Keka Sarkar

Effect of iron oxide and gold nanoparticles on bacterial growth leading towards biological application

BackgroundNanoparticle-metal oxide and gold represents a new class of important materials that are increasingly being developed for use in research and health related activities. The biological system being extremely critical requires the fundamental understanding on the influence of inorganic nanoparticles on cellular growth and functions. Our study was aimed to find out the effect of iron oxide (Fe3O4), gold (Au) nanoparticles on cellular growth of Escherichia coli (E. coli) and also try to channelize the obtained result by functionalizing the Au nanoparticle for further biological applications.ResultFe3O4 and Au nanoparticles were prepared and characterized using Transmission electron microscopy (TEM) and Dynamic Light Scattering (DLS). Preliminary growth analysis data suggest that the nanoparticles of iron oxide have an inhibitory effect on E. coli in a concentration dependant manner, whereas the gold nanoparticle directly showed no such activity. However the phase contrast microscopic study clearly demonstrated that the effect of both Fe3O4 and Au nanoparticle extended up to the level of cell division which was evident as the abrupt increase in bacterial cell length. The incorporation of gold nanoparticle by bacterial cell was also observed during microscopic analysis based on which glutathione functionalized gold nanoparticle was prepared and used as a vector for plasmid DNA transport within bacterial cell.ConclusionAltogether the study suggests that there is metal nanoparticle-bacteria interaction at the cellular level that can be utilized for beneficial biological application but significantly it also posses potential to produce ecotoxicity, challenging the ecofriendly nature of nanoparticles.

Ecological significance and phosphorus release potential of phosphate solubilizing bacteria in freshwater ecosystems

Phosphorus (P) is a limiting nutrient in some freshwater ecosystems. Phosphate solubilizing bacteria (PSB) are candidates for enhancing P availability in rhizoplane, but their P release potential in freshwater environments needs further evaluations. This study conducted in floodplain wetlands correlated PSB abundance, decline in sediment pH, and natural mobilization of sediment Ca–P. PSB were abundantly present in floodplain wetland waters, sediments, and in river and ponds, showing low to moderate Ca–P solubilization activity; PSB from Churni River and Bhomra wetland sediments had comparatively higher activity than those from other environments. In laboratory sediment microcosms, PSB were effective in enhancing available P concentration in interstitial water indicating their P release potential. However, P-fractionation of incubated sediments showed only a short-term decline in Ca–P by PSB, suggesting that Ca–P might not be their sole or preferred metabolic target. Despite low to moderate activity in culture medium, high population density and efficacy in P release in sediment suggest significant role of PSB in P cycling in freshwater environments.

Potential application of superparamagnetic nanoparticles for extraction of bacterial genomic DNA from contaminated food and environmental samples

BACKGROUND Isolation of high-molecular-weight DNA is essential for many molecular biology applications. Owing to the presence of polymerase chain reaction (PCR) inhibitors, there is a scarcity of suitable protocols for PCR-ready DNA extraction from food and natural environments. The conventional chemical methods of DNA extraction are time consuming and laborious and the yield is very low. Thus the aim of this research was to develop a simple, rapid, cost-effective method of genomic DNA extraction from food (milk and fruit juice) and environmental (pond water) samples and to detect bacterial contaminants present in those samples. RESULTS This approach is efficient for both Gram-positive and Gram-negative bacteria from all the studied samples. Herein super paramagnetic bare iron oxide nanoparticles were implemented for bacterial genomic DNA isolation. The method was also compared to the conventional phenol-chloroform method in the context of quality, quantity and timing process. This method took only half an hour or less to obtain high-molecular-weight purified DNA from minimum bacterial contamination. Additionally, the method was directly compatible to PCR amplification. CONCLUSION The problem of availability of suitable generalized methods for DNA isolation from various samples including food and environmental has been solved by a nanobiotechnological approach that may prove to be extremely useful in biotechnological applications.

A Simple One Pot Purification of Bacterial Amylase From Fermented Broth Based on Affinity Toward Starch-Functionalized Magnetic Nanoparticle

Surface-functionalized adsorbant particles in combination with magnetic separation techniques have received considerable attention in recent years. Selective manipulation on such magnetic nanoparticles permits separation with high affinity in the presence of other suspended solids. Amylase is used extensively in food and allied industries. Purification of amylase from bacterial sources is a matter of concern because most of the industrial need for amylase is met by microbial sources. Here we report a simple, cost-effective, one-pot purification technique for bacterial amylase directly from fermented broth of Bacillus megaterium utilizing starch-coated superparamagnetic iron oxide nanoparticles (SPION). SPION was prepared by co-precipitation method and then functionalized by starch coating. The synthesized nanoparticles were characterized by transmission electron microscopy (TEM), a superconducting quantum interference device (SQUID, zeta potential, and ultraviolet–visible (UV-vis) and Fourier-transform infrared (FTIR) spectroscopy. The starch-coated nanoparticles efficiently purified amylase from bacterial fermented broth with 93.22% recovery and 12.57-fold purification. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) revealed that the molecular mass of the purified amylase was 67 kD, and native gel showed the retention of amylase activity even after purification. Optimum pH and temperature of the purified amylase were 7 and 50°C, respectively, and it was stable over a range of 20°C to 50°C. Hence, an improved one-pot bacterial amylase purification method was developed using starch-coated SPION.

RETRACTED: Localized surface plasmon resonance-based DNA detection in solution using gold-decorated superparamagnetic Fe3O4 nanocomposite

In the field of nucleic acid-based biosensor technology, DNA-conjugated nanocomposites have attracted much attention due to their unique properties and multimodal applicability. However, quantitative estimation of sequence-specific oligonucleotide in a simpler way is still a challenge. Precise positioning of DNA probes over the surface of the nanocomposite can overcome problems such as steric hindrance of the surface-bound molecules to enable further sensing as well as nonspecific folding of the DNA molecule over the surface of the gold (Au) nanolayer. Considering such objectives, we have developed glutathionated Fe3O4@Au core/shell nanocomposite, fabricated with DNA molecules and applied for sensing complementary oligo spectrophotometrically, using the localized surface plasmon resonance (LSPR) properties of the synthesized nanocomposite. When hybridization experiments were performed with 10 to 100 fM complementary DNA and DNA-conjugated nanocomposite, a strong linear relationship was observed between DNA concentration and surface plasmon resonance (SPR). Discrimination even at the single-base level was also observed when further experiments were performed with complementary DNA, but with a sequential decrease of bases from the single level to the fifth level.

Isolation, Identification and Efficacy of Inorganic Phosphate-Solubilizing Bacteria from Oxbow Lakes of West Bengal, India

Microbial mobilization of sediment calcium-bound P constitutes an important process of P cycling in aquatic environments. The present study was conducted to identify the bacterial community responsible for inorganic phosphate solubilization in tropical oxbow lakes. Fifty eight phosphate-solubilizing bacteria were isolated from bottom soil, water, and fish gut and examined for solubilization of tricalcium phosphate. Results revealed aquatic PSB to be low-to-moderately capable in P solubilization (mean: 33.5 mg P L−1; range: 6.3–68.8 mg P L−1), and bacteria from wetland sediment and water were more effective than those from fish gut. The PSB were identified to belong to diverse genera, viz. Bacillus, Brevibacillus, Enterobacter, Agrobacterium, Pseudomonas, Acinetobacter, Microbacterium, Curtobacterium, Stenotrophomonas and Novosphingobium. The findings help in understanding the microbial role in inorganic P solubilization and identifying important P solubilizers in freshwater environments.

Silver nanoparticles in hydrogels and microemulsions?a comparative account of their properties and bio-activity

Stable silver nanoparticles were prepared in sodium Aerosol OT (AOT) based microemulsions and hydrogels. The various gel and microemulsion compositions used for nanoparticle synthesis were obtained from the phase diagram of the AOT/n-heptane/H2O system. It was found that only in gels can AOT play a dual role of stabilizer as well as reducing agent. In microemulsions, AOT acts as a stabilizer only. In gels, the commonly used NaBH4 reduction results in spherical silver nanoparticles while the AOT based reduction yields highly facetted particles. In microemulsion however, larger particles of undefined shapes are formed in low yield while for the gels, a large number of particles are formed. The synthesized silver nanoparticles show strong antibacterial activity.

Draft Genome Sequence of the Aquatic Phosphorus-Solubilizing and -Mineralizing Bacterium Bacillus sp. Strain CPSM8.

ABSTRACT Bacillus sp. strain CPSM8 is an efficient solubilizer and mineralizer of phosphorus. Here, we present the 4.39-Mb draft genome sequence of the strain, providing insight into the phosphorus-releasing genes related to productivity in aquatic habitats.

SPION-mediated soil DNA extraction and comparative analysis with conventional and commercial kit-based protocol

Direct isolation of soil DNA comes as an emerging technology to understand the microbial diversity of a particular environment circumventing the dependency on culturable methods. Soil DNA isolation is tough due to the presence of various organic components present in soil which interfere in extraction procedure. Here, we report a novel direct soil DNA extraction protocol utilizing bare superparamagnetic iron oxide nanoparticles and its comparison with conventional and commercial kit-based soil DNA extraction methods. The quality, quantity and feasibility of the recovered DNA from all the three methods towards various molecular techniques were checked. Our magnetic nanoparticle-based soil DNA extraction successfully yields pure DNA without any RNA or protein contamination as revealed by the nanodrop spectrophotometer and agarose gel electrophoretic study. Different methods of soil DNA extraction were evaluated on the basis of PCR, denaturing gradient gel electrophoresis and real-time PCR. Soil DNA extracted using conventional method fails to carry out critical molecular biology techniques where as magnetic nanoparticle-based soil DNA extraction gave good results which is comparable to commercial kit. This comparative study suggests that protocol described in this report is novel, less time consuming, cost effective with fewer handling steps and yields high quantity, good quality DNA from soil.

Molecular Techniques for the Study of Microbial Diversity with Special Emphasis on Drug Resistant Microbes

Abstract The advent of antibiotics has revolutionized medical science and has profound applications both in human and veterinary treatment. Diseases like cellulitis, syphilis, and rheumatic fever have become treatable. In addition, antibiotics have ensured a dip in death rates as far as invasive medical procedures like organ transplants are concerned. Unfortunately, bacteria are evolving rapidly to develop resistance against these antibiotics from as early as the 1940s. This has given rise to a scenario where there isn’t a single antibiotic against which there is no recorded resistance. These organisms are different and in a sense diverse from their antibiotic sensitive counterparts. This chapter outlines the principle molecular techniques that are most widely used in studying these resistant organisms in both clinical and environmental backdrops. The chapter will also give the reader an idea about bacterial resistance acquisition as well as the methods by which they are studied in the laboratories worldwide.