Heat-Passing Framework for Robust Interpretation of Data in Networks

Researchers are regularly interested in interpreting the multipartite structure of data entities according to their functional relationships. Data is often heterogeneous with intricately hidden inner structure. With limited prior knowledge, researchers are likely to confront the problem of transforming this data into knowledge. We develop a new framework, called heat-passing, which exploits intrinsic similarity relationships within noisy and incomplete raw data, and constructs a meaningful map of the data. The proposed framework is able to rank, cluster, and visualize the data all at once. The novelty of this framework is derived from an analogy between the process of data interpretation and that of heat transfer, in which all data points contribute simultaneously and globally to reveal intrinsic similarities between regions of data, meaningful coordinates for embedding the data, and exemplar data points that lie at optimal positions for heat transfer. We demonstrate the effectiveness of the heat-passing framework for robustly partitioning the complex networks, analyzing the globin family of proteins and determining conformational states of macromolecules in the presence of high levels of noise. The results indicate that the methodology is able to reveal functionally consistent relationships in a robust fashion with no reference to prior knowledge. The heat-passing framework is very general and has the potential for applications to a broad range of research fields, for example, biological networks, social networks and semantic analysis of documents.     

The role of axial ligands for the structure and function of chlorophylls

We have studied the effect of axial ligation of chlorophyll and bacteriochlorophyll using density functional calculations. Eleven different axial ligands have been considered, including models of histidine, aspartate/glutamate, asparagine/glutamine, serine, tyrosine, methionine, water, the protein backbone, and phosphate. The native chlorophylls, as well as their cation and anion radical states and models of the reaction centres P680 and P700, have been studied and we have compared the geometries, binding energies, reduction potentials, and absorption spectra. Our results clearly show that the chlorophylls strongly prefer to be five-coordinate, in accordance with available crystal structures. The axial ligands decrease the reduction potentials, so they cannot explain the high potential of P680. They also redshift the Q band, but not enough to explain the occurrence of red chlorophylls. However, there is some relation between the axial ligands and their location in the various photosynthetic proteins. In particular, the intrinsic reduction potential of the second molecule in the electron transfer path is always lower than that of the third one, a feature that may prevent back-transfer of the electron.     

Ecological characterisation of <Emphasis Type="Italic">Steinernema siamkayai</Emphasis> (Rhabditida: Steinernematidae), a warm-adapted entomopathogenic nematode isolate from India

Our study describes basic ecological properties of Steinernema siamkayai Tiruchirappalli strain from India. The effect of temperature on nematode infectivity and development, laboratory host range and foraging behaviour were determined. The data showed that S. siamkayai is a warm-adapted nematode species with larval mortality observed between 15°C and 37.5°C and nematode reproduction occurring between 20°C and 35°C. All insect species used in this study were susceptible to S. siamkayai under laboratory conditions. Sixty infective juveniles (IJs) per insect were used and the lepidopterans, Galleria mellonella (100%) and Spodoptera exigua (85%), were the most susceptible species followed by the dipteran, Ceratitis capitata (60%), and lepidopteran, Cydia splendana (55%), and the coleopteran, Tenebrio molitor (45%), whereas the coleopteran, Curculio elephas (25%), was the least susceptible species. S. siamkayai infective juveniles (IJs) stood on their tails and jumped and could also attach to a mobile host at a rate of 27 IJs larvae⁻¹ out of 1000 IJs in 10 min. Larval mortality of G. mellonella by S. siamkayai on different substrates (sand, filter paper, filter paper sprinkled with sand) was 100% on all substrates. Number of IJs out of 100 IJs that penetrated into a G. mellonella host at different soil depths was the highest at the surface (44 IJs larva⁻¹) and the lowest at 5 cm depth (13 IJs larva⁻¹) with no larval mortality observed at 10 cm depth. In addition, the symbiotic bacterium of S. siamkayai was identified as Xenorhabdus stockiae based on genotypic and phenotypic characterisation. Bacterial growth was observed between 15°C and 41°C.     

Towards Biomimicking Wood: Fabricated Free-standing Films of Nanocellulose,Lignin, and a Synthetic Polycation

Woody materials are comprised of plant cell walls that contain a layered secondary cell wall composed of structural polymers of polysaccharides and lignin. Layer-by-layer (LbL) assembly process which relies on the assembly of oppositely charged molecules from aqueous solutions was used to build a freestanding composite film of isolated wood polymers of lignin and oxidized nanofibril cellulose (NFC). To facilitate the assembly of these negatively charged polymers, a positively charged polyelectrolyte, poly(diallyldimethylammomium chloride) (PDDA), was used as a linking layer to create this simplified model cell wall. The layered adsorption process was studied quantitatively using quartz crystal microbalance with dissipation monitoring (QCM-D) and ellipsometry. The results showed that layer mass/thickness per adsorbed layer increased as a function of total number of layers. The surface coverage of the adsorbed layers was studied with atomic force microscopy (AFM). Complete coverage of the surface with lignin in all the deposition cycles was found for the system, however, surface coverage by NFC increased with the number of layers. The adsorption process was carried out for 250 cycles (500 bilayers) on a cellulose acetate (CA) substrate. Transparent free-standing LBL assembled nanocomposite films were obtained when the CA substrate was later dissolved in acetone. Scanning electron microscopy (SEM) of the fractured cross-sections showed a lamellar structure, and the thickness per adsorption cycle (PDDA-Lignin-PDDA-NC) was estimated to be 17 nm for two different lignin types used in the study. The data indicates a film with highly controlled architecture where nanocellulose and lignin are spatially deposited on the nanoscale (a polymer-polymer nanocomposites), similar to what is observed in the native cell wall.     

Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential

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High-performance thin-layer chromatographic determination of ibuprofen in plasma

A high-performance thin-layer chromatographic (HPTLC) method for quantitation of ibuprofen from plasma is described. The drug was extracted from acidified plasma with hexane-isopropanol (85:15). The mobile phase composition was n-hexane-ethyl acetate-anhydrous acetic acid (75:25:2). Densitometric analysis of ibuprofen was carried out at 222 nm. The calibration curves of ibuprofen in chloroform and in plasma were linear over the range 2–20 μg. The mean values of intercept, slope and correlation coefficient were 0.0422±0.0018, 0.0356±0.0213 and 0.9976±0.0013 for standard curves in chloroform and 0.1044±0.003, 0.8759±0.0213 and 0.9939±0.001 for standard curves in plasma, respectively. The limit of detection of ibuprofen from human plasma (assay sensitivity) was 50 ng and no interference was found from endogenous compounds. The recovery of ibuprofen from human plasma using the described extraction procedure was about 85%. The mean relative standard deviations for within-day and between-day analyses were 2.24 and 2.6% for 5 μg and 3.67 and 3.2% for 15μg ibuprofen concentration, respectively. The method was utilized to monitor the plasma concentration of ibuprofen post administration of sustained release capsules in human patient volunteers.