NTRFinder: a software tool to find nested tandem repeats

We introduce the software tool NTRFinder to search for a complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that NTRs can be used as phylogenetic and population markers. We have tested our algorithm on both real and simulated data, and present some real NTRs of interest. NTRFinder can be downloaded from http://www.maths.otago.ac.nz/~aamatroud/.     

Anxiety,depression-like behaviors and biochemistry disorders induced by cannabis extract in female mice

Cannabis is an annual herbaceous plant sometimes grown for decoration and used as bird food that looks like flax. The study wanted to determine if a Cannabis extract may have an effect on how anxious and depressed the female mice behaved. forty healthy female mice were divided into four groups. Tap water was administered to the first group (control). Ethanol was administered to second group (positive control). The third and four groups were given 1 and 2 mg/kg cannabis extract respectively. Treatment continued for 14 days. After therapy, the light–dark chamber, forced swimming, tail suspension, plus lamb and open field tests were done to assess anxiety and depressive behavior. The results indicated that the anxiety and depression were increased in treated females significantly compared to control. Biochemical results showed that DA,5-HT, AChE, GSH, GST, CAT and SOD were decreased while TBARS, corticosterone and cortisol were increased. In conclusion, cannabis effects this kind of females’ behavior but the mechanisms are not clear yet. We need more researches on this trend.     

HK022 bacteriophage Integrase mediated RMCE as a potential tool for human gene therapy

HK022 coliphage site-specific recombinase Integrase (Int) can catalyze integrative site-specific recombination and recombinase-mediated cassette exchange (RMCE) reactions in mammalian cell cultures. Owing to the promiscuity of the 7 bp overlap sequence in its att sites, active ‘attB’ sites flanking human deleterious mutations were previously identified that may serve as substrates for RMCE reactions for future potential gene therapy. However, the wild type Int proved inefficient in catalyzing such RMCE reactions. To address this low efficiency, variants of Int were constructed and examined by integrative site-specific recombination and RMCE assays in human cells using native ‘attB’ sites. As a proof of concept, various Int derivatives have demonstrated successful RMCE reactions using a pair of native ‘attB’ sites that were inserted as a substrate into the human genome. Moreover, successful RMCE reactions were demonstrated in native locations of the human CTNS and DMD genes whose mutations are responsible for Cystinosis and Duchene Muscular Dystrophy diseases, respectively. This work provides a steppingstone for potential downstream therapeutic applications.     

Prevalence of energy drink consumption and association with dietary habits among governmental university students in Riyadh

To determine the prevalence of Energy Drinks (ED) consumption, and the adverse effects experienced by consumers among governmental university students in Riyadh, and to assess the relationship between ED consumption and dietary habits. This is a cross-sectional study carried out in 2020 in a random sample of students at government universities in Riyadh (King Saud University (KSU) and Imam Muhammad Ibn Saud Islamic University (IMSIU). The study was conducted within a time frame of 3 months which included a total of 546 students. The data collection tool was an online self-administered questionnaire that included three sections. The first section addressed the characteristics of the students, the second section addressed ED consumption, and the third section addressed the dietary habits of ED consumers. A SPSS software-based analysis revealed that the percentage of ED consumers in our cohort was 29.3%. Moreover, we found a significant association between ED consumption and consumption of fewer than three meals, skipping breakfast, and fast food intake (χ² = 0.002, P = 0.364; χ² = 0.028, P = 0.341; and (χ² = 0.010, P = 0.369, respectively), with moderate correlation. No association was found between the consumption of EDs and that of fruits, vegetables, and snacks. Moreover, 36% of the consumers experienced jolt-and-crash symptoms and signs after ED consumption, with 84.5% of them exhibiting increased consumption of salty snacks, sweets, and fast food during the episodes. Our findings showed that ED consumption is not a common practice among governmental university students in Riyadh. Furthermore, the consumption of EDs was correlated with unhealthy dietary habits. Creating educational programs for school going students and providing healthy alternative options to the students is highly recommend. Future research should be conducted using a larger sample and including universities from the private sector, to compare the results.     

Within-Subject Interlaboratory Variability of QuantiFERON-TB Gold In-Tube Tests

Background

The QuantiFERON®-TB Gold In-Tube test (QFT-GIT) is a viable alternative to the tuberculin skin test (TST) for detecting Mycobacterium tuberculosis infection. However, within-subject variability may limit test utility. To assess variability, we compared results from the same subjects when QFT-GIT enzyme-linked immunosorbent assays (ELISAs) were performed in different laboratories.

Methods

Subjects were recruited at two sites and blood was tested in three labs. Two labs used the same type of automated ELISA workstation, 8-point calibration curves, and electronic data transfer. The third lab used a different automated ELISA workstation, 4-point calibration curves, and manual data entry. Variability was assessed by interpretation agreement and comparison of interferon-γ (IFN-γ) measurements. Data for subjects with discordant interpretations or discrepancies in TB Response >0.05 IU/mL were verified or corrected, and variability was reassessed using a reconciled dataset.

Results

Ninety-seven subjects had results from three labs. Eleven (11.3%) had discordant interpretations and 72 (74.2%) had discrepancies >0.05 IU/mL using unreconciled results. After correction of manual data entry errors for 9 subjects, and exclusion of 6 subjects due to methodological errors, 7 (7.7%) subjects were discordant. Of these, 6 (85.7%) had all TB Responses within 0.25 IU/mL of the manufacturer''s recommended cutoff. Non-uniform error of measurement was observed, with greater variation in higher IFN-γ measurements. Within-subject standard deviation for TB Response was as high as 0.16 IU/mL, and limits of agreement ranged from −0.46 to 0.43 IU/mL for subjects with mean TB Response within 0.25 IU/mL of the cutoff.

Conclusion

Greater interlaboratory variability was associated with manual data entry and higher IFN-γ measurements. Manual data entry should be avoided. Because variability in measuring TB Response may affect interpretation, especially near the cutoff, consideration should be given to developing a range of values near the cutoff to be interpreted as “borderline,” rather than negative or positive.     

An algorithm to solve the motif alignment problem for approximate nested tandem repeats in biological sequences

An approximate nested tandem repeat (NTR) in a string T is a complex repetitive structure consisting of many approximate copies of two substrings x and X ("motifs") interspersed with one another. NTRs fall into a class of repetitive structures broadly known as subrepeats. NTRs have been found in real DNA sequences and are expected to be important in evolutionary biology, both in understanding evolution of the ribosomal DNA (where NTRs can occur), and as a potential marker in population genetic and phylogenetic studies. This article describes an alignment algorithm for the verification phase of the software tool NTRFinder developed for database searches for NTRs. When the search algorithm has located a subsequence containing a possible NTR, with motifs X and x, a verification step aligns this subsequence against an exact NTR built from the templates X and x, to determine whether the subsequence contains an approximate NTR and its extent. This article describes an algorithm to solve this alignment problem in O(|T|(|X| + |x|)) space and time. The algorithm is based on Fischetti et al.'s wrap-around dynamic programming.     

Molecular docking of phenolic compounds and screening of antioxidant and antidiabetic potential of Moringa oleifera ethanolic leaves extract from Qassim region,Saudi Arabia

IntroductionOxidative stress is crucial in diabetic pathophysiology, hence the prerequisite of ingesting naturally derived antioxidants as a remedial target. This study investigates the naturally occurring antioxidant and antidiabetic potential of Moringa oleifera ethanolic leaves extract.MethodsMoringa oleifera leaves were macerated (MOLE) by using 70% ethanol. Physiochemical and phytochemical examinations of MOLE was assayed using standard methods. The antioxidant activity was analyzed by DPPH (1, 1-diphenyl-2-picrylhydrazil) radical scavenging assay. In vitro antidiabetic was analyzed by pancreatic α-amylase enzyme inhibitory assay. The molecular docking was performed using AutoDock Vina v1.1.2 in PyRx 30.8.ResultsEthanolic extraction of MOLE by maceration technique, 14 % yield. Loss on drying, foreign organic matters and total ash value of OLE showed 0.27 w/w, 0.8 % and 19 %, respectively. Phytochemical test on MOLE confirmed starch, carbohydrate, flavonoid, gum, glycoside, saponin, tannin, and phenol presences. The total phenolic and flavonoid contents of MOLE are 260 mg GAE/g and 755 mg RUE/g of extract. MOLE (IC 50 55.6 ± 0.18 µg/mL) showed functional DPPH scavenging assay comparable to ascorbic acid (IC 50 46.71 ± 0.24 µg/mL). In the alpha-amylase inhibitory activity, Acarbose showed an IC 50 value of 19.45 ± 0.26 µg/mL, while MOLE portrayed an IC 50 value of 27.54 ± 0.07 µg/mL. Docking studies revealed that most phenolic compounds found within MOLE have minimum docking scores and high binding affinity against Human pancreatic alpha-amylase.ConclusionsThe invitro and docking results suggest that MOLE has been a viable natural bioactive source and might be a great potential source for future antidiabetic medicine.