Dominant Driving Forces in Human Telomere Quadruplex Binding-Induced Structural Alterations

Recently various pathways of human telomere (ht) DNA folding into G-quadruplexes and of ligand binding to these structures have been proposed. However, the key issue as to the nature of forces driving the folding and recognition processes remains unanswered. In this study, structural changes of 22-mer ht-DNA fragment (Tel22), induced by binding of ions (K⁺, Na⁺) and specific bisquinolinium ligands, were monitored by calorimetric and spectroscopic methods and by gel electrophoresis. Using the global model analysis of a wide variety of experimental data, we were able to characterize the thermodynamic forces that govern the formation of stable Tel22 G-quadruplexes, folding intermediates, and ligand-quadruplex complexes, and then predict Tel22 behavior in aqueous solutions as a function of temperature, salt concentration, and ligand concentration. On the basis of the above, we believe that our work sets the framework for better understanding the heterogeneity of ht-DNA folding and binding pathways, and its structural polymorphism.     

Heterogeneity of Equilibrium Molten Globule State of Cytochrome c Induced by Weak Salt Denaturants under Physiological Condition

While many proteins are recognized to undergo folding via intermediate(s), the heterogeneity of equilibrium folding intermediate(s) along the folding pathway is less understood. In our present study, FTIR spectroscopy, far- and near-UV circular dichroism (CD), ANS and tryptophan fluorescence, near IR absorbance spectroscopy and dynamic light scattering (DLS) were used to study the structural and thermodynamic characteristics of the native (N), denatured (D) and intermediate state (X) of goat cytochorme c (cyt-c) induced by weak salt denaturants (LiBr, LiCl and LiClO₄) at pH 6.0 and 25°C. The LiBr-induced denaturation of cyt-c measured by Soret absorption (Δε ₄₀₀) and CD ([θ]₄₀₉), is a three-step process, N ↔ X ↔ D. It is observed that the X state obtained along the denaturation pathway of cyt-c possesses common structural and thermodynamic characteristics of the molten globule (MG) state. The MG state of cyt-c induced by LiBr is compared for its structural and thermodynamic parameters with those found in other solvent conditions such as LiCl, LiClO₄ and acidic pH. Our observations suggest: (1) that the LiBr-induced MG state of cyt-c retains the native Met80-Fe(III) axial bond and Trp59-propionate interactions; (2) that LiBr-induced MG state of cyt-c is more compact retaining the hydrophobic interactions in comparison to the MG states induced by LiCl, LiClO₄ and 0.5 M NaCl at pH 2.0; and (3) that there exists heterogeneity of equilibrium intermediates along the unfolding pathway of cyt-c as highly ordered (X1), classical (X2) and disordered (X3), i.e., D ↔ X3 ↔ X2 ↔ X1 ↔ N.     

Brucellosis and Coxiella burnetii Infection in Householders and Their Animals in Secure Villages in Herat Province,Afghanistan: A Cross-Sectional Study

Background

Brucellosis and coxiellosis are known to be endemic in ruminant populations throughout Afghanistan, but information about their prevalence and factors that affect prevalence in householders and livestock under diverse husbandry systems and pastoral settings is sparse.

Methods/Principal Findings

We conducted a cross-sectional survey to investigate the seroprevalence of brucellosis and Coxiella burnetii in humans and livestock in six secure districts in Herat from 26^th December 2012–17^th January 2013. A total of 204 households with livestock were surveyed in six Kuchi and five sedentary type villages. Blood samples from 1,017 humans, 1,143 sheep, 876 goats and 344 cattle were tested for brucellosis and Q fever. About one in six households (15.7%) had at least one Brucella seropositive person, about one in eight households (12.3%) had at least one Brucella seropositive animal and about one in four (24.5%) had either seropositive animals or humans. Ninety-seven percent of households had at least one C. burnetii seropositive person and 98.5% of households had one or more C. burnetii seropositive animals. Forty- seven householders had serological evidence of exposure to both C. burnetii and Brucella and eight animals were serologically positive for both diseases. Drinking unpasteurised milk (OR 1.6), treating animals for ticks (OR 1.4), milking sheep (OR 1.4), male gender (OR 1.4) and seropositivity to Brucella (OR 4.3) were identified as risk factors for seropositivity to C. burnetii in householders. Household factors associated with households having either Brucella seropositive animals or humans were Kuchi households (OR 2.5), having ≤4 rooms in the house (OR 2.9) and not owning land (OR 2.9).

Conclusions

The results from this study provide baseline information for the planning and monitoring of future interventions against these diseases. The implementation of this study greatly improved collaboration, coordination and capability of veterinary and public health professionals from government, NGOs and donor funded projects.     

Functional Connectivity Alterations in Epilepsy from Resting-State Functional MRI

The study of functional brain connectivity alterations induced by neurological disorders and their analysis from resting state functional Magnetic Resonance Imaging (rfMRI) is generally considered to be a challenging task. The main challenge lies in determining and interpreting the large-scale connectivity of brain regions when studying neurological disorders such as epilepsy. We tackle this challenging task by studying the cortical region connectivity using a novel approach for clustering the rfMRI time series signals and by identifying discriminant functional connections using a novel difference statistic measure. The proposed approach is then used in conjunction with the difference statistic to conduct automatic classification experiments for epileptic and healthy subjects using the rfMRI data. Our results show that the proposed difference statistic measure has the potential to extract promising discriminant neuroimaging markers. The extracted neuroimaging markers yield 93.08% classification accuracy on unseen data as compared to 80.20% accuracy on the same dataset by a recent state-of-the-art algorithm. The results demonstrate that for epilepsy the proposed approach confirms known functional connectivity alterations between cortical regions, reveals some new connectivity alterations, suggests potential neuroimaging markers, and predicts epilepsy with high accuracy from rfMRI scans.     

Geochemical Speciation and Risk Assessment of Heavy Metals in Sediments of a River in Bangladesh

The surface sediment of a downstream river (Paira) connected to the marine ecosystems of the Bay of Bengal was assessed by sequential extraction technique. The objectives of this study were to evaluate the mobility and dynamics of heavy metals and their probable ecological risks. The results revealed high environmental risk of Cd due to higher availability in the exchangeable fraction (21%) and a considerable portion in the carbonate bound fraction due to the special affinity towards carbonate and co-precipitation with its minerals. Toxic metals like Cr, Ni, and Cd are of concern, and can occasionally be associated with adverse biological effects. The risk assessment code (RAC) suggests that the highest mobility of Cd poses a higher environmental risk and threat to the aquatic biota, as well.     

Titanium Dioxide Nanoparticle-Based Interdigitated Electrodes: A Novel Current to Voltage DNA Biosensor Recognizes E. coli O157:H7

Nanoparticle-mediated bio-sensing promoted the development of novel sensors in the front of medical diagnosis. In the present study, we have generated and examined the potential of titanium dioxide (TiO₂) crystalline nanoparticles with aluminium interdigitated electrode biosensor to specifically detect single-stranded E.coli O157:H7 DNA. The performance of this novel DNA biosensor was measured the electrical current response using a picoammeter. The sensor surface was chemically functionalized with (3-aminopropyl) triethoxysilane (APTES) to provide contact between the organic and inorganic surfaces of a single-stranded DNA probe and TiO₂ nanoparticles while maintaining the sensing system’s physical characteristics. The complement of the target DNA of E. coli O157:H7 to the carboxylate-probe DNA could be translated into electrical signals and confirmed by the increased conductivity in the current-to-voltage curves. The specificity experiments indicate that the biosensor can discriminate between the complementary sequences from the base-mismatched and the non-complementary sequences. After duplex formation, the complementary target sequence can be quantified over a wide range with a detection limit of 1.0 x 10^-13M. With target DNA from the lysed E. coli O157:H7, we could attain similar sensitivity. Stability of DNA immobilized surface was calculated with the relative standard deviation (4.6%), displayed the retaining with 99% of its original response current until 6 months. This high-performance interdigitated DNA biosensor with high sensitivity, stability and non-fouling on a novel sensing platform is suitable for a wide range of biomolecular interactive analyses.     

Multigenic and morphometric differentiation of ground squirrels (Spermophilus, Scuiridae, Rodentia) in Turkey, with a description of a new species

This study reports on the molecular phylogenetics of ground squirrels, genus Spermophilus, in Turkey using cytochrome b (1140bp), part of the D-loop and flanking tRNAs (572bp), X chromosome (867-1051bp) and Y chromosome (983-989bp) DNA sequences. Individuals also were characterized by karyotype and with geometric morphometric analyses of mandibles and skulls. Two hundred fourteen individuals from 91 localities were studied. All the data support the recognition of a new species in SW Anatolia: the Taurus ground squirrel Spermophilus taurensis sp. nov. The new species has a small distribution in the Taurus Mountains in an area that is a hotspot for biodiversity. Molecular clock analysis suggests that the new species diverged from the European ground squirrel, Spermophilus citellus, about 2.5 million years ago and that the ancestor of these two species diverged from the widespread Anatolian ground squirrel, Spermophilus xanthoprymnus, about 5 million years ago. Morphometric differentiation in skull and mandible shape among the three species is incomplete, but statistically significant. S. xanthoprymnus is subdivided into five cytochrome b phylogroups and we use these data to infer the location of glacial refugia where the species lived during the last glacial maximum. This study illustrates the potential of combined molecular and morphometric studies to uncover new Anatolian species and to reconstruct their phylogeographic history. The new species is important for squirrel taxonomy and for understanding Eurasian mammal evolution.     

Carbon and nitrogen pools in a mangrove stand of <Emphasis Type="Italic">Kandelia obovata</Emphasis> (S., L.) Yong: vertical distribution in the soil–vegetation system

Attempts were made to quantify the carbon and nitrogen pools in a monospecific and pioneer mangrove stand of Kandelia obovata Sheue, Liu & Yong, Okinawa Island, Japan. The leaf C and N concentrations on a leaf area basis decreased with increasing PPFD (Photosysthetic Photon Flux Density). The total C and N stocks in foliage were estimated as 3.55 Mg ha^–1 and 0.105 Mg ha^–1, respectively. The bark (45.6–48.6% for C and 0.564–0.842% for N) contained significantly higher amount of C (P < 0.05) and N (P < 0.01) than wood (46.2–47.8% for C and 0.347–0.914% N). The total C stock of stem was 23.2 Mg ha^–1 in wood and 8.33 Mg ha^–1 in bark, and the total N stock was 0.222 Mg ha^–1 in wood and 0.116 Mg ha^–1 in bark. The root wood (37.1–45.0%) contained significantly higher amount of C than root bark (35.4–40.7%) (P < 0.01). The total C stock of root was 14.2 Mg ha^–1 in wood and 12.6 Mg ha^–1 in bark, and the total N stock of root was 0.157 Mg ha^–1 in wood and 0.155 Mg ha^–1 in bark. The soil organic C and total N stocks within 1 m soil depth were estimated as 57.3 Mg ha^–1 and 2.73 Mg ha^–1, respectively. The C pool in aboveground biomass (35.1 Mg ha^–1) was 1.3 times as large as that in belowground biomass (26.9 Mg ha^–1). However, the soil organic C pool (57.3 Mg ha^–1) was similar to the total C pool (62.0 Mg ha^–1) of vegetation, indicating that the mangrove stored a large part of production in the soil. About 50% of the C was in the soil. The N pool in aboveground biomass (0.442 Mg ha^–1) was 1.4 times as large as that in belowground biomass (0.312 Mg ha^–1). The soil N stock was 3.3 times as large as the biomass N stock (0.754 Mg ha^–1).     

Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 1: design, synthesis and biological activity

HTS screening identified 1 with micromolar inhibitory activity against PDK1. Optimization of 1 afforded 4i (BX-517) which has single-digit nanomolar activity against PDK1 and excellent selectivity against PKA.     

Characterization of lignin isolated from some nonwood available in Bangladesh

Lignins isolated from cotton stalks, jute stick and dhaincha by acidolytic dioxane were characterized using alkaline nitrobenzene oxidation, elemental analysis, methoxyl analysis and molecular weight analysis and UV, IR (1)H NMR spectroscopy. The C(9) formulas for cotton stalks, jute stick and dhaincha (Sesbania aculeata) lignin were C(9)H(9.36)O(4.50)(OCH(3))(1.23), C(9)H(9.02)O(4.57)(OCH(3))(1.35) and C(9)H(8.88)O(4.65)(OCH(3))(1.50), respectively. All three lignins were of the guaiacyl-syringyl type. Cotton stalks lignin contained more p-hydroxy phenyl unit than dhaincha and jute stick lignins as observed by alkaline nitrobenzene oxidation products. The beta-O-4 units in these nonwood lignins had predominately erythro stereochemistry type.