Computational design and experimental verification of pseudoknotted ribozymes

The design of new RNA sequences that retain the function of a model RNA structure is a challenge in bioinformatics because of the structural complexity of these molecules. RNA can fold into its secondary and tertiary structures by forming stem-loops and pseudoknots. A pseudoknot is a set of base pairs between a region within a stem-loop and nucleotides outside of this stem-loop; this motif is very important for numerous functional structures. It is important for any computational design algorithm to take into account these interactions to give a reliable result for any structures that include pseudoknots. In our study, we experimentally validated synthetic ribozymes designed by Enzymer, which implements algorithms allowing for the design of pseudoknots. Enzymer is a program that uses an inverse folding approach to design pseudoknotted RNAs; we used it in this study to design two types of ribozymes. The ribozymes tested were the hammerhead and the glmS, which have a self-cleaving activity that allows them to liberate the new RNA genome copy during rolling-circle replication or to control the expression of the downstream genes, respectively. We demonstrated the efficiency of Enzymer by showing that the pseudoknotted hammerhead and glmS ribozymes sequences it designed were extensively modified compared to wild-type sequences and were still active.

Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes

Pseudoknots are important motifs for stabilizing the structure of functional RNAs. As an example, pseudoknotted hammerhead ribozymes are highly active compared to minimal ribozymes. The design of new RNA sequences that retain the function of a model RNA structure includes taking in account pseudoknots presence in the structure, which is usually a challenge for bioinformatics tools. Our method includes using "Enzymer," a software for designing RNA sequences with desired secondary structures that may include pseudoknots. Enzymer implements an efficient stochastic search and optimization algorithm to sample RNA sequences from low ensemble defect mutational landscape of an initial design template to generate an RNA sequence that is predicted to fold into the desired target structure.

Antiviral activity of a standardized root water extract of Eurycoma longifolia (Physta®) against dengue virus

The aim of this study was to investigate the antiviral property of Eurycoma longifolia Jack (EL) against dengue virus. A propriety standardized extract of Eurycoma longifolia Jack (Physta®) was tested for anti-viral activity after viral adsorption in Vero cell line. Viral yield was measured by qRT-PCR in four serotypes of dengue virus. The antiviral activity was further investigated in an in vivo AG129 mouse model for dengue inhibitory candidates. 100 mg/kg EL extract was fed twice daily and challenged with a lethal dose of (~1x10⁵ PFU per mouse) of DENV-2 over a period of six days. Antiviral activity with IC₅₀ of 33.84, 33.55, 58.35 and 119 µg/ml for DENV-1, DENV-2, DENV-3 and DENV-4 serotypes respectively was observed. The selectivity index (SI) values determined as the ratio of cytotoxic concentration (CC₅₀) to inhibitory concentration (IC₅₀) was the lowest for DENV-2 at 28.9. The dengue virus (DENV) replication measured by qRT-PCR showed a reduction of 100% for DENV-1, DENV-2, DENV-3 and 80% for DENV-4 at day 2 of exposure. In the in vivo AG129 mouse model, a lower weight reduction, 30% lower viral load and 12% higher platelet in the extract group compared to the control was observed at day 6. The extract of E. longifolia has potential anti-dengue properties with improving trends in platelet counts. E. longifolia supplementation is potentially a two-pronged approach in treating dengue fever.

An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures

Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer.

First report on the seroprevalence of the Crimean-Congo haemorrhagic fever virus, a tick-borne virus, in Malaysia's Orang Asli population

OBJECTIVE

The Crimean-Congo haemorrhagic fever virus (CCHFV), which is transmitted by the ticks of Hyalomma spp. in general and H. marginatumin particular, can cause severe disease in humans, with mortality rates of 3-30%. Other than from the bites of infected ticks, CCHFV can also be transmitted through contact with patients with the acute phase of infection or contact with blood or tissues from viraemic livestock.  Outbreaks of human cases of haemorrhagic manifestations have been documented since 1945 and described in parts of Africa, Asia, Eastern Europe and the Middle East and most recently India in 2011. In addition, serological evidence of the disease has been reported in some countries where no human cases were reported. As regional neighbours China and India have been affected by this virus, this study was conducted to determine the seroprevalence of CCHFV among Orang Asli population of Malaysia as the most at risk people who residing in the deep forests.

PATIENTS AND METHODS

A total of 682 serum samples were collected from the Orang Asli population residing in eight states in peninsular Malaysia and analysed for the presence of anti-CCHFV immunoglobulin G (IgG) using a commercial enzyme-linked immunosorbent assay kit.

RESULTS

The study subjects comprised 277 (40.6%) men and 405 (59.4%) women. However, anti-CCHFV IgG was detected in only one female serum sample (0.1%). The presence of anti-CCHFV IgG could not be correlated to age or sex from these findings.

CONCLUSIONS

The results of this screening survey showed that the seroprevalence of the anti-CCHFV IgG among Malaysia's Orang Asli population is too low for detection or totally negative compared with that in neighbouring countries, such as India and China.

In vitro characterization and mechanical properties of β-calcium silicate/POC composite as a bone fixation device

Calcium silicate (CS, CaSiO3 ) is a bioactive, degradable, and biocompatible ceramic and has been considered for its potential in the field of orthopedic surgery. The objective of this study is the fabrication and characterization of the β-CS/poly(1.8-octanediol citrate) (POC) biocomposite, with the goals of controlling its weight loss and improving its biological and mechanical properties. POC is one of the most biocompatible polymers, and it is widely used in biomedical engineering applications. The degradation and bioactivity of the composites were determined by soaking the composites in phosphate-buffered saline and simulated body fluid, respectively. Human osteoblast cells were cultured on the composites to determine their cell proliferation and adhesion. The results illustrated that the flexural and compressive strengths were significantly enhanced by a modification of 40% POC. It was also concluded that the degradation bioactivity and amelioration of cell proliferation increased significantly with an increasing β-CS content.

Antiviral activity of Holothuria sp. a sea cucumber against herpes simplex virus type 1 (HSV-1)

BACKGROUND

Finding the new bioactive compounds with antiviral activity from the natural resources are in interest of many drug discovery scientists. Sea cucumber is among the marine organisms a traditional food item in Asia with different applications in traditional medicine.

METHODS

In current study, a cold water extract of the Holothuria sp, one type Persian Gulf's sea cucumber was evaluated for its antiviral effects against KOS strain of Herpes Simplex Virus tyoe 1 (HSV-1) in cell culture. The half maximal inhibitory concentration (IC50) values were calculated for anti-adsorption activity and intracellular antiviral activity of the crude extract separately.

RESULTS

The extract exhibited antiviral activity not only against the virus adsorption to the cells, but also on virus intracellular replication. The CC50 for sea cucumber extract was 32.57 mg/ml. The IC50 values for the inhibition of the virus adsorption to the cells and virus intracellular replication were 120.2 and 189.9 µg/ml respectively. Selectivity index (SI) value for anti-adsorption activity was 189 while that value for the extract's intracellular antiviral activity was 172.

CONCLUSIONS

The results showed that Holothuria sp, water extract has remarkable antiviral effect against HSV-1 in cell culture and it is crucial to investigate the mechanism(s) of action of extract. Moreover, identification of the effective compound(s) within the extract would be necessary for future studies towards developing the new natural antiviral agent against HSV-1.

Evaluation of antibodies against glycoprotein D (gD) and glycoprotein G (gG) in HSV-1 infected individuals' serum samples

BACKGROUND AND OBJECTIVES

Glycoproteins D (gD) and G (gG) of herpes simplex virus type 1 (HSV-1) are virus envelope glycoproteins that are able to induce HSV-1 antibody production in infected persons. Therefore, those proteins could be in interest to develop the serodiagnostic test(s) for HSV antibody detection. The aim of present study was the comparison of anti-gD and anti-gG antibodies in HSV-1 infected individuals' serum samples.

MATERIALS AND METHODS

In this study, recombinant gD and gG were prepared and used for western blot test to detect the antibodies against HSV-1.

RESULTS

Our data showed the total gD antibody titer was higher than gG antibody titer in the HSV-1 infected patient's sera but the gG antibody titer was high significantly.

CONCLUSIONS

According to our results, gD and gG can be used for designing the diagnostic laboratory tests to evaluate total antibody against HSV-1 and HSV-2.

In vitro study of antibacterial activity of the alga Sargassum oligocystum from the Persian Gulf

BACKGROUND AND OBJECTIVES

With due attention to the development of drug-resistant bacteria, discovering of new antibacterial compounds is needed. Algae produce numerous bioactive substances which may have pharmacological properties such as antibacterial activity. The objective of this investigation was to in vitro study of antibacterial activity of brown alga Sargassum oligocystum collected along the Bushehr coast of Persian Gulf (south west of Iran).

MATERIALS AND METHODS

Hot water extract, cold water extract, and hot glycerin extract were prepared. The effect of the extracts were investigated on Staphylococcus aureus (ATCC 25923), Staphylococcus epidermidis (ATCC 14990), Pseudomonas aeruginosa (ATCC 27853), and Escherichia coli (ATCC 25922).

RESULTS

Hot water extract exhibited antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis, and Pseudomonas aeruginosa. Cold water extract and hot glycerin extract did not show antibacterial activity on any of the four test bacteria. The minimum inhibitory concentration (MIC) of hot water extract for both Staphylococcus aureus and Staphylococcus epidermidis was 3.175 mg/ml. However, the MIC of this extract for Pseudomonas aeruginosa was 9.556 mg/ml.

DISCUSSION

In this study gram-positive bacteria were more susceptible to hot water extract than gram-negative bacteria. Extract of Sargassum oligocystum could be a candidate for purification and further in vivo studies.

Rapid detection of Streptococcus pyogenes in throat swab specimens by fluorescent in situ hybridization

BACKGROUND AND OBJECTIVES

Streptococcus pyogenes (S. pyogenes) is an important cause of pharyngitis. Rapid detection of this microorganism in throat specimens is essential to promptly start antibiotic therapy which could be lead to prevent complications and stop transmission of infection to other individuals. In the present study, fluorescent in situ hybridization (FISH) was compared with culture method for the detection of S. pyogenes in throat swab specimens.

MATERIALS AND METHODS

One hundred eleven patients with pharyngitis were included in this study. The throat swab specimens of these patients were investigated by both conventional culturing and FISH.

RESULTS

Based on the results of this investigation, the sensitivity and specificity of FISH were 88.9% and 97.8%, respectively. Strikingly, in the specimen of one patient who had received antibiotic previous to clinical sampling, S. pyogenes was detected by means of FISH, whereas the culture method could not detect this bacterium.

CONCLUSIONS

It seems that FISH is a suitable method for quick identification of S. pyogenes in throat swab specimens. When FISH is positive, culturing is not necessary. But because of the limited sensitivity of FISH for detection of S. pyogenes in throat swab specimens, culturing shoud be performed if FISH was negative.

Molecular epidemiology of hepatitis C virus genotypes in Bushehr province, Iran

BACKGROUND AND OBJECTIVES

Molecular epidemiology of hepatitis C virus (HCV) is very important for the treatment of hepatitis C infection. The aim of this study was to determine the distribution of HCV genotypes in Bushehr province (South West of Iran).

MATERIALS AND METHODS

A total of 100 patients who were detected as positive for HCV antibody (by using ELISA method and RIBA test) referred to Arya Virology Laboratory between 2007-2009 in order to molecular diagnosis and furthermore virus genotyping. After detection of HCV, RNA genotyping of virus was done by using genotype specific primers.

RESULTS

Genotype 1a was found in 49% of the patients and genotype 3a was found in 40% of the patients and 1b in 5% of patients, while the genotype of the virus could not be identified in 5% of the patients. Finally, in 1% of patients coinfection due to 1a-3a genotypes was identified.

CONCLUSION

The dominant genotype of HCV in Bushehr province, Iran, was determined as 1a.

Anticancer activity of Sargassum oligocystum water extract against human cancer cell lines

BACKGROUND AND OBJECTIVES

Antitumor drug resistance and side effects of antitumor compounds are the most common problems in medicine. Therefore, finding new antitumor agents with low side effects could be interesting. This study was designed to assay antitumor activity of the extract from brown alga Sargassum oligocystum, gathered from Persian Gulf seashore, against K562 and Daudi human cancer cell lines.

MATERIALS AND METHODS

The research was performed as an in vitro study. The effect of the alga extract on proliferation of cell lines were measured by two methods: MTT assay and trypan blue exclusion test.

RESULTS AND CONCLUSION

The most effective antitumor activity has been shown at concentrations 500 microg/ml and 400 microg/ml of the alga extract against Daudi and K562 cell lines, respectively. The results showed that the extracts of brown alga Sargassum oligocystum have remarkable antitumor activity against K562 and Daudi cell lines. It is justified to be suggested for further research such as algal extract fractionation and purification and in vivo studies in order to formulate natural compounds with antitumor activities.

Antigen-specific lymphocyte proliferation assay and virus neutralization test for measurement of measles-specific immunity in 15-19 years old high school students in Tehran, Iran

Limited information is available concerning the role of measles-specific cell mediated immunity as a correlate of long-term protection from measles infection. Although serological responses are determined in epidemiological studies and high antibody titer is a good indicator of protection, the role of Cell-Mediated Immunity (CMI) has to be defined more clearly. In this study, Lymphocyte Proliferation (LP) and Viral Neutralization Test (VNT) were used in order to measure measles-specific cellular and humoral immune responses of 100 high school students in Tehran. From total number of subjects studied, 33 were girls and 67 were boys and all were in good health. Of these, 77 had protective neutralizing measles antibody titers and 23 did not have such titer. The results of LP showed that 89 subjects had protective cellular immune responses and 11 did not. A quantitative relationship between humoral and cellular immune responses was not observed. These findings suggest that measles-specific protective CMI is measurable for longer time in comparison to humoral immunity. These data suggest that LP responses may be better sustained than antibody titers in some children.