Hybridization of 2'-ribose modified mixed-sequence oligonucleotides: thermodynamic and kinetic studies

In this study, we characterize the thermodynamics of hybridization, binding kinetics and conformations of four ribose-modified (2′-fluoro, 2′-O-propyl, 2′-O-methoxyethyl and 2′-O-aminopropyl) decameric mixed-sequence oligonucleotides. Hybridization to the complementary non-modified DNA or RNA decamer was probed by fluorescence and circular-dichroism spectroscopy and compared to the same duplex formed between two non-modified strands. The thermal melting points of DNA–DNA duplexes were increased by 1.8, 2.2, 0.3 and 1.3°C for each propyl, methoxyethyl, aminopropyl and fluoro modification, respectively. In the case of DNA–RNA duplexes, the melting points were increased by 3.1, 4.1 and 1.0°C for each propyl, methoxyethyl and aminopropyl modification, respectively. The high stability of the duplexes formed with propyl-, methoxyethyl- and fluoro-modified oligonucleotides correlated with high preorganization in these single-strands. Despite higher thermodynamic duplex stability, hybridization kinetics to complementary DNA or RNA was slower for propyl- and methoxyethyl-modified oligonucleotides than for the non-modified control. In contrast, the positively-charged aminopropyl-modified oligonucleotide showed rapid binding to the complementary DNA or RNA.     

Validation of the use of microbial consortium as standard seeding material in BOD determination

An attempt is made to validate the use of a microbial consortium in BOD analysis. A uniform dehydrated microbial consortium, `BODSEED', has been used as a seeding material in BOD analysis of synthetic and other industrial effluents. Statistical analysis of the obtained BOD values shows that conventional seeding material such as sewage can be replaced by `BODSEED'.     

Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas putida S11

Here we report the genome sequence of a plant growth-promoting rhizobacterium, Pseudomonas putida S11. The length of the draft genome sequence is approximately 5,970,799 bp, with a G+C content of 62.4%. The genome contains 6,076 protein-coding sequences.     

Investigating the pharmacodynamic durability of GalNAc–siRNA conjugates

One hallmark of trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNAs is the remarkable durability of silencing that can persist for months in preclinical species and humans. Here, we investigated the underlying biology supporting this extended duration of pharmacological activity. We found that siRNA accumulation and stability in acidic intracellular compartments is critical for long-term activity. We show that functional siRNA can be liberated from these compartments and loaded into newly generated Argonaute 2 protein complexes weeks after dosing, enabling continuous RNAi activity over time. Identical siRNAs delivered in lipid nanoparticles or as GalNAc conjugates were dose-adjusted to achieve similar knockdown, but only GalNAc–siRNAs supported an extended duration of activity, illustrating the importance of receptor-mediated siRNA trafficking in the process. Taken together, we provide several lines of evidence that acidic intracellular compartments serve as a long-term depot for GalNAc–siRNA conjugates and are the major contributor to the extended duration of activity observed in vivo.     

Population Structure of a Hybrid Clonal Group of Methicillin-Resistant Staphylococcus aureus,ST239-MRSA-III

The methicillin-resistant Staphylococcus aureus (MRSA) clonal group known as ST239-MRSA-III is notable for its hybrid origin and for causing sustained hospital epidemics worldwide since the late 1970s. We studied the population structure of this MRSA clonal group using a sample of 111 isolates that were collected over 34 years from 29 countries. Genetic variation was assessed using typing methods and novel ascertainment methods, resulting in approximately 15 kb of sequence from 32 loci for all isolates. A single most parsimonious tree, free of homoplasy, partitioned 28 haplotypes into geographically-associated clades, including prominent European, Asian, and South American clades. The rate of evolution was estimated to be approximately 100× faster than standard estimates for bacteria, and dated the most recent common ancestor of these isolates to the mid-20th century. Associations were discovered between the ST239 phylogeny and the ccrB and dru loci of the methicillin resistance genetic element, SCCmec type III, but not with the accessory components of the element that are targeted by multiplex PCR subtyping tools. In summary, the evolutionary history of ST239 can be characterized by rapid clonal diversification that has left strong evidence of geographic and temporal population structure. SCCmec type III has remained linked to the ST239 chromosome during clonal diversification, but it has undergone homoplasious losses of accessory components. These results provide a population genetics framework for the precise identification of emerging ST239 variants, and invite a re-evaluation of the markers used for subtyping SCCmec.     

Adenosine nucleotides in rat bone measured by ion-pair reversed-phase high-performance liquid chromatography: effect of hemorrhagic shock, with and without retransfusion of blood

The measurement of bone adenosine nucleotides (ATP, ADP, AMP) using a simple HPLC procedure is described for rat tibia; the response to hemorrhagic shock with and without blood retransfusion is also described. With respect to the measurement of nucleotides, a number of validation criteria are met. In the anesthetized intact rat (Normal) there was a declining gradient of the three nucleotides, expressed as nmol per g dry matter, from proximal over middle to distal diaphysis, with the mean ratio ATP/ADP (0.21, 0.20, 0.20) and the mean energy charge (0.34, 0.31, 0.30) being low. Irrespective of the anatomic site, hemorrhagic shock of 30-min duration evoked a further decrease versus Normal of ATP, ATP/ADP and energy charge. Blood retransfusion after shock kept nucleotides and other variables in the proximal and distal, but not the middle, diaphysis within normal limits. It was concluded that: (i) bone nucleotides are reliably measurable by HPLC, allowing the described method to be recommended for wider use in bone research and related areas; (ii) in contrast to more parenchymatous tissues, low ATP, ATP/ADP and energy charge may be characteristic for long bones, pointing towards different energy metabolism; and (iii) bone is a “shock organ”, reflecting blood hypoperfusion, O₂ deficiency and decreased ATP in this situation.     

Ligand dynamics controlled reverse spin cross over in bis pyrazolyl pyridine based Fe(II) complex cation with metallodithiolato anions with an example of a ferromagnetic 2:1 cocrystal of mixed Ni(III)/Ni(II) oxidation states

We report here the crystal and molecular structures of three compounds [FeL₂] [Ni(mnt)₂] (1), [FeL₂]₂ [Ni(mnt)₂]₃·2H₂O (2) and [FeL₂] [Cu(mnt)₂]·2CH₃CN (3) where L = 2,6-bis(3,5-dimethylpyrazol-1-ylmethyl)pyridine and mnt = maleonitriledithiolate, and their detailed spectroscopic and magnetic properties using variable temperature Mössbauer, EPR, susceptibility studies, along with room temperature electron spectroscopy for chemical analysis (ESCA) studies. The observed temperature dependant high spin/low spin (HS/LS) ratios of [FeL₂]²⁺ cations in these lattices, exhibiting ‘reverse spin cross-over’ measured unequivocally by Mössbauer, have been interpreted as resulting from differing amount of ‘void space’ in the lattice, a measure of the ease of lattice dynamics originating from ligand L. Differential scanning calorimetric data points this HS/LS transition to order-disorder type of second order phase transitions. While trying to test this lattice dynamics controlled property of [FeL₂]²⁺ cations an unusual behavior of cocrystallization of two planar complex anions of the same type in two different oxidation states, viz. [Ni(mnt)₂]²⁻ and [Ni(mnt)₂]⁻, was observed in [FeL₂]₂ [Ni(mnt₂)]₃, supported by crystallography, ESCA chemical shifts of Ni 2p_3/2 and EPR. The susceptibility data in combination with ESCA chemical shifts of S 2p_3/2 and Ni 2p_3/2 on all the compounds reveal the importance of charge transfer between the two counter ions.     

Biosynthesized silver nanoparticles using Caulerpa taxifolia against A549 lung cancer cell line through cytotoxicity effect/morphological damage

The Caulerpa taxifolia is excellent marine green algae, which produced enormous bioactive compounds with more biological activities. Also, it is an excellent source for synthesis of Ag NPs with increased bioactivity against various infections. In our study, the marine algae marine algae Caulerpa taxifolia mediated Ag NPs was synthesized effectively. The synthesized Ag NPs was characterized well using UV-spectrometer and X-ray powder diffraction (XRD) and confirmed as synthesized particle was Ag NPs. The available structure of the Ag NPs was morphologically identified by scanning electron microscope (SEM), and exact minimum size, polydispersive spherical shape of the entire Ag NPs structure was confirmed by Transmission electron microscope (TEM). Further, the anti-cancer efficiency of biosynthesized Ag NPs against A549 lung cancer cells was found at 40 µg/mL concentration by cytotoxicity experiment. In addition, the phase contrast images of the result were supported the Ag NPs, which damaged the A549 morphologically clearly. Finally, florescence microscopic images were effectively proved the anti-cancerous effect against A549 lung cancer cells due to the condensed morphology of increased death cells. All the confirmed in-vitro results were clearly stated that the Caulerpa taxifolia mediated Ag NPs has superior anti-cancer agent against A549 lung cancer cells.     

Anti-bacterial activity of chitosan loaded plant essential oil against multi drug resistant K. pneumoniae

The development of antibiotic resistant in K. pneumoniae is an emerging thread worldwide due to the poor antimicrobial drugs. To overcome this issue, researchers are focused on plant material and their essential oils to fight against multi drug resistant bacteria. In this context, the current study was concentrated in medicinal plant of guva leaves and their essential oils to combat multi drug resistant bacterial infections. The essential oils were successfully screened and confirmed by HRLC-MS analysis. The anti-bacterial ability of the compounds were loaded into the chitosan nanoparticles and proved by FT-IR analysis. In addition, the chitosan loaded essential oils morphology was compared with chitosan alone in SEM analysis and suggested that the material was loaded successfully. Further, the anti-bacterial ability of the chitosan loaded essential oils were primarily confirmed by agar well diffusion method. At the 100 µg/mL of lowest concentration of chitosan loaded essential oils, the multi-drug resistant K. pneumoniae was inhibited with 96% and confirmed by minimum inhibition concentration experiment. Hence, all the experiments were proved that the essential oils were successfully loaded into the chitosan nanoparticles, and it has more anti-bacterial activity against multi-drug resistant K. pneumoniae.