In Vitro Models of Traumatic Brain Injury: A Systematic Review

Traumatic brain injury (TBI) is a major public health challenge that is also the third leading cause of death worldwide. It is also the leading cause of long-term disability in children and young adults worldwide. Despite a large body of research using predominantly in vivo and in vitro rodent models of brain injury, there is no medication that can reduce brain damage or promote brain repair mainly due to our lack of understanding in the mechanisms and pathophysiology of the TBI. The aim of this review is to examine in vitro TBI studies conducted from 2008-2018 to better understand the TBI in vitro model available in the literature. Specifically, our focus was to perform a detailed analysis of the in vitro experimental protocols used and their subsequent biological findings. Our review showed that the uniaxial stretch is the most frequently used way of load application, accounting for more than two-thirds of the studies reviewed. The rate and magnitude of the loading were varied significantly from study to study but can generally be categorized into mild, moderate, and severe injuries. The in vitro studies reviewed here examined key processes in TBI pathophysiology such as membrane disruptions leading to ionic dysregulation, inflammation, and the subsequent damages to the microtubules and axons, as well as cell death. Overall, the studies examined in this review contributed to the betterment of our understanding of TBI as a disease process. Yet, our review also revealed the areas where more work needs to be done such as: 1) diversification of load application methods that will include complex loading that mimics in vivo head impacts; 2) more widespread use of human brain cells, especially patient-matched human cells in the experimental set-up; and 3) need for building a more high-throughput system to be able to discover effective therapeutic targets for TBI.

The role of diffusion tensor imaging in characterizing injury patterns on athletes with concussion and subconcussive injury: a systematic review

Traumatic brain injury (TBI) is a major public health problem. The majority of TBIs are in the form of mild TBI (also known as concussion) with sports-related concussion (SRC) receiving public attention in recent years.Here we have performed a systematic review of the literature on the use of Diffusion Tensor Imaging (DTI) on sports-related concussion and subconcussive injuries. Our review found different patterns of change in DTI parameters between concussed and subconcussed groups. The Fractional Anisotropy (FA) was either unchanged or increased for the concussion group, while the subconcussed group generally experienced a decrease in FA. A reverse pattern was observed for Mean Diffusivity (MD) - where the concussed group experienced a decrease in MD while the subconcussed group showed an increase in MD. However, in general, discrepancies were observed in the results reported in the literature - likely due to the huge variations in DTI acquisition parameters, and image processing and analysis methods used in these studies. This calls for more comprehensive and well-controlled studies in this field, including those that combine the advanced brain imaging with biomechancial modeling and kinematic sensors - to shed light on the underlying mechanisms behind the structural changes observed from the imaging studies.

Effect of fractional blood flow on plasma skimming in the microvasculature

Although redistribution of red blood cells at bifurcated vessels is highly dependent on flow rate, it is still challenging to quantitatively express the dependence of flow rate in plasma skimming due to nonlinear cellular interactions. We suggest a plasma skimming model that can involve the effect of fractional blood flow at each bifurcation point. To validate the model, it is compared with in vivo data at single bifurcation points, as well as microvascular network systems. In the simulation results, the exponential decay of the plasma skimming parameter M along fractional flow rate shows the best performance in both cases.

Abstract A48: Computational modeling of vessel growth and blood flow in the tumor microvasculature

Tumor-induced angiogenesis is important to understand the mechanism of tumor growth. However, due to its heterogeneous microenvironment, it is challenging to elucidate the correlation between tumor growth and angiogenesis. In this talk, we develop a computational model of tumor-induced angiogenesis with blood flow. The complex steps of angiogenesis are expressed by mathematical models from diffusion of growth factor, sprouting from existing vessels, vessel growth and anastomosis. Furthermore, the blood flow in the new vessels is simulated by using one dimensional flow model with hematocrit redistribution. First of all, the computational model will be validated by comparing with experimental data. In addition, the developed model will be tested in predicting tumor-induced angiogenesis with different model parameters. Finally, the future perspectives of computational modeling in tumor-induced angiogenesis will be fully discussed.

Note: This abstract was not presented at the conference.

Citation Format: Tae-Rin Lee, Sung Sic Yoo, Junhong Jo, Anna Go, Hyung-Kwon Seo. Computational modeling of vessel growth and blood flow in the tumor microvasculature. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A48.

Interferon-inducible T-cell alpha chemoattractant (ITAC) induces the melanocytic migration and hypopigmentation through destabilizing p53 via histone deacetylase 5: a possible role of ITAC in pigment-related disorders

BACKGROUND

Cell migration plays a major role in the immune response and in tumorigenesis. Interferon-inducible T-cell alpha chemoattractant (ITAC) elicits a strong chemotactic response from immune cells.

OBJECTIVES

To examine the effect of ITAC on melanocyte migration and pigmentation and its involvement in related disorders, and to investigate potential key players in these processes.

METHODS

Human melanocytes or melanoma cells were treated with ITAC and a migration assay was carried out. Global gene expression analysis was performed to find genes regulated by ITAC treatment. The function of key players involved in ITAC-induced cellular processes was addressed using knockdown or overexpression experiments in combination with ITAC treatment. ITAC expression in the inflammation-associated hypopigmentary disorder, vitiligo, was examined.

RESULTS

Among CXCR3 ligands, only ITAC induced melanocyte migration. ITAC treatment upregulated the expression of histone deacetylase 5 (HDAC5) and downregulated that of p53, a known target of HDAC5. Through knockdown or overexpression of HDAC5 and p53, we confirmed that HDAC5 mediates ITAC-induced migration by decreasing levels of p53 via deacetylation. In addition, ITAC treatment could decrease pigmentation in a p53- and HDAC5-dependent manner. Finally, the increased migration of human melanoma cells by ITAC treatment and the increased ITAC expression in the epidermis of vitiligo skin were verified.

CONCLUSIONS

This study provides in vitro evidence for the migratory and hypopigmentation effects of ITAC on melanocytic cells, gives translational insights into the roles of ITAC in pathological conditions, and suggests that HDAC5 and its substrate p53 are potent targets for regulating ITAC-induced cellular processes.

High shear-induced exfoliation of graphite into high quality graphene by Taylor–Couette flow

A scalable method to produce high-quality graphene by shear-exfoliation of graphite is presented. High shear mixing of graphite in the Taylor vortex flow regime allows for the bulk production of few-layer graphene with low content of defects.

Correction: High shear-induced exfoliation of graphite into high quality graphene by Taylor–Couette flow

Correction for ‘High shear-induced exfoliation of graphite into high quality graphene by Taylor–Couette flow’ by Tuan Sang Tran et al., RSC Adv., 2016, 6, 12003–12008.

A physical sciences network characterization of circulating tumor cell aggregate transport

Circulating tumor cells (CTC) have been implicated in the hematogenous spread of cancer. To investigate the fluid phase of cancer from a physical sciences perspective, the multi-institutional Physical Sciences-Oncology Center (PS-OC) Network performed multidisciplinary biophysical studies of single CTC and CTC aggregates from a patient with breast cancer. CTCs, ranging from single cells to aggregates comprised of 2-5 cells, were isolated using the high-definition CTC assay and biophysically profiled using quantitative phase microscopy. Single CTCs and aggregates were then modeled in an in vitro system comprised of multiple breast cancer cell lines and microfluidic devices used to model E-selectin mediated rolling in the vasculature. Using a numerical model coupling elastic collisions between red blood cells and CTCs, the dependence of CTC vascular margination on single CTCs and CTC aggregate morphology and stiffness was interrogated. These results provide a multifaceted characterization of single CTC and CTC aggregate dynamics in the vasculature and illustrate a framework to integrate clinical, biophysical, and mathematical approaches to enhance our understanding of the fluid phase of cancer.

Skin dryness in apparently healthy human skin is associated with decreased expression of bleomycin hydrolase in the stratum corneum

BACKGROUND

Maintenance of water balance in the stratum corneum (SC) is determined by the content of intercellular lipids and natural moisturizing factors (NMFs) in corneocytes.

AIM

To investigate the association between the NMFs and (pro)filaggrin and the proteases responsible for the processing of (pro)filaggrin to NMFs in the SC of hydrated and dry skin areas of healthy human subjects.

METHODS

The SC hydration state and the transepidermal water loss (TEWL) were measured using a Corneometer and a Tewameter, respectively. Proteases, (pro)filaggrin and NMFs were extracted from SC samples obtained by tape-stripping of the tested skin. Expression levels of (pro)filaggrin were determined by dot blotting and western blotting, and total NMFs by ultra-high performance liquid chromatography. Expression of the proteases caspase-14, calpain-1 and bleomycin hydrolase was measured by western blotting.

RESULTS

The levels of (pro)filaggrin were not significantly different between hydrated and dry skin, whereas the level of total NMFs was significantly reduced in dry skin. A negative correlation between (pro)filaggrin and NMFs was found in dry skin (Pearson correlation coefficient r = - 0.57, *P < 0.05). Bleomycin hydrolase expression was significantly decreased in the SC of dry skin.

CONCLUSIONS

These results suggest that the low hydration state of dry skin may be due to the reduction in (pro)filaggrin degradation caused by decreased bleomycin hydrolase expression.

Impact of atmospheric boundary layer depth variability and wind reversal on the diurnal variability of aerosol concentration at a valley site

The development of the atmospheric boundary layer (ABL) plays a key role in affecting the variability of atmospheric constituents such as aerosols, greenhouse gases, water vapor, and ozone. In general, the concentration of any tracers within the ABL varies due to the changes in the mixing volume (i.e. ABL depth). In this study, we investigate the impact on the near-surface aerosol concentration in a valley site of 1) the boundary layer dilution due to vertical mixing and 2) changes in the wind patterns. We use a data set obtained during a 10-day field campaign in which a number of remote sensing and in-situ instruments were deployed, including a ground-based aerosol lidar system for monitoring of the ABL top height (zi), a particle counter to determine the number concentration of aerosol particles at eight different size ranges, and tower-based standard meteorological instruments. Results show a clearly visible decreasing trend of the mean daytime zi from 2900 m AGL (above ground level) to 2200 m AGL during a three-day period which resulted in increased near-surface pollutant concentrations. An inverse relationship exists between the zi and the fine fraction (0.3-0.7 μm) accumulation mode particles (AMP) on some days due to the dilution effect in a well-mixed ABL. These days are characterized by the absence of daytime upvalley winds and the presence of northwesterly synoptic-driven winds. In contrast, on the days with an onset of an upvalley wind circulation after the morning transition, the wind-driven local transport mechanism outweighs the ABL-dilution effect in determining the variability of AMP concentration. The interplay between the ABL depth evolution and the onset of the upvalley wind during the morning transition period significantly governs the air quality in a valley and could be an important component in the studies of mountain meteorology and air quality.

Quantifying uncertainties in the microvascular transport of nanoparticles

The character of nanoparticle dispersion in the microvasculature is a driving factor in nanoparticle-based therapeutics and bio-sensing. It is difficult, with current experimental and engineering capability, to understand dispersion of nanoparticles because their vascular system is more complex than mouse models and because nanoparticle dispersion is so sensitive to in vivo environments. Furthermore, uncertainty cannot be ignored due to the high variation of location-specific vessel characteristics as well as variation across patients. In this paper, a computational method that considers uncertainty is developed to predict nanoparticle dispersion and transport characteristics in the microvasculature with a three step process. First, a computer simulation method is developed to predict blood flow and the dispersion of nanoparticles in the microvessels. Second, experiments for nanoparticle dispersion coefficients are combined with results from the computer model to suggest the true values of its unknown and unmeasurable parameters-red blood cell deformability and red blood cell interaction-using the Bayesian statistical framework. Third, quantitative predictions for nanoparticle transport in the tumor microvasculature are made that consider uncertainty in the vessel diameter, flow velocity, and hematocrit. Our results show that nanoparticle transport is highly sensitive to the microvasculature.

On the near-wall accumulation of injectable particles in the microcirculation: smaller is not better

Although most nanofabrication techniques can control nano/micro particle (NMP) size over a wide range, the majority of NMPs for biomedical applications exhibits a diameter of ~100 nm. Here, the vascular distribution of spherical particles, from 10 to 1,000 nm in diameter, is studied using intravital microscopy and computational modeling. Small NMPs (≤100 nm) are observed to move with Red Blood Cells (RBCs), presenting an uniform radial distribution and limited near-wall accumulation. Larger NMPs tend to preferentially accumulate next to the vessel walls, in a size-dependent manner (~70% for 1,000 nm NMPs). RBC-NMP geometrical interference only is responsible for this behavior. In a capillary flow, the effective radial dispersion coefficient of 1,000 nm particles is ~3-fold larger than Brownian diffusion. This suggests that sub-micron particles could deposit within diseased vascular districts more efficiently than conventional nanoparticles.

A statistical study on nanoparticle movements in a microfluidic channel

Microfluidic channels have received much attention because they can be used to control and transport nanoscale objects such as nanoparticles, nanowires, carbon nanotubes, DNA and cells. However, so far, practical channels have not been easy to design because they require very expensive fabrication and sensitive experiments. Numerical approaches can be alternatives or supplementary measures to predict the performance of new channels because they efficiently explain nanoscale multi-physics phenomena and successfully solve nanowire alignment and cell adhesion problems. In this paper, a newly updated immersed finite element method that accounts for collision force and Brownian motion as well as fluid-solid interaction is proposed, and is applied to simulate nanoparticle movements in a microfluidic channel. As part of the simulation, Brownian motion effects in a single nanoparticle focusing lens system are examined under different temperature conditions, and the resulting transport efficiencies are discussed. Furthermore, nanoparticle movements in a double focusing lens system are predicted to show the enhancement of focusing efficiency.

Numerical simulation of a nanoparticle focusing lens in a microfluidic channel by using immersed finite element method

Lap-on-a-chip system is one of challenging parts in nano and bio engineering fields, for instance, microfluidic channels on the chip are useful for selecting a target particle and mass transferring of boiomolecules in fluid. However, since experimental approach is highly expensive both in time and cost, alternative reliable methods are required to conceive optimized channels. The purpose of this research is to simulate a nanoparticle focusing lens in a microfluidic channel from nanoparticle control point of view. A promising immersed finite element method is expanded to estimate the path of randomly moving nanoparticles through a focusing lens. The channel flow is assumed as incompressible viscous fluid and Brownian motion effects as well as initial position of particle are quantitatively examined. As a representative result, while the nanoparticles with/without Brownian motion were focused along the center of the channel, the concentration factor representing focusing efficiency was calculated. Therefore, it is expected that the newly proposed numerical method considering Brownian motion will be efficiently applicable to design the microfluidic channel containing various particles, molecules and so forth in the near future.

Prognostic nomogram for predicting the 5-year probability of developing metastasis after neo-adjuvant chemotherapy and definitive surgery for AJCC stage II extremity osteosarcoma

BACKGROUND

In this retrospective study, we developed and internally validate a nomogram for predicting 5-year metastasis probability for nonmetastatic extremity osteosarcoma.

PATIENTS AND METHODS

We reviewed 365 osteosarcoma patients treated at our institute from 1990 to 2003. Clinicopathologic variables were recorded. Multivariate analysis using Cox proportional hazards regression was done and this Cox model was used as the basis for the nomogram.

RESULTS

By American Joint Committee on Cancer (AJCC) staging system, 141 patients (38.6%) were stage IIA and 224 (61.4%) were stage IIB. Multivariate Cox model identified patient age at diagnosis, tumor size, humeral location, and tumor necrosis rate after chemotherapy as correlated with metastasis-free survival. The degree of contribution of each covariate to the total point was tumor location, tumor necrosis rate, maximal tumor diameter, and age in decreasing order. The concordance index for the model was 0.78. Nomogram discrimination was superior to that of AJCC stage (concordance index 0.78 versus 0.68; P = 0.02) and histologic response grouping (concordance index 0.78 versus 0.69; P = 0.0004).

CONCLUSIONS

We devised a nomogram for nonmetastatic osteosarcoma that proposes improved estimates of metastasis over AJCC staging system or tumor necrosis rate. We suggest that this nomogram allows individualized risk assessments and could be used as the basis for risk-adapted therapy.

Slc11a1 (formerly Nramp1) polymorphisms and susceptibility to post-transplant lymphoproliferative disease following pediatric liver transplantation

BACKGROUND

Polymorphisms of the solute carrier family 11 member 1 (Slc11a1) gene have previously been associated with susceptibility to infectious disease, anti-tumor defenses, and autoimmune diseases. We postulated that polymorphisms of the gene may also be associated with susceptibility to post-transplant lymphoproliferative disease (PTLD), a disease thought to be related to an impaired immune response to Epstein-Barr virus (EBV) in immunosuppressed patients.

METHODS

Whole blood samples were obtained from 45 pediatric patients who underwent liver transplantation. Polymerase chain reaction (PCR) was used to amplify a 3' region of the gene that includes an exon 15 single-nucleotide substitution (referred to as D543N) and a 4-bp deletion polymorphism (referred to as 3'-UTR). PCR products were digested using AvaII and FokI restriction enzymes for the D543N and 3'-UTR polymorphisms, respectively. PTLD disease status and EBV virus serum titers of all patients were obtained from hospital records.

RESULTS

Six of the 45 pediatric transplant recipients developed PTLD. An association was found between 3'-UTR polymorphisms of Slc11a1 and incidence of PTLD after liver transplantation (P = 0.005). In addition, post-transplant serum EBV titers were higher (P = 0.009) for recipients with certain Slc11a1 polymorphisms. No association was found between the D543N polymorphism and incidence of PTLD.

CONCLUSION

3'-UTR polymorphisms of the Slc11a1 gene appear to be associated with susceptibility to PTLD and the immune response to EBV in pediatric liver transplant recipients. Genotyping of pediatric patients undergoing liver transplantation may enable early identification of patients at high risk for developing high EBV titers and/or PTLD.

Positive regulation of hepatic carnitine palmitoyl transferase 1A (CPT1A) activities by soy isoflavones and L-carnitine

BACKGROUND

Genistein increases CPT1A, a rate-limiting enzyme in the beta-oxidation pathway, enzyme activity by increasing CPT1A transcription in HepG2 cells and, consequently, suppresses high fat induced obesity in C57BL/6J mice. Genistein and daidzein are the most abundant isoflavones in soy.

AIM OF STUDY

To investigate the effect of co-treatment of genistein and L-carnitine on CPT1A enzyme activity and to determine whether daidzein also increases CPT1A activity and to establish a cell line that can be used to screen chemicals to regulate CPT1A transcription.

METHODS

The enzyme activities of CPT1A were determined after HepG2 cells were incubated with 10 microM genistein or 10 microM daidzein or 1 mM L-carnitine or in combination with 10 microM genistein and 1 mM L-carnitine or in combination with 10 microM daidzein and 1 mM L-carnitine. The mRNA expression levels of CPT1A were determined by real time PCR method after HepG2 cells were incubated with 10 microM genistein or 10 microM daidzein. A suggested CPT1A promoter region was cloned from human genomic DNA and the CPT1A promoter-luciferase reporter gene construct was made, and the promoter-reporter gene construct was transfected into human hepatoma cell line Huh7.

RESULTS

The enzyme activity of CPT1A was at least 2.3- fold higher in L-carnitine and genistein co-treated HepG2 cells than either single-agent treated cells. Daidzein also significantly increased the mRNA expression of CPT1A as well as the enzyme activity of CPT1A. A stable Huh7 cell line, which was selected after Huh7 cells were transfected with CPT1A promoter luciferase reporter gene construct, was characterized by confirming that luciferase activity of the cell line can be regulated by genistein and daidzein as well as clofibrate, a well-known CPT1A mRNA up-regulating drug.

CONCLUSIONS

Genistein and daidzein can up-regulate CPT1A enzyme activity through up-regulation of CPT1A transcription. Co-treatment of L-carnitine and genistein additively increases CPT1A enzyme activity in HepG2 cells. A stable Huh7 cell line transfected with the CPT1A promoter luciferase reporter gene was established and characterized.

Probing the local structure and mechanical response of nanostructures using force modulation and nanofabrication

Nanostructures of self-assembled monolayers (SAMs) are designed and produced using coadsorption and nanografting techniques. Because the structures of these artificially engineered domains are predesigned and well-characterized, a systematic investigation is possible to study the mechanical responses to force modulation under atomic force microscope tips. Force modulation imaging reveals characteristic contrast sensitivity to changes in molecular-level packing, molecule chain lengths, domain boundaries, and surface chemical functionalities in SAMs. By means of actively tuning the driving frequency, the resonances at the tip-surface contact are selectively activated. Therefore, specific surface features, such as the edges of the domains and nanostructures or desired chemical functionalities, can be selectively enhanced in the amplitude images. These observations provide a new and active approach in materials characterization and the study of nanotribology using atomic force microscopy.

Academic goals, achievement, and age at first sexual intercourse: longitudinal, bidirectional influences

This study examined bidirectional relationships between age at first sexual intercourse and academic goals and achievement. It was hypothesized that lower educational goals and achievement would be associated with initiating sexual intercourse at a younger age, and that initiating sexual activity early would be associated with a decrease in subsequent academic achievement and goals. In longitudinal data spanning 11 years, evidence was found for bidirectional effects. One interpretation of these results is that adolescents with high educational goals and achievement delay having intercourse because of the perceived risks (e.g., pregnancy and sexually transmitted diseases may jeopardize their plans for the future). Conversely, adolescents who engage in sexual intercourse at young ages might undergo a change in attitudes, including reduced interest in academic achievement and goals. The specific educational variables most strongly related to adolescent sexual intercourse in this study differed substantially by race and gender.

Transcriptional regulation of the Bacillus subtilis bscR-CYP102A3 operon by the BscR repressor and differential induction of cytochrome CYP102A3 expression by oleic acid and palmitate

The adjacent yrhI and yrhJ genes were identified by the Bacillus subtilis genome sequencing project. We now report that yrhJ (renamed CYP102A3) encodes a cytochrome P450 and that yrhI (renamed bscR) encodes a repressor that negatively regulates the transcription of the bscR-CYP102A3 operon. The transcriptional initiation site of bscR has been mapped by primer extension analysis. An 18-bp perfect palindromic sequence centered 65.5 bp downstream from the transcriptional initiation site of bscR has been identified as the binding site for BscR by gel mobility shift assays. Base substitutions in the 18-bp inverted repeat resulted in derepression of the bscR-xylE transcriptional fusion in vivo. bscR-xylE fusion studies and Northern blot analysis revealed that oleic acid and palmitate could induce the expression of the bscR-CYP102A3 operon to a considerable extent. However, only oleic acid was capable of preventing the binding of BscR to its operator DNA in vitro, suggesting that the induction of CYP102A3 expression by oleic acid and palmitate in B. subtilis might be mediated through different mechanisms.

Kinetics of the cis,cis to trans,trans isomerization of 1,1,2,2,5,5,6,6-octamethyl-1,2,5,6-tetrasilacycloocta-3,7-diene

The kinetics of the ruthenium-promoted cis,cis to trans,trans isomerization of 1,1,2,2,5,5,6,6-octamethyl-1,2,5,6-tetrasilacycloocta-3,7-diene were investigated. Incubation of a ruthenium alkylidene complex, (Cy(3)P)RuCl(2)(==CHPh)Ru(p-cymene)Cl(2), in CD(2)Cl(2) for 5 days at 40 degrees C afforded a catalytically active ruthenium species that was shown to be responsible for promoting the isomerization. The isomerization was observed to proceed in two steps: (1) conversion of the starting cis,cis isomer to a proposed cis,trans intermediate and (2) subsequent conversion of the intermediate to the product trans,trans isomer. Kinetic studies demonstrated that the two steps are first-order with respect to the concentrations of the cis,cis isomer, the intermediate, and the ruthenium alkylidene complex. The data were further consistent with a mechanism involving bimolecular hydride addition-elimination during the two isomerization steps.

The cis-trans isomerization of 1,2,5,6-tetrasilacycloocta-3,7-dienes: analysis by mechanistic probes and density functional theory

A series of alkyl- and aryl-substituted derivatives of cis,cis-1,2,5,6-tetrasilacycloocta-3,7-diene were prepared. Isomerization of these compounds to the corresponding trans,trans-1,2,5,6-tetrasilacycloocta-3,7-dienes by exposure to Ru and Zr hydride complexes was explored. Experimental probes of the isomerization were consistent with a stepwise mechanism involving metal hydride addition/elimination rather than one involving radical intermediates. Analysis of the low energy conformers of the various cis and trans isomers of 1,1,2,2,5,5,6,6-octamethyl-1,2,5,6-tetrasilacycloocta-3,7-diene using density functional theory suggested the following trend in stability: trans,trans > cis,trans > cis,cis. The calculated trend in stability was consistent with the experimentally observed unidirectional isomerization of the carbon-carbon double bonds from all cis to all trans and supports a cis,trans isomer as a tenable intermediate.

From consensus sequence peptide to high affinity ligand, a "library scan" strategy

A wide variety of proteins have been shown to recognize and bind to specific amino acid sequences on other proteins. These sequences can be readily identified using combinatorial peptide libraries. However, peptides containing these preferred sequences ("consensus sequence peptides") typically display only modest affinities for the consensus sequence-binding site on the intact protein. In this report, we describe a parallel synthesis strategy that transforms consensus sequence peptides into high affinity ligands. The work described herein has focused on the Lck SH2 domain, which binds the consensus peptide acetyl-Tyr(P)-Glu-Glu-Ile-amide with a K(D) of 1.3 micrometer. We employed a strategy that creates a series of spatially focused libraries that challenge specific subsites on the target protein with a diverse array of functionality. The final lead compound identified in this study displayed a 3300-fold higher affinity for the Lck SH2 domain than the starting consensus sequence peptide.

Molecular rulers: an assessment of distance and spatial relationships of Src tyrosine kinase Sh2 and active site regions

The three-dimensional structures of the inactive conformations of Hck and Src, members of the Src protein-tyrosine kinase family, have recently been described. In both cases, the catalytic domain lies on the opposite face of the enzyme from the SH2 and SH3 domains. The active conformation of these enzymes has not yet been described. Given the known role of the SH2 and SH3 domains in promoting substrate binding, enzyme activation likely reorients the relative spatial arrangement between the SH2/SH3 domains and the active site region. We describe herein a series of "molecular rulers" and their use in assessing the topological and spatial relationships of the SH2 and active site regions of the Src protein-tyrosine kinase. These synthetic compounds contain sequences that are active site-directed (-Glu-Glu-Ile-Ile-(F(5))Phe-, where (F(5))Phe is pentafluorophenylalanine) and SH2-directed (-Tyr(P)-Glu-Glu-Ile-Glu-), separated by a sequence of variable length. The most potent bivalent compound, acetyl-Glu-Glu-Leu-Leu-(F(5))Phe-(GABA)(3)-Tyr(P)-Glu-Glu-Ile-Glu-amide (where GABA is gamma-aminobutyric acid), displays a >120-fold enhancement in inhibitory potency relative to the simple monovalent active site-directed species, acetyl-Glu-Glu-Leu-Leu-(F(5))Phe-amide. The short linker length (3 GABA residues) between the active site- and SH2-directed peptide fragments suggests that the corresponding domains on the Src kinase can assume a nearly contiguous spatial arrangement in the active form of the enzyme.

Nonhypoglycemic effects of thiazolidinediones

The thiazolidinediones are a new class of compounds for treatment of type 2 diabetes. Troglitazone became available in the United States in 1997 but was withdrawn from the market in March 2000 because it caused severe idiosyncratic liver injury. Rosiglitazone and pioglitazone have been available since 1999. Because these drugs directly improve insulin resistance and decrease plasma insulin levels (a risk factor for coronary artery disease), they may decrease risk for cardiovascular disease in patients with type 2 diabetes. Research on the non-glucose lowering effects of troglitazone and, to a lesser extent, of rosiglitazone and pioglitazone have demonstrated changes in several cardiovascular risk factors associated with the insulin resistance syndrome. These beneficial effects include a decrease in blood pressure, correction of diabetic dyslipidemia, improvement of fibrinolysis, and decrease in carotid artery intima-media thickness. Other in vitro effects related to the ability of these agents to bind a newly described class of receptors (peroxisome proliferator-activated receptors) may also have implications for atherosclerosis. However, these drugs increase low-density lipoprotein (LDL) cholesterol levels and may favorably change LDL particle size and susceptibility to oxidation (although the implications of the latter changes are not dear). Furthermore, these drugs tend to cause weight gain. The authors' enthusiasm for these drugs has diminished somewhat because of reported adverse events, including rare liver failure. Nevertheless, because of the mechanism of action of the thiazolidinediones, clinical trials designed to determine whether they (or similar "insulin sensitizers") decrease cardiovascular events in people with type 2 diabetes will be of interest.

SH2-directed ligands of the Lck tyrosine kinase

Two separate libraries, prepared via parallel synthesis, were employed to identify low-molecular-weight SH2-targeted ligands for the Lck tyrosine protein kinase. These libraries were constructed to furnish non-amino acid analogues of the (1) Glu-Glu and (2) Ile residues of the Lck SH2 domain peptide ligand Ac-pTyr-Glu-Glu-Ile-amide. The lead compound acquired in this study exhibits a dissociation constant for the Lck SH2 domain that is comparable to that displayed by Ac-pTyr-Glu-Glu-Ile-amide. These results demonstrate that the standard amino acid residues Glu-Glu-Ile can be completely replaced with non-amino acid moieties without loss of SH2 affinity.

Fullerene pipes

Single-wall fullerene nanotubes were converted from nearly endless, highly tangled ropes into short, open-ended pipes that behave as individual macromolecules. Raw nanotube material was purified in large batches, and the ropes were cut into 100- to 300-nanometer lengths. The resulting pieces formed a stable colloidal suspension in water with the help of surfactants. These suspensions permit a variety of manipulations, such as sorting by length, derivatization, and tethering to gold surfaces.

Rate-determining steps for tyrosine phosphorylation by the kinase domain of v-fps

The rate-determining steps in the phosphorylation of four tyrosine-containing peptides by the kinase domain of the nonreceptor tyrosine protein kinase v-fps were measured using viscosometric methods. The peptides were phosphorylated by a fusion protein of glutathione-S-transferase and the kinase domain of v-fps (GST-kin) and the initial velocities were determined by a coupled enzyme assay. Peptides I (EEEIYEEIE), II (EAEIYEAIE), and III (DADIYDAID) were phosphorylated by GST-kin with similar kinetic constants. The viscosogens, glycerol and sucrose, were found to have intermediate effects on kcat and no effect on kcat/Kpeptide for the phosphorylation of these three peptides. The data are interpreted according to the Stokes-Einstein equation and a simple three-step mechanism involving substrate binding, phosphoryl group transfer, and net product release. Two competitive inhibitors (EAEIFEAIE and DADIFDAID) exhibited K1 values that are 6-10-fold higher than the Kpeptide values for their analogous peptide substrates. The data imply that peptides I-III are in rapid equilibrium with the enzyme and that kcat is partially limited by both phosphoryl group transfer (40-100 s-1) and product release (17-22 s-1). GST-kin phosphorylates peptide IV (R5AENLEYamide) with a low Km (100 microM) and a kcat that is 40-fold lower than that for peptide I. No effect of solvent viscosity was observed for the phosphorylation of this peptide on either kcat or kcat/Kpeptide. This suggests that highly viscous solutions do not perturb structure and that the rate-determining step for this poor substrate is phosphoryl group transfer. The data indicate that the kinase domain of v-fps phosphorylates its best substrate with a chemical rate constant that is at least 5-fold lower than that for the serine-specific cAMP-dependent protein kinase and its best substrate LRRASLG (Adams & Taylor, 1992). Interestingly, both enzymes exhibit a similar affinity for their substrates and both enzymes release their products at a similar rate. This implies that the differences in catalytic efficiency between serine- and tyrosine-specific protein kinases lie exclusively in the rate constants for phosphoryl group transfer and not in substrate absorption or product desorption.

Is protein kinase substrate efficacy a reliable barometer for successful inhibitor design?

We have addressed the question of whether protein kinase substrate efficacy is a reliable barometer for successful inhibitor design by assessing the dependence of kcat and kcat/Km for eight separate alcohol-bearing residues on solvent viscosity. We have found that the Km for three structurally distinct primary alcohol-containing peptides overestimates the affinity that these species exhibit for the cAMP-dependent protein kinase. In all three cases, the rate-determining step is product release, and substrate binding is best described as rapid equilibrium. In contrast, peptides containing the following phosphorylatable residues all provide Km values that are accurate assessments of substrate affinity for the protein kinase: a secondary alcohol, a simple phenol, and a primary alcohol with a relatively long side chain. In the latter three instances, the rate-determining step is phosphoryl transfer. Finally, two aromatic alcohol-containing residues that possess lipophilic side chains exhibit Michaelis constants that underestimate enzyme affinity. These results demonstrate that while it may be tempting to employ structural elements from the most efficient substrates (e.g. primary alcohols) for inhibitor design, less effective substrates may serve as a more accurate assessment of inhibitory success.

Precision substrate targeting of protein kinases v-Abl and c-Src

The active site substrate specificities of v-Abl and c-Src are compared and contrasted. Both enzymes catalyze the phosphorylation of a broad assortment of peptide-bound aliphatic and aromatic alcohols, such as achiral and simple straight chain residues. In addition, both protein kinases exhibit a "dual specificity" with respect to the ability to utilize D- and L-configurational isomers as substrates. However, c-Src and v-Abl are extremely inefficient as catalysts for certain structural arrangements, including secondary alcohols and primary alcohols containing large substituents in close proximity to the hydroxyl moiety. In addition to these similarities, these enzymes also display noteworthy differences in catalytic behavior. Whereas c-Src exhibits a modest preference for aromatic versus aliphatic alcohols, v-Abl does not. Most dramatic is the ability of c-Src to utilize short chain alcohols as substrates, an activity virtually absent from the catalytic repertoire of v-Abl. The implications of these observations are 2-fold. First, because both enzymes are able to accommodate a wide variety of structural variants within their respective active site regions, there exists a substantial degree of flexibility with respect to inhibitor design. Second, because these enzymes exhibit disparate active site specificities, it is possible that other tyrosine-specific protein kinases will display unique substrate specificities as well. Consequently, it may ultimately be possible to exploit these differences to generate inhibitors that precisely target specific protein kinases.

The extraordinary active site substrate specificity of pp60c-src. A multiple specificity protein kinase

We report the first active site substrate specificity analysis of a tyrosine-specific protein kinase, namely pp60c-src. Like the cAMP-dependent protein kinase and protein kinase C, pp60c-src will phosphorylate an assortment of achiral residues attached to active site-directed peptides. Furthermore, pp60c-src phosphorylates both aromatic and aliphatic alcohols. However, the substrate specificity of pp60c-src is much broader than that of the two previously examined serine/threonine-specific protein kinases. We have previously shown that both the cAMP-dependent protein kinase and protein kinase C will utilize a wide array of non-amino acid residues as substrates, as long as the distance between the hydroxyl moiety and the adjacent peptide backbone is comparable with that present in serine and threonine (Kwon, Y.-G., Mendelow, M., and Lawrence, D. S. (1994) J. Biol. Chem. 269, 4839-4844). In marked contrast, pp60c-src does not discriminate against substrates on the basis of chain length, catalyzing the phosphorylation of residues that contain anywhere from 2-12 carbons between the alcohol functional group and the adjacent peptide bond. In addition, pp60c-src phosphorylates L-serine in an active site-directed peptide. The possible structural basis for the multiple specificity of pp60c-src is discussed. Finally, the active site specificity of pp60c-src is not just limited to L-amino acid residues, but also extends into the realm of D-amino acids as well.

Phenol kinase activity of the serine/threonine-specific cAMP-dependent protein kinase: steric and electronic effects

We have found that the cAMP-dependent protein kinase catalyzes the phosphorylation of a wide variety of peptide-based aromatic alcohols, thereby greatly amplifying the range of compounds recognized as substrates by this enzyme. This newly discovered enzyme-catalyzed reaction is sensitive to both steric and electronic effects. Substituents on the aromatic ring that are positioned para to the hydroxyl moiety lower the observed Km, presumably via a favorable interaction with an adjacent hydrophobic pocket. In contrast, electron-withdrawing substituents have a slight adverse effect on the kinetics of phosphoryl transfer, an observation which is consistent with the notion that the rate of substrate turnover is dependent upon the nucleophilicity of the phosphorylatable hydroxyl moiety. As a corollary, electron-donating groups on the aromatic nucleus promote the rate of phosphoryl transfer to such an extent that the observed Vmax values approach those exhibited by aliphatic alcohols. This suggests that analogously appended electron-donating groups on tyrosine moieties could dramatically improve the modest Vmax values that are typical for tyrosine kinase-catalyzed reactions.

The active site substrate specificity of the cAMP-dependent protein kinase

cAMP-dependent protein kinase substrates have been synthesized employing an unusually efficient method that allows the alcohol-bearing residue to be incorporated into the peptide after solid phase peptide synthesis. These peptide substrates have been utilized to map the active site substrate specificity of the protein kinase. Only alpha- or beta-substituted alcohol-bearing residues containing the proper absolute configuration are phosphorylated by the enzyme. However, the cAMP-dependent protein kinase will phosphorylate achiral residues. The implications of the observed protein kinase substrate specificity with respect to inhibitor design are discussed.

Oxygen transfer from the nitro group of a nitroaromatic radiosensitizer to a DNA sugar damage product

Mechanisms based on one-electron oxidation appear incomplete in explaining cellular radiosensitization by nitroaromatic compounds such as misonidazole. Evidence is presented for a novel mechanism that may be involved in enhancing DNA strand breakage due to a variety of agents, including ionizing radiation, that generate carbon-centered radicals on DNA deoxyribose. Under anaerobic conditions the carbon-centered radical generated selectively at C-5' of deoxyribose of thymidylate residues in DNA by the antitumor antibiotic neocarzinostatin reacts with misonidazole to produce a DNA damage product in the form of 3'-(formyl phosphate)-ended DNA. In an 18O-transfer experiment we find that the carbonyl oxygen of the activated formyl moiety (trapped as formyl-Tris) is derived from the nitro group oxygen of misonidazole. This result strongly supports a mechanism in which a nitroxide radical adduct, formed by the addition of misonidazole to the radical at C-5' of deoxyribose, cleaves between the N and O so as to form an oxy radical precursor of the formyl moiety and a two-electron reduction species of misonidazole.

Enzyme cytochemistry of blood and marrow cells

Diseases of the blood and bone marrow are commonly associated with abnormalities of oxido-reductase and lysosomal enzymes within individual erythrocytes and leucocytes. There are considerable technical difficulties, however, in adapting enzyme histochemical techniques to the study of haemopoietic tissue since individual cells are readily disrupted during processing, show variable enzyme activity according to the stage of maturation, and possess a lipoprotein cytoplasmic membrane which hinders reagent penetration. Cytochemical techniques for the study of oxido-reductase systems are of importance in the study of the neutrophil in infected patients, the erythrocyte in glucose-6-phosphate dehydrogenase deficiency, and the primitive blast cell in acute leukaemia. Lysosomal enzymes are of importance in the study of the neutrophil in infected patients and in the differential diagnosis of acute leukaemia. Some examples of recent studies of these enzyme systems are given to illustrate technical procedures involving cytocentrifugation of cells on to glass slides, adjustment of the osmolality of the reaction mixture, and the study of smeared cells as opposed to cells incubated in suspension.

The cytocentrifuge NBT test

The NBT test is a non-specific test of neutrophil membrane stimulation which has application to the study of neutrophil function, particularly in the septicaemic patient. An improved cytochemical test which eliminates potential sources of laboratory error has been developed. Venous or capillary blood samples may be studied and the technique can be applied to the neutropenic patient since available neutrophils are concentrated by cytocentrifugation. Clinical evaluation in 443 patients is described.