Residue Distributions Research Articles

GeoNet enables the accurate prediction of protein-ligand binding sites through interpretable geometric deep learning.

The identification of protein binding residues is essential for understanding their functions invivo. However, it remains a computational challenge to accurately identify binding sites due to the lack of known residue binding patterns. Local residue spatial distribution and its interactive biophysical environment both determine binding patterns. Previous methods could not capture both information simultaneously, resulting in unsatisfactory performance. Here, we present GeoNet, an interpretable geometric deep learning model for predicting DNA, RNA, and protein binding sites by learning the latent residue binding patterns. GeoNet achieves this by introducing a coordinate-free geometric representation to characterize local residue distributions and generating an eigenspace to depict local interactive biophysical environments. Evaluation shows that GeoNet is superior compared to other leading predictors and it shows a strong interpretability of learned representations. We present three test cases, where interaction interfaces were successfully identified with GeoNet.

Supramolecular organization and dynamics of mannosylated phosphatidylinositol lipids in the mycobacterial plasma membrane

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), a disease that claims ~1.6 million lives annually. The current treatment regime is long and expensive, and missed doses contribute to drug resistance. Therefore, development of new anti-TB drugs remains one of the highest public health priorities. Mtb has evolved a complex cell envelope that represents a formidable barrier to antibiotics. The Mtb cell envelop consists of four distinct layers enriched for Mtb specific lipids and glycans. Although the outer membrane, comprised of mycolic acid esters, has been extensively studied, less is known about the plasma membrane, which also plays a critical role in impacting antibiotic efficacy. The Mtb plasma membrane has a unique lipid composition, with mannosylated phosphatidylinositol lipids (phosphatidyl-myoinositol mannosides, PIMs) comprising more than 50% of the lipids. However, the role of PIMs in the structure and function of the membrane remains elusive. Here, we used multiscale molecular dynamics (MD) simulations to understand the structure-function relationship of the PIM lipid family and decipher how they self-organize to shape the biophysical properties of mycobacterial plasma membranes. We assess both symmetric and asymmetric assemblies of the Mtb plasma membrane and compare this with residue distributions of Mtb integral membrane protein structures. To further validate the model, we tested known anti-TB drugs and demonstrated that our models agree with experimental results. Thus, our work sheds new light on the organization of the mycobacterial plasma membrane. This paves the way for future studies on antibiotic development and understanding Mtb membrane protein function.

Predicting the rapid devolatilization of mineral-free cellulose

This paper extends the validation of a reaction mechanism for the devolatilization of mineral-free cellulose called “cel-FC.” A single set of model parameters accurately interprets the partitioning of raw cellulose into oil, noncondensables, and solid residue and oil molecular weight distributions (MWDs) for temperatures to 600 °C, heating rates from 60 to 6000°C/s, contact times to 120 s, and pressures of vacuum and 0.1 MPa. The analysis incorporates depolymerization via random scission and unzipping from chain ends; charring via monomer decomposition, spontaneous charring, and thermal annealing; fragmentation statistics, and the flash distillation analogy. Random depolymerization is responsible for the induction of primary cellulose devolatilization and eventually generates chains short enough to vaporize. The accompanying surge in the relative concentrations of chain ends activates the unzipping process. The fastest oil production rates are driven by scission plus unzipping and mediated by flash distillation. Whenever vaporization of longer oil precursors is limited, unzipping delivers monomer derivatives into the oil. Whenever longer volatile chains can freely vaporize they are no longer subject to unzipping or scission, so there are necessarily fewer monomers in oil. This is why ultimate oil yields are essentially the same across broad ranges of heating rate, temperature (given sufficient contact time at low temperatures), and pressure, and why oil MWDs shift toward heavier molecular weights for progressively faster heating rates, hotter temperatures, and lower pressures. Cel-FC interprets the optimal primary products - 94 wt% oil plus a mixture of light oxygenates, CO2, and CO in H2O – as the limit of depolymerization via scission and unzipping without any charring reactions. Monomer decomposition and spontaneous charring produce hardly any bio-char from mineral-free cellulose but are major sources of noncondensable gases and responsible for greater gas yields for slower heating rates, hotter temperatures, and higher pressures.

Multi-Year Survey and Bayesian Modeling Approach for Characterizing Arsenic Pollution in Marine Clams Cultivated Along the Tidal Flats of Mid-Eastern China

Marine clam is one of the main sources of arsenic (As), and the tidal flats of Jiangsu Province are considered major culturing areas for clams in mid-eastern China. In view of increasingly severe pollution in this region, concerns have been raised by the consumers with the safety of clams they purchased or may purchase. To address these concerns, we conducted a multi-year survey to determine the levels of As and As species in five major clam species cultivated in eight production areas of this region. Based on the above analysis data, Bayesian statistics used a Markov Chain Monte Carlo approach was applied to predict the toxic As residue distributions in clams produced in this region and their health risks to Chinese adults. It was found that the bioaccumulation ability of total As (tAs) and inorganic As (iAs) was species-specific, while Mactra veneriformis (MV) had the strongest accumulation capacity for toxic iAs (0.22–2.85 mg/kg dw). Up to 6.7% of the tested MV samples exceeding the iAs limit of China Food and Drug Administration. The content of iAs was also found to be related significantly to the harvest seasons, with clam in the spawning period (June) having the lowest iAs concentrations. The non-carcinogenic and carcinogenic health risk from dietary exposure to iAs associated with MV consumption was rather high, which suggested that specific attention should be paid to the safety of clam consumption in this region.

Evaluation of Dissipation Behavior, Residues, and Dietary Risk Assessment of Fludioxonil in Cherry via QuEChERS Using HPLC-MS/MS Technique.

The chemical fungicide fludioxonil is widely used to control post-harvest fungal disease in cherries. This study was implemented to investigate the dissipation behaviours and residues of fludioxonil on cherries. A reliable and efficient analytical method was established. Cherry samples from four product areas were analyzed by QuEChERS and HPLC-MS/MS methods with acceptable linearity (R2 > 0.99), accuracy (recoveries of 81–94%), and precision (relative standard deviation of 2.5–11.9%). The limits of quantification (LOQs) and limits of detection (LODs) of cherries were 0.01 mg/kg and 0.005 mg/kg. The dissipation of fludioxonil on cherries followed first order kinetics with half-lives of 33.7–44.7 days. The terminal residues of fludioxonil were all lower than 5.00 mg/kg, which is the MRL recommended by the European Commission. According to Chinese dietary patterns and terminal residue distributions, the risk quotient (RQs) of fludioxonil was 0.61%, revealing that the evaluated cherries exhibited an acceptably low dietary risk to consumers.

Systematic characterization and prediction of coenzyme A-associated proteins using sequence and network information.

Coenzyme A-associated proteins (CAPs) are a category of functionally important proteins involved in multiple biological processes through interactions with coenzyme A (CoA). To date, unfortunately, the specific differences between CAPs and other proteins have yet to be systemically investigated. Moreover, there are no computational methods that can be used specifically to predict these proteins. Herein, we characterized CAPs from multifaceted viewpoints and revealed their specific preferences. Compared with other proteins, CAPs were more likely to possess binding regions for CoA and its derivatives, were evolutionarily highly conserved, exhibited ordered and hydrophobic structural conformations, and tended to be densely located in protein-protein interaction networks. Based on these biological insights, we built seven classifiers using predicted CoA-binding residue distributions, word embedding vectors, remote homolog numbers, evolutionary conservation, amino acid composition, predicted structural features and network properties. These classifiers could effectively identify CAPs in Homo sapiens, Mus musculus and Arabidopsis thaliana. The complementarity among the individual classifiers prompted us to build a two-layer stacking model named CAPE for improving prediction performance. We applied CAPE to identify some high-confidence candidates in the three species, which were tightly associated with the known functions of CAPs. Finally, we extended our algorithm to cross-species prediction, thereby developing a generic CAP prediction model. In summary, this work provides a comprehensive survey and an effective predictor for CAPs, which can help uncover the interplay between CoA and functionally relevant proteins.

Sandstone Ground Stone Technology: a Multi-level Use Wear and Residue Approach to Investigate the Function of Pounding and Grinding Tools

Ground stone tool (GST) technology includes artefacts utilized in pounding or grinding activities and characterized by long life cycles and multiple uses. The introduction of such technology dates back to early prehistory, and for this reason, it is used as prime evidence for tackling a wide range of archaeological questions such as the origins of technology, patterns of daily subsistence and lifeways. In this paper, we contribute to the field of study of GSTs by discussing the application of a novel multi-level analytical approach combining use wear and residue observations at low and high magnification with residue spatial distribution investigated using GIS. We aim to assess the potential of a combined use wear and residue approach to (1) discriminate specific gestures and worked materials on sandstone GSTs and (2) understand the potential of residue distributions for reconstructing ancient GST functions and, more specifically, the role of GSTs recovered at Mesolithic sites of the Danube Gorges region in the Central Balkans. We identified diagnostic surface modifications associated with the use of GSTs in different activities involving both animal and plant materials. Morphological characteristics of residues have been described under reflected and transmitted light and characterized using biochemical staining. Finally, we mapped residues across the utilized surfaces of experimental tools to link patterns of residue spatial distribution to specific materials and gestures. We expect our methodological approach will be taken up by other researchers in order to produce comparable datasets on GSTs and improve our understanding of their ancient functional biographies.

Fate, residues and dietary risk assessment of the fungicides epoxiconazole and pyraclostrobin in wheat in twelve different regions, China

The fungicides epoxiconazole and pyraclostrobin have been widely used to control wheat fusarium head blight. This study was designed to investigate the dissipation behaviors in different climate regions and provide data for the modification of maximum residue limits of the two fungicides. Wheat samples were collected from field sites in twelve different regions, China and analyzed with an HPLC-MS/MS method for simultaneous detection of epoxiconazole and pyraclostrobin in wheat. The average recoveries of epoxiconazole and pyraclostrobin in wheat matrix were 87–112% and 85–102%, respectively, with the relative standard deviations ≤8.1%. The limits of quantification of epoxiconazole and pyraclostrobin in grain and straw were both 0.01 mg/kg. The dissipations of epoxiconazole and pyraclostrobin followed first-order kinetics, with the half-lives of 10.3 days and 7.6 days, respectively. The terminal residues of epoxiconazole and pyraclostrobin in grain were below 0.034 and 0.028 mg/kg, separately, both lower than the maximum residue limits recommended by China. Based on Chinese dietary pattern and terminal residue distributions, the risk quotients of epoxiconazole and pyraclostrobin were 13.9% and 65.9%, respectively, revealing the evaluated wheat exhibited an acceptably low dietary risk to consumers.

Pred-MutHTP: Prediction of disease-causing and neutral mutations in human transmembrane proteins.

Membrane proteins are unique in that segments thereof concurrently reside in vastly different physicochemical environments: the extracellular space, the lipid bilayer, and the cytoplasm. Accordingly, the effects of missense variants disrupting their sequence depend greatly on the characteristics of the environment of the protein segment affected as well as the function it performs. Because membrane proteins have many crucial roles (transport, signal transduction, cell adhesion, etc.), compromising their functionality often leads to diseases including cancers, diabetes mellitus or cystic fibrosis. Here, we report a suite of sequence-based computational methods "Pred-MutHTP" for discriminating between disease-causing and neutral alterations in their sequence. With a data set of 11,846 disease-causing and 9,533 neutral mutations, we obtained an accuracy of 74% and 78% with 10-fold group-wise cross-validation and test set, respectively. The features used in the models include evolutionary information, physiochemical properties, neighboring residue information, and specialized membrane protein attributes incorporating the number of transmembrane segments, substitution matrices specific to membrane proteins as well as residue distributions occurring in specific topological regions. Across 11 disease classes, the method achieved accuracies in the range of 75-85%. The model designed specifically for the transmembrane segments achieved an accuracy of 85% on the test set with a sensitivity and specificity of 86% and 83%, respectively. This renders our method the current state-of-the-art with regard to predicting the effects of variants in the transmembrane protein segments. Pred-MutHTP allows predicting the effect of any variant occurring in a membrane protein-available at https://www.iitm.ac.in/bioinfo/PredMutHTP/.

ChromaClade: combined visualisation of phylogenetic and sequence data

BackgroundStudying site-specific amino acid frequencies by eye can reveal biologically significant variability and lineage-specific adaptation. This so-called ‘sequence gazing’ often informs bioinformatics and experimental research. But it is important to also account for the underlying phylogeny, since similarities may be due to common descent rather than selection pressure, and because it is important to distinguish between founder effects and convergent evolution. We set out to combine phylogenetic and sequence data to produce evolutionarily insightful visualisations.ResultsWe present ChromaClade, a convenient tool with a graphical user-interface that works in concert with popular tree viewers to produce colour-annotated phylogenies highlighting residues found in each taxon and at each site in a sequence alignment. Colouring branches according to residues found at descendent tips also quickly identifies lineage-specific residues and those internal branches where key substitutions have occurred. We demonstrate applications of ChromaClade to human immunodeficiency virus and influenza A virus datasets, illustrating cases of conservative, adaptive and convergent evolution.ConclusionsWe find this to be a powerful approach for visualising site-wise residue distributions and detecting evolutionary patterns, especially in large datasets. ChromaClade is available for Windows, macOS and Unix or Linux; program executables and source code are available at github.com/chrismonit/chroma_clade.

Effect of terminal arrangement of tryptophan on biological activity of symmetric α-helix-forming peptides.

It is traditionally believed that the distribution of tryptophan (Trp) residues is critical for the novo design of antimicrobial peptides (AMPs). However, there is scarce knowledge regarding Trp residues arrangement at the head group level. Thus, a set of α-helical AMPs containing different Trp residue arrangements at the N-/C-terminal of sequence were designed to increase the strategy database and analyze their biological activities. The arrangement of the N-terminal Trp residue significantly improved the bacteriostatic activity of the peptides, but the C-terminal Trp residue arrangement reduced the biocompatibility of them. WL and LW were effective against Gram-negative microbes and had high selectivity for bacteria as compared to human erythrocytes and mammalian cells. They both maintained a relatively desirable activity in the presence of physiological salts and serum. It is observed through electron microscope, flow cytometry and fluorescence spectroscopy that target peptides can penetrate bacterial cell membrane and kill it by damaging cell membrane integrity. Collectively, we determined the structure-activity relationship of Trp residue distributions in a symmetric sequence structure and filled the gap in knowledge related to Trp arrangements at the head group level. The obtained results will be helpful in designing of artificial peptide-based antimicrobials.

Evaluating Forest Biomass Recovery in South Central Alabama Pine Plantations

AbstractImproved use of forest biomass has been presented as a viable option to satisfy a portion of the demand for sustainable alternative sources of energy. Yet, there are considerable gaps in our understanding related to the efficiencies of current state-of-the-art forest biomass recovery systems. Southern pine plantation biomass stands typically exhibit higher stand densities and smaller-diameter trees than conventional stands, which, in turn, may result in reduced recovery efficiencies. In this study, the impact of new harvest systems for biomass recovery was investigated in typical southern pine plantation biomass harvests. Specifically, spatial and temporal effects on residue distribution were examined following biomass harvest of 14- and 24-year-old loblolly pine plantations. Preharvest total standing biomass for the younger site at 90 t ac–1 (220 t hectare–1) was half that of the older site at 160 t ac–1 (390 t hectare–1). Although the analysis detected no significant temporal effects on residue distributions, the preharvest condition exhibited 100 percent ground cover, whereas postharvest conditions had nearly 20 percent of the area designated as bare. Two of the five residue classifications, light debris and litter-herbaceous, were found to have a significantly higher incidence of occurrence than the other residue classifications on the sites based on a multinomial regression. In general, we found recovery efficiencies for both sites of 80 percent or greater for both methods of determination, by destructive sampling and based on load tickets.

Recognition of sites of functional specialisation in all known eukaryotic protein kinase families.

The conserved function of protein phosphorylation, catalysed by members of protein kinase superfamily, is regulated in different ways in different kinase families. Further, differences in activating triggers, cellular localisation, domain architecture and substrate specificity between kinase families are also well known. While the transfer of γ-phosphate from ATP to the hydroxyl group of Ser/Thr/Tyr is mediated by a conserved Asp, the characteristic functional and regulatory sites are specialized at the level of families or sub-families. Such family-specific sites of functional specialization are unknown for most families of kinases. In this work, we systematically identify the family-specific residue features by comparing the extent of conservation of physicochemical properties, Shannon entropy and statistical probability of residue distributions between families of kinases. An integrated discriminatory score, which combines these three features, is developed to demarcate the functionally specialized sites in a kinase family from other sites. We achieved an area under ROC curve of 0.992 for the discrimination of kinase families. Our approach was extensively tested on well-studied families CDK and MAPK, wherein specific protein interaction sites and substrate recognition sites were successfully detected (p-value < 0.05). We also find that the known family-specific oncogenic driver mutation sites were scored high by our method. The method was applied to all known kinases encompassing 107 families from diverse eukaryotic organisms leading to a comprehensive list of family-specific functional sites. Apart from other uses, our method facilitates identification of specific protein interaction sites and drug target sites in a kinase family.

Dissipation behavior, residue distribution and dietary risk assessment of chlorfenapyr and clothianidin in leek using RRLC-QqQ-MS/MS technique

Commercial suspension emulsion (SE) of (8% chlorfenapyr+20% clothianidin), as a pre-registered product in China, was firstly investigated under Chinese open-field conditions. A MWCNTs-based QuEChERS method for simultaneous determination of chlorfenapyr and clothianidin in leek was established and validated through rapid resolution liquid chromatography triples quadrupole tandem mass spectrometry (RRLC-QqQ-MS/MS). Based on this method, the dissipation behaviors, residue distributions and dietary risk probability of these fungicides in leek from two representative locations in China in 2016, which were previously treated with these insecticides at the doses of 420–630g a.i./ha twice applications, were further investigated for food safety. Dissipation behavior of chlorfenapyr and clothianidin in leek followed first-order kinetics with the half-lives of 2.9–7.2days, and the highest residues (HR) of these insecticides in leek were below 0.3811mg/kg and 0.2989mg/kg, respectively, at the pre-harvest interval (PHI, 7days). For dietary risk assessments, the risk quotients (RQs) of chlorfenapyr and clothianidin in leek were evaluated by comparing the value of national estimated daily intake (NEDI) with acceptable daily intake (ADI), based on the trials data under good agricultural practices (GAP) conditions. The results indicated that RQs of chlorfenapyr and clothianidin in leek were 21.5% and 0.29%, respectively, which exhibited an acceptably low health risk to leek consumption. The current study could not only guide reasonable usage of the formulation, but also facilitate the setting of maximum residue limits (MRLs) of chlorfenapyr and clothianidin in leek for Chinese authorities

Corn Residue Particle Size Affects Soil Surface Properties

Core Ideas Corn harvesting practices generate characteristic residue particle size distributions. Corn residue particle size influences its composition and decomposition. Residue particle composition and decomposition influence soil properties, i.e., soil C and N. Mechanical harvesting operations affect soil properties via residue size distributions. Field operations may differentially influence crop residue size distributions, altering residue decomposition rates and soil carbon (C) and nitrogen (N) dynamics. In a laboratory microcosm study modeling corn residue distributions observed in a no‐till cropping system, microbial respiration was initially (first 30 d) inversely proportional to residue particle size across four size classes. Subsequently (30–60 d), respiration in the smallest particle size decreased in relation to the larger size classes. Residue particle size significantly increased soil C levels, with the smallest sizes producing the longest‐lasting effects (150 d). Smaller residue size classes initially (30 d) immobilized more soil N compared with larger size classes; however, at 150 d, the smaller size classes had mobilized increasing amounts of N while the larger size classes had progressively immobilized more N. We conclude that crop residue management operations changed characteristic residue size distributions that moderate decomposition activities and result in unique soil C and N dynamics, possibly influencing soil properties, including nutrient availability.

Local and global anatomy of antibody-protein antigen recognition.

Deciphering antibody-protein antigen recognition is of fundamental and practical significance. We constructed an antibody structural dataset, partitioned it into human and murine subgroups, and compared it with nonantibody protein-protein complexes. We investigated the physicochemical properties of regions on and away from the antibody-antigen interfaces, including net charge, overall antibody charge distributions, and their potential role in antigen interaction. We observed that amino acid preference in antibody-protein antigen recognition is entropy driven, with residues having low side-chain entropy appearing to compensate for the high backbone entropy in interaction with protein antigens. Antibodies prefer charged and polar antigen residues and bridging water molecules. They also prefer positive net charge, presumably to promote interaction with negatively charged protein antigens, which are common in proteomes. Antibody-antigen interfaces have large percentages of Tyr, Ser, and Asp, but little Lys. Electrostatic and hydrophobic interactions in the Ag binding sites might be coupled with Fab domains through organized charge and residue distributions away from the binding interfaces. Here we describe some features of antibody-antigen interfaces and of Fab domains as compared with nonantibody protein-protein interactions. The distributions of interface residues in human and murine antibodies do not differ significantly. Overall, our results provide not only a local but also a global anatomy of antibody structures.

Simultaneous Determination of Pyraclostrobin, Prochloraz, and its Metabolite in Apple and Soil Via RRLC-MS/MS

A sensitive and high-efficiency method for simultaneous detection of pyraclostrobin, prochloraz, and its metabolite in apple and soil based on QuEChERS pretreatment combined with rapid resolution liquid chromatography tandem mass spectrometry was established and validated. The limits of quantification of three compounds in two matrixes were 0.005 mg kg−1. The average recoveries of pyraclostrobin, prochloraz, and 2,4,6-trichlorophenol in soil matrix were in the ranges of 87–105%, 86–95%, and 90–96%, respectively, with all the relative standard deviations (RSDs) of < 9.6%, while recoveries were 89–93%, 83–97%, and 89–101% in apple with the RSDs of < 6.5% at three spiking levels. For verify the applicability of this method, the real samples from three representative locations were detected. The degradation behaviors and residue distributions of pyraclostrobin and prochloraz and its metabolite in apple ecosystem were investigated. The field experiment data showed that the dissipation of pyraclostrobin and prochloraz in apple and soil followed pseudo-first-order kinetic models. The half-lives of pyraclostrobin in soil and apple were 8.6–19.8 and 7.9–15.1 days, while prochloraz were 8.9–21 and 5.8–12.4 days. The highest terminal residue of total prochloraz and pyraclostrobin in apple, after spraying three to four times with the interval of 28 days, was far below the maximum residue limits recommended by China. This research could provide guidance on a reasonable usage of prochloraz and pyraclostrobin in apple orchard.

Dissipation behaviour, residue distribution and dietary risk assessment of tetraconazole and kresoxim-methyl in greenhouse strawberry via RRLC-QqQ-MS/MS technique

20% commercial suspension emulsion (SE) of (8% tetraconazole + 12% kresoxim-methyl), as a pre-registered product in China, was firstly investigated under Chinese greenhouse-field conditions. A MWCNTs-based QuEChERS method for simultaneous determination of tetraconazole and kresoxim-methyl in strawberry was developed and validated via RRLC-QqQ-MS/MS. On basis of this method, the dissipation behaviours, residue distributions and dietary risk probability of these fungicides in strawberry were further investigated for food safety. The dissipations of tetraconazole and kresoxim-methyl followed first-order kinetics with the half-lives of 8.0–18.2 days. The highest residues (HRs) of these fungicides in the supervised trials at the pre-harvest interval (PHI, 3 days) were below 0.8970mgkg−1. The total national estimated daily intake (NEDI) of tetraconazole and kresoxim-methy in strawberry at the PHI 3day was 0.2784mg and 0.4031mg, respectively, based on Chinese dietary pattern and terminal residue distributions under good agricultural practices (GAP) conditions. The risk quotients (RQs) of tetraconazole and kresoxim-methy at PHI 3 days were below 82.7% and 1.6%, respectively, showing that the evaluated strawberry exhibited an acceptably low dietary risk to consumers. The current study could not only guide reasonable usage of the formulation, but also facilitate the setting of maximum residue limits (MRLs) of tetraconazole in strawberry.

Two-domain analysis of JmjN-JmjC and PHD-JmjC lysine demethylases: Detecting an inter-domain evolutionary stress.

Residues at different positions of a multiple sequence alignment sometimes evolve together, due to a correlated structural or functional stress at these positions. Co-evolution has thus been evidenced computationally in multiple proteins or protein domains. Here, we wish to study whether an evolutionary stress is exerted on a sequence alignment across protein domains, i.e., on longer sequence separations than within a single protein domain. JmjC-containing lysine demethylases were chosen for analysis, as a follow-up to previous studies; these proteins are important multidomain epigenetic regulators. In these proteins, the JmjC domain is responsible for the demethylase activity, and surrounding domains interact with histones, DNA or partner proteins. This family of enzymes was analyzed at the sequence level, in order to determine whether the sequence of JmjC-domains was affected by the presence of a neighboring JmjN domain or PHD finger in the protein. Multiple positions within JmjC sequences were shown to have their residue distributions significantly altered by the presence of the second domain. Structural considerations confirmed the relevance of the analysis for JmjN-JmjC proteins, while among PHD-JmjC proteins, the length of the linker region could be correlated to the residues observed at the most affected positions. The correlation of domain architecture with residue types at certain positions, as well as that of overall architecture with protein function, is discussed. The present results thus evidence the existence of an across-domain evolutionary stress in JmjC-containing demethylases, and provide further insights into the overall domain architecture of JmjC domain-containing proteins.

Influence of various parts of sweet corn ears on pesticide residue levels.

Pesticide residue levels in various parts of sweet corn ears were analyzed. For this purpose, five pesticides were sprayed on corn in two different fields, and the harvested samples were separated into four portions, namely kernels, cobs, silks, and husks. Each of these portions was then separately analyzed. Pesticide residues were predominantly distributed in the silk and husk portions, which constituted ≥91% of the whole crop, whereas relatively minimal residues remained in the kernel and cob portions. Further, residue distributions in the silks and husks were found to differ between the two fields. The calculated residue levels in kernels with the cob and silk were obviously higher than the residue levels in the kernel alone (max. >62 times different). This result suggests that the silk portion could greatly affect pesticide residue levels in the edible portion of corn.