Goat testis calmodulin: Purification and physicochemical characterization

Calmodulin has been purified in large quantities from goat (Capra hiscus) testis. The procedure includes heat treatment, hydrophobic interaction chromatography, and gel filtration. Goat testis calmodulin closely resembles other mammalian testis calmodulin studied so far. The protein has an extinction coefficient value (E _1cm ^1% ) of 2.09 at 280 nm, a Stokes radius of 23.2 Å at 0.15 M KCl, and a frictional ratio of 1.38. Ca²⁺, and Tb³⁺ binding studies demonstrate that the protein has four Ca²⁺-binding sites with aK _d of 52.5 µM. Goat testis calmodulin shows close similarity to other calmodulins in the amino acid composition and in demonstrating an altered migration on SDS/PAGE upon Ca²⁺ binding. The protein also exhibits anomalously high values for molecular weight and Stokes radius as determined from the analytical gel chromatography and a change in its elution volume with the change of salt concentration in the eluant. These results have been discussed in view of the recently available knowledge from the crystallographic studies of rat testis calmodulin.     

SMARTp: A SMART design for nonsurgical treatments of chronic periodontitis with spatially referenced and nonrandomly missing skewed outcomes

This paper proposes dynamic treatment regimes (DTRs) as effective individualized treatment strategies for managing chronic periodontitis. The proposed DTRs are studied via SMARTp —a two-stage sequential multiple assignment randomized trial (SMART) design. For this design, we propose a statistical analysis plan and a novel cluster-level sample size calculation method that factors in typical features of periodontal responses such as non-Gaussianity, spatial clustering, and nonrandom missingness. Here, each patient is viewed as a cluster, and a tooth within a patient's mouth is viewed as an individual unit inside the cluster, with the tooth-level covariance structure described by a conditionally autoregressive structure. To accommodate possible skewness and tail behavior, the tooth-level clinical attachment level (CAL) response is assumed to be skew-t, with the nonrandomly missing structure captured via a shared parameter model corresponding to the missingness indicator. The proposed method considers mean comparison for the regimes with or without sharing an initial treatment, where the expected values and corresponding variances or covariance for the sample means of a pair of DTRs are derived by the inverse probability weighting and method of moments. Simulation studies are conducted to investigate the finite-sample performance of the proposed sample size formulas under a variety of outcome-generating scenarios. An R package SMARTp implementing our sample size formula is available at the Comprehensive R Archive Network for free download.     

Secondary structure at the beginning of the poly(A) sequence of mouse beta-actin messenger RNA.

A portion of the beta-actin mRNA of mammalian cells is believed to lack a poly(A) tail, because of its failure to bind to oligo(dT)-cellulose. S1 mapping and Northern blot analysis of this mRNA shows it to contain a poly(A) sequence of about 60 nucleotides. Only about 20-40 nucleotides are available for interaction with oligo(dT). The rest is masked, presumably by base-pairing with a poly(U) stretch present in the 3' non-coding region of the mRNA. A similar configuration occurs in the bulk of the actin mRNA, which carries a poly(A) tail with sizes ranging from approximately 60 to 200 nucleotides.     

Cervical cancer isolate PT3, super-permissive for adeno-associated virus replication, over-expresses DNA polymerase δ, PCNA, RFC and RPA

Background  

Adeno-associated virus (AAV) type 2 is an important virus due to its use as a safe and effective human gene therapy vector and its negative association with certain malignancies. AAV, a dependo-parvovirus, autonomously replicates in stratified squamous epithelium. Such tissue occurs in the nasopharynx and anogenitals, from which AAV has been clinically isolated. Related autonomous parvoviruses also demonstrate cell tropism and preferentially replicate in oncogenically transformed cells. Combining these two attributes of parvovirus tropism, squamous and malignant, we assayed if AAV might replicate in squamous cervical carcinoma cell isolates.     

A Combined Spectroscopic and Theoretical Analysis of Plasmonic Silver Nanoparticle Sensor Towards Detailed Microscopic Understanding of Heavy Metal Detection

Plasmonic nanoparticles are of great importance owing to their highly responsive ‘localized surface plasmon resonance’ (LSPR) behaviour to self-agglomeration/aggregation leading to the development of various nanosensors. Herein, we demonstrated the definite self-assembly of citrate functionalized silver nanoparticles (AgNPs) into a one-dimensional linear chain in presence of charged lead ions (Pb²⁺), one of the most toxic heavy metal pollutants. We have explored detail mechanism using a variety of spectroscopic tools and electron microscopy. The self-aggregation of AgNPs leads to the generation of new LSPR modes due to coupling of nearby existing modes. The conclusion of our experimental findings is duly supported by our developed numerical modelling based on the quasi-static approximation that the generated new LSPR modes are solely due to formation of chain-like aggregation of AgNPs. We have also monitored the LSPR spectra in the presence of other metal ions; however, only Pb²⁺ found to give such unique self-assembled geometry may due to its high interaction affinity with citrate. These findings play a key role for citrate functionalised AgNPs to be used as a low cost highly selective and sensitive lead ion sensor for potential application in industrial lead pollution monitoring. We have further varied several sensor parameters such as AgNPs size, concentration, and the allowed reaction time for it to be practically implemented as an efficient lead sensor meeting the Environmental Protection Agency recommendations.

Graphical abstract

The possible sensing mechanism of citrate-functionalized silver nanoparticles towards Pb2?+?followed by unique chain-like aggregation for potential atmospheric and industrial lead pollution monitoring.

     

DNA barcoding to map the microbial communities: current advances and future directions

During the last two decades, the DNA barcode development towards microbial community has increased dramatically. DNA barcode development is related to error-free and quick species identification which aid in understanding the microbial biodiversity, as well as the diseases related to microbial species. Here, we seek to evaluate the so-called barcoding initiatives for the microbial communities and the emerging trends in this field. In this paper, we describe the development of DNA marker-based DNA barcoding system, comparison between routine species identification and DNA barcode, and microbial biodiversity and DNA barcode for microbial communities. Two major topics, such as the molecular diversity of viruses and barcode for viruses have been discussed at the same time. We demonstrate the current status and the maker of DNA barcode for bacteria, algae, fungi, and protozoa. Furthermore, we argue about the promises, limitations, and present and future challenges of microbial barcode development.     

Unbinding free energy of acetylcholinesterase bound oxime drugs along the gorge pathway from metadynamics‐umbrella sampling investigation

Because of the pivotal role that the nerve enzyme, acetylcholinesterase plays in terminating nerve impulses at cholinergic synapses. Its active site, located deep inside a 20 Å gorge, is a vulnerable target of the lethal organophosphorus compounds. Potent reactivators of the intoxicated enzyme are nucleophiles, such as bispyridinium oxime that binds to the peripheral anionic site and the active site of the enzyme through suitable cation–π interactions. Atomic scale molecular dynamics and free energy calculations in explicit water are used to study unbinding pathways of two oxime drugs (Ortho‐7 and Obidoxime) from the gorge of the enzyme. The role of enzyme‐drug cation–π interactions are explored with the metadynamics simulation. The metadynamics discovered potential of mean force (PMF) of the unbinding events is refined by the umbrella sampling (US) corrections. The bidimensional free energy landscape of the metadynamics runs are further subjected to finite temperature string analysis to obtain the transition tube connecting the minima and bottlenecks of the unbinding pathway. The PMF is also obtained from US simulations using the biasing potential constructed from the transition tube and are found to be consistent with the metadynamics‐US corrected results. Although experimental structural data clearly shows analogous coordination of the two drugs inside the gorge in the bound state, the PMF of the drug trafficking along the gorge pathway point, within an equilibrium free energy context, to a multistep process that differs from one another. Routes, milestones and subtlety toward the unbinding pathway of the two oximes at finite temperature are identified. Proteins 2014; 82:1799–1818. © 2014 Wiley Periodicals, Inc.     

Synthesis of HPMC stabilized nickel nanoparticles and investigation of their magnetic and catalytic properties

Nickel nanoparticles synthesized from NiCl₂·6H₂O by hydrazine hydrate in mixed solvent of ethanol and water in the presence of hydroxypropylmethylcellulose (HPMC) as protective and stabilizing agents. The morphology and sizes of synthesized Ni nanoparticles were studied by field-emission-scanning-electron microscopy (FESEM). Structural properties of nanoparticles were examined by X-ray diffraction (XRD). The polymer stabilized Ni nanoparticles were characterized by Fourier-transform infrared (FTIR) spectroscopy. The magnetic measurement showed that the resultant Ni nanoparticles were ferromagnetic. Also, the saturation magnetization (M_S), remanent magnetization (M_R) and coercivity (M_R) were observed to increase with decreasing temperature. The results of magnetic characterization showed that the magnetic properties of the HPMC stabilized Ni nanoparticles are quite different from those of the bared Ni nanoparticles. All the observed magnetic properties essentially reflected the very typical nanoparticle type nature. Consequently, the resulting Ni nanoparticles were found to be highly active and recyclable catalyst for Suzuki coupling reactions.