Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity.

Soybean nodulation is a highly controlled process that involves complex gene regulation at both transcriptional and post-transcriptional levels. In the present study, we profiled gene expression changes, alternative splicing events, and DNA methylation patterns during nodule formation, development, and senescence. The transcriptome data uncovered key transcription patterns of nodule development that included 9669 core genes and 7302 stage-specific genes. Alternative splicing analysis uncovered a total of 2323 genes that undergo alternative splicing events in at least one nodule developmental stage, with activation of exon skipping and repression of intron retention being the most common splicing events in nodules compared to roots. Approximately 40% of the differentially spliced genes were also differentially expressed at the same nodule developmental stage, implying a substantial association between gene expression and alternative splicing. Genome-wide-DNA methylation analysis revealed dynamic changes in nodule methylomes that were specific to each nodule stage, occurred in a sequence-specific manner, and impacted the expression of 1864 genes. An attractive hypothesis raised by our data is that increased DNA methylation may contribute to the efficiency of alternative splicing. Together, our results provide intriguing insights into the associations between gene expression, alternative splicing, and DNA methylation that may shape transcriptome complexity and proteome specificity in developing soybean nodules.

How Charge and Triple Size-Selective Membrane Separation of Peptides from Salmon Protein Hydrolysate Orientate their Biological Response on Glucose Uptake.

The valorization of by-products from natural organic sources is an international priority to respond to environmental and economic challenges. In this context, electrodialysis with filtration membrane (EDFM), a green and ultra-selective process, was used to separate peptides from salmon frame protein hydrolysate. For the first time, the simultaneous separation of peptides by three ultrafiltration membranes of different molecular-weight exclusion limits (50, 20, and 5 kDa) stacked in an electrodialysis system, allowed for the generation of specific cationic and anionic fractions with different molecular weight profiles and bioactivity responses. Significant decreases in peptide recovery, yield, and molecular weight (MW) range were observed in the recovery compartments depending on whether peptides had to cross one, two, or three ultrafiltration membranes. Moreover, the Cationic Recovery Compartment 1 fraction demonstrated the highest increase (42%) in glucose uptake on L6 muscle cells. While, in the anionic configuration, both Anionic Recovery Compartment 2 and Anionic Recovery Compartment 3 fractions presented a glucose uptake response in basal condition similar to the insulin control. Furthermore, Cationic Recovery Compartment 3 was found to contain inhibitory peptides. Finally, LC-MS analyses of the bioassay-guided bioactive fractions allowed us to identify 11 peptides from salmon by-products that are potentially responsible for the glucose uptake improvement.

Selection of risk factors to be included in the Canadian Food Inspection Agency risk assessment inspection model for food establishments.

The Canadian Food Inspection Agency (CFIA) is developing a risk assessment model for food establishments. Previous research on the significance of food safety risk factors determined by literature review and expert advice served as the bases for the current study, to further refine, discriminate and select the most important criteria to be included in the model. This process considered the availability of data sources, the clarity and measurability of the selected factors, undertook the elimination of lower-rated risk factors and grouped those with similar focus of attention, enabling the selection of a final list of risk factors for the model. A method of assessment for the remaining factors was then proposed to allow the quantification of individual risk factors within the model. From the 155 risk factors initially identified, 17 consolidated factors were kept and will be considered for the development of the risk assessment model.

Low-Molecular-Weight Peptides from Salmon Protein Prevent Obesity-Linked Glucose Intolerance, Inflammation, and Dyslipidemia in LDLR-/-/ApoB100/100 Mice.

BACKGROUND: We previously reported that fish proteins can alleviate metabolic syndrome (MetS) in obese animals and human subjects. OBJECTIVES: We tested whether a salmon peptide fraction (SPF) could improve MetS in mice and explored potential mechanisms of action. METHODS: ApoB(100) only, LDL receptor knockout male mice (LDLR(-/-)/ApoB(100/100)) were fed a high-fat and -sucrose (HFS) diet (25 g/kg sucrose). Two groups were fed 10 g/kg casein hydrolysate (HFS), and 1 group was additionally fed 4.35 g/kg fish oil (FO; HFS+FO). Two other groups were fed 10 g SPF/kg (HFS+SPF), and 1 group was additionally fed 4.35 g FO/kg (HFS+SPF+FO). A fifth (reference) group was fed a standard feed pellet diet. We assessed the impact of dietary treatments on glucose tolerance, adipose tissue inflammation, lipid homeostasis, and hepatic insulin signaling. The effects of SPF on glucose uptake, hepatic glucose production, and inducible nitric oxide synthase activity were further studied in vitro with the use of L6 myocytes, FAO hepatocytes, and J774 macrophages. RESULTS: Mice fed HFS+SPF or HFS+SPF+FO diets had lower body weight (protein effect, P = 0.024), feed efficiency (protein effect, P = 0.018), and liver weight (protein effect, P = 0.003) as well as lower concentrations of adipose tissue cytokines and chemokines (protein effect, P ≤ 0.003) compared with HFS and HFS+FO groups. They also had greater glucose tolerance (protein effect, P < 0.001), lower activation of the mammalian target of rapamycin complex 1/S6 kinase 1/insulin receptor substrate 1 (mTORC1/S6K1/IRS1) pathway, and increased insulin signaling in liver compared with the HFS and HFS+FO groups. The HFS+FO, HFS+SPF, and HFS+SPF+FO groups had lower plasma triglycerides (protein effect, P = 0.003; lipid effect, P = 0.002) than did the HFS group. SPF increased glucose uptake and decreased HGP and iNOS activation in vitro. CONCLUSIONS: SPF reduces obesity-linked MetS features in LDLR(-/-)/ApoB(100/100) mice. The anti-inflammatory and glucoregulatory properties of SPF were confirmed in L6 myocytes, FAO hepatocytes, and J774 macrophages.

Interaction of protamine with gram-negative bacteria membranes: possible alternative mechanisms of internalization in Escherichia coli, Salmonella typhimurium and Pseudomonas aeruginosa.

This study was concerned with the interaction between the cationic antimicrobial peptide, protamine (Ptm) and the cytoplasmic membranes of the gram-negative bacteria Escherichia coli, Salmonella typhimurium and Pseudomonas aeruginosa. The objective of the study was to explain the observed paradox of internalization without permanent disruption of the cell envelope. We carried out Monte Carlo computer simulation of Ptm in an aqueous environment in the presence of ~100 mM NaCl and model membranes consisting of either (65:35) or (75:25) PE:PG molar ratios. The (75:25) model, representative of the gram-negative cytoplasmic membrane, showed that the Ptm center of mass remained at least 7 nm from the membrane surface leading to the prediction that Ptm would not internalize via disruption of the inner membrane. By using immunoelectron microscopy of Ptm-treated cells, we showed that Ptm internalization to the cytoplasm took place rapidly in the presence or absence of the outer envelope. Ultrastructural examination revealed no obvious morphological changes to cells that were treated with subinhibitory or bactericidal levels of Ptm. Reconstituted phospholipid bilayers were constructed and were unperturbed by Ptm treatment over a wide range of concentrations and applied transmembrane voltages. We conclude that in the cases of the cell envelopes of E. coli, S. typhimurium and P. aeruginosa, Ptm internalized by means independent of the phospholipid bilayer, most likely mediated by one or more membrane proteins such as cation-selective barrel-like proteins. Work is currently underway to test this hypothesis.

Glucoregulatory and Anti-Inflammatory Activities of Peptide Fractions Separated by Electrodialysis with Ultrafiltration Membranes from Salmon Protein Hydrolysate and Identification of Four Novel Glucoregulatory Peptides.

Natural bioactive peptides are suitable candidates for preventing the development of Type 2 diabetes (T2D), by reducing the various risk factors. The aim of this study was to concentrate glucoregulatory and anti-inflammatory peptides, from salmon by-products, by electrodialysis with ultrafiltration membrane (EDUF), and to identify peptides responsible for these bioactivities. Two EDUF configurations (1 and 2) were used to concentrate anionic and cationic peptides, respectively. After EDUF separation, two fractions demonstrated interesting properties: the initial fraction of the EDUF configuration 1 and the final fraction of the EDUF configuration 2 both showed biological activities to (1) increase glucose uptake in L6 muscle cells in insulin condition at 1 ng/mL (by 12% and 21%, respectively), (2) decrease hepatic glucose production in hepatic cells at 1 ng/mL in basal (17% and 16%, respectively), and insulin (25% and 34%, respectively) conditions, and (3) decrease LPS-induced inflammation in macrophages at 1 g/mL (45% and 30%, respectively). More impressive, the initial fraction of the EDUF configuration 1 (45% reduction) showed the same effect as the phenformin at 10 µM (40%), a drug used to treat T2D. Thirteen peptides were identified, chemically synthesized, and tested in-vitro for these three bioactivities. Thus, four new bioactive peptides were identified: IPVE increased glucose uptake by muscle cells, IVDI and IEGTL decreased hepatic glucose production (HGP) of insulin, whereas VAPEEHPTL decreased HGP under both basal condition and in the presence of insulin. To the best of our knowledge, this is the first time that (1) bioactive peptide fractions generated after separation by EDUF were demonstrated to be bioactive on three different criteria; all involved in the T2D, and (2) potential sequences involved in the improvement of glucose uptake and/or in the regulation of HGP were identified from a salmon protein hydrolysate.

Salmon peptides limit obesity-associated metabolic disorders by modulating a gut-liver axis in vitamin D-deficient mice.

OBJECTIVE: This study investigated the effects of a low-dose salmon peptide fraction (SPF) and vitamin D3 (VitD3 ) in obese and VitD3 -deficient mice at risk of metabolic syndrome (MetS). METHODS: Obese and VitD3 -deficient low-density lipoprotein receptor (LDLr)-/- /apolipoprotein B100 (ApoB)100/100 mice were treated with high-fat high-sucrose diets, with 25% of dietary proteins replaced by SPF or a nonfish protein mix (MP). The SPF and MP groups received a VitD3 -deficient diet or a supplementation of 15,000 IU of VitD3 per kilogram of diet. Glucose homeostasis, atherosclerosis, nonalcoholic fatty liver disease, and gut health were assessed. RESULTS: VitD3 supplementation increased plasma 25-hydroxyvitamin D to optimal status whereas the VitD3 -deficient diet maintained moderate deficiency. SPF-treated groups spent more energy and accumulated less visceral fat in association with an improved adipokine profile. SPF lowered homeostatic model assessment of insulin resistance compared with MP, suggesting that SPF can improve insulin sensitivity. SPF alone blunted hepatic and colonic inflammation, whereas VitD3 supplementation attenuated ileal inflammation. These effects were associated with changes in gut microbiota such as increased Mogibacterium and Muribaculaceae. CONCLUSIONS: SPF treatment improves MetS by modulating hepatic and gut inflammation along with gut microbiota, suggesting that SPF operates through a gut-liver axis. VitD3 supplementation has limited influence on MetS in this model.

Pseudoalteromonas bacteria are capable of degrading paralytic shellfish toxins.

Marine bacterial isolates cultured from the digestive tracts of blue mussels (Mytilus edulis) contaminated with paralytic shellfish toxins (PSTs) were screened for the ability to reduce the toxicity of a PST mixture. Seven isolates reduced the overall toxicity of the algal extract by > or = 90% within 3 days. These isolates shared at least 99% 16S rRNA gene sequence similarity with five Pseudoalteromonas spp. Phenotypic tests suggested that all are novel strains of Pseudoalteromonas haloplanktis.

Improving Education in Agricultural Biosciences through Studying Abroad in the United States.

Studying abroad in agricultural biosciences can develop students' cultural, academic, and communication skills and enhance employability. However, in the United States, discussions of study abroad are limited to either one-way directionality (U.S. students to other countries) or to the experiences of international students who come to the United States for degree programs. We analyzed the perspectives and experiences of studying abroad by Zamorano University (Honduras) students who completed an agricultural bioscience pasantía (four-month internship) during the final year of their undergraduate program. We used mixed methods to collect data via focus group discussions and a survey with Zamorano students who had completed a pasantía in 2017, as well as key informant interviews with Zamorano pasantía coordinators. Study-abroad experiences were compared between students who completed their pasantía in the United States (37%) and those who completed their pasantía in any of 17 other countries worldwide. Significant relationships were identified (p < 0.05) between: doing a pasantía in the United States (compared with going elsewhere) and improving science and theoretical knowledge; having a hands-on experience and science and theory improvement; improving communication and confidence in using scientific methods. The Zamorano pasantía model lends insights into the value of study abroad for agricultural bioscience education.

Estudiar en el extranjero puede desarrollar habilidades culturales, académicas y de comunicación en los estudiantes de biociencias agrícolas, sobre todo potencializar la empleabilidad. Sin embargo, las discusiones en los Estados Unidos sobre estudios en el extranjero son limitadas a vías unidireccionales (estudiantes de EE.UU. hacia otros países) o las experiencias de estudiantes internacionales durante sus estudios superiores en los Estados Unidos. Analizamos la perspectiva y experiencia de estudiar en el extranjero con estudiantes de la Universidad Zamorano (Honduras), quienes completaron una pasantía en biociencias agrícolas durante su último año del programa de pregrado. Utilizamos métodos mixtos para obtener datos a través de entrevistas con los coordinadores de las pasantías en Zamorano, discusión de grupos focales y encuestas a los estudiantes de Zamorano quienes habían completado su pasantía en el 2017. Se compararon estudios en el exterior entre estudiantes que completaron su pasantía en Estados Unidos (37%) contra aquellos que completaron su pasantía en cualquiera de los otros 17 países del mundo. Se identificaron relaciones significativas (P < 0.05) entre: realizar una pasantía en Estados (comparada a realizarla en cualquier otro lugar) y el aumento del conocimiento teórico y científico; teniendo experiencias prácticas y mejoras en la ciencia y la teoría; mejoras en la comunicación y la confianza en el uso de métodos científicos. El modelo de pasantía de Zamorano brinda información sobre el valor de estudios sobre biociencias agrícolas en el extranjero.

Source attribution at the food sub-product level for the development of the Canadian Food Inspection Agency risk assessment model.

Decreasing the health burden caused by foodborne pathogens is challenging and it depends on the identification of the most significant hazards and food sources causing illnesses, so adequate mitigation strategies can be implemented. In this regard, the Canadian Food Inspection Agency (CFIA) has developed the Establishment-based Risk Assessment (ERA) model, so that a more effective and efficient allocation of resources can be assigned to the highest food safety risk areas. To assess risk, the model considers the type of food sub-products being manufactured by establishments and its scope is limited to the 17 most important foodborne pathogens representing the highest level of food safety risk. However, the information on source attribution at the sub-product level based on a structured approach is limited. To overcome this challenge, an expert elicitation was conducted in 2016 to estimate the relative contribution and associated certainty of each sub-product for 31 pathogen-commodity combinations to the total Canadian health burden associated with foodborne illnesses (expressed in DALYs). These DALYs represent 78% of the total Canadian health burden associated with federally-regulated food commodities considered within the model. A total of 49 Canadian experts recruited using a "snow ball" sampling strategy participated in the study by completing an electronic survey. Results of the elicitation displayed variable levels of health burden allocation between the pathogens and the different commodity sub-products. Assessment of the certainty levels showed some combinations being evaluated with more confidence (e.g., Campylobacter and eggs/poultry sub-products) than others, where a bimodal distribution of certainty was observed (e.g., Toxoplasma in pork sub-products). Furthermore, no participant raised concerns on the food classification scheme, suggesting their agreement with the proposed sub-products categorization of the elicitation. Relative contribution estimates will be included in the CFIA ERA model and used to enhance its applicability for risk prioritization and effective resource allocation during food establishment inspections. While substantial uncertainty around the central tendency estimates was found, these estimates provide a good basis for regulatory oversight and public health policy.

Bacterial degradation of paralytic shellfish toxins.

Bacteria isolated from the digestive tracts of blue mussels (Mytilus edulis) contaminated with paralytic shellfish toxins (PSTs) were screened for the ability to reduce the toxicity of a PST mixture in vitro. Bacteria were isolated on marine agar and grown in marine broth supplemented with a mussel extract and an algal extract containing PSTs (saxitoxin, neosaxitoxin, gonyautoxins 2 and 3, decarbamoyl-gonyautoxins 2 and 3 and C1/C2 toxins). Toxin levels were measured before and after 5d of incubation, using high performance liquid chromatography (HPLC) and reduction of overall toxicity verified by mouse bioassays. Of the 73 bacterial cultures screened, seven isolates were designated "competent" PST degraders, individually reducing the overall toxicity of the PSTs by at least 90% within 3d. Most isolates degraded 100% of the saxitoxin and neosaxitoxin within 1-3d. In all cases, the overall kinetics of degradation of the toxicities was first order, as were the individual degradation kinetics of most of the individual toxins. This is the first report of nearly complete elimination of PSTs through bacterial action and may perhaps result in the development of a practical means to eliminate or reduce the risk of PSP intoxication associated with shellfish consumption.

Thermal denaturation and aggregation properties of Atlantic salmon myofibrils and myosin from white and red muscles.

Thermal denaturation and aggregation abilities of salmon myofibrils and myosin were studied measuring turbidity, intrinsic fluorescence, 8-anilino-1-naphthalene sulfonic acid binding, and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide cross-linking. The thermal behaviors of protein preparation from white and red muscles were compared, and the relationship with thermal gelation properties is discussed. The low gelation ability of salmon muscle proteins was related to a limited extent of protein denaturation and aggregation upon heating. These properties seemed to be carried by myosin molecules as a similar behavior was observed for both myofibrils and myosin preparations. The higher thermal stability observed for red muscle proteins with higher transition temperatures in rheological profiles was related to a shift to higher temperature in denaturation and aggregation processes. The extent of denaturation and aggregation was very similar for both muscle types as was the final rigidity of the gels formed.

Astaxanthin binding protein in Atlantic salmon.

The rubicund pigmentation in salmon and trout flesh is unique and is due to the deposition of dietary carotenoids, astaxanthin and canthaxanthin in the muscle. The present study was undertaken to determine which protein was responsible for pigment binding. Salmon muscle proteins were solubilized by sequential extractions with non-denaturing, low ionic strength aqueous solutions and segregated as such into six different fractions. Approximately 91% of the salmon myofibrillar proteins were solubilized under non-denaturing conditions using a protocol modified from a method described by Krishnamurthy et al. [Krishnamurthy, G., Chang, H.S., Hultin, H.O., Feng, Y., Srinivasan, S., Kelleher. S.D., 1996. Solubility of chicken breast muscle proteins in solutions of low ionic strength. J. Agric. Food Chem. 44: 408-415.] for the dissolution of avian muscle. To our knowledge, this is the first time this solubilization approach has been applied to the study of molecular interactions in myofibrillar proteins. Astaxanthin binding in each fraction was determined using an in vitro binding assay. In addition, SDS-PAGE and quantitative densitometry were used to separate and determine the relative amounts of each of the proteins in the six fractions. The results showed that alpha-actinin was the only myofibrillar protein correlating significantly (P<0.05) with astaxanthin binding. Alpha-actinin was positively identified using electrophoretic techniques and confirmed by tandem mass spectroscopy. Purified salmon alpha-actinin bound synthetic astaxanthin in a molar ratio of 1.11:1.00. The study was repeated using halibut alpha-actinin, which was found to have a molar binding ratio of astaxanthin to alpha-actinin of 0.893:1. These results suggest that the difference in pigmentation between white fish and Atlantic salmon is not due to binding capacity in the muscle, but rather differences in the metabolism or transport of pigment.

Inhibition of foodborne bacteria by native and modified protamine: importance of electrostatic interactions.

Protamine is a naturally occurring cationic antimicrobial peptide (CAP) that has shown some promise for control of microorganisms in food. It was hypothesized that the antibacterial effect is partially due to protamine's electrostatic affinity to the negatively charged cell envelopes of actively growing bacteria. However, nonspecific binding of the CAPs to negatively charged food particles may reduce the effect in food systems. To test the hypothesis, the antibacterial efficacies of native and reduced charge protamines (chemically modified by randomly blocking 10 to 71% of the guanido groups of the arginine residues) were compared in model and food systems. In Tryptic Soy Broth, moderate reductions of charge (<26%) resulted in either a similar or slightly improved antimicrobial efficacy, measured as the minimum inhibitory concentration (MIC) toward 21 food-related bacteria. Further reductions in positive charge led to lower antimicrobial activity. Compared to protamine, the affinity of reduced charge protamines (10 and 20%) for binding to Listeria monocytogenes cells was higher at pH 7 and 8. As perhaps would be expected, L. monocytogenes is most sensitive to modified protamines in this pH range. Protamine with reduced charge (14 and 23%) inhibited growth of L. monocytogenes in milk as well as total bacteria and coliforms in ground beef significantly (P<0.05) better than native protamine, demonstrating that the reduced charge peptides were more inhibitory in these high protein food matrices. Electrophoretic analysis of the 21 bacteria revealed a statistically significant (P<0.01) relationship with antimicrobial activity, where the most negatively charged bacteria were also the most susceptible to protamine. In conclusion, components of food matrices interfered with the antibacterial effects of the peptides, however; these undesirable interferences were reduced by altering the electrostatic properties of protamine.

Kinetics of the inhibition of renin and angiotensin I-converting enzyme by cod (Gadus morhua) protein hydrolysates and their antihypertensive effects in spontaneously hypertensive rats.

BACKGROUND: Cod muscle has a balanced protein profile that contains potentially bioactive amino acid sequences. However, there is limited information on release of these peptides from the parent proteins and their ability to modulate mammalian blood pressure. OBJECTIVE: The aim of this study was to generate cod antihypertensive peptides with potent in vitro inhibitory effects against angiotensin-converting enzyme (ACE) and renin. The most active peptides were then tested for systolic blood pressure (SBP)-reducing ability in spontaneously hypertensive rats (SHRs). DESIGN: Cod protein hydrolysate (CPH) was produced by subjecting the muscle proteins to proteolysis first by pepsin and followed by trypsin+chymotrypsin combination. In order to enhance peptide activity, the CPH was subjected to reverse-phase (RP)-HPLC separation to yield four fractions (CF1, CF2, CF3, and CF4). The CPH and RP-HPLC fractions were each tested at 1 mg/mL for ability to inhibit in vitro ACE and renin activities. CPH and the most active RP-HPLC fraction (CF3) were then used for enzyme inhibition kinetics assays followed by oral administration (200 and 30 mg/kg body weight for CPH and CF3, respectively) to SHRs and SBP measurements within 24 h. RESULTS: The CPH, CF3, and CF4 had similar ACE-inhibitory activities of 84, 85, and 87%, which were significantly (p<0.05) higher than the values for CF1 (69%) and CF2 (79%). Conversely, the CF3 had the highest (63%) renin-inhibitory activity (p<0.05) when compared to CPH (43%), CF1 (15%), and CF4 (44%). CPH and CF3 exhibited uncompetitive mode of ACE inhibition, whereas renin inhibition was non-competitive. Even at a 6.7-fold lower dosage, the CF3 significantly (p<0.05) reduced SBP (maximum -40.0 mmHg) better than CPH (maximum -19.1 mmHg). CONCLUSIONS: RP-HPLC fractionation led to enhanced antihypertensive effects of cod peptides, which may be due to a stronger renin-inhibitory activity.

Evaluation of the in vitro antioxidant properties of a cod (Gadus morhua) protein hydrolysate and peptide fractions.

Mechanically-deboned cod muscle proteins were sequentially hydrolysed using pepsin and a trypsin+chymotrypsin combination, which was followed by passing the digest through a 1 kDa equipped tangential flow filtration system; the permeate (<1 kDa peptides) was collected as the cod protein hydrolysate (CPH). Reversed-phase high performance liquid chromatography (RP-HPLC) was used to separate the CPH into four peptide fractions (CF1-CF4) and their in vitro antioxidant properties investigated. Results showed that most of the peptide fractions (CF2-CF4) displayed significantly higher (p<0.05) oxygen radical absorbance capacity values (698-942 µM Trolox equivalents, TE/g) and 2,2-diphenyl-1-picrylhydrazyl scavenging activities (17-32%) than those of CPH (613 µM TE/g and 19%, respectively). However, the unfractionated CPH displayed improved capability to scavenge superoxide and hydroxyl radicals as well as significantly higher (p<0.05) ferric iron reduction and chelation of iron than the RP-HPLC peptides. The CPH and peptide fractions displayed a dose-dependent inhibition of linoleic acid oxidation.

Physical interactions of fish protamine and antisepsis peptide drugs with bacterial membranes revealed by combination of specular x-ray reflectivity and grazing-incidence x-ray fluorescence.

As a defined model of outer membranes of gram negative bacteria, we investigated the interaction of monolayers of lipopolysacchrides from Salmonella enterica rough strains R90 (LPS Ra) with natural and synthetic peptides. The fine structures perpendicular to the membrane plane and the ion distribution near the interface were determined by specular x-ray reflectivity (XRR) and grazing-incidence x-ray fluorescence (GIXF) in the presence and absence of divalent cations. The unique combination of XRR and GIXF allows for the quantitative identification of different modes of interactions in a high spatial resolution, which cannot be assessed by other experimental methods. Natural fish protamine disrupts the stratified membrane structures in the absence of Ca(2+) ions, while staying away from the membrane surface in the presence of Ca(2+) ions. In contrast, synthetic antisepsis peptide Pep 19-2.5 weakly adsorbs to the membrane and stays near the uncharged sugar units even in the absence of Ca(2+). In the presence of Ca(2+), Pep 19-2.5 can reach the negatively charged inner core without destroying the barrier capability against ions.

Crucial roles of charged saccharide moieties in survival of gram negative bacteria against protamine revealed by combination of grazing incidence x-ray structural characterizations and Monte Carlo simulations.

Grazing incidence x-ray scattering techniques and Monte Carlo (MC) simulations are combined to reveal the influence of molecular structure (genetic mutation) and divalent cations on the survival of gram negative bacteria against cationic peptides such as protamine. The former yields detailed structures of bacterial lipopolysaccharide (LPS) membranes with minimized radiation damages, while the minimal computer model based on the linearized Poisson-Boltzmann theory allows for the simulation of conformational changes of macromolecules (LPSs and peptides) that occur in the time scale of ms. The complementary combination of the structural characterizations and MC simulation demonstrates that the condensations of divalent ions (Ca2+ or Mg2+) in the negatively charged core saccharides are crucial for bacterial survival.