Proficient Detection of Multi-Drug-Resistant Mycobacterium tuberculosis by Padlock Probes and Lateral Flow Nucleic Acid Biosensors.

Tuberculosis is a major communicable disease. Its causative agent, Mycobacterium tuberculosis, becomes resistant to antibiotics by acquisition of point mutations in the chromosome. Multi-drug-resistant tuberculosis (MDR-TB) is an increasing public health threat, and prompt detection of such strains is of critical importance. As rolling circle amplification of padlock probes can be used to robustly distinguish single-nucleotide variants, we combined this technique with a sensitive lateral flow nucleic acid biosensor to develop a rapid molecular diagnostic test for MDR-TB. A proof-of-concept test was established for detection of the most common mutations [rpoB 531 (TCG/TTG) and katG 315 (AGC/ACC)] causing MDR-TB and verification of loss of the respective wild type. The molecular diagnostic test produces visual signals corresponding to the respective genotypes on lateral flow strips in approximately 75 min. By detecting only two mutations, the test can detect about 60% of all MDR-TB cases. The padlock probe-lateral flow (PLP-LF) test is the first of its kind and can ideally be performed at resource-limited clinical laboratories. Rapid information about the drug-susceptibility pattern can assist clinicians to choose suitable treatment regimens and take appropriate infection control actions rather than prescribing empirical treatment, thereby helping to control the spread of MDR-TB in the community.

Bioanalytical advantages of a novel recombinant apyrase enzyme in ATP-based bioluminescence methods.

Ultrasensitive measurements of intracellular ATP (intATP) based on the firefly luciferase reactions are frequently used to enumerate bacterial or mammalian cells. During clinical applications, extracellular ATP (extATP) should be depleted in biological samples since it interferes with intATP and affects the quantification of bacteria. The extATP can be eliminated by ATP-degrading enzymes but complete hydrolysis of extATP remains a challenge for today's commercial enzymes. The catalytic efficiency of ATP-degrading enzymes depends on enzyme characteristics, sample composition and the ability to deplete diphosphates, triphosphates and their complexes generated during the reaction. This phenomenon restricts the usage of bioluminescence-based ATP methods in clinical diagnostics. In light of this, we have developed a recombinant Shigella flexneri apyrase (RSFA) enzyme and analysed its ATP depletion potential with five commercial biochemical sources including potato apyrase, acid phosphatase, alkaline phosphatase, hexokinase and glycerol kinase. The RSFA revealed superior activity by completely eliminating the extracellular ATP and ATP-complexes, even in biological samples like urine and serum. Therefore, our results can potentially unwrap the chemical and bio-analytical applications of ATP-based bioluminescence tests to develop highly sensitive point-of-care diagnostics.

Dimerization of a flocculent protein from Moringa oleifera: experimental evidence and in silico interpretation.

Many proteins exist in dimeric and other oligomeric forms to gain stability and functional advantages. In this study, the dimerization property of a coagulant protein (MO2.1) from Moringa oleifera seeds was addressed through laboratory experiments, protein-protein docking studies and binding free energy calculations. The structure of MO2.1 was predicted by homology modelling, while binding free energy and residues-distance profile analyses provided insight into the energetics and structural factors for dimer formation. Since the coagulation activities of the monomeric and dimeric forms of MO2.1 were comparable, it was concluded that oligomerization does not affect the biological activity of the protein.

In silico modeling and experimental evidence of coagulant protein interaction with precursors for nanoparticle functionalization.

The design of novel protein-nanoparticle hybrid systems has applications in many fields of science ranging from biomedicine, catalysis, water treatment, etc. The main barrier in devising such tool is lack of adequate information or poor understanding of protein-ligand chemistry. Here, we establish a new strategy based on computational modeling for protein and precursor linkers that can decorate the nanoparticles. Moringa oleifera (MO2.1) seed protein that has coagulation and antimicrobial properties was used. Superparamagnetic nanoparticles (SPION) with precursor ligands were used for the protein-ligand interaction studies. The molecular docking studies reveal that there are two binding sites, one is located at the core binding site; tetraethoxysilane (TEOS) or 3-aminopropyl trimethoxysilane (APTES) binds to this site while the other one is located at the side chain residues where trisodium citrate (TSC) or Si60 binds to this site. The protein-ligand distance profile analysis explains the differences in functional activity of the decorated SPION. Experimentally, TSC-coated nanoparticles showed higher coagulation activity as compared to TEOS- and APTES-coated SPION. To our knowledge, this is the first report on in vitro experimental data, which endorses the computational modeling studies as a powerful tool to design novel precursors for functionalization of nanomaterials; and develop interface hybrid systems for various applications.

Small RNA fragments in complex culture media cause alterations in protein profiles of three species of bacteria.

Efforts to delineate the basis for variations in protein profiles of different membrane fractions from various bacterial pathogens led to the finding that even the same medium [e.g., Luria Bertani (LB) broth] purchased from different commercial sources generates remarkably dissimilar protein profiles despite similar growth characteristics. Given the pervasive roles small RNAs play in regulating gene expression, we inquired if these source-specific differences due to media arise from disparities in the presence of small RNAs. Indeed, LB media components from two different commercial suppliers contained varying, yet significant, amounts of 10-80 bp small RNAs. Removal of small RNA from LB using RNaseA during media preparation resulted in significant changes in bacterial protein expression profiles. Our studies underscore the fact that seemingly identical growth media can lead to dramatic alterations in protein expression patterns, highlighting the importance of utilizing media free of small RNA during bacteriological studies. Finally, these results raise the intriguing possibility that similar pools of small RNAs in the environment can influence bacterial adaptation.

Evaluation of solid (disc diffusion)- and liquid (turbidity)-phase antibiogram methods for clinical isolates of diarrheagenic E. coli and correlation with efflux.

Multiple drug resistance (MDR) in bacteria causes higher mortality and morbidity, complicates treatment and increases health-care outlay. With no new-generation antibiotics in sight, its rapid spread through the environment poses grave danger. Therefore, rapid detection to identify effective antibiotics and to prevent their indiscriminate use is imperative. However, the widely used clinical method for antibiogram, the Kirby-Bauer disc-diffusion method (DDM), requires 2-3 days, has inherent shortcomings of solid-phase assays and is not suitable for high-throughput operations. In our research on MDR associated with childhood diarrhea, we determined the antibiogram of 73 clinical diarrheagenic Escherichia coli strains using both the DDM and the more reliable liquid turbidity method (LTM) performed in 96-microwell plates. The results were further correlated with a dye-exclusion efflux assay using fluorescein diacetate. Although LTM is apparently superior in saving critical time, suitability to high-throughput operations and reliability, we found that the serious shortcomings of DDM could be effectively countered by just doubling the dosage of antibiotics currently used in discs or by using two discs in place of one. With 48 of the 49 MDR strains being positive for efflux and the 12 strains 'susceptible' to all the antibiotics being negative, the efflux assay could be useful as an integral component of the antibiogram test or for additional confirmation. The presence of 65% of MDR strains among diarrheagenic E. coli is a matter of serious concern, although most of them could be treated with either Gentamycin or Amikacin, as is the practice by experience.

Apyrase-based colorimetric test for detection of Shigella and enteroinvasive Escherichia coli in stool.

For lack of simple inexpensive early detection methods for Shigella spp. and enteroinvasive Escherichia coli (EIEC), bacillary dysentery remains a major cause of childhood mortality and morbidity in India and other developing countries. Rapid stool testing for apyrase, a specific periplasmic enzyme essential for the pathogen's intracellular spread, may provide a solution. We have developed a whole-cell colorimetric pyrophosphate hydrolysis assay based on cheap, stable, and locally available reagents. An innovative filtration-cum-inoculation step eliminates interfering stool solids and ensures sufficient bacterial growth and apyrase expression in 6 to 7 h at 37 degrees C. In a limited double-blind study of 57 clinical isolates of common enterobacteria, the test showed 100% sensitivity and 80% specificity for Shigella spp. and EIEC. Requiring only widely available equipment and inexpensive consumables, this affordable test is readily adaptable for determining antibiograms and for surveillance of food and water samples for the presence of Shigella and EIEC.