Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP inhibitor-resistant advanced breast cancer

BACKGROUND

Resistance to therapies that target homologous recombination deficiency (HRD) in breast cancer limits their overall effectiveness. Multiple, preclinically validated, mechanisms of resistance have been proposed, but their existence and relative frequency in clinical disease are unclear, as is how to target resistance.

PATIENTS AND METHODS

Longitudinal mutation and methylation profiling of circulating tumour (ct)DNA was carried out in 47 patients with metastatic BRCA1-, BRCA2- or PALB2-mutant breast cancer treated with HRD-targeted therapy who developed progressive disease-18 patients had primary resistance and 29 exhibited response followed by resistance. ctDNA isolated at multiple time points in the patient treatment course (before, on-treatment and at progression) was sequenced using a novel >750-gene intron/exon targeted sequencing panel. Where available, matched tumour biopsies were whole exome and RNA sequenced and also used to assess nuclear RAD51.

RESULTS

BRCA1/2 reversion mutations were present in 60% of patients and were the most prevalent form of resistance. In 10 cases, reversions were detected in ctDNA before clinical progression. Two new reversion-based mechanisms were identified: (i) intragenic BRCA1/2 deletions with intronic breakpoints; and (ii) intragenic BRCA1/2 secondary mutations that formed novel splice acceptor sites, the latter being confirmed by in vitro minigene reporter assays. When seen before commencing subsequent treatment, reversions were associated with significantly shorter time to progression. Tumours with reversions retained HRD mutational signatures but had functional homologous recombination based on RAD51 status. Although less frequent than reversions, nonreversion mechanisms [loss-of-function (LoF) mutations in TP53BP1, RIF1 or PAXIP1] were evident in patients with acquired resistance and occasionally coexisted with reversions, challenging the notion that singular resistance mechanisms emerge in each patient.

CONCLUSIONS

These observations map the prevalence of candidate drivers of resistance across time in a clinical setting, information with implications for clinical management and trial design in HRD breast cancers.

A Peer-to-Peer Collaborative Learning Approach for the Implementation of Evidence-Informed Interventions to Improve HIV-Related Health Outcomes

The nationwide scale-up of evidence-based and evidence-informed interventions has been widely recognized as a crucial step in ending the HIV epidemic. Although the successful delivery of interventions may involve intensive expert training, technical assistance (TA), and dedicated funding, most organizations attempt to replicate interventions without access to focused expert guidance. Thus, there is a grave need for initiatives that meaningfully address HIV health disparities while addressing these inherent limitations. Here, the Health Resources and Services Administration HIV/AIDS Bureau (HRSA HAB) initiative Using Evidence-Informed Interventions to Improve HIV Health Outcomes among People Living with HIV (E2i) piloted an alternative approach to implementation that de-emphasized expert training to naturalistically simulate the experience of future HIV service organizations with limited access to TA. The E2i approach combined the HAB-adapted Institute for Healthcare Improvement's Breakthrough Series Collaborative Learning Model with HRSA HAB's Implementation Science Framework, to create an innovative multi-tiered system of peer-to-peer learning that was piloted across 11 evidence-informed interventions at 25 Ryan White HIV/AIDS Program sites. Four key types of peer-to-peer learning exchanges (i.e., intervention, site, staff role, and organization specific) took place at biannual peer learning sessions, while quarterly intervention cohort calls and E2i monthly calls with site staff occurred during the action periods between learning sessions. Peer-to-peer learning fostered both experiential learning and community building and allowed site staff to formulate robust site-specific action plans for rapid cycle testing between learning sessions. Strategies that increase the effectiveness of interventions while decreasing TA could provide a blueprint for the rapid uptake and integration of HIV interventions nationwide.

Concurrent urinary organophosphate metabolites and acetylcholinesterase activity in Ecuadorian adolescents

BACKGROUND

Organophosphates are insecticides that inhibit the enzymatic activity of acetylcholinesterase (AChE). Because of this, AChE is considered a physiological marker of organophosphate exposure in agricultural settings. However, limited research exists on the associations between urinary organophosphate metabolites and AChE activity in children.

METHODS

This study included 526 participants from 2 exams (April and July-October 2016) of ages 12-17 years living in agricultural communities in Ecuador. AChE activity was measured at both examinations, and organophosphate metabolites, including para-nitrophenol (PNP), 3,5,6-trichloro-2-pyridinol (TCPy), and malathion dicarboxylic acid (MDA) were measured in urine collected in July-October. We used generalized estimating equation generalized linear model (GEEGLM), adjusting for hemoglobin, creatinine, and other demographic and anthropometric covariates, to estimate associations of urinary metabolite concentrations with AChE activity (July-October) and AChE% change between April and July-October.

RESULTS

The mean (SD) of AChE and AChE% change (April vs July-October) were 3.67 U/mL (0.54) and -2.5% (15.4%), respectively. AChE activity was inversely associated with PNP concentration, whereas AChE% change was inversely associated with PNP and MDA. There was evidence of a threshold: difference was only significant above the 80th percentile of PNP concentration (AChE difference per SD increase of metabolite = -0.12 U/mL [95%CI: 0.20, -0.04]). Likewise, associations with AChE% change were significant only above the 80th percentile of TCPy (AChE % change per SD increase of metabolite = -1.38% [95%CI: 2.43%, -0.32%]) and PNP -2.47% [95%CI: 4.45%, -0.50%]). PNP concentration at ≥80th percentile was associated with elevated ORs for low AChE activity of 2.9 (95% CI: 1.5, 5.7) and for AChE inhibition of ≤ -10% of 3.7 (95% CI: 1.4, 9.8).

CONCLUSIONS

Urinary organophosphate metabolites, including PNP, TCPy and MDA, particularly at concentrations above the 80th percentile, were associated with lower AChE activity among adolescents. These findings bring attention to the value of using multiple constructs of pesticide exposure in epidemiologic studies.

Influenza B-associated encephalitis with rapid improvement with oseltamivir

A 25-year-old female veterinarian presented with 1-week of flu-like symptoms followed by progressive encephalopathy. She was originally from Nicaragua and had been in the USA for 4 months. In the emergency department, she was confused and non-verbal with meningismus and facial myoclonus, but with an otherwise non-focal neurological exam. MRI brain abnormalities were consistent with viral encephalitides. Influenza B was detected via nasopharyngeal swab PCR. Mental status improved rapidly with oseltamivir. In such presentations, especially during flu season, influenza encephalitis must be considered, to facilitate early recognition of this entity and allow for targeted treatment.

Endothelial STAT3 Modulates Protective Mechanisms in a Mouse Ischemia-Reperfusion Model of Acute Kidney Injury

STAT3 is a transcriptional regulator that plays an important role in coordinating inflammation and immunity. In addition, there is a growing appreciation of the role STAT3 signaling plays in response to organ injury following diverse insults. Acute kidney injury (AKI) from ischemia-reperfusion injury is a common clinical entity with devastating consequences, and the recognition that endothelial alterations contribute to kidney dysfunction in this setting is of growing interest. Consequently, we used a mouse with a genetic deletion of Stat3 restricted to the endothelium to examine the role of STAT3 signaling in the pathophysiology of ischemic AKI. In a mouse model of ischemic AKI, the loss of endothelial STAT3 signaling significantly exacerbated kidney dysfunction, morphologic injury, and proximal tubular oxidative stress. The increased severity of ischemic AKI was associated with more robust endothelial-leukocyte adhesion and increased tissue accumulation of F4/80+ macrophages. Moreover, important proximal tubular adaptive mechanisms to injury were diminished in association with decreased tissue mRNA levels of the epithelial cell survival cytokine IL-22. In aggregate, these findings suggest that the endothelial STAT3 signaling plays an important role in limiting kidney dysfunction in ischemic AKI and that selective pharmacologic activation of endothelial STAT3 signaling could serve as a potential therapeutic target.

Copepods' Response to Burgers' Vortex: Deconstructing Interactions of Copepods with Turbulence

This study examined the behavioral response of two marine copepods, Acartia tonsa and Temora longicornis, to a Burgers' vortex intended to mimic the characteristics of a turbulent vortex that a copepod is likely to encounter in the coastal or near-surface zone. Behavioral assays of copepods were conducted for two vortices that correspond to turbulent conditions with mean dissipation rates of turbulence of 0.009 and 0.096 cm(2) s(-3) (denoted turbulence level 2 and level 3, respectively). In particular, the Burgers' vortex parameters (i.e., circulation and rate of axial strain rate) were specified to match a vortex corresponding to the median rate of dissipation due to viscosity for each target level of turbulence. Three-dimensional trajectories were quantified for analysis of swimming kinematics and response to hydrodynamic cues. Acartia tonsa did not significantly respond to the vortex corresponding to turbulence level 2. In contrast, A. tonsa significantly altered their swimming behavior in the turbulence-level-3 vortex, including increased relative speed of swimming, angle of alignment of the trajectory with the axis of the vortex, ratio of net-to-gross displacement, and acceleration during escape, along with decreased turn frequency (relative to stagnant control conditions). Further, the location of A. tonsa escapes was preferentially in the core of the stronger vortex, indicating that the hydrodynamic cue triggering the distinctive escape behavior was vorticity. In contrast, T. longicornis did not reveal a behavioral response to either the turbulence level 2 or the level 3 vortex.

The Second National Ballistics Imaging Comparison (NBIC-2)

In response to the guidelines issued by the American Society of Crime Laboratory Directors/Laboratory Accreditation Board (ASCLD/LAB-International) to establish traceability and quality assurance in U.S. crime laboratories, NIST and the ATF initiated a joint project, entitled the National Ballistics Imaging Comparison (NBIC). The NBIC project aims to establish a national traceability and quality system for ballistics identifications in crime laboratories utilizing ATF's National Integrated Ballistics Information Network (NIBIN). The original NBIC was completed in 2010. In the second NBIC, NIST Standard Reference Material (SRM) 2461 Cartridge Cases were used as reference standards, and 14 experts from 11 U.S. crime laboratories each performed 17 image acquisitions and correlations of the SRM cartridge cases over the course of about half a year. Resulting correlation scores were collected by NIST for statistical analyses, from which control charts and control limits were developed for the proposed quality system and for promoting future assessments and accreditations for firearm evidence in U.S. forensic laboratories in accordance with the ISO 17025 Standard.

Simplifying fuzzy rule-based models using orthogonal transformation methods

An important issue in fuzzy-rule-based modeling is how to select a set of important fuzzy rules from a given rule base. Even though it is conceivable that removal of redundant or less important fuzzy rules from the rule base can result in a compact fuzzy model with better generalizing ability, the decision as to which rules are redundant or less important is not an easy exercise. In this paper, we introduce several orthogonal transformation-based methods that provide new or alternative tools for rule selection. These methods include an orthogonal least squares (OLS) method, an eigenvalue decomposition (ED) method, a singular value decomposition and QR with column pivoting (SVD-QR) method, a total least squares (TLS) method, and a direct singular value decomposition (D-SVD) method. A common attribute of these methods is that they all work on a firing strength matrix and employ some measure index to detect the rules that should be retained and eliminated. We show the performance of these methods by applying them to solving a nonlinear plant modeling problem. Our conclusions based on analysis and simulation can be used as a guideline for choosing a proper rule selection method for a specific application.

The California Pertussis Epidemic 2010: A Review of 986 Pediatric Case Reports From San Diego County

BACKGROUND

The California Department of Public Health (CDPH) declared a pertussis epidemic on 23 June 2010. More cases were reported in 2010 (9146) than in any year since 1947. We describe the characteristics of pertussis epidemiology and disease from 986 reported cases in children in San Diego County (population 3.2 million).

METHODS

Descriptive statistics were abstracted from CDPH pertussis case report forms that were completed by public health nurses investigating reports of positive laboratory results for pertussis and reports of illnesses compatible with pertussis.

RESULTS

Of 1144 reported adult and pediatric cases, 753 (66%) were confirmed and 391 were probable/suspect. Children aged <19 years comprised 86% of all reported cases in San Diego County; of these, 22% were aged 11-18 years, 29% were aged 6-10 years, 27% were aged 1-5 years, and 22% were aged <1 year (with 70% aged <6 months). Case rates were highest in infants aged <6 months (651 per 100 000 population). Of those aged >1 year, the highest attack rates were in preschool children aged 1-5 years (114 per 100 000) and elementary school children aged 6-10 years (141 per 100 000). Of 51 children hospitalized, 82% were aged <6 months; 2 deaths occurred in these young infants. Paroxysmal cough was noted in over 70% of children in all age groups; post-tussive vomiting occurred in 36% (aged 11-18 years) to 57% (aged <6 months) of children.

CONCLUSIONS

Pertussis vaccine efficacy may decrease more rapidly than previously believed, facilitating spread of pertussis in elementary school-aged children. The highest case rates and the only mortality occurred in infants aged <6 months.

Efficacy and tolerability of amlodipine/valsartan combination therapy in hypertensive patients not adequately controlled on amlodipine monotherapy

ABSTRACT (ARB), in essential hypertensive patients not adequately controlled by amlodipine monotherapy.

METHODS

This was a multi-centre, randomised, double-blind, active-controlled study in patients with essential hypertension. After a washout period followed by a single-blind amlodipine 10 mg run-in period, patients with mean sitting diastolic blood pressure (msDBP) > or =90 mmHg and <110 mmHg were randomised to receive amlodipine/valsartan (10/160 mg o.d.) or amlodipine (10 mg o.d.) for 8 weeks.

TRIAL REGISTRATION NUMBER

NCT00171002.

MAIN OUTCOME MEASURES

The primary efficacy variable was change from baseline in msDBP at study endpoint. Secondary efficacy variables were change from baseline in mean sitting systolic blood pressure (msSBP), responder rate (msDBP <90 mmHg or > or =10 mmHg reduction from baseline) and DBP control rate (msDBP <90 mmHg).

RESULTS

Of the 1283 patients enrolled in single-blind period, 944 were randomised to receive amlodipine/valsartan 10/160 mg (n = 473) and amlodipine 10 mg (n = 471). Statistically significant greater reductions (p < 0.0001) from baseline in msSBP/msDBP were observed with combination therapy (12.9/11.4 mmHg) compared to monotherapy (10.0/9.3 mmHg). Responder rate was significantly greater (p = 0.0011) with combination therapy (79.0%) compared to monotherapy (70.1%). The percentage of patients with controlled DBP was also significantly (p < 0.0001) higher with combination therapy (77.8%) compared to monotherapy (66.5%). Incidence of peripheral oedema was slightly higher with amlodipine monotherapy (9.4%) compared to combination therapy (7.6%).

CONCLUSION

The combination of amlodipine/valsartan in this 8-week double-blind study provided additional BP control and was well tolerated in patients inadequately controlled with amlodipine monotherapy. Results should be interpreted with the knowledge that study entry criteria may limit application to a wider population.

Efficacy and tolerability of amlodipine/valsartan combination therapy in hypertensive patients not adequately controlled on valsartan monotherapy

OBJECTIVE

To demonstrate additional BP-lowering effects of amlodipine/valsartan combination in patients whose BP was not adequately controlled on valsartan alone.

METHODS

This was a multi-centre, randomised, double-blind, active-controlled study in patients with essential hypertension. After a washout period followed by a single-blind valsartan 160 mg run-in period, patients with mean sitting diastolic blood pressure (DBP) >or= 90 mmHg and < 110 mmHg were randomised to receive amlodipine/valsartan (10/160 mg or 5/160 mg o.d.) or valsartan (160 mg o.d.) for 8 weeks.

TRIAL REGISTRATION

NCT00170963 MAIN OUTCOME MEASURES: Primary efficacy variable was change from baseline in mean DBP at study end. Secondary efficacy variables included change from baseline in mean sitting systolic blood pressure (SBP), responder rate (mean DBP < 90 mmHg or >or= 10 mmHg reduction from baseline), and DBP control rate (mean DBP < 90 mmHg). Safety was also assessed.

RESULTS

Of 1136 patients enrolled in single-blind phase, 947 (mean age: 54.6 years) were randomised. Statistically significantly greater reductions in mean SBP/DBP were observed in both amlodipine/valsartan combinations (10/160 mg: 14.3/11.5 mmHg, 5/160 mg: 12.2/9.6 mmHg; both p < 0.0001) compared to valsartan 160 mg (8.3/6.7 mmHg). The 10/160 mg combination (p < 0.05) showed statistically significantly greater reductions in mean SBP/DBP compared to 5/160 mg (p < 0.001). Responder rates were higher in both combination therapy groups (10/160 mg: 81% [p < 0.0001]; 5/160 mg: 68% [p = 0.0018], respectively) compared to monotherapy (57%). Peripheral oedema was the most frequent adverse event, reported in amlodipine/valsartan 10/160 mg (9.1%), 5/160 mg (0.9%), and valsartan 160 mg (1.3%).

CONCLUSIONS

The combination of amlodipine/valsartan in this 8-week double-blind study provided additional BP control and was well-tolerated in patients inadequately controlled with valsartan monotherapy.

ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection

The ORFDB (http://orf.invitrogen.com/) represents an ongoing effort at Invitrogen Corporation to integrate relevant scientific data with an evolving collection of human and mouse Open Reading Frame (ORF) clones (Ultimate ORF Clones). The ORFDB serves as a central data warehouse enabling researchers to search the ORF collection through its web portal ORFBrowser, allowing researchers to find the Ultimate ORF clones by blast, keyword, GenBank accession, gene symbol, clone ID, Unigene ID, LocusLink ID or through functional relationships by browsing the collection via the Gene Ontology (GO) Browser. As of October 2003, the ORFDB contains 6200 human and 2870 mouse Ultimate ORF clones. All Ultimate ORF clones have been fully sequenced with high quality, and are matched to public reference protein sequences. In addition, the cloned ORFs have been extensively annotated across six categories: Gene, ORF, Clone Format, Protein, SNP and Genomic links, with the information assembled in a format termed the ORFCard. The ORFCard represents an information repository that documents the sequence quality, alignment with respect to public protein sequences, and the latest publicly available information associated with each human and mouse gene represented in the collection.

DDT resistance in Drosophila correlates with Cyp6g1 over-expression and confers cross-resistance to the neonicotinoid imidacloprid

Mutagenesis can be used as a means of predicting likely mechanisms of resistance to novel classes of insecticides. We used chemical mutagenesis in Drosophila to screen for mutants that had become resistant to imidacloprid, a neonicotinoid insecticide. Here we report the isolation of two new dominant imidacloprid-resistant mutants. By recombinational mapping we show that these map to the same location as Rst(2)DDT. Furthermore, we show that pre-existing Rst(2)DDT alleles in turn confer cross-resistance to imidacloprid. In order to localize the Rst(2)DDT gene more precisely, we mapped resistance to both DDT and imidacloprid with respect to P-element markers whose genomic location is known. By screening for recombinants between these P-elements and resistance we localized the gene between 48D5-6 and 48F3-6 on the polytene chromosome map. The genomic sequence in this interval shows a cluster of cytochrome P450 genes, one of which, Cyp6g1, is over-expressed in all resistant strains examined. We are now testing the hypothesis that resistance to both compounds is associated with over-expression of this P450 gene.

DNA-based vaccination for the treatment of food allergy

At present, avoidance is the only therapeutic option available for individuals with food allergies. However, studies suggest that DNA-based vaccination might be an effective therapeutic option for the reversal of allergic hypersensitivities, including allergies to foods. Because severe anaphylactic reactions represent a life-threatening risk for individuals with food allergies, we and others have evaluated the effectiveness of DNA-based vaccination for the prevention of anaphylactic hypersensitivity in murine models. Our investigations demonstrated that primary gene and protein/immunostimulatory sequence oligodeoxynucleotide (ISS-ODN) vaccination of subsequently Th2-sensitized mice reduced the risk of death after anaphylactic challenge, significantly. In addition, gene and protein/ISS-ODN vaccination reduced post challenge plasma histamine levels. Analysis of the immune profiles of mice receiving DNA-based vaccines showed that both gene and protein/ISS-ODN vaccination effectively prevented the development of Th2-biased immune profiles after sensitization. In contrast, vaccination with protein alone, the experimental equivalent of the traditional protein-based immunotherapy (IT) reagents used in clinical practice provided no protection from anaphylaxis, nor did it prevent the development of a Th2-biased immune profile after allergen sensitization. These studies justify continued optimism in the potential of DNA-based vaccination for the desensitization of food allergic individuals.

Porphyromonas gingivalis DPP-7 represents a novel type of dipeptidylpeptidase

A novel dipeptidylpeptidase (DPP-7) was purified from the membrane fraction of Porphyromonas gingivalis. This enzyme, with an apparent molecular mass of 76 kDa, has the specificity for both aliphatic and aromatic residues in the P1 position. Although it belongs to the serine class of peptidases, it does not resemble other known dipeptidylpeptidases. Interestingly, the amino acid sequence around the putative active site serine residue shows significant similarity to the C-terminal region of the Staphylococcus aureus V-8 endopeptidase. The genes encoding homologues of DPP-7 were found in genomes of Xylella fastidiosa, Shewanella putrefaciens, and P. gingivalis. It is likely that at least in P. gingivalis, DPP-7 and its homologue, in concert with other di- and tripeptidases, serve nutritional functions by providing dipeptides to this asaccharolytic bacterium.

Life in transition: balancing inertial and viscous forces by planktonic copepods

Copepods (1-10 mm aquatic crustaceans moving at 1-1000 mm s(-1)) live at Reynolds numbers that vary over 5 orders of magnitude, from 10(-2) to 10(3). Hence, they live at the interface between laminar and turbulent regimes and are subject to the physical constraints imposed by both viscous and inertial realms. At large scales, the inertially driven system enforces the dominance of physically derived fluid motion; plankton, advected by currents, adjust their life histories to the changing oceanic environment. At Kolmogorov scales, a careful interplay of evenly matched forces of biology and physics occurs. Copepods conform or deform the local physical environment for their survival, using morphological and behavioral adaptations to shift the balance in their favor. Examples of these balances and transitions are observed when copepods engage in their various survival tasks of feeding, predator avoidance, mating, and signaling. Quantitative analyses of their behavior give measures of such physical properties of their fluid medium as energy dissipation rates, molecular diffusion rates, eddy size, and eddy packaging. Understanding the micromechanics of small-scale biological-physical-chemical interactions gives insight into factors influencing large-scale dynamics of copepod distribution, patchiness, and encounter probabilities in the sea.

Emerging family of proline-specific peptidases of Porphyromonas gingivalis: purification and characterization of serine dipeptidyl peptidase, a structural and functional homologue of mammalian prolyl dipeptidyl peptidase IV

Porphyromonas gingivalis is an asaccharolytic and anaerobic bacterium that possesses a complex proteolytic system which is essential for its growth and evasion of host defense mechanisms. In this report, we show the purification and characterization of prolyl dipeptidyl peptidase IV (DPPIV) produced by this organism. The enzyme was purified to homogeneity, and its enzymatic activity and biochemical properties were investigated. P. gingivalis DPPIV, like its human counterpart, is able to cleave the N terminus of synthetic oligopeptides with sequences analogous to those of interleukins 1beta and 2. Additionally, this protease hydrolyzes biologically active peptides including substance P, fibrin inhibitory peptide, and beta-casomorphin. Southern blot analysis of genomic DNA isolated from several P. gingivalis strains reveal that a single copy of the DPPIV gene was present in all strains tested.

A fuzzy logic approach to identifying brain structures in MRI using expert anatomic knowledge

We report a novel computer method for automatic labeling of structures in 3D MRI data sets using expert anatomical knowledge that is coded in fuzzy sets and fuzzy rules. The method first identifies major structures and then uses spatial relationships to these landmarks to recognize other structures. This labeling process simulates the iterative process that we ourselves use to locate structures in images. We demonstrate its application in three data sets, labeling brain MRI by locating the longitudinal and lateral fissures and the central sulci and then determining boundaries for the frontal lobes. Our method is adaptable to the identification of other anatomical structures.

Potent dipeptidylketone inhibitors of the cysteine protease cathepsin K

Cathepsin K (EC 3.4.22.38) is a cysteine protease of the papain superfamily which is selectively expressed within the osteoclast. Several lines of evidence have pointed to the fact that this protease may play an important role in the degradation of the bone matrix. Potent and selective inhibitors of cathepsin K could be important therapeutic agents for the control of excessive bone resorption. Recently a series of peptide aldehydes have been shown to be potent inhibitors of cathepsin K. In an effort to design more selective and metabolically stable inhibitors of cathepsin K, a series of electronically attenuated alkoxymethylketones and thiomethylketones inhibitors have been synthesized. The X-ray co-crystal structure of one of these analogues in complex with cathepsin K shows the inhibitor binding in the primed side of the enzyme active site with a covalent interaction between the active site cysteine 25 and the carbonyl carbon of the inhibitor.

Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic

Modeling of metabolic pathway dynamics requires detailed kinetic equations at the enzyme level. In particular, the kinetic equations must account for metabolite effectors that contribute significantly to the pathway regulation in vivo. Unfortunately, most kinetic rate laws available in the literature do not consider all the effectors simultaneously, and much kinetic information exists in a qualitative or semiquantitative form. In this article, we present a strategy to incorporate such information into the kinetic equation. This strategy uses fuzzy logic-based factors to modify algebraic rate laws that account for partial kinetic characteristics. The parameters introduced by the fuzzy factors are then optimized by use of a hybrid of simplex and genetic algorithms. The resulting model provides a flexible form that can simulate various kinetic behaviors. Such kinetic models are suitable for pathway modeling without complete enzyme mechanisms. Three enzymes in Escherichia coli central metabolism are used as examples: phosphoenolpyruvate carboxylase; phosphoenolpyruvate carboxykinase; and pyruvate kinase I. Results show that, with fuzzy logic-augmented models, the kinetic data can be much better described. In particular, complex behavior, such as allosteric inhibition, can be captured using fuzzy rules. The resulting models, even though they do not provide additional physical meaning in enzyme mechanisms, allow the model to incorporate semiquantitative information in metabolic pathway models.

Short-term cell/substrate contact dynamics of subconfluent endothelial cells following exposure to laminar flow

The manner in which fluid stresses are transmitted from the apical to the basal surface of the endothelium will influence the dynamics of cell/substrate contacts. Such dynamics could be important in the design of synthetic vascular grafts to promote endothelial cell adhesion. To examine whether the initial response of cell/substrate contact sites to flow depends on the magnitude of the applied shear stress, subconfluent monolayers of endothelial cells were exposed to flow at 10, 20, and 30 dyn cm-2 wall shear stresses for 20 min. Cell/substrate contact sites were visualized with total internal reflection fluorescence microscopy. Flow induced a rapid fluctuation in the membrane topography, which was reflected in dynamic changes in cell/substrate contacts. Exposure to flow caused marked changes in contact area. Contact movement occurred normal and parallel to the direction of flow. Contact sites demonstrated significant variability in contact area at 30 dyn cm-2 during the experiment but no significant movement of the contact sites in flow direction after 20 min of flow. Mean square displacements of the contact center of mass were described in terms of a directed diffusion model. Prior to onset of flow, contact movement was random. Flow induced a significant convective component to contact movement for 300-600 s, followed by reestablishment of diffusive growth and movement of contacts. These results suggest that fluid stresses are rapidly transmitted from the apical to the basal surface of the cell via the cytoskeleton.

Following the invisible trail: kinematic analysis of mate-tracking in the copepod Temora longicornis

We have analysed the fine-scale kinematics of movement of male and female copepods, Temora longicornis, to resolve how these small animals find their mates. Location of the trail initially involves rapid random turning and high rates of directional change. Males subsequently increase their rate of movement as they follow the trail, and execute a regular pattern of counter turns in both x,z and y,z planes to stay near or within the central axis of the odour field. Pursuit behaviour of males is strongly associated with female swimming behaviour, suggesting that quantifiable variations in the structure of the odour signal released by females affects male tracking. The behavioural components of mate tracking in Temora are very similar to those of other animals that employ chemically mediated orientation in their search for mates and food, and we conclude that male Temora find their mates using chemoperception. The kinematic analysis indicates both sequential and simultaneous taxis mechanisms are used by Temora to follow the odour signal. This, in turn, indicates that rather than responding to a diffuse plume, males are following a signal more accurately characterized as a chemical trail, and copepods appear to use mechanisms that are similar to those employed by trail-following terrestrial insects such as ants. While Temora expresses similar behaviours to those of a variety of chemosensory organisms, the ability to track a three-dimensional odour trail appears unique, and possibly depends on the persistence of fluid-borne odour signals created in low Reynolds number hydrodynamic regimes.

The fluid physics of signal perception by mate-tracking copepods

Within laboratory-induced swarms of the marine copepod Temora longicornis, the male exhibits chemically mediated trail-following behaviour, concluding with fluid mechanical provocation of the mate-capture response. The location and structure of the invisible trail were determined by examining the specific behaviour of the female copepods creating the signal, the response of the male to her signal, and the fluid physics of signal persistence. Using the distance of the mate-tracking male from the ageing trail of the female, we estimated that the molecular diffusion coefficient of the putative pheromonal stimulant was 2.7 x 10(-5) cm2 s-1, or 1000 times slower than the diffusion of momentum. Estimates of signal strength levels, using calculations of diffusive properties of odour trails and attenuation rates of fluid mechanical signals, were compared to the physiological and behavioural threshold detection levels. Males find trails because of strong across-plume chemical gradients; males sometimes go the wrong way because of weak along-plume gradients; males lose the trail when the female hops because of signal dilution; and mate-capture behaviour is elicited by suprathreshold flow signals. The male is stimulated by the female odour to accelerate along the trail to catch up with her, and the boundary layer separating the signal from the chemosensitive receptors along the copepod antennule thins. Diffusion times, and hence reaction times, shorten and behavioural orientation responses can proceed more quickly. While 'perceptive' distance to the odour signal in the trail or the fluid mechanical signal from the female remains within 1-2 body lengths (< 5 mm), the 'reactive' distance between males and females was an order of magnitude larger. Therefore, when nearest-neighbour distances are 5 cm or less, as in swarms of 10(4) copepods m-3, mating events are facilitated. The strong similarity in the structure of mating trails and vortex tubes (isotropic, millimetre-centimetre scale, 10:1 aspect ratio, 10s persistence), indicates that these trails are constrained by the same physical forces that influence water motion in a low Reynolds number fluid regime, where viscosity limits forces to the molecular scale. The exploratory reaches of mating trails appear inscribed within Kolmogorov eddies and may represent a measure of eddy size. Biologically formed mating trails, however, are distinct in their flow velocity and chemical composition from common small-scale turbulent features; and mechanoreceptive and chemoreceptive copepods use their senses to discriminate these differences. Zooplankton are not aimless wanderers in a featureless environment. Their ambit is replete with clues that guide them in their efforts for survival in the ocean.

Human placental norepinephrine transporter mRNA: expression and correlation with fetal condition at birth

The purpose of this study was to determine the primary form of human placental norepinephrine transporter (hNET) mRNA expressed in the human placenta and to compare the level of expression in normal pregnancies and in pregnancies complicated by drug exposure or other forms of physiological derangement. We used the hNET cDNA to measure RNA extracted from placenta and examined placental RNA following complicated and uncomplicated pregnancies. To compare transporter expression and its relation to fetal condition at birth, umbilical arterial plasma catecholamine levels, umbilical arterial blood gases and placental transporter mRNA level were compared by linear regression analysis. Uncomplicated pregnancies had a higher level of placental norepinephrine transporter mRNA than complicated pregnancies. An inverse relationship between umbilical cord norepinephrine level and transporter expression was demonstrated. We conclude that placental transporter expression represents an important and newly described metabolic function of the placenta. Placental catecholamine clearance mediated via the placental NET may be important in the pathophysiology of disorders associated with placental dysfunction, impaired placental blood flow or intrauterine growth retardation. This may also explain the adverse effects of drugs, such as cocaine, which block catecholamine transport.

A clinical phase I/II study of recombinant human interleukin-1 receptor in glucocorticoid-resistant graft-versus-host disease

Graft-versus-host disease (GVHD) is the major complication of allogeneic bone marrow transplantation. GVHD is accompanied by the release of inflammatory cytokines, including interleukin (IL)-1, and previous work has demonstrated that IL-1 participates in the pathogenesis of GVHD. The recombinant human IL-1 receptor (rhuIL-1R) is the soluble form of the type I IL-1 receptor that can bind to IL-1 and prevent cellular activation. We report a phase I/II trial utilizing the rhuIL-1R in the treatment of allogeneic bone narrow transplant patients not improving with glucocorticoid therapy. RhuIL-R was given at four dose levels for 21 days to 14 patients with progressive or persistent acute GVHD. The study drug had no clinical or persistent hematopoiesis and the treatment was tolerated by patients without toxicity at all dose levels. Eight of 14 patients (57%) had an improvement of GVHD after rhuIL-1R therapy. Improvement in GVHD was noted at each dose level, although a dose-response effect for rhuIL-1R treatment was not observed. This work supports the concept that IL-1 plays a role in the inflammation associated with acute GVHD. A controlled study of the rhuIL-1R for treatment of prophylaxis of GVHD is warranted.

Survival factors in 186 patients younger than 40 years old with colorectal adenocarcinoma

BACKGROUND

We sought to determine the clinical factors and tumor characteristics associated with the reported poor prognosis in young patients with carcinoma of the colon and rectum.

STUDY DESIGN

A retrospective review was performed of 186 patients younger than 40 years of age who were treated for primary colorectal adenocarcinoma. The median age was 34.3 years, and the median follow-up period was 9.4 years. Clinical and tumor histopathologic parameters were analyzed.

RESULTS

Regional lymph node metastases, distant metastases, or both, were seen at first examination in 65.6 percent of young patients. Histopathologic indicators of more aggressive tumor biology were present at a significantly higher frequency in young patients compared with patients older than 40 years (p < 0.001). Poorly differentiated tumor grade was present in 41.0 percent, signet-ring cell tumors were found in 11.1 percent, and infiltrating tumor leading edges were present in 69.0 percent of young patients. Among young patients with stage II disease, vascular invasion was a significant negative prognostic variable (p < 0.05).

CONCLUSIONS

We have demonstrated an increased incidence of three biological indicators of aggressive and potentially metastatic tumor biology in 186 young patients with carcinoma of the colon and rectum: signet-ring cell carcinoma, infiltrating tumor edges, and aggressive histologic grade in the primary adenocarcinoma. The increased incidence of these three histologic measures of more aggressive carcinoma of the colon and rectum in part accounts for the higher rate of advanced disease at presentation in patients younger than 40.

Transformation by FosB requires a trans-activation domain missing in FosB2 that can be substituted by heterologous activation domains

Two functionally distinct proteins derived from the FosB gene by alternative splicing have recently been described. FosB protein transforms fibroblasts efficiently, whereas FosB2 protein, a carboxy-terminally truncated form of FosB, does not, despite the fact that both proteins can participate in high-affinity, sequence-specific DNA binding as part of a heterodimeric complex with c-Jun protein. We show here that the functional difference between these proteins is the result of the presence of a potent proline-rich transcriptional activation domain in the carboxy-terminal amino acids unique to FosB. This conclusion is supported by three lines of evidence: (1) Mutations in the carboxy-terminal region of FosB that impair transcriptional activation also reduce transforming potential, despite the fact that DNA binding as part of a complex with c-Jun is not affected; (2) the carboxy-terminal region unique to FosB functions as an activation domain when fused to the DNA-binding domain of GAL4; and (3) transforming potential can be conferred on FosB2 by fusing any of several different well-characterized trans-activation domains. These results identify an additional functional requirement for transformation by Fos proteins and have implications for the mechanism(s) of mitogenic signaling by the AP-1 transcription complex.

An alternative spliced form of FosB is a negative regulator of transcriptional activation and transformation by Fos proteins

Two forms of FosB transcript and their products can be identified in mouse NIH 3T3 cells following serum induction. The larger RNA codes for a 338-amino acid protein, whereas the smaller RNA results from the removal of an additional 140 nucleotides from FosB mRNA by alternative splicing. This alternative splicing event places a stop codon following the "leucine zipper" region and results in a shorter protein (FosB2) of 237 amino acids that lacks 101 amino acids at the carboxyl terminus. FosB2 is able to form heterodimers with c-Jun and bind to an AP-1 site but is not able to activate the transcription of promoters containing AP-1 sites. Furthermore, FosB2 can not only suppress the transcriptional activation by c-Fos and c-Jun of promoters containing an AP-1 site but also interferes with the transforming potential of viral and cellular Fos proteins. We propose that FosB2 protein functions as a trans-negative regulator.

A rapid in vitro cytotoxicity assay for the detection of tumor necrosis factor on human BT-20 cells

This report describes a rapid, reproducible in vitro bioassay to quantitate the cytotoxic activity of human tumor necrosis factor-alpha using a human rather than murine cell line in the absence of metabolic inhibitors. The target cells are BT-20 (breast carcinoma) cultured at 39 degrees C in the presence of recombinant human tumor necrosis factor-alpha (rHuTNF-alpha) in 96-well microtiter plates for 2 days. Cytotoxicity is measured by the crystal violet dye uptake of the remaining viable cells. This bioassay is sensitive to 1.5 ng/ml of rHuTNF-alpha, with an assay range to 130 ng/ml. Samples spiked into human plasma are measurable from 0.5 to 150 ng/ml. The specificity of this cytotoxic effect on the BT-20 cell line was demonstrated using rHuTNF-alpha neutralizing antibodies. A panel of cytokines including interferons, interleukins, and tumor necrosis factors was also analyzed using this assay system. Of the cytokines assayed, only recombinant murine tumor necrosis factor-alpha and recombinant human tumor necrosis factor-beta demonstrated measurable cytotoxic activity when assayed independently, while recombinant human interferon-gamma was the only cytokine to demonstrate greater than additive activity in combination with rHuTNF-alpha. The simplicity and reproducibility of this assay on a human cell line makes it useful for the routine determination of the biological activity of human tumor necrosis factor-alpha.