Science: Uncovering and Discovering

Mercury (Hg), the only metallic element that is liquid at normal temperature and pressure, has fascinated people since ancient times. It forms a variety of electrovalent compounds (for example, HgCl2, Hg(NO3)2, HgSO4, Hg2SO2) and covalent compounds (such as phenyl mercuric acetate, alkyl mercuric acetate, fluorescein mercuric acetate) due to the presence of vacant d-orbitals. Because of its unique properties, the use and dispersion of mercuric compounds has increased vastly, resulting in extensive heavy metal pollution. Current uses of Hg are predominantly in the production of chlorine and extraction of gold from ore, a use which is estimated to release 50-70 tonnes Hg per annum to the environment. There are over 3000 industrial uses of Hg including devices such as thermometers, thermostats, electrodes, batteries, fluorescent lights and switches. It is also used in skin creams, dental fillings, paints, preservatives, antiseptics, and some pesticides. (more…)

Carbonic anhydrase (CA) catalyzes reversible hydration of CO2 to HCO3-. The first carbonic anhydrase was purified from erythrocytes in 1933. Zn was shown to play a specific role in its catalytic function. In fact, CA was the first Zn metalloenzyme to be identified. (more…)

Physico-chemical remediation technologies use the physical and/or chemical properties of the contaminants or of the contaminated media to destroy, convert, separate, or contain the contamination. (more…)

Biological remediation/bioremediation is defined as the process whereby wastes are biologically degraded or converted either to an innocuous state or to levels below concentration limits established by regulatory authorities. Bioremediation has been used in various media such as soil, ground water, wastewater, sludge, and gases. (more…)

The goal of remediation is to degrade, detoxify or contain hazardous substances to an extent that is established as safe or acceptable by regulatory agencies. This can be achieved by several approaches such as destruction or alteration of contaminants, extraction or separation of contaminants from environmental media, and immobilization of contaminants. (more…)

Environmental pollution with chemicals, especially the xenobiotics, has been of growing concern. Persistent toxic substances (PTSs) constitute a very important class of chemical pollutants. They take a very long time to break down biotically and/or abiotically in the environment. They can be both natural (for example, mercury, lead) or anthropogenic in origin. While the amount of natural PTSs on earth’s surface does not change, anthropogenic PTSs are continuously piling up and hence, constitute a more serious threat. Some important anthropogenic PTSs are aldrin, DDT, polychlorinated biphenyls (PCB), endosulfan, lindane, benzidine, and polyaromatic hydrocarbons (PAH). (more…)

Until the middle of 19th century, all dyes came from natural sources. The earliest written record of the use of natural dyes was found in China dated 2600BC. A red fabrics found in the tomb of King Tutankhamen in Egypt showed the presence of alizarin, a pigment extracted from madder. Most of these natural dyes were ancient dyes obtained from plants (for example, madder and indigo), lichens (for example, cudbear) and animals (for example, Kermes from the Kermes insect and purple from a mollusk), and even the methods of their application had changed little from ancient times. Hence, the dye-making industry was in the hands of the natural dye extractors, merchants and dyers. (more…)

Carbonic anhydrase (CA) has been of interest recently for its potential application in CO2 sequestration. Several groups have attempted application of CA enzymes or whole cells for this purpose. (more…)

Carbonic anhydrase (CA; EC 4.2.1.1) is a zinc-containing metalloenzyme catalyzing the reversible hydration of CO2. It has been found in all kingdoms of life, including both prokaryotic and eukaryotic subdivisions. Phylogenetically, CA can be divided into three distinct classes (α, β, and γ) that have no sequence homology and are supposed to have evolved independently. CA is important in biological systems because the uncatalyzed interconversion between CO2 and HCO3- is slow around neutral pH. Its high efficiency catalysis is fundamental to many biological processes, such as metabolism, photosynthesis, respiration, pH homeostasis and ion transport. (more…)

As discussed in the previous blog, the major disadvantage of chemical cloud seeding is that it uses harmful chemicals which get deposited in aquatic and terrestrial habitats following rain fall. Here they can have undesirable toxic and ecological effects on biota including plants and human beings. Secondly, abiotic particles such as dust and silver iodide are good at collecting water at temperatures below -8°C, but biological particles seem to be the main active nuclei at higher temperatures. Hence, there is a growing interest in biological particles which can act as cloud condensation nuclei. (more…)

From nowhere, artificial cloud seeding suddenly found itself making the headlines during the recent Olympic event in China. Many came to know about this phenomenon for the first time. However, you will be surprised to know that it is a very old science. So we can definitely spare some time to know more about it. (more…)

A zygote inherits a haploid set of chromosomes from both parents. Hence, its phenotype is supposed to result from co-expression of both alleles received from the sperm and the ovum. However, in mammals, gametes do not contribute equal genetic functions to the embryo due to the phenomenon of genomic imprinting. (more…)

As discussed in last blog, genome sequencing has revolutionized several fields in biology, antibiotic target discovery being one of them. Antibiotic targets can be of 2 types:
1) Proteins those are essential for bacterial growth.
2) Proteins those are required for virulence.
Such proteins can be identified by mutating all the genes from a pathogen, one at a time, and observing for the desired phenotype. STM is still another approach (discussed in previous blog). All these approaches, however, are labour intensive. (more…)

Advent of genome sequencing has revolutionized biology to its base. Development in approaches towards vaccine design is a good example of it. Vaccines have come a long way since their discovery by Jenner, a time when even their mode of action was unknown. Major development in vaccination then came up with the advent of recombinant DNA technology, which allowed selection and production of pure immunogens from pathogenic organisms. (more…)

The basic yeast two-hybrid system has been a widely used approach for general protein-protein interaction studies (as discussed in previous blog). With time researchers have modified it in many ways for certain special proteins that are not amenable to the basic system. Some of the modifications can even detect protein-nucleic acid and protein-ligand interactions. (more…)

The basic yeast two-hybrid system is based on the fact that eukaryotic transcriptional activators consist of a DNA binding domain (BD) and an activation domain (AD). Both these domains can be separately fused to 2 different polypeptides X and Y. if X and Y interact with each other, they can bring together BD and AD. This interaction can be monitored by transcriptional activation of a suitable reporter gene. (more…)

Application of proteomic techniques like 2-D gel electrophoresis (2-D GE) directly to crude cell extracts leads to loss of several protein constituents. This is due to the necessity of generalizing conditions for accommodating majority of proteins, rather than using conditions for a specific class of proteins. The resolution also decreases due to the broad range of separation parameters used in such techniques. These shortcomings have led researchers to use prefractionation techniques for enrichment of a particular group of proteins before separation by 2-D GE. (more…)

With increasing availability of whole gnome sequences, a new challenge has arised, that of understanding the function of each gene product, such as role in disease progression. The traditional methods involving testing mutants individually in animal models cannot handle genome-wide information. This has led to development of high throughput signature tagged mutagenesis (STM) approach. (more…)

One of the major challenges in bacterial expression profiling is the requirement for large amount of total RNA. This has led to development of amplification methods that can decrease the amount of starting material required and at the same time maintain the relative proportion of different mRNAs constant. (more…)

In the previous blog extraction of bacterial mRNA for global gene expression analysis was discussed. The next step in the analysis involves synthesis of cDNA from mRNAs before hybridization to microarray reporters. In eukaryotes this is relatively easy as mRNA molecules are polyadenylated, allowing use of oligo(dT) primers. For prokaryotes random hexamers have to be used. However, this may lead to inclusion of undesirable mRNAs, say from tissue/cells of interacting partner in case of interaction studies. (more…)