Dirigent isoflavene-forming PsPTS2: 3D structure, stereochemical, and kinetic characterization comparison with pterocarpan-forming PsPTS1 homolog in pea

Pea phytoalexins (-)-maackiain and (+)-pisatin have opposite C6a/C11a configurations, but biosynthetically how this occurs is unknown. Pea dirigent-protein (DP) PsPTS2 generates 7,2'-dihydroxy-4',5'-methylenedioxyisoflav-3-ene (DMDIF), and stereoselectivity toward four possible 7,2'-dihydroxy-4',5'-methylenedioxyisoflavan-4-ol (DMDI) stereoisomers was investigated. Stereoisomer configurations were determined using NMR spectroscopy, electronic circular dichroism, and molecular orbital analyses. PsPTS2 efficiently converted cis-(3R,4R)-DMDI into DMDIF 20-fold faster than the trans-(3R,4S)-isomer. The 4R-configured substrate's near β-axial OH orientation significantly enhanced its leaving group abilities in generating A-ring mono-quinone methide (QM), whereas 4S-isomer's α-equatorial-OH was a poorer leaving group. Docking simulations indicated that the 4R-configured β-axial OH was closest to Asp51, whereas 4S-isomer's α-equatorial OH was further away. Neither cis-(3S,4S)- nor trans-(3S,4R)-DMDIs were substrates, even with the former having C3/C4 stereochemistry as in (+)-pisatin. PsPTS2 used cis-(3R,4R)-7,2'-dihydroxy-4'-methoxyisoflavan-4-ol [cis-(3R,4R)-DMI] and C3/C4 stereoisomers to give 2',7-dihydroxy-4'-methoxyisoflav-3-ene (DMIF). DP homologs may exist in licorice (Glycyrrhiza pallidiflora) and tree legume Bolusanthus speciosus, as DMIF occurs in both species. PsPTS1 utilized cis-(3R,4R)-DMDI to give (-)-maackiain 2200-fold more efficiently than with cis-(3R,4R)-DMI to give (-)-medicarpin. PsPTS1 also slowly converted trans-(3S,4R)-DMDI into (+)-maackiain, reflecting the better 4R configured OH leaving group. PsPTS2 and PsPTS1 provisionally provide the means to enable differing C6a and C11a configurations in (+)-pisatin and (-)-maackiain, via identical DP-engendered mono-QM bound intermediate generation, which PsPTS2 either re-aromatizes to give DMDIF or PsPTS1 intramolecularly cyclizes to afford (-)-maackiain. Substrate docking simulations using PsPTS2 and PsPTS1 indicate cis-(3R,4R)-DMDI binds in the anti-configuration in PsPTS2 to afford DMDIF, and the syn-configuration in PsPTS1 to give maackiain.

Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody-Antigen Interactions

This perspective sheds light on the transformative impact of recent computational advancements in the field of protein therapeutics, with a particular focus on the design and development of antibodies. Cutting-edge computational methods have revolutionized our understanding of protein-protein interactions (PPIs), enhancing the efficacy of protein therapeutics in preclinical and clinical settings. Central to these advancements is the application of machine learning and deep learning, which offers unprecedented insights into the intricate mechanisms of PPIs and facilitates precise control over protein functions. Despite these advancements, the complex structural nuances of antibodies pose ongoing challenges in their design and optimization. Our review provides a comprehensive exploration of the latest deep learning approaches, including language models and diffusion techniques, and their role in surmounting these challenges. We also present a critical analysis of these methods, offering insights to drive further progress in this rapidly evolving field. The paper includes practical recommendations for the application of these computational techniques, supplemented with independent benchmark studies. These studies focus on key performance metrics such as accuracy and the ease of program execution, providing a valuable resource for researchers engaged in antibody design and development. Through this detailed perspective, we aim to contribute to the advancement of antibody design, equipping researchers with the tools and knowledge to navigate the complexities of this field.

Predicted Cardiac Toxicity in Daily Cone-Beam CT-Based Online Adaptive Stereotactic Partial Breast Irradiation with Decreased PTV Margins

PURPOSE/OBJECTIVE(S)

Partial breast irradiation (PBI) targets a smaller volume over less time compared to whole breast radiation, but the organ-at-risk (OAR) sparing allowed by its large (up to 1 cm) PTV can be improved. The heart is sensitive to low doses with conventional fractionation and NTCP models have been created for heart substructures. We hypothesized that daily online adaptive stereotactic PBI (A-SPBI) IMRT with 3-mm PTV improves dosimetry and predicted cardiac toxicity risk.

MATERIALS/METHODS

Patients treated with daily CBCT-based online A-SPBI IMRT were excluded if the minimum heart dose was <1 Gy. IMRT radiation plans with 3-mm PTV margins were recreated with 1-cm margins per the Florence APBI IMRT trial planning guideline. Dose statistics were converted to the equivalent doses in 2-Gy fractions (EQD2) using α/β = 3 for use in NTCP models and for comparison using paired t tests, with differences considered significant if p≤0.05.

RESULTS

The table details heart, left anterior descending artery (LAD), and left (LV) and right ventricle (RV) EQD2 statistics for 4 left-sided and 4 right-sided 3-mm PTV plans and their 1-cm PTV replans. For 2 patients with non-zero LV V5, 9-year excess cumulative risk of acute coronary event was <0.001% for both margin sizes. No plan reached thresholds for increased risk of non-cardiac death, major adverse cardiac event, or >10% decrease in LV ejection fraction.

CONCLUSION

Given the established relationship between low MHD and cardiac events, the significant decrease in MHD revealed in comparisons of 3-mm and 1-cm PTV A-SPBI plans of our first 8 patients is promising; we expect the forthcoming larger sample size to show significant differences in substructure doses. NTCP models created for non-IMRT breast plans and targets with higher heart exposure did not predict clinically-relevant differences in cardiac risk. NTCP model development for the low heart dose achieved with A-SPBI would define expected benefit in these patients; in their absence, daily adaptation should be considered in patients with unfavorable anatomy or cardiac risk factors.

Observed and Predicted Toxicity in Daily Cone-Beam CT-Based Online Adaptive Stereotactic Partial Breast Irradiation with Decreased PTV Margins

PURPOSE/OBJECTIVE(S)

Accelerated partial breast irradiation (APBI) delivers smaller radiation volumes over less time compared to whole breast irradiation (WBI), but the organ-at-risk (OAR) sparing allowed by its large (up to 1 cm) planning target volume (PTV) can be improved. PTV can be decreased with daily online adaptive planning, which we hypothesized yields low rates of adverse events observed and predicted by normal tissue complication probability (NTCP) models.

MATERIALS/METHODS

Intensity-modulated (IMRT) cone-beam CT (CBCT)-based daily online adaptive stereotactic PBI (A-SPBI) plans with 3-mm PTV from 8 patients were recreated with 1-cm PTV per the Florence APBI IMRT trial planning guideline. Dose statistics with evidence for association with toxicity were compared. Documented toxicities were collected for patients treated with A-SPBI with a minimum follow-up of 3.5 months and Common Terminology Criteria for Adverse Events (CTCAE) v.5.0 grade was assigned. Using α/β = 3 for breast and lung, dose statistics were converted to equivalent doses in 2-Gy fractions (EQD2) for use in NTCP models and for comparison using paired t tests, with differences considered significant if p≤0.05.

RESULTS

The table details EQD2 dose statistics for breast, lung, and cosmetic toxicity for A-SPBI plans with 3-mm PTV and their 1-cm PTV re-plans in 8 patients. PTV volume, mean lung dose (MLD), and lung V5, V20, and V30 were significantly lower in 1-cm plans. Acute, subacute (3-6 months), and late toxicities were collected for 30 patients followed for a median of 8 months (range 4-13 months). Radiation dermatitis was the most common acute toxicity (n = 16, 53%), followed by hyperpigmentation (n = 12, 40%), fibrosis (n = 9, 30%), and fatigue (n = 9, 30%). One grade 3 radiation dermatitis was the only grade ≥3 toxicity. Six patients (20%) acutely developed breast or axillary edema: 4 (13.3%) resolved, and 2 (6.7%) developed acutely and persist at last follow-up, >6 months after RT. No patient had a lung V20, V30, or MLD meeting thresholds for radiation-induced lung injury, radiation pneumonitis, or symptomatic or imaging-based pneumonitis models, respectively. The breast V55 model predicted a median risk of unfavorable cosmesis of 33% (range 26-44%) for A-SBPI plans and 35% (range 28-51) for 1-cm PTV plans (p = 0.28).

CONCLUSION

Observed acute toxicities are tolerable and rarely persist in patients treated with A-SPBI with 3-mm PTV margins with daily CBCT-based online adaptation. NTCP modeling predicts similar cosmetic outcome to 1-cm margins. The significant reduction in ipsilateral lung dose with a 3-mm PTV in our first 8 patients especially supports daily adaptation in low-risk breast cancer patients with smoking history and/or lung comorbidity.

A Comprehensive Deep Learning Framework for Automatic Target Volumes Segmentation in Post-Operative Stereotactic Partial Breast Irradiation (S-PBI)

PURPOSE/OBJECTIVE(S)

In S-PBI, accurate delineation of post-surgical tumor bed volume (TBV) and clinical target volume (CTV) are crucial tasks to achieve effective radiotherapy outcomes. However, manual contouring is labor intensive, time consuming, and largely relies on the experience of clinicians. We aimed to propose a deep learning (DL) approach which mimics physicians' contouring practice to accurately segment target volumes in post-operative breast CT images.

MATERIALS/METHODS

Our approach incorporated domain knowledge into a 3D U-Net based DL model for breast target volumes (TBV and CTV) delineation. Our TBV segmentation approach was inspired by the marker-guidance procedure in manual delineation, where the visual clues provided by the markers assist physicians in defining TBV. For this purpose, a distance-transformation coupled with a Gaussian filter was adopted to convert markers' locations on the CT images to saliency maps. Subsequently, the CT images and the corresponding saliency maps formed a two-channel input for the segmentation model. For CTV segmentation, TBV was incorporated as an input in addition to the CT images, guiding the model to encode the location-related image features. The architecture allowed the network to emulate the oncologist's manual delineation where CTV is derived from TBV via a margin expansion, followed by correcting the extensions for anatomical barriers of tumor invasion (e.g., skin, chest wall). We retrospectively collected 175 prone CT images from 35 post-operative breast cancer patients who received 5-fraction partial breast irradiation (PBI) regimen on a Co-60 prone based S-PBI unit. The 35 patients were randomly split into 25, 5, and 5 for model training, validation, and testing respectively.

RESULTS

We evaluated the performance of the developed DL model on the testing dataset by comparing the predicted volumes with the manually delineated contours (ground truth) using Dice similarity coefficient (DSC), 95th percentile Hausdorff distance (HD95), and average symmetric surface distance (ASD). For TBV segmentation, our model achieved mean (standard deviation) of 0.76 (±2.7), 6.76 (±1.83) mm, and 1.9 (±0.66) mm for DSC, HD95, and ASD respectively. For CTV segmentation, our model achieved 0.94 (±0.02), 2.46 (±0.5) mm, and 0.53 (±0.14) mm for DSC, HD95, and ASD respectively. The proposed auto-segmentation approach generated TBV and CTV masks in ∼11 seconds per CT volume, implying significantly improved efficiency compared to manual contouring.

CONCLUSION

We developed a comprehensive DL framework mimicking clinical contouring practice for auto-segmentation of target volumes in S-PBI. The results demonstrated high levels of agreement between the predicted contours and physicians' manual contours. The approach is promising for improving the efficiency and accuracy of the on-line treatment planning workflow, such as adaptive based S-PBI.

Shaping Nanobodies and Intrabodies against Proteoforms

Proteoforms expand genomic diversity and direct developmental processes. While high-resolution mass spectrometry has accelerated characterization of proteoforms, molecular techniques working to bind and disrupt the function of specific proteoforms have lagged behind. In this study, we worked to develop intrabodies capable of binding specific proteoforms. We employed a synthetic camelid nanobody library expressed in yeast to identify nanobody binders of different SARS-CoV-2 receptor binding domain (RBD) proteoforms. Importantly, employment of the positive and negative selection mechanisms inherent to the synthetic system allowed for amplification of nanobody-expressing yeast that bind to the original (Wuhan strain RBD) but not the E484 K (Beta variant) mutation. Nanobodies raised against specific RBD proteoforms were validated by yeast-2-hybrid analysis and sequence comparisons. These results provide a framework for development of nanobodies and intrabodies that target proteoforms.

The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes

The OSU/PNNL Superfund Research Program (SRP) represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons (PAHs) at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental toxicity model that provides quantitative measurements of the exposure to chemicals. Toward this end, we have linked over 150 PAHs found at Superfund sites to the effect of these same chemicals in zebrafish, creating a rich dataset that links environmental exposure to biological response. To quantify this response, we have implemented a dose-response modelling pipeline to calculate benchmark dose parameters which enable potency comparison across over 500 chemicals and 12 of the phenotypes measured in zebrafish. We provide a rich dataset for download and analysis as well as a web portal that provides public access to this dataset via an interactive web site designed to support exploration and re-use of these data by the scientific community at http://srp.pnnl.gov .

Graph identification of proteins in tomograms (GRIP-Tomo)

In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases for refinement. We hypothesized that the topological connectivity of protein structures is invariant, and they are distinctive for the purpose of protein identification from distorted data presented in volume densities. Three-dimensional densities of a protein or a complex from simulated tomographic volumes were transformed into mathematical graphs as observables. We systematically introduced data distortion or defects such as missing fullness of data, the tumbling effect, and the missing wedge effect into the simulated volumes, and varied the distance cutoffs in pixels to capture the varying connectivity between the density cluster centroids in the presence of defects. A similarity score between the graphs from the simulated volumes and the graphs transformed from the physical protein structures in point data was calculated by comparing their network theory order parameters including node degrees, betweenness centrality, and graph densities. By capturing the essential topological features defining the heterogeneous morphologies of a network, we were able to accurately identify proteins and homo-multimeric complexes from 10 topologically distinctive samples without realistic noise added. Our approach empowers future developments of tomogram processing by providing pattern mining with interpretability, to enable the classification of single-domain protein native topologies as well as distinct single-domain proteins from multimeric complexes within noisy volumes.

CPUE standardization for southern bluefin tuna (Thunnus maccoyii) in the Korean tuna longline fishery, accounting for spatiotemporal variation in targeting through data exploration and clustering

Accounting for spatial and temporal variation in targeting is a concern in many catch per unit effort (CPUE) standardization exercises. In this study we standardized southern bluefin tuna (Thunnus maccoyii, SBT) CPUE from the Korean tuna longline fishery (1996-2018) using generalized linear models (GLMs) with operational set by set data. Data were first explored to investigate the operational characteristics of Korean tuna longline vessels fishing for SBT, such as the spatial and temporal distributions of effort, and changes in the nominal catch rates among major species and species composition. Then we estimated SBT CPUE by area used for the stock assessment in the CCSBT (Commission for the Conservation of Southern Bluefin Tuna) and identified two separate areas in which Korean tuna longline vessels have targeted SBT and albacore tuna (T. alalunga), with targeting patterns varying spatially, seasonally and longer term. We applied two approaches, data selection and cluster analysis of species composition, and compared their ability to address concerns about the changing patterns of targeting through time. Explanatory variables for the GLM analyses were year, month, vessel identifier, fishing location (5° cell), number of hooks, moon phase, and cluster. GLM results for each area suggested that location, year, targeting, and month effects were the principal factors affecting the nominal CPUE. The standardized CPUEs for both areas decreased until the mid-2000s and have shown an increasing trend since that time.

A Comparative Multi-System Approach to Characterizing Bioactivity of Commonly Occurring Chemicals

A 2019 retrospective study analyzed wristband personal samplers from fourteen different communities across three different continents for over 1530 organic chemicals. Investigators identified fourteen chemicals (G14) detected in over 50% of personal samplers. The G14 represent a group of chemicals that individuals are commonly exposed to, and are mainly associated with consumer products including plasticizers, fragrances, flame retardants, and pesticides. The high frequency of exposure to these chemicals raises questions of their potential adverse human health effects. Additionally, the possibility of exposure to mixtures of these chemicals is likely due to their co-occurrence; thus, the potential for mixtures to induce differential bioactivity warrants further investigation. This study describes a novel approach to broadly evaluate the hazards of personal chemical exposures by coupling data from personal sampling devices with high-throughput bioactivity screenings using in vitro and non-mammalian in vivo models. To account for species and sensitivity differences, screening was conducted using primary normal human bronchial epithelial (NHBE) cells and early life-stage zebrafish. Mixtures of the G14 and most potent G14 chemicals were created to assess potential mixture effects. Chemical bioactivity was dependent on the model system, with five and eleven chemicals deemed bioactive in NHBE and zebrafish, respectively, supporting the use of a multi-system approach for bioactivity testing and highlighting sensitivity differences between the models. In both NHBE and zebrafish, mixture effects were observed when screening mixtures of the most potent chemicals. Observations of BMC-based mixtures in NHBE (NHBE BMC Mix) and zebrafish (ZF BMC Mix) suggested antagonistic effects. In this study, consumer product-related chemicals were prioritized for bioactivity screening using personal exposure data. High-throughput high-content screening was utilized to assess the chemical bioactivity and mixture effects of the most potent chemicals.

Tunable Heteroassembly of a Plant Pseudoenzyme-Enzyme Complex

Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is inactive remain uncertain. For pseudoenzyme-enzyme pairs, the similarity of both subunits can often hinder conventional characterization approaches. In plants, a pseudoenzyme, PDX1.2, positively regulates vitamin B₆ production by association with its active catalytic homologues such as PDX1.3 through an unknown assembly mechanism. Here we used an integrative experimental approach to learn that such pseudoenzyme-enzyme pair associations result in heterocomplexes of variable stoichiometry, which are unexpectedly tunable. We also present the atomic structure of the PDX1.2 pseudoenzyme as well as the population averaged PDX1.2-PDX1.3 pseudoenzyme-enzyme pair. Finally, we dissected hetero-dodecamers of each stoichiometry to understand the arrangement of monomers in the heterocomplexes and identified symmetry-imposed preferences in PDX1.2-PDX1.3 interactions. Our results provide a new model of pseudoenzyme-enzyme interactions and their native heterogeneity.

Shallow population structure of southern bluefin tuna, Thunnus maccoyii (Castelnau, 1872) between Indian and Atlantic Oceans inferred from mitochondrial DNA sequences

Southern bluefin tuna (Thunnus maccoyii Castelnau, 1872) is distributed across most of the southern temperate ocean and migrates extensively between 30°S and 50°S. Since T. maccoyii has been continually and heavily exploited, it is necessary to investigate the genetic diversity, population structure and demographic history of T. maccoyii for effective management and conservation. Thirty-seven gonad tissues of T. maccoyii were sampled from two locations, which were in the eastern Indian Ocean and the eastern Atlantic Ocean, by scientific observers onboard Korean T. maccoyii longline vessels in 2015. We compared 1240-bp sequences of combined mitochondrial DNA (mtDNA) from the cytochrome c oxidase subunit I (COI, 504-bp) and control region (CR, 736-bp) sequences. The pairwise fixation index (F_ST) and maximum-likelihood tree showed that two clades (A and B) were formed regardless of locations. Clade A occurred more commonly than clade B in both localities: the occurrence ratio of clade A was 69% in the Indian Ocean, and 79% in the Atlantic Ocean, respectively. Our findings suggest that a historic differentiation event may have occurred in T. maccoyii, but recently the connectivity between the two oceans may be possible in T. maccoyii populations.

Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps

We describe common approaches to atomistic structure modeling with single particle analysis derived cryo-EM maps. Several strategies for atomistic model building and atomistic model fitting methods are discussed, including selection criteria and implementation procedures. In covering basic concepts and caveats, this short perspective aims to help facilitate active discussion between scientists at different levels with diverse backgrounds.

Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

Long non-coding RNAs (lncRNAs) constitute a significant fraction of the transcriptome, playing important roles in development and disease. However, our understanding of structure-function relationships for this emerging class of RNAs has been limited to secondary structures. Here, we report the 3-D atomistic structural study of epigenetic lncRNA, Braveheart (Bvht), and its complex with CNBP (Cellular Nucleic acid Binding Protein). Using small angle X-ray scattering (SAXS), we elucidate the ensemble of Bvht RNA conformations in solution, revealing that Bvht lncRNA has a well-defined, albeit flexible 3-D structure that is remodeled upon CNBP binding. Our study suggests that CNBP binding requires multiple domains of Bvht and the RHT/AGIL RNA motif. We show that RHT/AGIL, previously shown to interact with CNBP, contains a highly flexible loop surrounded by more ordered helices. As one of the largest RNA-only 3-D studies, the work lays the foundation for future structural studies of lncRNA-protein complexes.

Cryo_fit: Democratization of flexible fitting for cryo-EM

Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in hardware and software. Flexible fitting of atomic models to three-dimensional (3D) cryo-EM reconstructions by molecular dynamics (MD) simulation is a popular technique but often requires technical expertise in computer simulation. This work introduces cryo_fit, a package for the automatic flexible fitting of atomic models in cryo-EM maps using MD simulation. The package is integrated with the Phenix software suite. The module was designed to automate the multiple steps of MD simulation in a reproducible manner, as well as facilitate refinement and validation through Phenix. Through the use of cryo_fit, scientists with little experience in MD simulation can produce high quality atomic models automatically and better exploit the potential of cryo-EM.

Boosting protein stability with the computational design of β-sheet surfaces

β-sheets often have one face packed against the core of the protein and the other facing solvent. Mutational studies have indicated that the solvent-facing residues can contribute significantly to protein stability, and that the preferred amino acid at each sequence position is dependent on the precise structure of the protein backbone and the identity of the neighboring amino acids. This suggests that the most advantageous methods for designing β-sheet surfaces will be approaches that take into account the multiple energetic factors at play including side chain rotamer preferences, van der Waals forces, electrostatics, and desolvation effects. Here, we show that the protein design software Rosetta, which models these energetic factors, can be used to dramatically increase protein stability by optimizing interactions on the surfaces of small β-sheet proteins. Two design variants of the β-sandwich protein from tenascin were made with 7 and 14 mutations respectively on its β-sheet surfaces. These changes raised the thermal midpoint for unfolding from 45°C to 64°C and 74°C. Additionally, we tested an empirical approach based on increasing the number of potential salt bridges on the surfaces of the β-sheets. This was not a robust strategy for increasing stability, as three of the four variants tested were unfolded.

A new species of Anchistrotos Brian, 1906 (Copepoda: Cyclopoida: Taeniacanthidae) from the filamentous shrimpgoby Myersina filifer (Valenciennes) (Perciformes: Gobiidae) in Korean waters

A new species of Anchistrotos Brian, 1906 (Copepoda: Cyclopoida: Taeniacanthidae), parasitic in the branchial cavities of the filamentous shrimpgoby Myersina filifer (Valenciennes) (Perciformes: Gobiidae) from Korea is described. The new species is most closely related to A. tangi Venmathi Maran, Moon & Adday, 2014, but differs from it by the following combination of characters in the adult female: the U-shaped rostrum, the distal margin of the anal somite lacks patches of spinules, the proximal segment of the maxilliped is without seta, and the maxilliped claw is armed with long and small naked setae. This is the tenth species of the genus and a key is provided to distinguish all nominal species.

Amphritea ceti sp. nov., isolated from faeces of Beluga whale (Delphinapterus leucas)

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated RA1T, was isolated from faeces collected from Beluga whale (Delphinapterus leucas) in Yeosu aquarium, South Korea. Strain RA1T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain RA1T joins the cluster comprising the type strains of three species of the genus Amphritea , with which it exhibited 95.8–96.0 % sequence similarity. Sequence similarities to the type strains of other recognized species were less than 94.3 %. Strain RA1T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain RA1T were phosphatidylethanolamine, phosphatidylglycerol, two unidentified lipids and one unidentified aminolipid. The DNA G+C content of strain RA1T was 47.4 mol%. The differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain RA1T is separated from other species of the genus Amphritea . On the basis of the data presented, strain RA1T is considered to represent a novel species of the genus Amphritea , for which the name Amphritea ceti sp. nov. is proposed. The type strain is RA1T ( = KCTC 42154T = NBRC 110551T).

Computational approaches to understanding protein aggregation in neurodegeneration

The generation of toxic non-native protein conformers has emerged as a unifying thread among disorders such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Atomic-level detail regarding dynamical changes that facilitate protein aggregation, as well as the structural features of large-scale ordered aggregates and soluble non-native oligomers, would contribute significantly to current understanding of these complex phenomena and offer potential strategies for inhibiting formation of cytotoxic species. However, experimental limitations often preclude the acquisition of high-resolution structural and mechanistic information for aggregating systems. Computational methods, particularly those combine both all-atom and coarse-grained simulations to cover a wide range of time and length scales, have thus emerged as crucial tools for investigating protein aggregation. Here we review the current state of computational methodology for the study of protein self-assembly, with a focus on the application of these methods toward understanding of protein aggregates in human neurodegenerative disorders.

P5-09-02: Reducing Excess Biopsies: Improving Screening through Risk Stratification and New Thresholds for Intervention

Background BI-RADS Category 4 patients have a 2–95% risk for malignancy and are generally recommended for breast biopsy with little discrimination for risk level or distinction between risk of invasive or in situ disease. Our study sought to determine if higher thresholds for biopsy based on stratifying for risk and distinguishing between risk of invasive cancer and DCIS could reduce biopsy rates and increase cancer-to-biopsy yields without missing cancers urgent for resolution.

Methods 108 BI-RADS 4 cases with final outcomes data were evaluated from a prospective cohort of 215 consecutive patients seen at a same-day multidisciplinary breast clinic for women with mammograms categorized as BI-RADS 0, 4, or 5 in 2006–07. Final outcomes were determined from pathologic diagnosis or two-year follow-up. Risk estimates (RE) for DCIS and invasive cancer were collected prospectively and re-assessed by a radiologist blinded to outcomes and prior reading assessments. Cases were stratified according to the risk ranges of the BI-RADS 4 subcategories and risk of invasive or in situ disease. Biopsy rates, cancer-to-biopsy yields, and number of malignancies missed were calculated for various thresholds for intervention.

Results A ROC curve for invasive cancer risk for the radiologist demonstrated a 98.5% level of accuracy (95% confidence interval [CI]: 96.9%, 100%). 60 cases had some risk for invasive cancer and 48 had some risk for DCIS. There were 14 invasive cancer and 11 DCIS outcomes, 3 of which were high-grade. Pathologic assessment from biopsy or surgery was available for 100 patients. The outcomes of 8 cases were determined by benign two-year follow-up.

There are several strategies for intervention that improve biopsy yield and reduce biopsies for benign disease as shown in Table 1.

Shewanella upenei sp. nov., a lipolytic bacterium isolated from bensasi goatfish Upeneus bensasi

A Gram-staining-negative, motile, non-spore-forming and rod-shaped bacterial strain, 20-23R(T), was isolated from intestine of bensasi goatfish, Upeneus bensasi, and its taxonomic position was investigated by using a polyphasic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 20-23R(T) belonged to the genus Shewanella. Strain 20-23R(T) exhibited 16S rRNA gene sequence similarity values of 99.5, 99.2, and 97.5% to Shewanella algae ATCC 51192(T), Shewanella haliotis DW01(T), and Shewanella chilikensis JC5(T), respectively. Strain 20-23R(T) exhibited 93.1-96.0% 16S rRNA gene sequence similarity to the other Shewanella species. It also exhibited 98.3-98.4% gyrB sequence similarity to the type strains of S. algae and S. haliotis. Strain 20-23R(T) contained simultaneously both menaquinones and ubiquinones; the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-8 and Q-7. The fatty acid profiles of strain 20-23R(T), S. algae KCTC 22552(T) and S. haliotis KCTC 12896(T) were similar; major components were iso-C(15:0), C(16:0), C(16:1) ω7c and/or iso-C(15:0) 2-OH and C(17:1) ω8c. The DNA G+C content of strain 20-23R(T) was 53.9 mol%. Differential phenotypic properties and genetic distinctiveness of strain 20-23R(T), together with the phylogenetic distinctiveness, revealed that this strain is distinguishable from recognized Shewanella species. On the basis of the data presented, strain 20-23R(T) represents a novel species of the genus Shewanella, for which the name Shewanella upenei sp. nov. is proposed. The type strain is 20-23R(T) (=KCTC 22806(T) =CCUG 58400(T)).

EaMEAD: Activation energy prediction of cytochrome P450 mediated metabolism with effective atomic descriptors

In an effort to improve drug design and predictions for pharmacokinetics (PK), an empirical model was developed to predict the activation energies (Ea) of cytochrome P450 (CYP450) mediated metabolism. The model, EaMEAD (Activation energy of Metabolism reactions with Effective Atomic Descriptors), predicts the Ea of four major metabolic reactions of the CYP450 enzyme: aliphatic hydroxylation, N-dealkylation, O-dealkylation, and aromatic hydroxylation. To build and validate the empirical model, the E(a) values of the substrates with diverse chemical structures (394 metabolic sites for aliphatic hydroxylation, 27 metabolic sites for N-dealkylation, 9 metabolic sites for O-dealkylation, and 85 metabolic sites for aromatic hydroxylation) were calculated by AM1 molecular orbital (MO). Empirical equations, Quantitative Structure Activity Relationship (QSAR) models, were derived using effective atomic charge, effective atomic polarizability, and bond dipole moments of the substrates as descriptors. EaMEAD is shown to accurately predict Ea with a correlation coefficient (R) of 0.94 and root-mean-square error (RMSE, unit is kcal/mol) of 0.70 for aliphatic hydroxylation, N-dealkylation, and O-dealkylation, and R of 0.83 and RMSE of 0.80 for aromatic hydroxylation, respectively. Physical origin and the role of the effective atomic descriptors of the models are presented in detail. With this model, the Ea of the metabolism can be rapidly predicted without any experimental parameters or time-consuming QM calculation. Regioselectivity prediction with our model is presented in the case of CYP3A4 metabolism. The reliability and ease of use of this model will greatly facilitate early stage PK predictions and rational drug design. Moreover, the model can be applied to develop the Ea prediction model of various types of chemical reactions.

Regioselectivity prediction of CYP1A2-mediated phase I metabolism

A kinetic, reactivity-binding model has been proposed to predict the regioselectivity of substrates meditated by the CYP1A2 enzyme, which is responsible for the metabolism of planar-conjugated compounds such as caffeine. This model consists of a docking simulation for binding energy and a semiempirical molecular orbital calculation for activation energy. Possible binding modes of CYP1A2 substrates were first examined using automated docking based on the crystal structure of CYP1A2, and binding energy was calculated. Then, activation energies for CYP1A2-mediated metabolism reactions were calculated using the semiempirical molecular orbital calculation, AM1. Finally, the metabolic probability obtained from two energy terms, binding and activation energies, was used for predicting the most probable metabolic site. This model predicted 8 out of 12 substrates accurately as the primary preferred site among all possible metabolic sites, and the other four substrates were predicted into the secondary preferred site. This method can be applied for qualitative prediction of drug metabolism mediated by CYP1A2 and other CYP450 family enzymes, helping to develop drugs efficiently.

Fish oil, atherogenesis, and thrombogenesis

Marine fish consumption is known to reduce mortality from ischemic heart disease. The use of fish oil as a dietary supplement, however, is not universally recommended. In large doses, fish oil reduces plasma cholesterol and triacylglycerol but increases low density lipoprotein (LDL) levels and the potential for free radical generation and bleeding. Moderate marine fish consumption is known to reduce mortality without altering commonly measured variables, i.e., plasma cholesterol levels, in vitro platelet aggregation, and bleeding times. In swine, we observed that monocyte adhesions and platelet clumps over the lesion surface of proximal left anterior descending (LAD) coronary arteries are markedly reduced when an atherogenic diet was supplemented with cod-liver oil, even when the cholesterol levels were equalized with the untreated group. These findings suggest that fish oil is hypothrombogenic. We developed an in vitro assay to delineate the mechanism whereby fish oil reduced monocyte-endothelial cell interactions in vivo. The effects of supplementing the culture medium with different fatty acids on adhesions between lipopolysaccharide (LPS) stimulated swine aortic endothelial cells (SAEC) and the human monocyte-like cell line, U937, was investigated in a 10 minute adhesion assay at 37 degrees C. Exposure of SAEC for 6 hours to media containing 50-200 microMs eicosapentaenoic (EPA), stearic, oleic, linoleic, and arachidonic acid, respectively, revealed that only EPA reduced U937-SAEC adhesion. Exposure of U937 to EPA also reduced adhesions. EPA was not effective when added to the SAEC more than 2 hours after they were stimulated with LPS. Exposure of human umbilical vein endothelial cells (HUVEC) to EPA reduced the expression of VCAM-1, ELAM-1, and ICAM-1 after 5 hours of stimulation with LPS. These results suggest that EPA may functionally impair the induction/expression of adhesion molecules.

E-cadherin expression in prostatic carcinoma biopsies: correlation with tumor grade, DNA content, pathologic stage, and clinical outcome

We compared tumor grade and DNA content with expression of E-cadherin (E-CD), a cell adhesion molecule associated with cell-cell and cell-matrix interaction, leukocyte function, and tumor invasion and metastases, on 56 prostate carcinoma needle biopsies. The findings were correlated with final pathologic stage at subsequent prostatectomy, preoperative serum prostate-specific antigen level and further development of metastases during an initial 2.4-yr mean clinical follow-up period (range 0.5 to 5.5 yr). E-CD expression (uvomorulin, L-CAM, cell CAM 80/120, ARC-1, Sigma, St. Louis, MO) was measured by double-linked immunoalkaline phosphatase immunohistochemistry quantified with a the Roche RPW image analyzer (Roche Image Analysis Systems, Elon College, NC). DNA ploidy was determined on formalin-fixed, paraffin-embedded Feulgen-stained 5-microns tissue sections of the narrow-bore initial prostate carcinoma biopsies with the Roche RPW image analyzer. The 51% mean positive area E-CD expression in the group of 56 adenocarcinomas was significantly less than the 76% expression level for 15 normal control prostate tissues (P < 0.001). E-CD expression was also decreased in aneuploid (39%) versus diploid tumors (54%, P < 0.001); and in high-grade (44%) versus low-grade lesions (54%; P < 0.01). The 44% E-CD expression level in patients with metastases was lower than the 52% level in the nonmetastatic cases, but this finding was not statistically significant.(ABSTRACT TRUNCATED AT 250 WORDS)

Exponential relationship between plasma cholesterol levels and atherosclerotic lesion size in hyperlipidemic swine

The effect of fish oil supplements on atherogenesis is controversial, especially when fish oil does not lower plasma cholesterol. Some studies in swine have shown that a fish oil supplement to a butter-cholesterol diet reduces atherogenesis. The fish oil supplement also frequently reduces average plasma cholesterol levels. The reduction in lesion size has been shown to be greater than can be expected from average plasma cholesterol reductions, if a linear relationship between lesion size and plasma cholesterol was assumed. However, in an experiment in which we equalized time-weighted average plasma cholesterol levels, there was no significant reduction in lesion size in the fish oil supplemented group. This led us to question the validity of the linear relationship between lesion size and plasma cholesterol level. In this study we have combined the results of eight study blocks with a total of 76 swine fed a similar hyperlipidemic, butter-cholesterol diet. Of these, 24 received a fish oil supplement (BT+fish oil) and 52 swine received no fish oil supplement (BT). The average lesion size as measured by nuclear profiles per cross section of a fixed site in the abdominal aorta (ABNpCx) was 7704 +/- 778 (mean +/- SEM) for the BT group and 2360 +/- 1145 for the BT+fish oil group. Total plasma cholesterol levels were measured at the outset and at monthly intervals until sacrifice. For each animal we obtained a time-weighted average based on the trapezoidal rule.(ABSTRACT TRUNCATED AT 250 WORDS)

Dietary fish oil reduces microthrombi over atherosclerotic lesions in hyperlipidemic swine even in the absence of plasma cholesterol reduction

We have investigated in swine the effect of fish oil additives to a butter-cholesterol hyperlipidemic diet (BT) on atherogenesis and thrombogenesis when average plasma cholesterol levels were kept similar in fish oil-treated and untreated BT groups. The studies included evaluation of lesion sizes and cell numbers, counts of adherent monocytes over lesions, and counts of platelet clumps (microthrombi) over lesions either attached directly to endothelium or to adherent monocytes. Anatomic sites studied for lesion development were the left anterior descending coronary artery (LAD), the distal 1/5 of the abdominal aorta, and a proximal portion of the thoracic aorta. Counts of attached monocytes and platelet clumps were made by scanning electron microscopy only for the LAD and expressed per mm2 of surface. The most striking new result was in regard to the platelet clumps. These were reduced by the fish oil from 996 +/- 295/mm2 in the untreated BT group to 313 +/- 59 and 364 +/- 105 in BT+cod liver oil and BT+menhaden oil groups, respectively. Most of the platelet clumps were adherent to attached monocytes in all groups and the number of attached monocytes were greatly reduced by the fish oil additive. Thus there were close relationships among platelet clumps, monocytes, and lesion endothelium. Numbers of attachments over nonlesion endothelium were much less than those over lesions in all dietary groups. The most surprising result was the lack of retardation of lesion growth by the fish oil additives in spite of the reduction in attached monocytes and platelet clumps. In previous studies where the high plasma cholesterol levels in the BT swine had been modestly reduced (about 25%) there had been a marked retardation of lesion growth. The current result suggests that plasma cholesterol is the major factor controlling lesion growth in this model through under milder conditions and longer observation periods other factors might become apparent.

Reductions in serum thromboxane, prostacyclin, and leukotriene B4 levels in swine fed a fish oil supplement to an atherogenic diet

We have reported previously that fish oil rich in omega-3 fatty acids added to a butter-cholesterol atherogenic diet for swine resulted in marked retardation of the atherosclerotic process which many regard as largely an inflammatory response to injury by excessive lipids in the intima. In this report on the same swine we present serum levels of several eicosanoids derived from arachidonic acid via the cyclooxygenase and lipoxygenase pathways. The study involves six swine fed a high fat, high cholesterol diet (BT group) for 4 months, six swine fed the same diet but with 30 ml/day fish oil added (BT + FO), and five swine fed a low fat, low cholesterol mash diet (MA). The serum eicosanoids were measured by radioimmunoassay. Thromboxane B2 levels (ng/dl: means +/- SEM) were 543 +/- 49 for MA, 231 +/- 12 for BT, and 105 +/- 20 for BT + FO, and all differences were statistically highly significant, 6-Keto PGF1 alpha (a relatively stable prostacyclin metabolite) levels were 249 +/- 31 for MA, 184 +/- 12 for BT, and 101 +/- 10 for BT + FO, and all differences were significant. Leukotriene B4 levels at 4 months were 151 +/- 25 for MA, 112 +/- 11 for BT, and 84 +/- 11 for BT + FO. BT + FO was significantly different from both MA and BT, but BT was not significantly different from MA. Leukotriene C4 levels were not significantly different among the three groups. Of special interest was the effect of the BT diet without the FO additive in reducing several eicosanoid levels compared to MA values. The affected eicosanoid levels were reduced still further by the fish oil additive, indicating its ability to inhibit both the cyclooxygenase and the lipoxygenase pathways. The relation of the fish oil-induced inhibition to the observed retardation of atherogenesis is not as yet clear but there are several theoretical possibilities, including reduction in recruitment of monocytes and in proliferation of smooth muscle cells.

Comparison of effects of fish oil and corn oil supplements on hyperlipidemic diet induced atherogenesis in swine

The addition of a fish oil supplement rich in n - 3 unsaturated fatty acids to a high cholesterol, high saturated fat (BT) diet for swine has been shown previously to result in modest lowering of plasma cholesterol levels and in marked retardation of atherogenesis. It has been suggested that the effect was due to the change in polyunsaturated (PUFA) to saturated fatty acid ratios (P/S) and that a supplement of PUFA of the n - 6 series might have the same effect as the fish oil. We have tested this hypothesis in swine fed an atherogenic diet by comparing the effect of a fish oil supplement producing a P/S ratio of 0.28 to that of corn oil in the same amount producing a ratio of 0.46. The P/S ratio of the atherogenic diet without supplements was 0.16. Thirteen young male Yorkshire swine were fed either BT alone (n = 4), BT + cod liver oil (n = 4) or BT + corn oil (n = 5) for 6 months and then killed for quantitative studies of atherosclerosis in the aortas and coronary arteries including lesion areas, number of lesion cells, and number of monocytes attached to endothelium. Plasma cholesterol levels were determined periodically and lipoproteins were separated terminally by density gradient ultracentrifugation, Pevikon block electrophoresis and immunoelectrophoresis. The fish oil supplement resulted in a 30% reduction in time-weighted average plasma cholesterol levels, and a marked shift in terminal lipoprotein patterns from predominantly apo B and E containing ones to predominantly apo B only ones. Atherogenesis was reduced by the fish oil supplement as judged by several morphometric criteria including size of lesions, number of lesion cells, and number of monocytes attached to lesion endothelium. The corn oil supplement produced no significant reductions in any of these variables from those in swine fed the atherogenic BT diet without the supplement. We conclude that the n - 3 fatty acid rich fish oil supplemented diet retarded atherogenesis, but that this effect was not shared by the corn oil supplemented diet which had an even higher P/S ratio.

Dietary fish oil added to a hyperlipidemic diet for swine results in reduction in the excessive number of monocytes attached to arterial endothelium

Modest numbers of blood monocytes become attached at least temporarily to the endothelium of large arteries in normal swine fed low fat, low cholesterol diets. These numbers are increased several fold when the swine are fed a high saturated fat, high cholesterol atherogenic diet (BT). The main objective of this portion of a broader study was to see if the addition of fish oil (30 ml) to a BT diet (BT + FO) could prevent the increase in attached monocytes induced over arterial endothelium in BT fed swine. Six BT, 6 BT + FO and 5 control mash (MA) swine fed the respective diets for 4 months before killing were available for the current study. Other aspects of this experiment have been presented previously which in brief are that BT + FO resulted in retardation of atherosclerotic lesion development and a shift in lipoprotein components from predominantly apolipoprotein B,E containing with the BT diet to predominantly apo B only with BT + FO. There was a significant positive correlation between lesion development and apo B,E lipoproteins. In the current study we determined by scanning electron microscopy on the first portion of the left anterior descending coronary artery after perfusion fixation under pressure the number of monocytes per mm2 attached over or not over visible lesions. We also determined monocyte percentages in the circulating blood and analyzed the correlation of the numbers of attached monocytes and blood monocyte percentages with various lipoprotein components reported previously.(ABSTRACT TRUNCATED AT 250 WORDS)

Intestinal apolipoprotein B-48 synthesis and lymphatic cholesterol transport are lower in swine fed high fat, high cholesterol diet with soy protein than with casein

Effects of dietary proteins on intestinal lipoproteins were studied in 8 Yorkshire swine fed a high fat, high cholesterol diet with either casein or soy protein. After 5 weeks of feeding, the casein group exhibited moderately elevated levels of serum cholesterol (334 +/- 46 mg/dl). The soy protein group showed significantly less hypercholesterolemia as compared to the casein group (122 +/- 8 mg/dl). Swine were subjected to cannulation of mesenteric lymph duct under halothane anesthesia. A single dose of 250 microCi [14C]cholesterol and 10 mCi [3H]leucine was infused into the upper jejunum 2 h after one-fifth of daily food was given. The 3-h lymphatic transport of cholesterol in casein-fed swine was significantly higher than in those fed soy protein. Triglyceride transport values were similar in the 2 groups. The [3H]leucine incorporation study revealed that transport of apo B-48 bore a significant positive relationship to transport of cholesterol in both chylomicron and VLDL fractions of mesenteric lymph. A greater apo B-48 secretion with higher specific activity was probably responsible for the greater transport of cholesterol in chylomicrons in casein-fed than in soy protein-fed swine. Similarly, the transport of lymph VLDL cholesterol in swine fed casein or soy protein paralleled the amount of accompanying apo B-48. Dietary proteins probably influence the intestinal synthesis of apo B-48 which in turn affects cholesterol transport into the lymphatics.

Modification of lipoprotein patterns and retardation of atherogenesis by a fish oil supplement to a hyperlipidemic diet for swine

We have studied the effect of addition of 30 ml cod liver oil (FO) daily to a highly atherogenic butter (BT) diet for swine on lesion development in the coronary arteries and aorta, plasma lipoprotein (LP) patterns, plasma levels of thiobarbituric acid-reactive substances (TBARS) and on tritiated thymidine-labeling indices ([3H]TdR LI) of smooth muscle cells (SMC) and monocyte/macrophages (M/M phi) in the atherosclerotic lesions. Seventeen male Yorkshire swine (11.1 +/- 0.4 kg) were divided into 3 groups: BT (n = 6), BT + FO (n = 6) and mash (n = 5). They were fed the respective diets for 4 months. Terminally, fasting plasma was obtained and cholesterol contents were determined in various fractions of lipoproteins separated by density gradient ultracentrifugation, Pevikon block electrophoresis and immunoelectrophoresis. Apoprotein (B, A-I, E and C) contents of the plasma and lipoprotein fractions were determined by polyacrylamide gel electrophoresis and densitometry of gels stained with Coomassie blue. Swine were injected intramuscularly with 0.5 mCi/kg of [3H]TdR 2 h before death. The aorta and coronary arteries were perfusion fixed in situ under anesthesia. Samples were obtained for microscopic morphometry, autoradiography and immunohistochemistry from distal abdominal aorta, thoracic aorta, and proximal coronary arteries; left main (LM), left anterior descending (LAD), left circumflex (LCX), right main (RM), and right coronary artery (RCA). On the BT diet without FO there was extensive atherosclerotic (AS) lesion development, which was drastically reduced by the addition of FO to the BT diet in all sites by from 71 to 94%. The overall plasma cholesterol (CH) levels were reduced only modestly by the FO (816 +/- 64 to 629 +/- 14 mg/dl) but the distribution of CH in the various lipoprotein classes was remarkably altered. The CH in the large lipoprotein molecules containing both B and E apoproteins was reduced from 488 +/- 84 to 204 +/- 17 mg/dl by the FO with an almost corresponding increase in the conventional LDL molecules containing apo B only (158 +/- 29 to 344 +/- 15 mg/dl). We offer the hypothesis that the large apo B,E containing molecules are much more atherogenic than the smaller apo B containing molecules. This hypothesis is supported by a highly significant correlation between extent of lesion development in all arterial sites and plasma levels of CH in apo B,E containing lipoproteins. Plasma TBARS were elevated by the BT + FO diet but seemed to have no significant effect on the lesions.(ABSTRACT TRUNCATED AT 400 WORDS)

Endothelial cell denudation, labelling indices and monocyte attachment in advanced swine coronary artery lesions

This study shows that frank endothelial denudation, as measured by scanning electron microscopy, is associated with coronary artery atherosclerotic lesions in swine fed hyperlipidemic diets for 9 or 18 months. The largest areas of endothelial cell denudation were found to be associated with the most advanced atherosclerotic lesions, and lesser areas of denudation were present in less severely atherosclerotic arteries. Overall, the study suggests that frank endothelial denudation in swine coronaries occurs secondarily to advanced lesion development, and is proportionate to the amount of lesion present. In contrast attachment of monocytes to the endothelial surface was not proportionate to the amount of lesion present. While the number of attached monocytes after 9 or 18 months of a hyperlipidemic diet was much greater than in the mash-fed swine, there was no difference between the two hyperlipidemic groups. In both hyperlipidemic groups, the attached monocytes were concentrated over lesion areas. By scanning electron microscopy, most attached monocytes in these perfused coronary arteries showed a slender foot process extending into a gap between endothelial cells. Endothelial cell turnover, as measured by tritiated thymidine labelling indices, increased with the amount of coronary artery atherosclerosis. However, it did not become significantly greater than in mash-fed swine until advanced lesions developed.

The "turning off" of excessive cell replicative activity in advanced atherosclerotic lesions of swine by a regression diet

We studied progression of atherosclerotic lesions in the coronaries and abdominal aortas of swine fed hyperlipidemic (HL) diets producing serum cholesterol levels of about 700 mg/dl for up to 18 months with killings at 9, 13.5 and 18 months on diet. We studied changes in lesions in subsets given after 9 months on the HL diet a low fat, low cholesterol mash diet with killings at 4.5 and 9 months on the regression diet. Lesion cell numbers were evaluated using mean nuclear profiles per cross-section (Np/Cx) in an anatomically defined portion of artery as an index. Lesion sizes were evaluated using mean cross-sectional area (area/Cx) as an index. Tritiated thymidine labeling indices (LI) were used as an index of cell proliferative activity in the coronaries. We also determined the percentage of lesions occupied by lipid rich calcific necrotic debris. For further comparisons all of the same values were determined for normal intimal cell masses (ICM) in control groups fed a low fat, low cholesterol mash diet throughout. The atherosclerotic lesions in the HL swine appeared to arise mainly in the ICM. These became lesions and increased tremendously in size and cell numbers. The greatest increase was in the abdominal aorta even when lesion values were normalized by being expressed as percentages of the wall (intima + media). Lipid-rich calcific necrotic debris occupied about 25% of the lesion by 9 months and the percentage was similar at 18 months although size of lesions and their necrotic regions had increased 3-fold over the 9-month interval. Lesion [3H]thymidine LIs were 3-4-fold greater than in the control ICM. In the period 9-18 months on an HL diet lesions increased about 3-fold in size and cell numbers. In the swine put on a regression diet for the 9-18 month period growth of the lesions stopped completely. In fact, there was a numerical decrease in lesion sizes and cell numbers and this was statistically significant for the left anterior descending coronary. The lesion growth stoppage was partly accounted for by the "turning off" of excessive DNA synthesis activity of the lesion cells as indicated by the return of [3H] thymidine LIs to the normal values in the mash controls. Another factor was the lack of increase and in fact marked reduction in the size of the regions of lipid rich necrotic debris.(ABSTRACT TRUNCATED AT 400 WORDS)

Atherosclerotic lesions in the coronary arteries of hyperlipidemic swine. Part 1. Cell increases, divisions, losses and cells of origin in first 90 days on diet

The intima of the proximal portion of the coronary arteries of young swine is normally thickened by accumulations of cells about 90% of which are smooth muscle cells (SMC) and about 10% are of probable monocyte origin. Extracellular components such as collagen and elastic tissue are also present but we have chosen to emphasize their cellular nature by calling the regions of thickened intima, intimal cell masses (ICM). We have previously shown that atherosclerotic lesions produced in the coronary arteries of swine by 90 days of feeding a hyperlipidemic (HL) diet arise almost exclusively in the normally occurring ICM. We are reporting here a study of the pathogenesis of these lesions following killing at 0, 14, 49 and 90 HL diet days with comparisons between ICM in control mash-fed swine and ICM-lesions in the HL swine. We found that in the ICM: lipid accumulation was present by 14 days and increased thereafter; the lipid was mostly in SMC but percentage wise the monocyte-macrophages were involved as much or more, cell division activity was increased 3-4-fold by 49 days, cell numbers in ICM were similar in HL and control swine at 49 days but were about 6-fold greater in the HL swine at 90 days, (now in ICM-lesions), at 90 days, circa 90% of the cells appeared to be of SMC and circa 10% of monocyte origin both in the ICM-lesions of the HL swine and in the normal ICM of the controls. The data suggest but do not prove that early lipid accumulation precedes increased cell divisions especially among the SMC component and this in turn precedes increased numbers of cells in the ICM. Although SMC constitute the major cell component of the ICM-lesion at 90 days, the monocyte-macrophage-like cells also increase in number as a result of the HL diet and constitute a small but definite minor component. One possible explanation for the increased cell division activity is that one of the lipid constituents is acting as mitogen; another possibility is that the effect of a well known mitogen such as platelet-derived growth factor is enhanced by the lipid; another is that the monocytes are being stimulated to produce monocyte-derived growth factor. In any event in the very early stage of atherogenesis in the coronary arteries in these experiments excessive proliferation of resident SMC in the ICM appears to be the predominant feature.

Intimal cell mass-derived atherosclerotic lesions in the abdominal aorta of hyperlipidemic swine. Part 2. Investigation of endothelial cell changes and leukocyte adherence associated with early smooth muscle cell proliferative activity

We have investigated several aspects of endothelial cell (EC) behavior during the initiation and early development of intimal cell mass (ICM)-derived atherosclerotic lesions in the distal abdominal aortas of young swine fed hyperlipidemic (HL) diets for 0, 14, 49, or 90 days. By scanning electron microscopy no breaks in endothelial integrity or other abnormalities were observed even at 90 days on diet after lesions were well established. Also, counts of leukocytes adherent to the endothelium by both scanning and light microscopy revealed no greater numbers in HL than in mash control swine. Estimates of individual EC losses over ICM-lesions in the HL swine (based on calculations from tritiated thymidine labeling indices and EC growth rates determined by counts) suggested a loss of approximately one per 100 EC/day. This loss over ICM lesion was not significantly greater than that over ICM in mash controls, but was significantly greater than that of EC not over ICM lesions in the same HL animal. In any event, the estimated loss seems to be too trivial for the endothelial barrier to be compromised even transiently in a biologically significant fashion. A significant correlation was observed between tritiated thymidine labeling indices of cells within the ICM lesions and of those of the overlying EC that was not observed with the ICM in the controls. Possibly the positive correlation may be a result of the abluminal surface of the overlying EC being exposed to the abnormal milieu of the ICM lesion. It is emphasized that results reported here apply only to ICM-derived lesions at an early stage of development and that they do not contradict results obtained by others with other lesion types such as those derived from monocytes. Furthermore, in later stages of development of ICM-derived lesions in the same model we know that extensive endothelial cell damage can be demonstrated. Also, functional changes in endothelial permeability may have been present in early stages that would not have been detected with the methods used in this study.

Atherosclerotic lesions in coronary arteries of hyperlipidemic swine. Part 2. Endothelial cell kinetics and leukocyte adherence associated with early lesions

The role of endothelial cells (EC) in the development and progression of early swine intimal cell mass (ICM)-derived coronary artery lesions in 55 swine fed either a mash or hyperlipidemic diet for 14, 49 or 90 days was investigated. Characteristics studied were endothelial cell turnover (using tritiated thymidine autoradiography), adhesion of leukocytes (presumably chiefly monocytes) to endothelium, and the presence or absence of endothelial cell denudation. The major findings were: An increased adherence of leucocytes to endothelial cells over ICM-lesions in the HL-90 day group compared to the corresponding mash value at 90 days as well as to that of each of the other HL and mash groups. Significant positive correlation between the labeling indices (LI) of endothelial cells lying over coronary artery lesion cells and the labeling indices of the underlying ICM-lesion cells; also, a significant positive correlation between the labeling indices of endothelial cells over lesions of the abdominal aorta and those of the coronary arteries. At 90 days the endothelial cell LI over lesions in the HL group was significantly higher than the corresponding values in the mash group. Since the EC increase rates by growth in the two groups are also significantly different, the differences in LIs reflect at least in part EC growth differences and no strong conclusion can be made regarding possible cell turnover differences. No frank endothelial denudation was found. The findings suggest that in swine coronary arteries participation by monocytes from circulating blood is a factor in the early progression of the lesion as well as smooth muscle cell proliferation.

Association of plasma intermediate density lipoproteins with atherogenic intimal proliferative activity in abdominal aortas of hyperlipidemic swine

In an earlier study of swine fed hyperlipidemic (HL) diets containing either butter or corn oil we found wide differences in atherogenic intimal proliferative responses among the swine, especially in the corn oil group, that could not be entirely accounted for by differences in serum cholesterol levels. We hypothesized that there might be differences in some lipoprotein constituents other than total cholesterol that might better account for the differences in intimal proliferative responses. In the current experiment, 11 swine were fed HL diets containing butter (n = 5) or corn oil (n = 6). At 90 days on HL diet, plasma was obtained for lipoprotein fractionation. At 120 days the swine were killed and the lesion areas and number of nuclear profiles in the intima or lesions in multiple cross-sections of the distal abdominal aorta were determined under light microscopy. Tritiated thymidine labeling indices of the intima or lesion cells were also determined. On comparing the butter and corn oil groups, only IDL-cholesterol and tritiated thymidine labeling indices of the cells in the lesions were significantly different. Based on the number of nuclear profiles per cross-section (Np/Cx) 7 were classified as high intimal proliferative responders (5 butter, 2 corn oil) and 4 as low responders (4 corn oil). The high-proliferative responders had plasma IDL levels 6-fold greater than those of the low responders with no overlaps. LDL, VLDL and HDL were not significantly different between the high- and low-proliferative responders. Among correlation coefficients between Np/Cx and plasma lipoprotein variables for all swine (n = 11), IDL cholesterol level was best correlated with Np/Cx. However, in the high responder group LDL values showed a highly significant correlation with the amount of intimal proliferation.

Cell population kinetics in atherogenesis. Cell births and losses in intimal cell mass-derived lesions in the abdominal aorta of swine

Atherosclerotic lesions may arise in a number of different ways. The two most notable, perhaps, are by monocyte infiltration of the intima and by hyperplasia of normally occurring intimal cell masses. This report is limited to the ICM-derived lesion type induced by a hyperlipidemic diet in the abdominal aorta of swine. The HL diet results, by 49 days, in accumulation of lipid in about 50% of the ICM cells and increases in cell division activity, as indicated by tritiated thymidine LI fourfold greater than in ICM of control swine. Cell numbers are not significantly increased over controls at 49 days, but by 90 HL diet days, they have increased to eightfold over control values. Throughout the 90 days, about 95% of the cells in the ICM or ICM-lesions are smooth muscle cells. Monocytes appear to constitute no more than 5% of the cells. Calculated lesion cell deaths are small during the 90 days, and foci of necrosis are rarely found. By scanning electron microscopy, the endothelial cell integrity appears to be maintained even over the ICM-lesions at 90 days. Calculations from tritiated thymidine LI indicate endothelial cell losses equivalent to 50% of the LI, but they are not significantly greater for the HL swine than for controls. We suggest, then, that the lipid in the ICM (or something associated with it) is the most likely candidate for the SMC growth stimulatory agent accounting for the increased tritiated thymidine LI and the great increase in ICM-lesion cell numbers between HL diet days 49 and 90. Platelet- and/or monocyte-derived growth factors may also be involved in some subtle fashion, but this study provides no positive evidence to support this hypothesis. Progression of the ICM-derived lesions to the advanced atheromatous phase by 300 days on HL diet appears to be a much more complex process. By 300 days in the specific experiment cited, approximately 65% of the atherosclerotic lesion volume consisted of lipid-rich calcific necrotic debris; calculated death rates of lesion cells were very high compared to that at 90 days; calculated endothelial cell loss rates were considerably higher than in controls; and, large numbers of monocyte-macrophages were present in many areas generally associated with necrotic foci. These changes in the aggregate suggest a much more complex mode of pathogenesis for progression to advanced stages than for initiation and early development.

Endothelial cell labeling indices in swine aortas in relation to intimal cell mass-derived atherosclerotic lesions

In the swine abdominal aorta, most atherosclerotic lesions arise from naturally occurring collections of intimal cells called intimal cell masses. The main objective of this study was to determine if the tritiated thymidine labeling index of endothelial cells lying over intimal cell masses was greater than that of endothelial cells not over intimal cell masses. A higher endothelial cell labeling index over intimal cell masses would indicate possibly a greater turnover in the area. Such a finding would suggest possible transient but repeated breaks in the endothelial cell barrier that might contribute to the initiation of the atherosclerotic lesion in intimal cell masses. In 2 groups of mash-fed swine, 2 and 11 months old, no differences were found in labeling indices of endothelial cells lying over or not over intimal cell masses. It appears that the initiation of atherosclerosis in swine abdominal aorta is not dependent upon pre-existing altered endothelial cell kinetics as measured by tritiated thymidine labeling indices. The labeling index of cells within the intimal cell mass was significantly higher than in the media; this also is obviously not dependent upon an increased labeling index of the covering endothelial cells. Another group of swine were killed at 11 months of age after receiving a hyperlipidemic diet for 270 days. The labeling index of endothelial cells over atherosclerotic lesions was significantly higher than the labeling index of endothelial cells not over lesions in these swine, and also significantly higher than that of endothelial cells over intimal cell masses in the 11-month old mash-fed group.(ABSTRACT TRUNCATED AT 250 WORDS)

Intimal cell mass-derived atherosclerotic lesions in the abdominal aorta of hyperlipidemic swine. Part 1. Cell of origin, cell divisions and cell losses in first 90 days on diet

Atherosclerotic lesions may originate and develop in a variety of ways. In this study we are focusing our attention on atherosclerotic lesions arising in normally occurring intimal cell masses (ICM) in the abdominal aortas of hyperlipidemic (HL) swine. Times chosen for study were 0, 14, 49 and 90 days on HL diet; mash-fed swine were used as controls. Total numbers of cells in the ICM of HL and mash swine were similar at 14 and 49 days; by 90 days the number of cells had increased dramatically in the HL swine to 8-fold greater than control values. Changes present at 49 days and thus preceding increase in cell numbers included extensive intracellular lipid accumulation with by count nearly half of the ICM cells involved and elevated tritiated thymidine labeling indices (LI) 4-fold greater than control. Differential cell counts by transmission electron microscopy were made on the ICM lesions in the HL swine at 49 and 90 days. More than 95% of all cells were smooth muscle cells (SMC), with relatively few monocytes being present. Calculations from the LI and total cell counts showed that the entire increase in cell numbers could be accounted for by divisions among the resident SMC in the ICM. Further calculations suggested that cell losses (deaths) from the ICM were minimal. Scanning electron microscopy studies reported elsewhere revealed no loss of endothelial integrity. The results suggest: (1) that the lesions arise by stimulation of the resident SMC in the ICM to hyperplastic activity, (2) that the role of monocytes in the early development of these lesions is minimal if any, (3) that in view of the intact endothelium platelets are not likely to play an important role, (4) that ICM cell death is not a major factor, (5) that the most likely candidate for the cell growth stimulatory role (? mitogen) is some component(s) of the excess lipid that accumulates in the ICM.

Differential counts by electron microscopy of cell types in normal intimal cell masses in swine abdominal aortas

Hyperlipidemic diet-induced atherosclerotic lesions show a predilection for locating at the site of normal collections of intimal cells in the swine abdominal aorta. This implies that preexisting intimal cell masses (ICM) evolve into early diet-induced lesions. This study characterizes in detail the distal abdominal aortic ICM of young normal swine as a basis for a better understanding of lesion development. Seventeen male Yorkshire swine were used, from neonates to 20 weeks of age. Only three of six neonates showed multilayered ICM, the remaining three showed scattered individual cells or a single layer of cells. All older swine had multilayered ICM at a predictable ventral site corresponding to Evans blue in vivo staining. The majority of cells counted by electron microscopy were smooth muscle (89 to 94%), the remaining were macrophages (1 to 8%) and poorly differentiated cells (3 to 5%). Weanling and older swine showed high proportions of contractile smooth muscle cells. Ergastoplasm-rich smooth muscle cells comprised nearly half of the neonatal population. Stainable lipids were demonstrable in 20-week-olds, but not in younger swine. No foam cells were seen, but cells containing a few droplets totaled 2%; macrophages comprised a high proportion of these. Pyknotic dead cells were rare, being found in the neonate and 20-week-old swine. Mitoses were observed in two ergastoplasm-rich smooth muscle cells in the neonate and one each in contractile smooth muscle cells of a 14- and a 20-week-old swine. Saddlebag-shaped, atypical-appearing cells were present in all age groups, involving all three cell types, and ranging from 1 to 3%. These represented either bridged nuclei and cytoplasm or more likely artefactual distortion of relatively normal cells.

Endothelial and lesion cell growth patterns of early smooth-muscle cell atherosclerotic lesions in swine

This study shows that the endothelial cell turnover over the early porcine atherosclerotic lesion is more or less uniform in distribution. This is contrary to the findings in White Carneau pigeons where the increased endothelial cell turnover has a zonal pattern, being much greater at the lesion edge. The difference in the endothelial cell pattern of turnover in the two lesions probably is a reflection of their different manner of development. The porcine abdominal aortic lesion is derived from naturally occurring preexisting collections of intimal smooth-muscle cells called intimal cell masses. After 90 days of a hyperlipidemic diet these lesions are composed predominantly of smooth-muscle cells, with very few monocytes. The White Carneau pigeon lesion develops from circulating monocytes that have been shown to adhere to the edge of the lesion.

Intimal cell masses in the abdominal aortas of swine fed a low-fat, low-cholesterol diet for up to twelve years of age

The normal subendothelial intima of large arteries in man, swine and most other species is a variegated structure from birth onwards. In some regions it contains only a few scattered cells; in others there may be a continuous single layer of cells; and in still others the cells pile up to form what we have called intimal cell masses (ICM). The cells in the normal ICM are mostly smooth muscle cells although there is also a small resident population of monocyte-like cells. We have been studying the ICM in swine with emphasis on the abdominal aorta. We have found that atherosclerotic lesions in the abdominal aorta of swine induced by high-fat high-cholesterol diets begin by a hyperplastic reaction of the smooth muscle cells in the ICM and progress to form large lesions characterized by extensive regions of lipid-rich calcific necrotic debris similar to advanced lesions in man. Because of the putative key role of the ICM in atherogenesis we think that it is important to learn as much as possible about their natural history under conditions as normal as possible. In this report we present data on ICM in the abdominal aortas of 34 male and female Hormel miniature swine maintained on a low-fat low-cholesterol diet for up to 12 years of age. The ICM grow slowly with aging and in the distal portion of the aorta account for an average of 9% in the male and 15% in the female of the total cells in the aortic wall (intima + media).(ABSTRACT TRUNCATED AT 250 WORDS)

Quantification of intimal cell masses and atherosclerotic lesions in coronary arteries of control and hyperlipidemic swine

In the current study of swine coronary arteries, we have attempted to quantify the coronary intimal cell masses (ICM) with regard to two aspects: (1) percentage of total arterial wall cells (intimal plus medial) that are in the intima, and (2) percentage of arterial wall area occupied by intima. We have studied 4 coronary sites: left main stem (LMS), proximal right (RCA), proximal left circumflex (LCX), and proximal left anterial descending (LAD). In mash-fed ('normal') swine we carried out the study at 3 ages: 2, 5 and 12 months. In addition, we have carried out a similar study in swine fed hyperlipidemic (HL) diets for 3 or approximately 10 months starting at 2 months of age. In the control swine we found approximately 6% of the arterial wall occupied by intima at 2 months of age with no significant increases by 12 months. There were no consistent significant differences among the 4 coronary artery sites with regard to percentage of wall occupied by intima. When the HL diet was fed, there were significant increases in the percentage of the arterial wall occupied by intima (now atherosclerotic lesion) by 3 months on diet and much larger increases by 10 months (up to 87% of wall occupied by intimal lesion) with extensive regions of lipid-rich, calcific, necrotic debris. After 3 months on HL diet the RCA lesions occupied significantly greater percentages of areas than the other 3 sites but this difference had disappeared by 10 months on the HL diet.