieved from soil clone libraries were related to Sphingomonas. Members of the genus Sphingomonas were detected in all soils, and significant correlation (p < 0.05) was observed between the Sphingomonas abundance and the ratios of PAHs to total petroleum hydrocarbon (TPH). DGGE profiles revealed Sphingomonas population structures differed greatly in different sites. The Sphingomonas diversity was not statistically (p > 0.05) correlated with the contamination level. Some of the soil-derived sequences were not grouped phylogenetically with sequences of known Sphingomonas, indicating new members of the Sphingomonas genus might be present in the Shenfu irrigation zone.

CONCLUSION

The newly designed Sphingomonas-selective primers were specific and practicable for analyzing Sphingomonas abundance and diversity in petroleum-contaminated soils. The significant correlation between the abundance and the ratios of PAHs to TPH suggested an important role of Sphingomonas in PAH bioremediation.

Towards protein crystallization as a process step in downstream processing of therapeutic antibodies: screening and optimization at microbatch scale

Crystallization conditions of an intact monoclonal IgG4 (immunoglobulin G, subclass 4) antibody were established in vapor diffusion mode by sparse matrix screening and subsequent optimization. The procedure was transferred to microbatch conditions and a phase diagram was built showing surprisingly low solubility of the antibody at equilibrium. With up-scaling to process scale in mind, purification efficiency of the crystallization step was investigated. Added model protein contaminants were excluded from the crystals to more than 95%. No measurable loss of Fc-binding activity was observed in the crystallized and redissolved antibody. Conditions could be adapted to crystallize the antibody directly from concentrated and diafiltrated cell culture supernatant, showing purification efficiency similar to that of Protein A chromatography. We conclude that crystallization has the potential to be included in downstream processing as a low-cost purification or formulation step.

Fluorescence determination of DNA using the gatifloxacin-europium(III) complex

A method for the determination of DNA based on the fluorescence intensity of the gatifloxacin-europium(III) (GFLX-Eu(3+)) complex that could be enhanced by DNA was developed. The GFLX-Eu(3+) complex showed an up to 6-fold enhancement of luminescence intensity after adding DNA. Under the optimized experimental conditions, the system exhibited a linear relationship between the enhanced fluorescence intensity and the concentration of calf thymus DNA (ctDNA) over the range from 1.0 × 10(-8) to 1.5 × 10(-6) g mL(-1), with a correlation coefficient (R) of 0.997, and the detection limit (3σ) of the method was determined as 6.0 × 10(-9) g mL(-1). The mechanism of the fluorescence enhancement effect was also discussed.

Oligonucleotide-based luminescent detection of metal ions

Metal ions are prevalent in biological systems and are critically involved in essential life processes. However, excess concentrations of metals can pose a serious danger to living organisms. Oligonucleotides represent a versatile sensing platform for the detection of various molecular entities including metal ions. This review summarizes the recent advances in the development of oligonucleotide-based luminescent detection methods for metal ions.

Cell-free DNA in the blood as a solid tumor biomarker--a critical appraisal of the literature

Circulating cell-free DNA (cfDNA) has been suggested as a cancer biomarker. Several studies assessed the usefulness of quantitative and qualitative tumor-specific alterations of cfDNA, such as DNA strand integrity, frequency of mutations, abnormalities of microsatellites, and methylation of genes, as diagnostic, prognostic, and monitoring markers in cancer patients. Most of the papers that could be evaluated in this review resulted in a positive conclusion. However, methodical diversity without the traceability of data and differently designed and often underpowered studies resulted in divergent results between studies. In addition, the limited diagnostic sensitivity and specificity of cfDNA alterations temper the effusive hope of novel tumor markers, raising similar issues as those for other tumor markers. To validate the actual clinical validity of various cfDNA alterations as potential cancer biomarkers in practice for individual tumor types, the main problems of the observed uncertainties must be considered in future studies. These include methodical harmonization concerning sample collection, processing, and analysis with the traceability of measurement results as well as the realization of well-designed prospective studies based on power analysis and sample size calculations.