A novel Agrobacterium rhizogenes-mediated transformation method of soybean [Glycine max (L.) Merrill] using primary-node explants from seedlings

A novel Agrobacterium rhizogenes-mediated transformation method using a primary-node explant from Dairyland cultivar 93061 was developed for soybean using the disarmed Agrobacterium strain SHA17. Transformed plants regenerated from explants inoculated with SHA17 were fertile and phenotypically normal. In a comparative experiment, regeneration frequencies were not significantly different between explants inoculated with A. rhizogenes strain SHA17 and Agrobacterium tumefaciens strain AGL1; however, a 3.5-fold increase in transformation efficiency [(number of Southern or TaqMan-positive independent events/total number of explants inoculated) × 100] was found for explants cocultured with SHA17 compared to AGL1 (6.6 and 1.64%, respectively). Southern analysis of 48 T₀ plants suggested that 37.5, 23, and 39.6% of the T₀ plants contained 1, 2, and 3 or more T-DNA fragments integrated into the genome, respectively. Additionally, T₁ progeny analysis of 8 independent events resulted in typical Mendelian inheritance of T-DNA genes. Of seven T₀ plants that had two or more T-DNA fragments, six contained multiple loci segregating in T₁ progenies. Further analysis of four lines confirmed the presence of PAT, GUS, and/or DsRED2 proteins in transgenic plants that were encoded on the T-DNA into the T₂ generation.     

Are clonal plants more tolerant to grazing than co-occurring non-clonal plants in inland dunes?

Clonal traits such as clonal integration and storage functions of rhizomes or stolons may provide clonal plants with additional advantages against grazing over non-clonal plants. Here, we hypothesize that clonal species have a larger capacity for compensatory growth than co-occurring non-clonal species. In inland dunes in northern China, individual plants of two rhizomatous clonal species (Bromus ircutensis and Psammochloa villosa) and two non-clonal ones (Artemisia intramongolica and Astragalus melilotoides) were subjected to 0% (control), 50% (moderate) and 90% (heavy) shoot removal. Compared with control, heavy clipping greatly increased the relative growth rate in Bromus and Psammochloa, but decreased that in Artemisia and Astragalus. Heavy clipping affected above-ground dry weight and the number of modules more negatively in Artemisia and Astragalus than in Bromus and Psammochloa. These results support the hypothesis and suggest that clonal species are more tolerant to grazing than co-occurring non-clonal species in inland dunes.     

Modeling spatial integration in the ocular following response using a probabilistic framework

The machinery behind the visual perception of motion and the subsequent sensori-motor transformation, such as in ocular following response (OFR), is confronted to uncertainties which are efficiently resolved in the primate's visual system. We may understand this response as an ideal observer in a probabilistic framework by using Bayesian theory [Weiss, Y., Simoncelli, E.P., Adelson, E.H., 2002. Motion illusions as optimal percepts. Nature Neuroscience, 5(6), 598-604, doi:10.1038/nn858] which we previously proved to be successfully adapted to model the OFR for different levels of noise with full field gratings. More recent experiments of OFR have used disk gratings and bipartite stimuli which are optimized to study the dynamics of center-surround integration. We quantified two main characteristics of the spatial integration of motion: (i) a finite optimal stimulus size for driving OFR, surrounded by an antagonistic modulation and (ii) a direction selective suppressive effect of the surround on the contrast gain control of the central stimuli [Barthélemy, F.V., Vanzetta, I., Masson, G.S., 2006. Behavioral receptive field for ocular following in humans: dynamics of spatial summation and center-surround interactions. Journal of Neurophysiology, (95), 3712-3726, doi:10.1152/jn.00112.2006]. Herein, we extended the ideal observer model to simulate the spatial integration of the different local motion cues within a probabilistic representation. We present analytical results which show that the hypothesis of independence of local measures can describe the spatial integration of the motion signal. Within this framework, we successfully accounted for the contrast gain control mechanisms observed in the behavioral data for center-surround stimuli. However, another inhibitory mechanism had to be added to account for suppressive effects of the surround.     

Biodiversity informatics: organizing and linking information across the spectrum of life

Biological knowledge can be inferred from three major levels of information: molecules, organisms and ecologies. Bioinformatics is an established field that has made significant advances in the development of systems and techniques to organize contemporary molecular data; biodiversity informatics is an emerging discipline that strives to develop methods to organize knowledge at the organismal level extending back to the earliest dates of recorded natural history. Furthermore, while bioinformatics studies generally focus on detailed examinations of key 'model' organisms, biodiversity informatics aims to develop over-arching hypotheses that span the entire tree of life. Biodiversity informatics is presented here as a discipline that unifies biological information from a range of contemporary and historical sources across the spectrum of life using organisms as the linking thread. The present review primarily focuses on the use of organism names as a universal metadata element to link and integrate biodiversity data across a range of data sources.     

Comparative study of optical coherence tomography angiography algorithms for rodent retinal imaging

Optical coherence tomography angiography (OCTA) is a functional extension of optical coherence tomography for non-invasive in vivo three-dimensional imaging of the microvasculature of biological tissues. Several algorithms have been developed to construct OCTA images from the measured optical coherence tomography signals. In this study, we compared the performance of three OCTA algorithms that are based on the variance of phase, amplitude, and the complex representations of the optical coherence tomography signals for rodent retinal imaging, namely the phase variance, improved speckle contrast, and optical microangiography. The performance of the different algorithms was evaluated by comparing the quality of the OCTA images regarding how well the vasculature network can be resolved. Quantities that are widely used in ophthalmic studies including blood vessel density, vessel diameter index, vessel perimeter index, vessel complexity index were also compared. Results showed that both the improved speckle contrast and optical microangiography algorithms are more robust than phase variance, and they can reveal similar vasculature features while there are statistical differences in the calculated quantities.     

Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A

We developed a software package for improved free energy calculation, in which spherical solvent boundary potential, cell multipole method, and Nosé-Hoover equation are employed. The performance of the developed software package is demonstrated in the case of valine to alanine mutation of the 57th residue in chymotrypsin inhibitor 2. By using this package, we obtained results quantitatively comparable to experimental results. By the free energy component analysis, it is shown that leucine 51, arginine 65, arginine 67, and phenylalanine 69 residues contribute significantly to the total free energy shift, ΔΔG. Among them, contribution from the hydrophilic arginine 67 residue, which is in close contact with the mutation site, is the largest. Structure around the mutation site is largely changed by the mutation. The structure change is caused mainly by two effects, hydrophobic interaction and short-range interaction along the sequence. Effects of Nosé-Hoover algorithm and Kirkwood reaction field are also discussed. Proteins 30:388–400, 1998. © 1998 Wiley-Liss, Inc.     

Olfactory information processing in the brain: Encoding chemical and temporal features of odors

A fundamental problem in studying the neural mechanisms of odor recognition and discrimination in the olfactory system lies in determining the features or “primitives” of an odor stimulus that are analyzed by glomerular circuits at the first level of processing in the brain. Several recent studies support the idea that it is not simply the molecular features of odors that contain important information, but also the intermittent pattern of their presentation to the olfactory epithelium that helps determine the behavioral response to odor. © 1996 John Wiley & Sons, Inc.     

An ensemble approach for healthcare application and diagnosis using natural language processing

Integration of healthcare records into a single application is still a challenging process There are additional issues when data becomes heterogeneous, and its application based on users does not appear to be the same. Hence, we propose an application called MEDSHARE which is a web-based application that integrates the data from various sources and helps the patient to access all their health records in a single point of source. Apart just from the collection of data, this portal enables the process of diagnosis using Natural language processing. The process is carried out by fuzzy logic ruleset which is generated by using NLP packages. The resulted information is given to the SVM classifier which helps in the prediction of diseases resulting in 89% of accuracy and standing the best compared to other classifiers. Finally, the observations resulted are sent to the front end application and the concerned user mobile through text message in their own native language for which translation package is been used.