Chicoric acid: chemistry, distribution, and production
Though chicoric acid was first identified in 1958, it was largely ignored until recent popular media coverage cited potential health beneficial properties from consuming food and dietary supplements containing this compound. To date, plants from at least 63 genera and species have been found to contain chicoric acid, and while the compound is used as a processing quality indicator, it may also have useful health benefits. This review of chicoric acid summarizes research findings and highlights gaps in research knowledge for investigators, industry stakeholders, and consumers alike. Additionally, chicoric acid identification, and quantification methods, biosynthesis, processing improvements to increase chicoric acid retention, and potential areas for future research are discussed.

title: Determination of total monomeric anthocyanin pigment content of fruit juices, beverages, natural colorants, and wines by the pH differential method: collaborative study.
abstract: This collaborative study was conducted to determine the total monomeric anthocyanin concentration by the pH differential method, which is a rapid and simple spectrophotometric method based on the anthocyanin structural transformation that occurs with a change in pH (colored at pH 1.0 and colorless at pH 4.5). Eleven collaborators representing commercial laboratories, academic institutions, and government laboratories participated. Seven Youden pair materials representing fruit juices, beverages, natural colorants, and wines were tested. The repeatability relative standard deviation (RSDr) varied from 1.06 to 4.16%. The reproducibility relative standard deviation (RSDR) ranged from 2.69 to 10.12%. The HorRat values were < or = 1.33 for all materials. The Study Director recommends that the method be adopted Official First Action.

title: Effect of selenium fertilizer on free amino acid composition of broccoli (Brassica oleracea Cv. Majestic) determined by gas chromatography with flame ionization and mass selective detection.
abstract: Selenium-enriched broccoli florets, harvested from plants grown on soil fertilized with four levels of sodium selenate, were evaluated for their free amino acid composition using alkylchlorformate derivatization, solid-phase extraction, and GC-FID or GC-MS. The selenium-enriched florets contained 0.4 (control), 5.7 (treatment A), 98.6 (treatment B), and 879.2 (treatment C) microg/g Se (dry weight). Twenty-one free amino acids were identified in the control and all three treatments. The total free amino acid content of the broccoli florets ranged from 178 mmol/kg (dry weight), for the control, to 479 mmol/kg (dry weight), for treatment C. Broccoli from treatment C contained the highest level of Se, had the most total free amino acids, and had an extremely high level of glutamine (Gln) when compared to the control and the other two treatments. In general, the smallest addition of Se to the soil (treatment A) induced increased levels of all detectable amino acids when compared to the control, whereas increased additions of Se (treatments B and C) produced mixed responses. Florets from treatment A contained the highest essential amino acid content.

title: Establishing a case for improved food phenolic analysis
abstract: Future phenolic research findings using a multidisciplinary approach will ensure profitability and sustainability of specialty crop industries, while also improving the nutritional and economic choices available to increasingly health- and environmentally conscious consumers. Recent examples of phenolics used in commercial and research scenarios, and new phenolic research discoveries are discussed. Despite being a heavily researched topic, there remains a need to identify, develop, and define analyses targeted for specific quality-related plant metabolites.

title: Spectrum measurement of fast optical signal of neural activity in brain tissue and its theoretical origin
abstract: Functional brain imaging technologies have enabled recent advances in understanding human brain function. In particular, a noninvasive and fast optical technique will become one of the most promising tools for future studies. As a fundamental ex vivo study for the development of such a technique, this paper demonstrates the spectral measurement of fast optical changes associated with neural activity in bulk brain tissue. For this purpose, a high-speed confocal near-infrared spectrometer was built and used. The results verified that observed transient optical responses (tORs) are associated with neural activity by showing that the following: tORs were concurrent and correlated with local field potentials (LFPs); tORs disappeared following tetrodotoxin application; and tORs were reproducibly observed across preparations. In addition, the amplitude of tORs was statistically significantly larger in longer wavelengths (approximately 1200 nm). The time course of tORs, however, is quite different from that of LFPs. Since this difference implies that tORs may originate not directly from the electric potential variation but from other neurophysiological events accompanying excitation, this paper tested the hypothesis that tORs are attributed to transient cellular volume changes (tCVCs). With no previous dynamic equation to elucidate such different temporal dynamics of the optical responses, a novel mathematical neuron model to describe tCVCs was developed. This neuron model, along with finite-difference time-domain simulations, showed that tCVCs and tORs were similar in the temporal dynamics, order of magnitude, response direction, and detectability in the bulk tissue; thus supporting the hypothesis.

title: A derivation of the master equation from path entropy maximization.
abstract: The master equation and, more generally, Markov processes are routinely used as models for stochastic processes. They are often justified on the basis of randomization and coarse-graining assumptions. Here instead, we derive nth-order Markov processes and the master equation as unique solutions to an inverse problem. We find that when constraints are not enough to uniquely determine the stochastic model, an nth-order Markov process emerges as the unique maximum entropy solution to this otherwise underdetermined problem. This gives a rigorous alternative for justifying such models while providing a systematic recipe for generalizing widely accepted stochastic models usually assumed to follow from the first principles.

title: Target deconvolution techniques in modern phenotypic profiling.
abstract: The past decade has seen rapid growth in the use of diverse compound libraries in classical phenotypic screens to identify modulators of a given process. The subsequent process of identifying the molecular targets of active hits, also called 'target deconvolution', is an essential step for understanding compound mechanism of action and for using the identified hits as tools for further dissection of a given biological process. Recent advances in 'omics' technologies, coupled with in silico approaches and the reduced cost of whole genome sequencing, have greatly improved the workflow of target deconvolution and have contributed to a renaissance of 'modern' phenotypic profiling. In this review, we will outline how both new and old techniques are being used in the difficult process of target identification and validation as well as discuss some of the ongoing challenges remaining for phenotypic screening.

title: High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements
abstract: Approximately 80 long interspersed element (LINE-1 or L1) copies are able to retrotranspose actively in the human genome, and these are termed retrotransposition-competent L1s. The 5′ untranslated region (UTR) of the human-specific L1 contains an internal promoter and several transcription factor binding sites. To better understand the effect of the L1 5′ UTR on the evolution of human-specific L1s, we examined this population of elements, focusing on the sequence diversity and accumulated substitutions within their 5′ UTRs. Using network analysis, we estimated the age of each L1 component (the 5′ UTR, ORF1, ORF2, and 3′ UTR). Through the comparison of the L1 components based on their estimated ages, we found that the 5′ UTR of human-specific L1s accumulates mutations at a faster rate than the other components. To further investigate the L1 5′ UTR, we examined the substitution frequency per nucleotide position among them. The results showed that the L1 5′ UTRs shared relatively conserved transcription factor binding sites, despite their high sequence diversity. Thus, we suggest that the high level of sequence diversity in the 5′ UTRs could be one of the factors controlling the number of retrotransposition-competent L1s in the human genome during the evolutionary battle between L1s and their host genomes.

title: Development of near-infrared fluorophore (NIRF)-labeled activity-based probes for in vivo imaging of legumain.
abstract: Asparaginyl endopeptidase, or legumain, is a lysosomal cysteine protease that was originally identified in plants and later found to be involved in antigen presentation in higher eukaryotes. Legumain is also up-regulated in a number of human cancers, and recent studies suggest that it may play important functional roles in the process of tumorigenesis. However, detailed functional studies in relevant animal models of human disease have been hindered by the lack of suitably selective small molecule inhibitors and imaging reagents. Here we present the design, optimization, and in vivo application of fluorescently labeled activity-based probes (ABPs) for legumain. We demonstrate that optimized aza-peptidyl Asn epoxides are highly selective and potent inhibitors that can be readily converted into near-infrared fluorophore-labeled ABPs for whole body, noninvasive imaging applications. We show that these probes specifically label legumain in various normal tissues as well as in solid tumors when applied in vivo. Interestingly, addition of cell-penetrating peptides to the probes enhanced cellular uptake but resulted in increased cross-reactivity toward other lysosomal proteases as the result of their accumulation in lysosomes. Overall, we find that aza-peptidyl Asn ABPs are valuable new tools for the future study of legumain function in more complex models of human disease.