Mohamed S Eldin Badr

Mohamed S Eldin Badr
Ain Shams University · Department of Molecular Biology, Medical Research center

Professor
Mohamed S. Badr Professor Medical research center faculty of medicine Ain Shams University

About

36
Publications
11,590
Reads
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136
Citations
Additional affiliations
January 1994 - present
Ain Shams University
Position
  • Ain Shams University Medical Research Center
Education
June 2003 - September 2009
Ain Shams University
Field of study
  • MOLECULAR BIOLOGY - MEDICAL MICROBIOLOGY

Publications

Publications (36)
Article
Full-text available
The demand for using natural compounds as control methods for honey bee viruses have increased in recent decades. In this study, a chemical profile of honey bee venom (HBV) has been determined by FTIR spectroscopy and Egyptian ethanolic propolis (EP) extract by GC-MS and HPLC. Also, the enzymatic activities of HBV were determined. HBV and EP were t...
Article
Full-text available
Trichinellosis is one of the global food-borne parasitic diseases that can cause severe tissue damage. The traditionally used drugs for the treatment of trichinellosis have limited efficacy against the encysted larvae in the muscular phase of the disease. Therefore, this study aimed to evaluate the role of atorvastatin and mesenchymal stem cells co...
Article
Full-text available
Autism is a neurodevelopmental disorder with a significantly increased incidence rate across the world over the past few years. Toxoplasmosis and cytomegalovirus (CMV) infection are globally prevalent and have been associated with diverse neurological and psychiatric disorders. A few studies have demonstrated the role of toxoplasmosis and CMV as po...
Article
Full-text available
Purpose The relationship between the genetic diversity of Blastocystis and immune surveillance in precancerous colons with blastocystosis is still under investigation. This study aimed to identify the genetic Blastocystis variants among 54 symptomatic human isolates and their relationship to mucosal immune surveillance in the precancerous polyps of...
Article
Full-text available
Background Honeybees are one of the most important pollinators in the world, and their products are nowadays included in most anticancer, antiallergic, antimicrobial drugs and are included in cosmetic treatments. In the present study, honeybee venom and Egyptian ethanolic propolis extract (EP) were focused to test their effect on health and some ge...
Article
Full-text available
BACKGROUND: At present, there is little documented about the variability aspects of Entamoeba gingivalis (E. gingivalis) in relation to periodontal diseases. This is perhaps due to several specialists rejecting the notion that E. gingivalis can cause periodontal disease. AIM: The aim of the present study was to compare the morphological and genetic...
Article
Full-text available
White button mushroom, antiproliferative, Gene expressions, HepG2Bax,QSepharose, biomedical applications. The biological contents of the white button mushroom including(lectin and polysaccharides) were extracted from its dried fruiting bodies and purified through Q-Sepharose column which was considered a strong anion for adsorption of lectin with...
Preprint
Full-text available
The variability aspects of Entamoeba gingivalis concerning periodontal diseases are poorly studied. The reason is that many researchers rejected the notion that it can cause periodontal disease. The current study aimed to compare the morphological and genetic variability within trophozoites isolated from diseased and healthy periodontal sites. The...
Article
Over the past decades, the extensive use of pyrethroids insecticides for vector control has resulted in the development of insecticide resistance. Cytochrome P450 has been recognized to play a critical role in the metabolic detoxification of insecticides. In the current study, Culex pipiens mosquitoes were collected from Giza Governorate in Egypt a...
Article
Full-text available
Toxoplasmosis during pregnancy is known for inducing variable serious outcomes. In many previous studies, pregnancy was evaluated as a single event while in reality; it has different distinct immunological stages depending on gestational time and possible external factors as infectious agents. A state of immunological balance as well as a state of...
Article
Full-text available
BACKGROUND Toxoplasma gondii is a common parasitic infection of humans. Infection is usually mild. Serious complications can occur in pregnant and immunocompromised patients. AIM The present study aims to investigate the performance of 2 different PCR protocols; real-time quantitative molecular assays (qPCR) and conventional molecular assays (cPCR...
Article
Full-text available
AIM: The current study aimed to assess the practicability of a simple loop-mediated isothermal amplification (LAMP) about real-time quantitative PCR to diagnose primary toxoplasmosis among high-risk pregnant women. METHODS: Cloned Toxoplasma samples were used to calculate the analytical sensitivity while specificity was assessed using pooled DNA s...
Article
Full-text available
The aim of the current work was to evaluate the possibility of using a rapid and simple reagent strip test to investigate the viability of hydatid cysts intraoperatively, via testing certain biochemical parameters. Thirty eight HCF samples were processed and examined by different methods for determining the viability status. Using the reagent strip...
Article
Previous immunological studies targeting cystic echinococcosis infection have focused mainly on the dominating Th2 cell response to benefit parasite growth and development. However, the status of the adaptive immune cells and their contributions to E. granulosus cyst progression remains inadequately understood, especially in sensitized hosts. The a...
Article
Schistosoma mansoni causes a major chronic debilitating disease in more than 230 million people around the world. The pathognomonic granuloma is a major cause of the oxidative stress encountered as a consequence of infection not only in the liver, but also in other important organs as spleen, lung, brain and kidney. Resveratrol administration at a...
Article
Full-text available
Low parasite density in chronic infection with S. stercoralis is a challenging diagnostic issue. Generally, molecular techniques don't depend on parasite viability while copro-culture or Baermann concentration method relies on the presence of living larvae in fecal samples. Therefore, evaluation of PCR-based methods is important to increase the det...
Article
Full-text available
Schistosomiasis haematobium is a major endemic parasitic disease in many tropical regions including Egypt. Typical infection results in haematuria, dysuria, anaemia, genital as well as urinary tract lesions, with prospect of kidney damage in complicated cases. In addition, deposited eggs in the tissue, eventually leads to squamous cell carcinoma of...
Article
Full-text available
Toxoplasmosis caused by Toxoplasma gondii is one of the most prevalent parasitic diseases in human beings. Human toxoplasmosis can be associated with serious clinical manifestations, particularly in developing fetus. The aim of the current study was to identify the possible lineage type of Toxoplasma gondii, molecularly detected in placental sample...
Article
Introduction: Acute liver failure (ALF), like sepsis, is associated with an overwhelming activation of the immune response in which hepatic and circulating inflammatory cytokines play a pivotal role. Cholinesterase inhibition has been shown to have anti-inflammatory properties in experimental sepsis. We investigated the role of neostigmine in atten...
Article
Full-text available
Introduction Acute liver failure (ALF), like sepsis, is associated with an overwhelming activation of the immune response in which hepatic and circulating inflammatory cytokines play a pivotal role. Cholinesterase inhibition has been shown to have anti-inflammatory properties in experimental sepsis. We investigated the role of neostigmine in attenu...
Article
Full-text available
Abstract: Detection and monitoring of microbial load of variety of microbial targets could contribute immensely to research efforts aimed at understanding the pathogenicity of organisms and progression of microbial diseases. In the present study we aimed to find a specific and sensitive quantification method for detection and quantification of nucl...
Article
Full-text available
Single nucleotide polymorphisms (SNPs) in the IL-28B gene are considered one of the most important baseline predictors of sustained virological response (SVR) to peg-interferon (PegIFN) and ribavirin (Rbv) in patients with hepatitis C virus (HCV) genotype 1 infection, and much less so in HCV-2 and -3. Whether this holds true for HCV-4 patients too...

Questions

Question (1)
Question
Are microarray experiments more difficult to design than other studies?
No, but... Microarrays are still quite expensive to perform, so you would want to do them properly from the first step on. Also, a single microarray hybridization can generate as many data points as several "classical" Ph.D. theses, so expectations towards the results will be particularly high. Failure to interpret the data due to incorrect design can be particularly embarrassing.
What is a good microarray experiment?
Just as there are many uses for classical experimental techniques, there are many ways to exploit microarrays. One important consideration is that you should compare samples that are similar. Don't try to maximize the number of differentially expressed genes. Some special cases:
Knock-out animal models. If you compare two animals, try to take samples from comparable areas. The same tissue may not be the same anymore, after you knock out a major physiological process. E.g., the testis of a steroid receptor knock-out will have little resemblance to a wild-type testis, because spermatogenesis is abolished. Therefore almost all genes will be changed in expression to some extent - and the results may be close to impossible to interpret. Microarrays are very sensitive in picking out expression changes. As a rule of thumb, it may be good to use microarrays only on samples that are impossible to distinguish by eye.
Tissue comparisons. Here the problems described for knock-out models are aggravated. There are probably very few sensible experiments comparing samples from different tissues (except in the context of large-scale comprehensive expression surveys). It is often even recommendable to restrict analysis to specific cell types within the same tissue, if the quantitative composition changes between conditions.
Drug treatments. If you are interested in a drug effect, try to examine the earliest time point possible. This minimizes secondary effects and focuses on the drug-specific changes. Of course, a time-series can be helpful, but if you know the physiological time-scale in advance, it is often more efficient to increase the number of replicates on one early time point.
Stably transfected cell lines. To establish a cell line that has been stably transfected by some DNA, you usually have to go through a rigorous selection process, often even including a single-cell stage. Afterwards the newly established cell line may no longer be comparable to its parent line, especially if the effect of the transfection is rather mild. The observations could be dominated by individual differences between cells that have been "amplified" by the selection process. Therefore, it is important to use a mock transfected cell line as the control, preferably one that expresses an inactive point mutant of the construct of interest. Also, as the transfection process and the subsequent selection and gene integration are not reproducible, it is recommended to use independent transfectants for each replicate, even though this is more laborious.
Response studies vs. condition studies. If you want to compare two tissues that are quite different (wild type vs. mutant, healthy vs. diseased) it may be more effective to compare their responses to some stimulus (a drug, an hormone, a stressor), rather than comparing their conditions directly. In this setup, each hybridization could compare a single tissue in the stimulated and unstimulated state, which should be more similar, i.e. comparable, than the two different tissues.
Do I need statistical advise for my study design?
Microarray experiments are biological experiments, so the most important considerations will be biological. Especially in simple cases, where you want to use microarrays as a comprehensive Northern blot, microarray-specific statistical issues can be of secondary importance at the early stages. It will, however, be very useful to involve a statistician in the analysis/interpretation process to prevent some common pitfalls, such as underestimating the "multiple testing problem" involved in examining thousands of genes at once :
How do I analyze my results
And of course you should always be aware of the basic statistical and philosophical issues involved in any successful experimental design
What kind of microarrays should I use?
Standard arrays. If possible use arrays that many other people are using. This facilitates data exchange and the comparison of results. Your data will be much more useful and easier to interpret if you can directly compare them to other people's data. Cross-platform comparisons are possible but are presently quite tedious.
Whole-genome arrays. Nowadays, there are few good reasons to restrict your studies to an arbitrary selection of genes. Exceptions are experiments with organisms for which whole-genome arrays are unavailable or very focused specialized studies. However, it would be a mistake to choose a partial array just because a more comprehensive genome-wide study might yield too many unexpected (or currently unexplainable) results.
Single-color arrays (e.g. Affymetrix Genechip arrays) If you just compare two conditions (mutant vs. wild type; treated vs. untreated; healthy vs. diseased) two-color arrays are the obvious technique of choice. As soon as the study becomes a bit more complex (time-course of treatment; comparison of several mutants; inter-patient comparison), two-color arrays pose so many experimental design problems, that using a one-color technique is usually advisable, even if the single hybridizations may be more expensive.
Annotated arrays. For many biological studies, the interpretation will rely on the available functional annotation of the genes on an array. Although, sometimes, microarray experiments are used to fish for previously unknown genes involved in a certain process, attention will usually focus on those candidates that already have been functionally characterized in some other role. Differential expression of completely novel genes is very hard to interpret. This consideration can be important in the case of Affymetrix Genechiparrays, which in some cases are provided as chip pairs (A and B chips), where one member of a pair is enriched in all the functionally annotated genes. In these cases, consider using only the well-annotated member of the pair.
How many replicates do I need?
As many as possible! For an exploratory analysis 3 replicates are usually sufficient, unless the data are particularly noisy (e.g. samples from very small numbers of cells) or the expected effect is particularly small (e.g. changes occur only in very few, specialized cells in the sample). Using less than 3 replicates is not a good idea. Most important is the use of real replicates. Do equal numbers of replicates for each condition/comparison to keep the later analysis simple.
What is a real replicate?
A real - or biological - replicate is an independent sample that is varying all the variables that a colleague in another lab couldn't control. You want to report only observations that are general and reproducible. In an imaginary "ideal" experiment, each replicate would be performed in a different lab - so it may be advisable to approximate that situation as much as possible. That does not mean that you have to vary all the variables, if you are certain that some of them won't have any effect, e.g. the brand of standard chemicals, the phases of the moon, etc. But don't underestimate the sensitivity of microarrays, variables like batch of cells or time of day can very well have an observable effect. Most of all, be careful to prepare a perfectly matched control for every sample, even if you are going to use single-color arrays.
hould I do technical replicates?
No, unless you are planning a technical instead of a biological study. Repeated hybrization of the same biological sample is a waste of resources. Microarrays are reliable and it has been shown repeatedly that this kind of replication doesn't provide any biologically useful information.
Should I pool samples?
It is tempting to pool samples to save hybridization costs. Unless you do single-cell sampling, every samples is already a pool, as it contains mRNA from many cells. Especially if the number of cells obtained from each individual is very small, pooling is the best way of reducing the noise while keeping the number of hydridizations reasonably small. Unless you expect to find interesting inter-individual variations, e.g. in a medical study, there is little to argue against pooling. However, it is important to pool the biological material (tissue, cells), not the purified RNA or labeled cDNA! In this way, problems are far easier to spot. Don't ever include any sample that looks suspicious.
3. How do I analyze my results?
At the SHWFGF we have recently introduced two simple new statistical techniques (RankProducts [RP] and iterative GroupAnalysis [iGA]) that facilitate and enhance the interpretation of microarray experiments. Both methods provide rigorous significance estimates for your observations and perform considerably better than previous techniques, particularly for the small and noisy data sets that are often produced in biological experiments. The standard (recommended) analysis procedure used at the SHWFGF is described here and software is available for download at the GlaMA website
What else should I do?
Keep things simple (pair-wise comparisons, simple time-courses).
Try to define your expectations (hypotheses) in advance in as much detail as possible. Inventing ad hoc explanations later when you get your results is not best practice. As Ernst Wit writes in his Ethics of Chance: A statistical "method that makes use of a retrospective study of the data cannot [ever] reach the same significance level as a prior formulation of the hypothesis." This is a general issue for the performance and interpretation of scientific experiments and is particularly relevant for microarray studies with their large data sets and surprise observations.

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