Aflatoxin regulations and global pistachio trade: Insights from social network analysis

Aflatoxins, carcinogenic toxins produced by Aspergillus fungi, contaminate maize, peanuts, and tree nuts in many regions of the world. Pistachios are the main source of human dietary aflatoxins from tree nuts worldwide. Over 120 countries have regulations for maximum allowable aflatoxin levels in food commodities. We developed social network models to analyze the association between nations' aflatoxin regulations and global trade patterns of pistachios from 1996-2010. The main pistachio producing countries are Iran and the United States (US), which together contribute to nearly 75% of the total global pistachio market. Over this time period, during which many nations developed or changed their aflatoxin regulations in pistachios, global pistachio trade patterns changed; with the US increasingly exporting to countries with stricter aflatoxin standards. The US pistachio crop has had consistently lower levels of aflatoxin than the Iranian crop over this same time period. As similar trading patterns have also been documented in maize, public health may be affected if countries without aflatoxin regulations, or with more relaxed regulations, continually import crops with higher aflatoxin contamination. Unlike the previous studies on maize, this analysis includes a dynamic element, examining how trade patterns change over time with introduction or adjustment of aflatoxin regulations. © 2014 Bui-Klimke et al

Glycotope structures and intramolecular affinity factors of plant lectins for Tn/T antigens

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Are voltage-gated sodium channels on the dorsal root ganglion involved in the development of neuropathic pain?

Neuropathic pain is a common clinical condition. Current treatments are often inadequate, ineffective, or produce potentially severe adverse effects. Understanding the mechanisms that underlie the development and maintenance of neuropathic pain will be helpful in identifying new therapeutic targets and developing effective strategies for the prevention and/or treatment of this disorder. The genesis of neuropathic pain is reliant, at least in part, on abnormal spontaneous activity within sensory neurons. Therefore, voltage-gated sodium channels, which are essential for the generation and conduction of action potentials, are potential targets for treating neuropathic pain. However, preclinical studies have shown unexpected results because most pain-associated voltage-gated channels in the dorsal root ganglion are down-regulated after peripheral nerve injury. The role of dorsal root ganglion voltage-gated channels in neuropathic pain is still unclear. In this report, we describe the expression and distribution of voltage-gated sodium channels in the dorsal root ganglion. We also review evidence regarding changes in their expression under neuropathic pain conditions and their roles in behavioral responses in a variety of neuropathic pain models. We finally discuss their potential involvement in neuropathic pain

R2 imaging of ferritin iron in thalassaemia patients off and on iron-chelation therapy

Myocardial Tissue Characterization: Fat, Hemorrhage & Edema - Poster presentationAccurate assessment of iron burden is crucial for the management of iron-chelation therapy. MRI provides a means to non-invasively assess tissue iron concentration by exploiting the paramagnetic effects of iron on the relaxation rates of solvent protons. The most widely used method is R2* imaging, which has been shown to be sensitive to myocardial iron overload. Recently, a breath-hold fast spin echo sequence has been proposed for fast and accurate imaging of myocardial and hepatic R2. The purpose of this study was to determine which relaxation rates are sensitive to iron-chelation therapy.published_or_final_versionThe 17th Scientific Meeting & Exhibition of the International Society of Magnetic Resonance in Medicine (ISMRM), Honolulu, HI., 18-24 April 2009. In Proceedings of ISMRM 17th Scientific Meeting & Exhibition, 2009, p. 375

Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations

Understanding and control of structures and rates involved in protein-ligand binding are es- sential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations cannot di- rectly sample the excessively long residence and rearrangement times of tightly binding complexes. Here we exploit the recently developed multi-ensemble Markov model framework to compute full protein-peptide kinetics of the oncoprotein fragment 25−109Mdm2 and the nano-molar inhibitor peptide PMI. Using this system, we report, for the first time, direct estimates of kinetics beyond the seconds timescales using simulations of an all-atom MD model, with high accuracy and pre- cision. These results only require explicit simulations on the sub-milliseconds timescale and are tested against existing mutagenesis data and our own experimental measurements of the dissoci- ation and association rates. The full kinetic model reveals an overall downhill but rugged binding funnel with multiple pathways. The overall strong binding arises from a variety of conformations with different hydrophobic contact surfaces that interconvert on the milliseconds timescale.Funding is acknowledged by European Commission (ERC StG “pcCells” to F.N.), Deutsche Forschungsgemeinschaft (SFB 1114/C3, SFB 740/D7, and TRR 186/A12 to F.N. and SFB 1114/A4 to F.N. and T.W.). J.C. is a Wellcome Trust Senior Research Fellow (WT 095195MA). J.S. is a Marie Sklodowska-Curie Internationally outgoing fellow. M.D.C. is supported by a Biotechnology and Biological Sciences Research Council (BBSRC) studentship

Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix

Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other alternative structures. Various polymer models have been developed to capture these properties, with Monte-Carlo (MC) approaches dedicated to the inference of thermodynamic properties. In this chapter, we explain how to perform such Monte-Carlo simulations, following two objectives. On one hand, we present the self-avoiding supercoiled Worm-Like Chain (ssWLC) model, which is known to capture the folding properties of supercoiled DNA, and provide a detailed explanation of a standard MC simulation method. On the other hand, we explain how to extend this ssWLC model to include structural transitions of the helix.Comment: Book chapter to appear in The Bacterial Nucleoid, Methods and Protocols, Springer serie

Monitoring iron chelation effect in hearts of thalassaemia patients with improved sensitivity using reduced transverse relaxation rate (RR2)

Posters - Myocardial Viability: Human Models: No. 3660Accurate MRI characterization of myocardial iron is needed to improve the diagnosis and management of thalassaemia patients with transfusional iron overload. This study aimed to demonstrate that a new transverse relaxation index, the reduced R2 (RR2) that is estimated from non-monoexponential multi-echo CPMG signal decay and sensitive to ferritin iron, could detect the myocardial iron changes immediately following 1-week iron chelation suspension in thalassaemia patients at 3T.postprin

Heart and liver R2 and R2* measurements in patients with thalassaemia major at 3T

Myocardial Tissue Characterization: Fat, Hemorrhage & Edema - Poster presentationTo determine the feasibility of measurements of transverse relaxation times for assessment of tissue iron overload at high field, we compared results of determinations of R2 and R2* using breathhold multi-echo spin-echo (MESE) and multi-echo gradient echo (MEGE) sequences, respectively, at 3T and at 1.5T in normal subjects and patients with thalassaemia major. Our results, the first reported measurements of R2 at both 3T and 1.5T in iron overloaded patients, demonstrate significant correlations in heart and liver at the two field strengths. These results provide evidence that myocardial and hepatic R2 can be measured at 3T as indicators of iron overload.published_or_final_versionThe 17th Scientific Meeting & Exhibition of the International Society of Magnetic Resonance in Medicine (ISMRM), Honolulu, HI., 18-24 April 2009. In Proceedings of ISMRM 17th Scientific Meeting & Exhibition, 2009, p. 375

SMART: Unique splitting-while-merging framework for gene clustering

Copyright @ 2014 Fa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Successful clustering algorithms are highly dependent on parameter settings. The clustering performance degrades significantly unless parameters are properly set, and yet, it is difficult to set these parameters a priori. To address this issue, in this paper, we propose a unique splitting-while-merging clustering framework, named “splitting merging awareness tactics” (SMART), which does not require any a priori knowledge of either the number of clusters or even the possible range of this number. Unlike existing self-splitting algorithms, which over-cluster the dataset to a large number of clusters and then merge some similar clusters, our framework has the ability to split and merge clusters automatically during the process and produces the the most reliable clustering results, by intrinsically integrating many clustering techniques and tasks. The SMART framework is implemented with two distinct clustering paradigms in two algorithms: competitive learning and finite mixture model. Nevertheless, within the proposed SMART framework, many other algorithms can be derived for different clustering paradigms. The minimum message length algorithm is integrated into the framework as the clustering selection criterion. The usefulness of the SMART framework and its algorithms is tested in demonstration datasets and simulated gene expression datasets. Moreover, two real microarray gene expression datasets are studied using this approach. Based on the performance of many metrics, all numerical results show that SMART is superior to compared existing self-splitting algorithms and traditional algorithms. Three main properties of the proposed SMART framework are summarized as: (1) needing no parameters dependent on the respective dataset or a priori knowledge about the datasets, (2) extendible to many different applications, (3) offering superior performance compared with counterpart algorithms.National Institute for Health Researc

Composition of dissolved organic matter within a lacustrine environment

Freshwater dissolved organic matter (DOM) is a complex mixture of chemical components that are central to many environmental processes, including carbon and nitrogen cycling. However, questions remain as to its chemical characteristics, sources and transformation mechanisms. Here, we employ 1- and 2-D nuclear magnetic resonance (NMR) spectroscopy to investigate the structural components of lacustrine DOM from Ireland, and how it varies within a lake system, as well as to assess potential sources. Major components found, such as carboxyl-rich alicyclic molecules (CRAM) are consistent with those recently identified in marine and freshwater DOM. Lignin-type markers and protein/peptides were identified and vary spatially. Phenylalanine was detected in lake areas influenced by agriculture, whereas it is not detectable where zebra mussels are prominent. The presence of peptidoglycan, lipoproteins, large polymeric carbo- hydrates and proteinaceous material supports the substantial contribution of material derived from microorganisms. Evidence is provided that peptidoglycan and silicate species may in part originate from soil microbes