Science: Uncovering and Discovering

Due to its strong oxidizing properties, chlorine has long been used as cleansing and disinfecting agent. Chlorination is an ancient process used to treat drinking water as well as wastewater. Similarly, sodium hypochlorite is a cheap and powerful oxidizing agent widely used in household bleaches. Typical household bleach may contain between 1-5% NaOCl under alkaline conditions to maintain hypochlorite stability. Hypochlorite exhibits useful actions such as decolourization of soil/stains, breaking of soil matrix and killing of microorganisms. (more…)

In the last blog, some physical techniques for degradation of textile dyes were discussed. Now let’s jump over to their chemical alternatives. The chemical techniques are often expensive, and although the dyes are removed, accumulation of concentrated sludge creates a disposal problem. There is also the possibility that a secondary pollution problem will arise because of excessive chemical use. Recently, advanced oxidation processes, which are based on the generation of very powerful oxidizing agents such as hydroxyl radicals, have been applied with success for pollutant degradation. Although these methods are efficient, they are very costly and commercially unattractive. The high electrical energy demand and the consumption of chemical reagents are common problems. Major chemical methods used for treatment of dye wastewater are as follows: (more…)

Many industries, such as dyestuffs, textile, paper, plastic, food, pharmaceuticals and cosmetics use dyes. Since these dyes are designed to resist fading by different physical, chemical and biological agents, they are not degraded by conventional treatment processes and enter the environment. These coloured discharges are not only aesthetically unpleasing and drastically affect photosynthesis in aquatic ecosystem, but also pose ecological and public health risk. This has led to strict environmental regulations, making colour removal a very important issue for textile industries. (more…)

Mendel’s experiments demonstrated that for the production of single phenotypic traits of organisms, two alleles of a gene interacted with each other. Out of the two alleles, one always showed complete dominance over the other (Law of dominance). However, later on it was realized that the phenotypic traits studied by Mendel were governed by genes showing complete dominance. There are instances where one allele shows incomplete dominance over the other or both the alleles show equal expression or codominance. (more…)

The transmission of hereditary trait through nuclear genes is a well established phenomenon. However, there are enough evidences confirming inheritance of certain traits based on DNA elements present in the cytoplasm. This phenomenon is known as extra-nuclear or cytoplasmic inheritance. This has been observed in plants, animals as well as bacteria. It arises due to presence of extra-chromosomal elements in the cytoplasm in the form of organelles or symbionts or naked DNA in case of prokaryotes. (more…)

Molecular approaches are increasingly being used to characterize microorganisms and their activity in environmental samples to follow the progress of bioremediation processes. The major benefits of these techniques are that:

1) In contrast with classical microbiological techniques, they can detect both culturable and non-culturable microorganisms.

2) They give direct picture of the in situ microbial community and metabolic activity in the environment.

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GMOs (Genetically Modified Organisms) have been a subject of much hype since the advent of genetic engineering technologies, although with limited output. They were expected to find quick applicability in bioremediation of hazardous chemicals from the environment. However, there are still no (or very few, if any) documented evidences for the use of live GMOs in commercial bioremediation projects. There are several obstacles responsible for this. (more…)

Natural sources and human activities release significant amounts of heavy metals in surface water, wastewater and soils. These metals accumulate in living species and have toxic and carcinogenic effects. The most common treatment methods used to remove these metals from the wastewater include chemical precipitation, oxidation/reduction, adsorption, ion exchange, reverse osmosis etc. A great deal of research is being carried out to develop alternative and economical processes based on biosorption of metals. Some pilot plant studies have also been carried out to investigate the potential of microorganisms to remove metal ions from liquid and a few systems have been commercialized too. However, interaction between microorganisms and metals involves much more than simple adsorption. (more…)

Mycorrhizal fungi are widespread and form symbiosis with a large majority of plant species. They can be classified into 2 types:

1. Ectomycorrhiza, where fungal mycelium forms a compact mantle on the surface of the root and penetrates between cortical cells, forming Hartig net, which is the site of exchange of compounds between the partners.

2. Endomycorrhiza is far more diverse. Here, the mycelium penetrates not only the spaces between cells, but also the inside of live cortical cells. The mycelium develops into tree-like structures (arbuscles) inside the root cells. Hence, such associations are commonly known as Arbuscular Mycorrhizae (AM; formerly Vesicular-Arbuscular Mycorrhizae). This symbiosis is believed to be phylogenetically the most ancient type of mycorrhiza. (more…)

With number of people performing Ames test increasing as are the responses I am getting for an earlier article on the same topic, I guess, it is the correct time to blog on some tricks of the trade for it. Salmonella typhimurium his^- system is by far the most widely used system for mutagenicity testing as the diversity of tester strains available is high and their genetic features are better characterized as compared to trp^‑ system of E. coli. Hence, this article will concentrate on S. typhimurium system only. Although the problems can be many, some general precautions that may be taken are: (more…)

Mastigophores are a group of diverse flagellated protozoans, ranging from well-known parasites to free-living photosynthetic organisms. In a recent blog, people wanted more about one of these bugs, Volvox and why not, it is such a beautiful organism in this class. So here we go about it. (more…)

Despite some similarities between prions and viral diseases, these entities are very different. Prions lack a nucleic acid genome, making them unprecedented infectious particles. Although many investigators argued for a nucleic acid genome or at least a small polynucleotide, no nucleic acid has ever been found despite use of a wide variety of techniques and approaches. (more…)

Proteins interact with DNA to mediate a host of important cellular processes, such as, recombination, repair, expression, replication, packaging etc. Hence, a structural analysis of the individual components of nucleoprotein complexes is essential to understand these processes. While there are several techniques available for this, DNA footprinting might be the one you want to begin with. This technique was developed in 1977 and is commonly used for identifying the specific sequence of DNA that binds to a particular protein. The method can be performed on proteins which bind both double and single-stranded DNA. (more…)

Human eyes are very complicated structures, but this is not the case with all animals. We all know eye is a very important part of our body, but what about the animals that do not have an eye altogether or have a rudimentary form of it. The complexity and functionality of eyes is directly related to the complexity of animal itself. Thus, higher animals like humans tend to have more developed eyes. Eyes belong to a broad class of sensory organs (or should I say organelles in some of the animals?) known as photoreceptors i.e. organs responsible for reception of light. (more…)

Gas chromatograph (GC) is a very useful instrument to separate volatile and semi-volatile compounds with good resolution. However, it cannot identify them. Mass spectrometer (MS) can provide detailed structural information of most compounds, such that they can be exactly identified. However, the compounds must be separated beforehand as identification from mixtures is not possible. Therefore, a combination of the two techniques was suggested shortly after the development of GC in the mid-1950s.

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The amount of haploid nuclear DNA (C value) among eukaryotes varies more than 4 orders of magnitude. However, the C value is not directly related to the organismal complexity – C value paradox. This has been explained by variation in the noncoding DNA among eukaryotes. Although it answers the first question, it raises another query: reasons for the tremendous variations observed in noncoding DNA. (more…)

Quantification of RNA is normally carried out by RT-PCR (reverse transcription-polymerase chain reaction). It can be done in 2 ways: endpoint assay and real-time quantification. The real-time assay has distinct advantages of being more sensitive, less labour-intensive and capable of high-throughput as it does not require post-PCR probing/sequencing to confirm the identity of the amplicon generated. (more…)

As science is progressing, our knowledge base is increasing and new things are coming to light. Several of the older theories that were widely accepted once, are being replaced by new ones that better simulate the existing matter. Although we only try to understand the exiting theories, it is very interesting, and at times fascinating, to know how previous theories came in place, what facts were used to support them and how they contributed to the development of newer theories. (more…)

Mu phage is very similar to the well known lambda phage, having an icosahedral head and a contractile tail with tail fibers. However, it possesses several unique features that forced the scientific community to study it in detail, eventually culminating in its wide application in classical genetics.  To begin with, its name itself is descriptive. It has not been derived from Greek letters (e.g., lambda phage). The name “Mu” stands for its mutator phenotype. Mu is both a virus and transposable element i.e. it is a bacteriophage with transposition as obligatory part of its life cycle, although it carries no inverted repeats like other transposable elements.

Once into the host cell, its linear DNA integrates into the host DNA (chromosomal or plasmid) by conservative transposition. At this stage, it can enter either lysogeny or initiate lytic cycle. In lytic cycle, Mu undergoes several cycles of replicative transposition and the resulting phage DNA molecules integrate randomly in the host genome. The phage DNA molecules are then packed in phage heads by another interesting phenomenon. A transposase enzyme cuts on right end of the Mu DNA. This cut is, however, not made at the exact junction between the Mu DNA and the host DNA, but it is made at approximately 100 bp away in the adjacent host DNA. Now the DNA is packed in phage heads by headful mechanism and since Mu DNA is shorter than the required amount, some 1 Kbp of host DNA at the left end also gets packed in the phage head. Thus, Mu DNA is always flanked by host DNA on both sides and this is required for the conservative transposition that is has to undergo in the next infection cycle.

In the lysogenic phase, Mu DNA undergoes a unique transformation. It has a “G” segment carrying genes for host range specificity and flanked by inverted repeats. In lysogenic phase, Mu expresses a Gin protein that catalyzes inversion of this G segment. This results in change in host specificity. In a large population of Mu lysogens, 50% of cells have G in (+) orientation, while the remaining 50% have it in (–) orientation, resulting in mixed host specificity.

Due to its ability to randomly integrate in host DNA and inactivate the corresponding gene, it had found wide application in classical genetics. It has been manipulated to construct more user-friendly tools like Mud-lac phage, which have been of immense importance in understanding of several genes.

Everyone is familiar with the fact that no two persons can have the same fingerprints, which forms the basis of identification of suspects by fingerprinting in forensic science. In a similar manner, no 2 persons (except monozygotic twins) can have the same sequence of DNA bases in all chromosomes. This has led to the development of DNA fingerprinting (in analogy to the conventional fingerprinting). It has found wide usage in maternity/paternity disputes, identification of victims with damaged bodies, and criminal cases.

Although we all belong to same species (Homo sapiens) i.e. our DNA sequences are sufficiently related to cluster us as a single species, there are enough differences among the sequences to differentiate a person from others. However, it is not practical to sequence entire genome for confirming identity of a person. Hence, we resort to an indirect measure of sequence variation. It relies on variation in the number of short identical tandem repeats present in DNA sequences. Such tandem sequences are known as minisatellites and variation in their number is known as VNTR (variable number of tandem repeats). On restriction digestion, length of DNA fragments containing these minisatellites will depend on the number of repeats.

Thus, if individual A is homozygous for 5-repeat allele and individual B is homozygous for 10-repeat allele, corresponding restriction fragment of A will be smaller than B. This provides a very easy way to identify a person.

Development of molecular biology over recent years has really redefined our identity. Now we can know each other not only by our faces or names, but also by our DNAs!!!