A real-time DNase assay (ReDA) based on PicoGreen® fluorescence

DNA nucleases (DNases) perform a wide variety of important cellular functions and are also very useful for research and in biotechnological applications. Due to the biological and technological importance of DNases and their use in a wide range of applications, DNase activity assays are essential. Traditional DNase assays employ radiolabeled DNA substrates and require separation of the products of the reaction from the unreacted substrate before quantification of enzyme activity. As a consequence, these methods are discontinuous. In this report, we describe a continuous DNase assay based on the differential fluorescence output of a DNA dye ligand called PicoGreen®. The assay was developed to characterize a processive dsDNA exonuclease, lambda exonuclease. The assay appears to have general utility as it is also suitable for measuring the DNA digestion activities of a processive helicase/nuclease, RecBCD, a distributive exonuclease, T7 gene 6 exonuclease, and an endonuclease, DNaseI. The benefits of, and limitations to, the method are discussed.     

A preliminary study on the effects of E-Z Mixin® and EquiPlus® extenders supplemented with Edible Bird’s Nest on the quality of chilled Arabian stallion semen

The aim of this study was to evaluate the effects of adding different concentrations of edible bird’s nest (EBN) which is secreted by swiftlet birds (Aerodramus fuciphagus), into EquiPlus® and E-Z Mixin® extenders on the quality of chilled Arabian stallion semen at various storage times (0, 24 and 48 h). Ten ejaculates were collected from five stallions, and diluted using the two extenders containing 0% (control), 0.12%, 0.24% and 0.24% of EBN + seminal plasma (SP). All the diluted semen samples were then cooled and stored at 5 °C, and examined at 0, 24 and 48 h. Sperm kinetic parameters were assessed using computer assisted sperm analysis (CASA) and viability were assessed using Hoechst33342/PI stain. In both extenders, total motility (TM) and progressive motility (PM) were significantly higher at 0.12% and 0.24% compared to 0.24% + SP at 24 and 48 h. At 0.12%, E-Z mixin® treated semen had significantly higher TM and PM than EquiPlus^® at 24 and 48 h. At 0.12% and 0.24%, average path velocity (VAP), straight-line velocity (VSL) and curvilinear velocity (VCL) were significantly higher in E-Z mixin® treated semen compared to EquiPlus^® at 24 and 48 h. Comparisons between the two extender types at different concentrations of EBN showed no significant difference in lateral head amplitude (ALH), linearity (LIN), straightness (STR), beat cross frequency (BCF) and viability, irrespective of the storage time. The percentage of viable was significantly higher in E-Z mixin® than EquiPlus® at 0 and 48 h in control and 0.12%. Supplementation of the E-Z mixin^® extender with 0.12% and 0.24% EBN concentrations in the absence of SP provided better CASA parameters such as TM, PM, VAP, VSL, and VCL at 24 and 48 h storage time. In conclusion, the results of this study indicated that chilled semen from Arabian stallion that was extended using E-Z mixin® and supplemented with 0.12% and 0.24% EBN concentrations performed better and yielded superior results in sperm kinetic parameters and % viable compared to EquiPlus® at 24 and 48 h storage time.     

A bioenergetic model for zebrafish Danio rerio (Hamilton)

A bioenergetics model was developed from observed consumption, respiration and growth rates for zebrafish Danio rerio across a range (18–32° C) of water temperatures, and evaluated with a 50 day laboratory trial at 28° C. No significant bias in variable estimates was found during the validation trial; namely, predicted zebrafish mass generally agreed with observed mass.     

Benefits of Soleris® over the Conventional Method for Enumeration of Microbial Load in Salacia Herbal Extract

Stems and roots of Salacia genus plants have been used as a specific remedy for early-stage diabetes, and one of the four sulphonium sulphates, salacinol is the compound responsible for the anti-diabetic activity. Salacia is prone to microbial contamination and insect infestation; hence, methods to estimate the microbial load in such plants will enhance its nutritional value. This paper highlights the novel use of Soleris^® to quantify microbes of all types, namely bacteria, yeasts, molds, and coliforms in herbal extracts. The microbial analysis results obtained with Soleris^® test vial have been compared with the conventional method, and the results indicate that Soleris^® is equally efficient as the conventional method and in fact displays several advantages over the traditional method. The Soleris^® method is a real time monitoring system that is highly sensitive, user-friendly, and environmentally friendly since it generates very little biomedical waste and saves a large amount of time. The data presented here demonstrate that for highly contaminated samples, results are available within 24 h. For yeasts and molds, the Soleris^® method produces results in 48 h, thus offering considerable time savings compared to other commonly used methods.Key words: Salacia, salacinol, microbial load, bacteria, yeasts, herbals     

The zebrafish as a model for gastrointestinal tract–microbe interactions

The zebrafish (Danio rerio) has become a widely used vertebrate model for bacterial, fungal, viral, and protozoan infections. Due to its genetic tractability, large clutch sizes, ease of manipulation, and optical transparency during early life stages, it is a particularly useful model to address questions about the cellular microbiology of host–microbe interactions. Although its use as a model for systemic infections, as well as infections localised to the hindbrain and swimbladder having been thoroughly reviewed, studies focusing on host–microbe interactions in the zebrafish gastrointestinal tract have been neglected. Here, we summarise recent findings regarding the developmental and immune biology of the gastrointestinal tract, drawing parallels to mammalian systems. We discuss the use of adult and larval zebrafish as models for gastrointestinal infections, and more generally, for studies of host–microbe interactions in the gut.     

The zebrafish (Danio rerio) caudal complex – a model to study vertebral body fusion

Impairment of segmentation during embryonic development leads to congenital fusion of vertebrae. Nevertheless, vertebral fusion can also occur during post‐embryonic life. Fusion can cause reduction in mobility and may be pathological, but it can also be part of normal development and mechanically required, such as in the teleost caudal skeleton, or in the tetrapod sacrum. Using a series of closely spaced ontogenetic stages of zebrafish, stained for mineralized (Alizarin red) and cartilaginous (Alcian blue) structures, we have characterized all fusions occurring during the formation of the caudal skeleton. The urostyle results from the vertebral fusion of the compound centrum preural1‐ural1 [PU1⁺+U1] and ural2 [U2⁺]. Based on developmental and morphological characters: (i) number of vestigial haemal arches, (ii) occasional presence of a haemal arch rudiment, (iii) occasional individuals with separate centra rudiments or distinct mineralization time points, and (iv) evidence for internal separation, we propose that the urostyle forms as a fusion product of five, and not three vertebral centra, as previously described. The last fusion to occur in development, between the compound centrum [PU1⁺+U1] and U2⁺, is a relatively slow process that typically occurs in Cypriniformes and Salmoniformes and is therefore considered reliable to monitor the fusion process. The vertebrae adjacent to the urostyle, preurals 2 and 3, are highly susceptible to fusion, and thus inadequate as a negative control to fusion, in contrast to trunk vertebrae, where fusion is never observed. With this we have established the basis for a new model to study vertebral fusion and to unravel cellular and molecular events underlying this process.     

The developing zebrafish (Danio rerio): a vertebrate model for high-throughput screening of chemical libraries

The zebrafish, Danio rerio, a small, tropical freshwater species native to Pakistan and India, has become a National Institutes of Health-sanctioned model organism and, due to its many advantages as an experimental vertebrate, it has garnered intense interest from the world's scientific community. Some have labeled the zebrafish, the "vertebrate Drosophila," due to its genetic tractability, small size, low cost, and rapid development. The transparency of the embryo, external development, and the many hundreds of mutant and transgenic lines available add to the allure. Now it appears, the zebrafish can be used for high-throughput screening (HTS) of drug libraries in the discovery process of promising new therapeutics. In this review, various types of screening methods are briefly outlined, as are a variety of screens for different disease models, to highlight the range of zebrafish HTS possibilities. High-content screening (HCS) has been available for cell-based screens for some time and, very recently, HCS is being adapted for the zebrafish. This will allow analysis, at high resolution, of drug effects on whole vertebrates; thus, whole body effects as well as those on specific organs and tissues may be determined.     

Identification of new aryl hydrocarbon receptor (AhR) antagonists using a zebrafish model

A new series of 1,3-diketone, heterocyclic and α,β-unsaturated derivatives were synthesized and evaluated for their AhR antagonist activity using zebrafish and mammalian cells. Compounds 1b, 2c, 3b and 5b showed significant AhR antagonist activity in a transgenic zebrafish model. Among them, compound 3b, and 5b were found to have excellent AhR antagonist activity with IC₅₀ of 3.36 nM and 8.3 nM in a luciferase reporter gene assay. In stem cell proliferation assay, compound 5b elicited marked HSC expansion.     

The use of mature zebrafish (Danio rerio) as a model for human aging and disease

Zebrafish (Danio rerio) have been extensively utilized for understanding mechanisms of development. These studies have led to a wealth of resources including genetic tools, informational databases, and husbandry methods. In spite of all these resources, zebrafish have been underutilized for exploring pathophysiology of disease and the aging process. Zebrafish offer several advantages over mammalian models for these studies, including the ability to perform saturation mutagenesis and the capability to contain thousands of animals in a small space. In this review, we will discuss the use of mature zebrafish as an animal model and provide specific examples to support this novel use of zebrafish. Examples include demonstrating that clinical pathology can be performed in mature zebrafish and that age-associated changes in heat shock response can be observed in zebrafish. These highlights demonstrate the utility of zebrafish as a model for disease and aging.     

Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY® FL-labeled probe or primer

We have developed a simple method for the quantitative detection of specific DNA or RNA molecules based on the finding that BODIPY^® FL fluorescence was quenched by its interaction with a uniquely positioned guanine. This approach makes use of an oligonucleotide probe or primer containing a BODIPY^® FL-modified cytosine at its 5′-end. When such a probe was hybridized with a target DNA, its fluorescence was quenched by the guanine in the target, complementary to the modified cytosine, and the quench rate was proportional to the amount of target DNA. This widely applicable technique will be used directly with larger samples or in conjunction with the polymerase chain reaction to quantify small DNA samples.     

Clinical relevance of lipid panel and aminotransferases in the context of hepatic steatosis and fibrosis as measured by transient elastography (FibroScan®)

BackgroundNonalcoholic fatty liver disease (NAFLD) is one of the most common causes of chronic liver disease and is associated with various co-morbidities. Transient elastography (FibroScan®) is a non-invasive method to detect NAFLD using the controlled attenuation parameter (CAP). We aimed to evaluate the association of the lipid panel and aminotransferases concentrations with the presence or absence of steatosis and fibrosis.MethodsOne hundred and five patients with NAFLD were included. Hepatic steatosis was quantified by CAP (dB/m) and liver stiffness by Kilopascals (kPa), these values were then analyzed against patient lipid panel and serum concentrations of the liver enzymes aspartate aminotransferase (AST) and alanine aminotransferase (ALT). A correlation and multiple regression were used. Mann-Whitney U test was used as non-parametric analysis.ResultsWe observed an association between hepatic steatosis and total cholesterol (B = 0.021, p = 0.038, Exp (B) = 1.021, I.C = 1.001-1.041) as well as serum triglycerides (B = 0.017, p = 0.006, Exp (B) = 1.018 and I.C = 1.005-1.030). Similarly, we found an association between significant hepatic fibrosis and lower concentrations of total cholesterol (B = -0.019, p = 0.005, Exp (B) = 0.982 I.C = 0.969-0.995) and elevated AST (B = 0.042, p = 3.25 × 10^-4, Exp (B) = 1.043 I.C = 1.019-1.068) independent of age, gender and BMI.ConclusionsOur results suggest that, total cholesterol and triglyceride concentrations positively correlate with hepatic steatosis while significant hepatic fibrosis is associated with lower total cholesterol and higher AST concentrations.     

Effect of papaya (Carica papaya) leaf extract as dietary growth promoter supplement in red hybrid tilapia (Oreochromis mossambicus × Oreochromis niloticus) diet

The purpose of this experiment was to examine the potential use of Carica papaya leaf extract as a supplement to promote growth and improve feed utilization in red hybrid tilapia. Five diets were formulated containing isolipidic (80 g/kg) and isonitrogenic (350 g/kg) levels. All feeds contained similar types and amounts of raw materials but differed in the inclusion of papaya leaf extract (0, 5, 10, 20 and 40 g/kg feed). The initial size of fish used was 2.3 ± 0.01 g. Each diet was performed in triplicate tanks, and the feeding period was 12 weeks. Fish fed diet containing 2% papaya leaf extract (PLE) had the highest final weight, 31.14 ± 1.47 g, followed by 1% PLE (27.27 ± 1.75 g). These two diets (1% and 2%) were also showed significant improvements of weight gain, SGR, and feed efficiency of the red hybrid tilapia (p < 0.05). However, papaya leaf extract did not affect the HSI, VSI, PER, digestive enzymes activity, blood composition, and survival rate. Supplementing the diets with papaya leaf extract lowered serum urea. Findings of this research suggest that adding papaya leaf extract to the diet of red hybrid tilapia improves growth and feed efficiency without adversely affecting blood parameters. Therefore, an inclusion level between 1% and 2% of the papaya leaf extract is recommended as a feed additive to promote red hybrid tilapia fry growth.     

High-performance centrifugal partition chromatography (HPCPC) for efficient isolation of diphlorethohydroxycarmalol (DPHC) and screening of its antioxidant activity in a zebrafish model

High-performance centrifugal partition chromatography (HPCPC) can be used for the rapid isolation of biologically active metabolites from natural sources. The present study investigates the one-step isolation of diphlorethohydroxycarmalol (DPHC), an algal polyphenol, from the brown seaweed Ishige okamurae by HPCPC and its protective effect against 2,2’-azobis dihydrochloride (AAPH) induced oxidative stress in zebrafish embryos. HPCPC was found to be efficient and effective for the isolation of DPHC from Ishige okamurae under optimized solvent conditions, yielding a high purity product. The present purification method helps overcome compound wasting and possible degradation, which cause a low yield in conventional column separations. Further, zebrafish embryos exposed to AAPH were compared with and without DPHC treatment, two days after fertilization for ROS generation, cell death, lipid peroxidation, survival rate, and heartbeat rates. These evaluations revealed that DPHC treatment significantly enhanced protection against oxidative stress in zebrafish embryos. HPCPC was, therefore, established as an efficient DPHC isolation method and could be used for separating other complex phlorotannins from seaweeds.     

Laboratory evaluation of the rapid diagnostic tests for the detection of Vibrio cholerae O1 using diarrheal samples

BackgroundCholera, an acute diarrheal disease is a major public health problem in many developing countries. Several rapid diagnostic tests (RDT) are available for the detection of cholera, but their efficacies are not compared in an endemic setting. In this study, we have compared the specificity and sensitivity of three RDT kits for the detection of Vibrio cholerae O1 and compared their efficiency with culture and polymerase chain reaction (PCR) methods.MethodsFive hundred six diarrheal stool samples collected from patients from two different hospitals in Kolkata, India were tested using SD Bioline Cholera, SMART-II Cholera O1 and Crystal-VC RDT kits. All the stool samples were screened for the presence of V. cholerae by direct and enrichment culture methods. Stool DNA-based PCR assay was made to target the cholera toxin (ctxAB) and O1 somatic antigen (rfb) encoding genes. Statistical evaluation of the RDTs has been made using STATA software with stool culture and PCR results as the gold standards. The Bayesian latent class model (LCM) was used to evaluate the diagnostic tests in the absence of the gold standard.ResultsInvolving culture technique as gold standard, the sensitivity and specificity of the cholera RDT kits in the direct testing of stools was highest with SAMRT-II (86.1%) and SD-Cholera (94.4%), respectively. The DNA based PCR assays gave very high sensitivity (98.4%) but the specificity was comparatively low (75.3%). After enrichment, the high sensitivity and specificity was detected with SAMRT-II (78.8%) and SD-Cholera (99.1%), respectively. Considering PCR as the gold standard, the sensitivity and specificity of the RDTs remained between 52.3–58.2% and 92.3–96.8%, respectively. In the LCM, the sensitivity of direct and enrichment testing was high in SAMRT-II (88% and 92%, respectively), but the specificity was high in SD cholera for both the methods (97% and 100%, respectively). The sensitivity/specificity of RDTs and direct culture have also been analyzed considering the age, gender and diarrheal disease severity of the patients.ConclusionOverall, the performance of the RDT kits remained almost similar in terms of specificity and sensitivity. Performance of PCR was superior to the antibody-based RDTs. The RTDs are very useful in identifying cholera cases during outbreak/epidemic situations and for making them as a point-of-care (POC) testing tool needs more improvement.     

Malaria importada en población pediátrica de Alicante,España (1994-2019)

Introduction:

In recent years there has been an increase in imported malaria among children in whom it is a potentially serious and fatal disease.

Objective:

To describe the incidence and the clinical and epidemiological characteristics of malaria in children diagnosed in Alicante, Spain, over a 26-year period.

Materials and methods:

We conducted an observational retrospective study of malaria in children aged under 15 years diagnosed at the Alicante General University Hospital from 1994 to 2019.

Results:

Twenty-four cases were registered over the study period. The frequency of cases increased from 2 over the first five years to 11 in the last five years. The median age of the children was 6 years (interquartile range: 3-8); 91.6% came from sub-Saharan Africa. Over half (n=15, 62.5%) were children born in Spain to immigrant parents visiting friends and relatives (VFR); just one (6.7%) had received antimalarial chemoprophylaxis.The most frequent clinical signs were fever (86.9%), hepatosplenomegaly (70.8%), and anemia (70.8%). Plasmodium falciparum was the most frequently identified species (83.3%, n=20). The most common treatment was oral piperaquine/dihydroartemisinin (41.6%, n=10) with favorable outcomes in all cases.

Conclusions:

Imported childhood malaria shows an increasing incidence and a nonspecific clinical presentation. Professional awareness of this disease and a high degree of clinical suspicion are needed for the early initiation of treatment. Pre-travel preventive measures should be promoted when appropriate.     

Role of Chd7 in zebrafish: a model for CHARGE syndrome

CHARGE syndrome is caused by mutations in the CHD7 gene. Several organ systems including the retina, cranial nerves, inner ear and heart are affected in CHARGE syndrome. However, the mechanistic link between mutations in CHD7 and many of the organ systems dysfunction remains elusive. Here, we show that Chd7 is required for the organization of the neural retina in zebrafish. We observe an abnormal expression or a complete absence of molecular markers for the retinal ganglion cells and photoreceptors, indicating that Chd7 regulates the differentiation of retinal cells and plays an essential role in retinal cell development. In addition, zebrafish with reduced Chd7 display an abnormal organization and clustering of cranial motor neurons. We also note a pronounced reduction in the facial branchiomotor neurons and the vagal motor neurons display aberrant positioning. Further, these fish exhibit a severe loss of the facial nerves. Knock-down of Chd7 results in a curvature of the long body axis and these fish develop irregular shaped vertebrae and have a reduction in bone mineralization. Chd7 knockdown also results in a loss of proper segment polarity illustrated by flawed efnb2a and ttna expression, which is associated with later vascular segmentation defects. These critical roles for Chd7 in retinal and vertebral development were previously unrecognized and our results provide new insights into the role of Chd7 during development and in CHARGE syndrome pathogenesis.