Development of single-stranded DNA aptamers for specific Bisphenol a detection

The development of reagents with high affinity and specificity to small molecules is crucial for the high-throughput detection of chemical compounds, such as toxicants or pollutants. Aptamers are short and single-stranded (ss) oligonucleotides able to recognize target molecules with high affinity. Here, we report the selection of ssDNA aptamers that bind to Bisphenol A (BPA), an environmental hormone. Using SELEX process, we isolated high affinity aptamers to BPA from a 10(15) random library of 60 mer ssDNAs. The selected aptamers bound specifically to BPA, but not to structurally similar molecules, such as Bisphenol B with one methyl group difference, or 4,4'-Bisphenol with 2 methyl groups difference. Using these aptamers, we developed an aptamer-based sol-gel biochip and detected BPA dissolved in water. This novel BPA aptamer-based detection can be further applied to the universal and high-specificity detection of small molecules.     

Brain signal predictions from multi-scale networks using a linearized framework

Simulations of neural activity at different levels of detail are ubiquitous in modern neurosciences, aiding the interpretation of experimental data and underlying neural mechanisms at the level of cells and circuits. Extracellular measurements of brain signals reflecting transmembrane currents throughout the neural tissue remain commonplace. The lower frequencies (≲ 300Hz) of measured signals generally stem from synaptic activity driven by recurrent interactions among neural populations and computational models should also incorporate accurate predictions of such signals. Due to limited computational resources, large-scale neuronal network models (≳ 10⁶ neurons or so) often require reducing the level of biophysical detail and account mainly for times of action potentials (‘spikes’) or spike rates. Corresponding extracellular signal predictions have thus poorly accounted for their biophysical origin.Here we propose a computational framework for predicting spatiotemporal filter kernels for such extracellular signals stemming from synaptic activity, accounting for the biophysics of neurons, populations, and recurrent connections. Signals are obtained by convolving population spike rates by appropriate kernels for each connection pathway and summing the contributions. Our main results are that kernels derived via linearized synapse and membrane dynamics, distributions of cells, conduction delay, and volume conductor model allow for accurately capturing the spatiotemporal dynamics of ground truth extracellular signals from conductance-based multicompartment neuron networks. One particular observation is that changes in the effective membrane time constants caused by persistent synapse activation must be accounted for.The work also constitutes a major advance in computational efficiency of accurate, biophysics-based signal predictions from large-scale spike and rate-based neuron network models drastically reducing signal prediction times compared to biophysically detailed network models. This work also provides insight into how experimentally recorded low-frequency extracellular signals of neuronal activity may be approximately linearly dependent on spiking activity. A new software tool LFPykernels serves as a reference implementation of the framework.     

Lyotropic Liquid Crystalline Nanoparticles of Amphotericin B: Implication of Phytantriol and Glyceryl Monooleate on Bioavailability Enhancement

Implication of different dietary specific lipids such as phytantriol (PT) and glyceryl monooleate (GMO) on enhancing the oral bioavailability of amphotericin B (AmB) was examined. Liquid crystalline nanoparticles (LCNPs) were prepared using hydrotrope method, followed by in vitro characterization, Caco-2 cell monolayer uptake, and in vivo pharmacokinetic and toxicity evaluation. Optimized AmB-LCNPs displayed small particle size (<?210 nm) with a narrow distribution (~?0.2), sustained drug release and high gastrointestinal stability, and reduced hemolytic toxicity. PLCNPs presented slower release, i.e., ~?80% as compared to ~?90% release in case of GLCNPs after 120 h. Significantly higher uptake in Caco-2 monolayer substantiated the role of LCNPs in increasing the intestinal permeability followed by increased drug titer in plasma. Pharmacokinetic studies demonstrated potential of PT in enhancing the bioavailability (approximately sixfold) w.r.t. of its native counterpart with reduced nephrotoxicity as presented by reduced nephrotoxicity biomarkers and histology studies. These studies established usefulness of PLCNPs over GLCNPs and plain drug. It can be concluded that acid-resistant lipid, PT, can be utilized efficiently as an alternate lipid for the preparation of LCNPs to enhance bioavailability and to reduce nephrotoxicity of the drug as compared to other frequently used lipid, i.e., GMO.     

Genetic transformation technology: Status and problems

Summary Transfer of genes from heterologous species provides the means of selectively introducing new traits into crop plants and expanding the gene pool beyond what has been available to traditional breeding systems. With the recent advances in genetic engineering of plants, it is now feasible to introduce into crop plants, genes that have previously been inaccessible to the conventional plant breeder, or which did not exist in the crop of interest. This holds a tremendous potential for the genetic enhancement of important food crops. However, the availability of efficient transformation methods to introduce foreign DNA can be a substantial barrier to the application of recombinant DNA methods in some crop plants. Despite significant advances over the past decades, development of efficient transformation methods can take many years of painstaking research. The major components for the development of transgenic plants include the development of reliable tissue culture regeneration systems, preparation of gene constructs and efficient transformation techniques for the introduction of genes into the crop plants, recovery and multiplication of transgenic plants, molecular and genetic characterization of transgenic plants for stable and efficient gene expression, transfer of genes to elite cultivars by conventional breeding methods if required, and the evaluation of transgenic plants for their effectiveness in alleviating the biotic and abiotic stresses without being an environmental biohazard. Amongst these, protocols for the introduction of genes, including the efficient regeneration of shoots in tissue cultures, and transformation methods can be major bottlenecks to the application of genetic transformation technology. Some of the key constraints in transformation procedures and possible solutions for safe development and deployment of transgenic plants for crop improvement are discussed.     

Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid

Mycobacterium tuberculosis cell envelope is a treasure house of biologically active lipids of fascinating molecular architecture. Although genetic studies have alluded to an array of genes in biosynthesis of complex lipids, their mechanistic, structural, and biochemical principles have not been investigated. Here, we have dissected the molecular logic underlying the biosynthesis of a virulence lipid phthiocerol dimycocerosate (PDIM). Cell-free reconstitution studies demonstrate that polyketide synthases, which are usually involved in the biosynthesis of secondary metabolites, are responsible for generating complex lipids in mycobacteria. We show that PapA5 protein directly transfers the protein bound mycocerosic acid analogs on phthiocerol to catalyze the final esterification step. Based on precise identification of biological functions of proteins from Pps cluster, we have rationally produced a nonmethylated variant of mycocerosate esters. Apart from elucidating mechanisms that generate chemical heterogeneity with PDIMs, this study also presents an attractive approach to explore host-pathogen interactions by altering mycobacterial surface coat.     

Molecular heterogeneity in Yersinia enterocolitica and 'Y. enterocolitica-like' species--Implications for epidemiology, typing and taxonomy

Yersinia enterocolitica is an extremely heterogeneous species. Serotyping and biotyping have been used extensively, in the past, to study its heterogeneity and epidemiology. Application of methods like ribotyping, pulsed-field gel electrophoresis and a host of other genomic techniques have further revealed molecular heterogeneity in this species. Furthermore, these methods may be used effectively to supplement serotyping and biotyping schema for studying epidemiology of Y. enterocolitica. This is evident from the ability of some of these methods to subtype strains belonging to serogroups O:3, O:9 and O:8 - which are most commonly encountered in human Yersiniosis. Multilocus enzyme electrophoresis and nucleotide sequencing have reiterated the taxonomic relationships of this organism. However there is paucity of information about the molecular heterogeneity of 'Y. enterocolitica-like' species, which need to be addressed in the future. Also, newer techniques such as amplified fragment length polymorphism, VNTR-based typing and multilocus sequence typing should be applied to further understand epidemiology, population structure and evolutionary genetics of Y. enterocolitica and 'Y. enterocolitica-like' species.     

Developmental Studies in Porphyra Vietnamensis: a High-Temperature Resistant Species from the Indian Coast

Porphyra vietnamensis Tanaka & Pham-Hoang Ho (Bangiales, Rhodophyta) is a tropical seaweed collected from the west coast of India. Thalli of the blade phase are found growing only during the rainy season between July and September. They grow on rocky intertidal or subtidal substrata or as epiphytes on other seaweeds such as Enteromorpha flexuosa and Chaetomorpha media. The gametophytic thallus is monostromatic and covered with spines at the base. The species is monoecious. Male gametangia are found in patches that are distributed in the upper part of the thallus. Archeospores are found at the thallus margins and give rise to the blade phase after one week of germination even at 30 ^∘ C. Zygotospores germinated at 25 ^∘ C into conchocelis within three days from the date of their inoculation. Conchospores were released at 30 ^∘ C. The young blades grew at 32 ^∘ C in the laboratory.     

Determination of ultrasound phase velocity in trabecular bone using time dependent phase tracking technique

Ultrasound velocity is one of the key acoustic parameters for noninvasive diagnosis of osteoporosis. Ultrasound phase velocity can be uniquely measured from the phase of the ultrasound signal at a specified frequency. Many previous studies used fast Fourier transform (FFT) to determine the phase velocity, which may cause errors due to the limitations of FFT. The new phase tracking technique applied an adaptive tracking algorithm to detect the time dependent phase and amplitude of the ultrasound signal at a specified frequency. This overcame the disadvantages of FFT to ensure the accuracy of the ultrasound phase velocity. As a result, the new method exhibited high accuracy in the measurement of ultrasound phase velocity of two phantom blocks with the error less than 0.4%. 41 cubic trabecular samples from sheep femoral condyles were used in the study. The phase velocity of the samples using the new method had significantly high correlation to the bulk stiffness of the samples (r = 0.84) compared to the phase velocity measured using fast Fourier transform FFT (r = 0.14). In conclusion, the new method provided an accurate measurement of the ultrasound phase velocity in bone.