SIZ1-mediated SUMOylation during phosphate homeostasis in plants: Looking beyond the tip of the iceberg.

Availability of phosphate (Pi) is often limited in rhizospheres in different agroclimatic zones and adversely affects growth and development of plants. To circumvent this impasse, there is an urgent need and global consensus to develop Pi use efficient crops. To achieve this goal, it is essential to identify the molecular entities that exert regulatory influences on the sensing and signaling cascade governing Pi homeostasis. SIZ1 encodes a small ubiquitin-like modifier (SUMO E3) ligase, and plays a pivotal role in the post-translational SUMOylation of proteins. In this review, we discuss the reverse genetics approach conventionally used for providing circumstantial evidence towards the regulatory influences of SIZ1 on several morphophysiological and molecular traits that govern Pi homeostasis in taxonomically diverse Arabidopsis thaliana (Arabidopsis) and Oryza sativa (rice) model species. However, the efforts have been rather modest in identifying SUMO protein targets that play key roles in the maintenance of Pi homeostasis in these model plants contrary to the plethora of them now known in lower organisms and animals. Therefore, to predict the SIZ1-mediated SUMOylome involved in Pi homeostasis, the state-of-the-art high-throughput technologies often used for animals thus provide an attractive paradigm towards achieving the long-term goal of developing Pi use efficient crops.

Structural comparison, docking and substrate interaction study of modeled endo-1, 4-beta xylanase enzyme of Bacillus brevis.

Xylanase belongs to, Glycoside hydrolase family, playing a major role in xylan degradation. Bacterial and most of the fungal Xylanase, are categorized as true Xylanase belong to GH 10 and GH 11 families. Xylanase is an industrially important enzyme. Most of the research has progressed in the field of isolation, purification and characterization of Xylanases, without giving much emphasis on the interaction of the substrate and the enzyme. To study the structure and ligand interaction, xylanase form Bacillus brevis was modeled, docking studies were performed and ligand interactions were studied. The comparative study gave detailed insight into the conserved amino acids which are involved in ligand interaction and complex stability. The amino acids like Tyrosine, Glutamic acid, Aspartic acid, Aspartate, Arginine play a major role in placing the substrate accurately in the binding cavity; also interact with the ligand for the specific activity. This study clarifies that amino acid Tyrosine at position 69, 166 and 174, is conserved among the different microbial Xylanase, specifying its importance in ligand binding and enzyme activity.

Computational approaches for predicting mutant protein stability.

Mutations in the protein affect not only the structure of protein, but also its function and stability. Prediction of mutant protein stability with accuracy is desired for uncovering the molecular aspects of diseases and design of novel proteins. Many advanced computational approaches have been developed over the years, to predict the stability and function of a mutated protein. These approaches based on structure, sequence features and combined features (both structure and sequence features) provide reasonably accurate estimation of the impact of amino acid substitution on stability and function of protein. Recently, consensus tools have been developed by incorporating many tools together, which provide single window results for comparison purpose. In this review, a useful guide for the selection of tools that can be employed in predicting mutated proteins' stability and disease causing capability is provided.

Detection of DNA Sequence with Enhanced Sensitivity and Higher FRET Efficiency Using a Light-Emitting Polymer, Peptide Nucleic Acid Probe and Anionic Surfactant System.

An improved strategy has been developed for detection of DNA sequence by using water-soluble cationic conjugated polymer (PFP)/single-strand (ss) DNA and peptide nucleic acid labeled with fluorescent dye (PNAC*), where an anionic surfactant (sodium dodecyl sulphate, SDS) system has been used to improve the sensitivity of the sensor. The method of detection is simple to use, fast and cost-effective. This method uses the phenomenon of Forester Resonance Energy Transfer (FRET). The detection sensitivity of the biosensor has been improved by about ten times by using the anionic surfactant. It is observed that the effect of surfactant is to increase the photoluminescence (PL) intensity of the PNAC* when the sequence of the DNA is complementary (to that of PNA probe). On the other hand when the two sequences are non-complementary, the PL intensity of the PNAC* is further reduced as compared to the case when surfactant was absent.

Detection of known mutations for medical diagnostics by FRET spectroscopy.

A rapid, simple and low-cost method for the detection of known mutations in DNA oligonucleotide in a biothreat agent, Bacillus anthracis, has been reported. The technique is based on fluorescence resonance energy transfer (FRET), that utilizes a cationic conjugated polymer and a PNA probe labeled with Fluorescein dye (PNAC*). When the PNA probe is hybridized with a complementary target ssDNA and its mutated sequences separately, the energy transfer from polymer to PNAC*/ssDNA complex decreases with increasing number of mutations. It means that the efficiency of FRET or the degree of hybridization depends on the extent of mutations in the DNA sequence. The method is sensitive enough to detect upto 4 bases mismatch. We have, thus, explored a possible application of fluorescence-based technology for medical diagnostics.

2D polarization imaging of turbid media.

Cancer normally tends to result in the decrease of tissue elasticity; i.e., the cancerous region is more rigid than the normal surrounding areas. This would appear as differences in the distribution of internal birefringence that could be used to improve image contrast between the cancerous and normal tissue structures. Different filtering techniques are used to enhance the image to help us identify, locate, and diagnose an "object," such as a tumor inside a biological tissue.

Triple-FRET Technique for Energy Transfer Between Conjugated Polymer and TAMRA Dye with Possible Applications in Medical Diagnostics.

Three-component Förster resonance energy transfer (FRET) has been used to obtain efficient FRET between the cationic conjugated polymer (CCP) as donor and 5-carboxy tetramethylrhodamine (TAMRA) dye as acceptor, by using an intermediate donor, fluorescein. In spite of the fact that there is enough overlap between the emission spectra of CCP and absorption spectra of TAMRA, the efficiency of FRET between CCP and TAMRA is poor. The reason for this is that while the Förster critical distance is not very sensitive to the overlap, the FRET efficiency is extremely sensitive to it. However, it is observed that the FRET efficiency between CCP and TAMRA improves considerably when fluorescein is introduced in the solution. The triple FRET so obtained can be used for deoxyribonucleic acid sequence detection in medical diagnostics because the fluorescence emission from TAMRA is pH-insensitive.