Nature Precedings
Not a member yet
3446 research outputs found
Sort by
SBGN PD: Current status, future changes and unresolved issues.
Get PDFThe presentations reports and the current status of the SBGN-PD specification and highlights issues for further discussion
Genome sequence and genetic linkage analysis of Shiitake mushroom _Lentinula edodes_
Get PDF_Lentinula edodes_ (Shiitake/Xianggu) is an important cultivated mushroom. Understanding the genomics and functional genomics of _L. edodes_ allows us to improve its cultivation and quality. Genome sequence is a key to develop molecular genetic markers for breeding and genetic manipulation. We sequenced the genome of _L. edodes_ monokaryon L54A using Roche 454 and ABI SOLiD genome sequencing. Sequencing reads of about 1400Mb were de novo assembled into a 40.2 Mb genome sequence. We compiled the genome sequence into a searchable database with which we have been annotating the genes and analyzing the metabolic pathways. In addition, we have been using many molecular techniques to analyze genes differentially expressed during development. Gene ortholog groups of _L. edodes_ genome sequence compared across genomes of several fungi including mushrooms identified gene families unique to mushroom-forming fungi. We used a mapping population of haploid basidiospores of dikaryon L54 for genetic linkage analysis. High-quality variations such as single nucleotide polymorphisms, insertions, and deletions of the mapping population formed a high-density genetic linkage map. We compared the linkage map to the _L. edodes_ L54A genome sequence and located selected quantitative trait loci. The Shiitake community will benefit from these resources for genetic studies and breeding.

Non-viral delivery and optimized optogenetic stimulation of retinal ganglion cells led to behavioral restoration of vision
Get PDFStimulation of retinal neurons using optogenetics via use of chanelrhodopsin-2 (ChR2) has opened up a new direction for restoration of vision for treatment of retinitis pigmentosa (RP). Here, we report non-viral in-vivo electroporation of degenerated retina of adult RP-mice with ChR2-plasmids and subsequent in-vivo imaging of retina to confirm expression. Further, we demonstrate that in addition to efficient non-viral delivery of ChR2 to a specific retinal layer, threshold level of stimulation light needs to be delivered onto the retina for achieving successful behavioral outcome. Measurement of intensity of light reaching the retina of RP-mouse models along with geometrical optics simulation of light propagation in the eye is reported in order to determine the stimulating source position for optimal light delivery to the retina. The light-guided navigation of mice with ChR2 expressing retinal ganglion cells was found to be significantly improved over a long distance in correlation with stimulation intensity
Agriculture: Nanotechnology’s Green Field
No full textNatural agricultural production functions in open system, where energy and matter are exchanged freely between geosphere (especially pedosphere), biosphere, and atmosphere. The self regulation of biophysical processes in these spheres is crucial for global sustainability. However, modern farming practices have stressed the system to the extent that damaged C, N, and P cycles are threatening catastrophic consequences. High food-wastage coupled with high food price, high soil fertility zones but low crop productivity, and highly productive irrigated farming marred with ecological disasters are examples of global paradoxes associated with modern farming. High incidence of pesticide residues in soil and water bodies, low use efficiency of agricultural inputs, vulnerability to climate, and low conversion of energy by crops leaving high amount of residues and their subsequent burden on environment, and hunger and malnutrition in many parts of the world are threatening civilizations to crumble. Nanotechnology promises to break these vicious cycles, because technology is based on applying exact amounts of inputs for use by the crops, and only when they are required. Some of the examples are: nanofabricating nutrient ions to improve nutrient use efficiency, targeted use of nano-pesticides, holding of water and then releasing it at the time of crop need by nps, forecasting and elimination of diseases, packaging of food to improve shelf-life, protecting food during storage, DNA nanotechnology, smart treatment delivery systems, bioanalytical nanosensors, bioselective surfaces, nanobioprocessing, protection of the environment by the reduction and conversion of agricultural materials into valuable products, design and development of new nanocatalysts to convert vegetable oils into biobased fuels and biodegradable industrial solvents, and controlled ecological life support system
INCF Lithuanian Workshop on Neuroscience and Information Technology
Get PDFThe aim of this workshop was to give a current overview of neuroscience and informatics research in Lithuania, and to discuss the strategies for forming the Lithuanian Neuroinformatics Node and becoming a member of INCF. The workshop was organized by Dr. Aušra Saudargiene (Department of Informatics, Vytautas Magnus University, Kaunas, and Faculty of Natural Sciences, Vilnius University, Lithuania) and INCF.
The workshop was attended by 15 invited speakers, among them 4 guests and 11 Lithuanian neuroscientists, and over 20 participants. The workshop was organized into three main sessions: overview of the INCF activities including the Swedish and UK nodes of INCF; presentations on Neuroscience research carried out in Lithuania; discussion about the strategies for forming an INCF national node, and the benefits of having such a node in Lithuania (Appendix A: Program; Appendix B: Abstracts)
Neural Information Processing: between synchrony and chaos
Get PDFThe brain is characterized by performing many different processing tasks ranging from elaborate processes such as pattern recognition, memory or decision-making to more simple functionalities such as linear filtering in image processing. Understanding the mechanisms by which the brain is able to produce such a different range of cortical operations remains a fundamental problem in neuroscience. Some recent empirical and theoretical results support the notion that the brain is naturally poised between ordered and chaotic states. As the largest number of metastable states exists at a point near the transition, the brain therefore has access to a larger repertoire of behaviours. Consequently, it is of high interest to know which type of processing can be associated with both ordered and disordered states. Here we show an explanation of which processes are related to chaotic and synchronized states based on the study of in-silico implementation of biologically plausible neural systems. The measurements obtained reveal that synchronized cells (that can be understood as ordered states of the brain) are related to non-linear computations, while uncorrelated neural ensembles are excellent information transmission systems that are able to implement linear transformations (as the realization of convolution products) and to parallelize neural processes. From these results we propose a plausible meaning for Hebbian and non-Hebbian learning rules as those biophysical mechanisms by which the brain creates ordered or chaotic ensembles depending on the desired functionality. The measurements that we obtain from the hardware implementation of different neural systems endorse the fact that the brain is working with two different states, ordered and chaotic, with complementary functionalities that imply non-linear processing (synchronized states) and information transmission and convolution (chaotic states)
Identifying reliable traits across laboratory mouse exploration arenas: A meta-analysis
Get PDFThis study is a meta-analysis of 367 mice from a collection of behaviour neuroscience and behaviour genetic studies run in the same lab in Zurich, Switzerland. We employed correlation-based statistics to confirm and quantify consistencies in behaviour across the testing environments. All 367 mice ran exactly the same behavioural arenas: the light/dark box, the null maze, the open field arena, an emergence task and finally an object exploration task. We analysed consistency of three movement types across those arenas (resting, scanning, progressing), and their relative preference for three zones of the arenas (home, transition, exploration). Results were that 5/6 measures showed strong individual-differences consistency across the tests. Mean inter-arena correlations for these five measures ranged from +.12 to +.53. Unrotated principal component factor analysis (UPCFA) and Cronbach’s alpha measures showed these traits to be reliable and substantial (32-63% of variance across the five arenas). UPCFA loadings then indicate which tasks give the best information about these cross-task traits. One measure (that of time spent in “intermediate” zones) was not reliable across arenas. Conclusions centre on the use of individual differences research and behavioural batteries to revise understandings of what measures in one task predict for behaviour in others. Developing better behaviour measures also makes sound scientific and ethical sense
Identification of transcription regulation associated proteins in plants and stramenopiles
Get PDFThe generation of biodiversity is tied to the evolution and re-wiring of gene regulatory networks (GRNs). One component of these GRN are transcription factors and other transcriptional regulators. We have devised a pipeline for the identification of TFs and TRs, exploiting the domain architecture of these proteins. Currently we have a set of rules, representing 138 proteins families, that we have applied to the identification of ~20 different plant species and several species of Stramenopiles, where important plant pathogens are found. Results for plant species are available at http://plntfdb.uniandes.edu.co/; we are now developing a newer interface for Stramenopiles
Virtual screening for NS5B inhibitors of Hepatitis C virus
Get PDFHepatitis C Virus (HCV) infection is a serious cause of chronic liver disease worldwide with more than 170 million infected individuals at a risk of developing significant morbidity and mortality. To date there is no effective drug for the treatment or vaccine to prevent this infection. The present study aims to discover novel inhibitors which target an allosteric binding site of RNA dependent RNA polymerase enzyme of HCV. A structure based virtual screening of Zinc database by computational docking and the post docking analysis of energy calculations and interactions followed by ADMET studies were conducted. Our study revealed 10 compounds which has more potential than the existing inhibitor to be considered as lead compounds.

Microparticles specific for lung delivery: in-vivo drug distribution in monkeys
Get PDFIn spite of extensive research in tuberculosis (TB), it is still one of the major infectious diseases and cause of high mortality worldwide. To enhance efficacy with lower dosing, newer drug delivery systems has been developed which provide targeted drug delivery and controlled release at the primary site of infection, i.e., the lung macrophage. Our lab has previously reported poly(D, L-lactic acid) (PLA) microparticles containing rifabutin (RFB) and isoniazid (INH) for pulmonary delivery and explored various facets of treatment with microparticle DPI. We have utilized this dry powder aerosol drug delivery system to deposit drugs directly at the site of infection in lungs and have been investigating such DPI as a novel approach to increase therapeutic efficacy, patient compliance and lower toxicity. Data from murine models of DPI delivery suggests that aerosolized delivery of anti-TB drugs is more effective than conventional drug therapies in maintaining therapeutic concentration at the site of infection. Most of the previous studies were primarily concerned with acute administration of drug-containing delivery systems and evaluation of their pharmacokinetic profile in rodents. The aim of present study was to evaluate pharmacokinetics, biodistribution and toxicity parameters of RFB and INH incorporated in DPI microparticles after ninety days of repeated dosing in rhesus macaques in order to establish steady-stae pharmacokinetics and preclinical safety of the formulation prior to humans clinical trials