Extending transfer entropy improves identification of effective connectivity in a spiking cortical network model.

Transfer entropy (TE) is an information-theoretic measure which has received recent attention in neuroscience for its potential to identify effective connectivity between neurons. Calculating TE for large ensembles of spiking neurons is computationally intensive, and has caused most investigators to probe neural interactions at only a single time delay and at a message length of only a single time bin. This is problematic, as synaptic delays between cortical neurons, for example, range from one to tens of milliseconds.

Tracking cellular metabolomics in lipoapoptosis- and steatosis-developing liver cells.

Palmitate (PA) is known to induce reactive oxygen species (ROS) formation and apoptosis in liver cells, whereas concurrent treatment of oleate (OA) with PA predominately induces steatosis without ROS in liver cells. We previously reported that PA treatment induces the decoupling of glycolysis and tricarboxylic acid cycle (TCA cycle) fluxes, but OA co-treatment restored most metabolic fluxes to their control levels. However, the mechanisms by which metabolites are linked to metabolic fluxes and subsequent lipoapoptotic or steatotic phenotypes remain unclear.

Effect of anaplerotic fluxes and amino acid availability on hepatic lipoapoptosis.

To identify metabolic pathways involved in hepatic lipoapoptosis, metabolic flux analysis using [U-(13)C(5)]glutamine as an isotopic tracer was applied to quantify phenotypic changes in H4IIEC3 hepatoma cells treated with either palmitate alone (PA-cells) or both palmitate and oleate in combination (PA/OA-cells). Our results indicate that palmitate inhibited glycolysis and lactate dehydrogenase fluxes while activating citric acid cycle (CAC) flux and glutamine uptake. This decoupling of glycolysis and CAC fluxes occurred during the period following palmitate exposure but preceding the onset of apoptosis.

Automated and Unbiased Image Analyses as Tools in Phenotypic Classification of Small-Spored Alternaria spp.

ABSTRACT For more than 25 years, controversy has surrounded the characterization and differentiation of small-spored Alternaria spp. And, therefore, the application of names of several species that are involved in the pathology of diseases related to host-specific toxin production. The name A.

Computerized screening for novel producers of Monascus-like food pigments in Penicillium species.

Monascus pigments have been used as natural food colorants in Asia for centuries. They are not authorized for use in the European Union and the United States mainly due to the risk of coproduction of the mycotoxin citrinin by Monascus spp. In the present study, we screened for novel producers of Monascus-like pigments from ascomycetous filamentous fungi belonging to Penicillium subgenus Biverticillium that are not reported to produce citrinin or any other known mycotoxins.

A method for comparison of growth media in objective identification of Penicillium based on multi-spectral imaging.

We consider the problems of using excessive growth media for identification and performing objective identification of fungi at the species level. We propose a method for choosing the subset of growth media, which provides the best discrimination between several fungal species. Furthermore, we propose the use of multi-spectral imaging as a means of objective identification.

A comparison of direct infusion MS and GC-MS for metabolic footprinting of yeast mutants.

Recent technical advances in mass spectrometry (MS) have propelled this technology to the forefront of methods employed in metabolome analysis. Here, we compare two distinct analytical approaches based on MS for their potential in revealing specific metabolic footprints of yeast single-deletion mutants. Filtered fermentation broth samples were analyzed by GC-MS and direct infusion ESI-MS.

Phenotypic taxonomy and metabolite profiling in microbial drug discovery.

Microorganisms and in particular actinomycetes and microfungi are known to produce a vast number of bioactive secondary metabolites. For industrially important fungal genera such as Penicillium and Aspergillus the production of these compounds has been demonstrated to be very consistent at the species level. This means that direct metabolite profiling techniques such as direct injection mass spectrometry or NMR can easily be used for chemotyping/metabolomics of strains from both culture collections and natural samples using modern informatics tools.

X-Hitting: an algorithm for novelty detection and dereplication by UV spectra of complex mixtures of natural products.

A major challenge in lead discovery is to detect well-known and trivial compounds rapidly, a process known as dereplication, so that isolation, structure elucidation, and pharmacological investigations can be focused on novel compounds. In this paper, we present a new algorithm, X-hitting, based on cross sample comparison of full UV spectra from HPLC analysis of highly complex natural product extracts/samples. X-Hitting allows automatic identification of known compounds but more important also allows finding of potentially new or similar compounds.

Discovery of new natural products by application of X-hitting, a novel algorithm for automated comparison of full UV spectra, combined with structural determination by NMR spectroscopy.

X-hitting, a newly developed algorithm for automated comparison of UV data, has been used for the tracking of two novel spiro-quinazoline metabolites, lapatins A (1) and B (2), in a screening study targeting quinazolines. The structures of 1 and 2 were elucidated by analysis of spectroscopic data, primarily 2D NMR.

Automated and unbiased classification of chemical profiles from fungi using high performance liquid chromatography.

In this paper we present a method for unbiased/unsupervised classification and identification of closely related fungi, using chemical analysis of secondary metabolite profiles created by HPLC with UV diode array detection. For two chromatographic data matrices a vector of locally aligned full spectral similarities is calculated along the retention time axis. The vector depicts the evaluating of the alikeness between two fungal extracts based upon eluted compounds and corresponding UV-absorbance spectra.

A new matching algorithm for high resolution mass spectra.

We present a new matching algorithm designed to compare high-resolution spectra. Whereas existing methods are bound to compare fixed intervals of ion masses, the accurate mass spectrum (AMS) distance method presented here is independent of any alignment. Based on the Jeffreys-Matusitas (JM) distance, a difference between observed peaks across pairs of spectra can be calculated, and used to find a unique correspondence between the peaks.

Visual clone identification of Penicillium commune isolates.

A method for visual clone identification of Penicillium commune isolates was developed. The method is based on images of fungal colonies acquired after growth on a standard medium and involves a high degree of objectivity, which in future studies will make it possible for non-experts to perform a qualified identification of different species as well as clones within a species. A total of 77 P.