Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees

The adaptive immune response to vaccination or infection can lead to the production of specific antibodies to neutralize the pathogen or recruit innate immune effector cells for help. The non-neutralizing role of antibodies in stimulating effector cell responses may have been a key mechanism of the protection observed in the RV144 HIV vaccine trial. In an extensive investigation of a rich set of data collected from RV144 vaccine recipients, we here employ machine learning methods to identify and model associations between antibody features (IgG subclass and antigen specificity) and effector function activities (antibody dependent cellular phagocytosis, cellular cytotoxicity, and cytokine release). We demonstrate via cross-validation that classification and regression approaches can effectively use the antibody features to robustly predict qualitative and quantitative functional outcomes. This integration of antibody feature and function data within a machine learning framework provides a new, objective approach to discovering and assessing multivariate immune correlates.     

Accuracy of Clinical Diagnosis of Dengue Episodes in the RV144 HIV Vaccine Efficacy Trial in Thailand

RV144 was a community-based HIV vaccine efficacy trial conducted in HIV-uninfected adults in Thailand, where dengue virus continues to cause a large number of infections every year. We attempted to document the accuracy of clinically diagnosed dengue episodes reported as serious adverse events (SAEs) and adverse events (AEs) and examine whether dengue serology would support the clinical diagnosis. Subjects without a clinical dengue diagnosis but with an infection or idiopathic fever were selected as a control population. Dengue serology was performed by hemagglutination inhibition on plasma samples. A total of 124 clinical dengue episodes were reported (103 SAEs and 21 AEs). Overall 82.6% of the clinically diagnosed dengue episodes were supported by a positive dengue serology: 71.4% of the AEs and 85.0% of the SAEs. Of the 100 subjects with both clinical dengue and positive serology, all presented with fever, 83% with leucopenia, 54% with thrombocytopenia, and 27% with hemorrhagic symptoms. All episodes resolved spontaneously without sequellae. Only two of 15 subjects with a negative serology presented with fever. The sensitivity and specificity of clinical dengue diagnosis were 90.9% and 74.4%, respectively, when compared to the control population, and with a positive predictive value of 82.6% and negative predictive value of 84.7% when compared to dengue serology. Clinical diagnosis of dengue is an accurate method of dengue diagnosis in adults in Thailand. Large-scale clinical trials offer the opportunity to systematically study infectious diseases such as dengue and other infections that may occur during the trial.     

Microfluidic conductimetric bioreactor

A microfluidic conductimetric bioreactor has been developed. Enzyme was immobilized in the microfluidic channel on poly-dimethylsiloxane (PDMS) surface via covalent binding method. The detection unit consisted of two gold electrodes and a laboratory-built conductimetric transducer to monitor the increase in the conductivity of the solution due to the change of the charges generated by the enzyme-substrate catalytic reaction. Urea–urease was used as a representative analyte-enzyme system. Under optimum conditions urea could be determined with a detection limit of 0.09 mM and linearity in the range of 0.1–10 mM (r = 0.9944). The immobilized urease on the microchannel chip provided good stability (>30 days of operation time) and good repeatability with an R.S.D. lower than 2.3%. Good agreement was obtained when urea concentrations of human serum samples determined by the microfluidic flow injection conductimetric bioreactor system were compared to those obtained using the Berthelot reaction (P < 0.05). After prolong use the immobilized enzyme could be removed from the PDMS microchannel chip enabling new active enzyme to be immobilized and the chip to be reused.     

Detecting penicillin G in milk with impedimetric label-free immunosensor

A label-free impedimetric flow injection immunosensor for the direct detection of penicillin G has been developed. Anti-penicillin G was immobilized on a gold working electrode modified with a self-assembled monolayer of thioctic acid. Real time monitoring of impedance was carried out at the optimum frequency of 160 Hz. Under optimum operating conditions the system provided a wide linear range between 1.0 x 10(-13) and 1.0 x 10(-8) M with a very low detection limit of 3.0 x 10(-15) M, much lower than the MRL of penicillin G in milk (1.2 x 10(-8) M). The immobilized anti-penicillin G on self-assembled thioctic acid monolayer gold electrode was very stable and provided good reproducible signal after regeneration up to 45 times with a relative standard deviation (R.S.D.) lower than 4%. Good recoveries and precisions were obtained when spiked raw milk samples were analyzed.     

Development and application of a real-time capacitive sensor

A real-time capacitive sensor based on a potentiostatic step method was developed. It can display in real-time the evoked current waveform, capacitance and the electrical resistance of elements serially connected to the insulation layer on the electrode as a function of time as well as the ohmic resistance of the insulation layer. These features enable the user to observe the association and dissociation of the affinity binding pairs and to evaluate the insulating property of the electrode surface during measurement. The system allows the setting of potential pulse height, pulse interval, gain, filter, and sampling frequency, enabling the system to be more flexible. The performance of the system was firstly evaluated with equivalent circuits. Under suitable parameter settings it provided good accuracy of both the capacitance and resistance. Using the affinity binding pair of human serum albumin (HSA) and anti human serum albumin (anti-HSA) the measured capacitance change was used for the direct detection of HSA. The developed system provided the same sensitivity as the commercially available potentiostat (P>0.05). The proposed system was then applied to analyse HSA in real urine samples and the results agreed well with the immunoturbidimetric assay (P>0.05). The proposed system can be applied for capacitance measurement to directly detect other target analytes using different affinity binding pairs. Other applications such as kinetics analysis of the interaction between affinity bindings, thickness analysis, and the study of the insulation property of the modified layer are also promising.     

Semi disposable reactor biosensors for detecting carbamate pesticides in water

Two flow-injection biosensor systems using semi disposable enzyme reactor have been developed to determine carbamate pesticides in water samples. Acetylcholinesterase was immobilized on silica gel by covalent binding. pH and conductivity electrodes were used to detect the ionic change of the sample solution due to hydrolysis of acetylcholine. Carbamate pesticides inhibited acetylcholinesterase and the decrease in the enzyme activity was used to determine these pesticides. Parameters influencing the performance of the systems were optimized to be used in the inhibition procedure. Carbofuran and carbaryl were used to test these systems. Detection limits for the potentiometric and conductimetric systems were both at 10% inhibition corresponding to 0.02 and 0.3 ppm of carbofuran and carbaryl, respectively. Both systems also provided the same linear ranges, 0.02-8.0 ppm for carbofuran, and 0.3-10 ppm for carbaryl. The analysis of pesticides was done a few times before the reactor was disposed. Percentages of inhibition obtained from different reactors were reproducible, therefore, no recalibration was necessary when changing the reactor. The biosensors were used to analyze carbaryl in water samples from six wells in a vegetable growing area. Both systems could detect the presence of carbaryl in the samples and provided good recoveries of the added carbaryl, i.e., 80-106% for the potentiometric system and 75-105% for the conductimetric system. The presence of carbaryl in water samples analyzed by the biosensors was confirmed by gas chromatography-mass spectrometric system. These biosensors do not require any sample preconcentration and are suitable for detecting pesticides in real water samples.     

Estimation of the total parasite biomass in acute falciparum malaria from plasma PfHRP2

BackgroundIn falciparum malaria sequestration of erythrocytes containing mature forms of Plasmodium falciparum in the microvasculature of vital organs is central to pathology, but quantitation of this hidden sequestered parasite load in vivo has not previously been possible. The peripheral blood parasite count measures only the circulating, relatively non-pathogenic parasite numbers. P. falciparum releases a specific histidine-rich protein (PfHRP2) into plasma. Quantitative measurement of plasma PfHRP2 concentrations may reflect the total parasite biomass in falciparum malaria.ConclusionPlasma PfHRP2 concentrations may be used to estimate the total body parasite biomass in acute falciparum malaria. Severe malaria results from extensive sequestration of parasitised erythrocytes.     

Partial characterization of allatinhibin,a neurohormone of Manduca sexta

During the last larval stage, corpora allata (CA) of Manduca sexta are inactivated by a factor from the brain. Apparently the same factor (allatinhibin, Al) is secreted by day 4 Vth instar brains kept overnight in Grace's medium. Al is rapidly inactivated by heat or acid but withstands exposure to alkali and can be recovered after freezing and lyophilization. Exposure to pronase, chymotrypsin, carboxypeptidases-A and-Y, as well as leucine aminopeptidase eliminated Al activity completely, whereas after exposure to trypsin and protease XVII-S, some residual activity remained. Inactivation by pyroglutamate aminopeptidase is interprefed as being due to prolinase activity of this enzyme. Incubation of CA with gentamicin, an aminoglycoside antibiotic, affects neither their ability to produce JH in vitro nor their viability in implantation assays. However, Al did not inactivate CA in the presence of low concentrations of gentamicin. This effect was used to guard against false positive assay results possibly produced by allatotoxic contamination. Al was purified by chromatography on Sephadex G-25. All activity recovered emerged from the columns in intermediate fractions with an apparent Mr of 1,000–2,000. © 1993 Wiley-Liss, Inc.     

Identification of New Regions in HIV-1 gp120 Variable 2 and 3 Loops that Bind to α4β7 Integrin Receptor

Background

The gut mucosal homing integrin receptor α4β7 present on activated CD4⁺ T cells interacts with the HIV-1 gp120 second variable loop (V2). Case control analysis of the RV144 phase III vaccine trial demonstrated that plasma IgG binding antibodies specific to scaffolded proteins expressing the first and second variable regions (V1V2) of HIV envelope protein gp120 containing the α4β7 binding motif correlated inversely with risk of infection. Subsequently antibodies to the V3 region were also shown to correlate with protection. The integrin receptor α4β7 was shown to interact with the LDI/V motif on V2 loop but recent studies suggest that additional regions of V2 loop could interact with the α4β7. Thus, there may be several regions on the V2 and possibly V3 loops that may be involved in this binding. Using a cell line, that constitutively expressed α4β7 receptors but lacked CD4, we examined the contribution of V2 and V3 loops and the ability of V2 peptide-, V2 integrin-, V3-specific monoclonal antibodies (mAbs), and purified IgG from RV144 vaccinees to block the V2/V3-α4β7 interaction.

Results

We demonstrate that α4β7 on RPMI8866 cells bound specifically to its natural ligand mucosal addressin cell adhesion molecule-1 (MAdCAM-1) as well as to cyclic-V2 and cyclic-V3 peptides. This binding was inhibited by anti-α4β7-specific monoclonal antibody (mAb) ACT-1, mAbs specific to either V2 or V3 loops, and by purified primary virions or infectious molecular clones expressing envelopes from acute or chronic subtypes A, C, and CRF01_AE viruses. Plasma from HIV-1 infected Thai individuals as well as purified IgG from uninfected RV144 vaccinees inhibited (0–50%) the binding of V2 and V3 peptides to α4β7.

Conclusion

Our results indicate that in addition to the tripeptide LDI/V motif, other regions of the V2 and V3 loops of gp120 were involved in binding to α4β7 receptors and this interaction was blocked by anti-V2 peptide, anti-V2 integrin, and anti-V3 antibodies. The ability of purified IgG from some of the uninfected RV144 vaccinees to inhibit α4β7 raises the hypothesis that anti-V2 and anti-V3 antibodies may play a role in blocking the gp120-α4β7 interaction after vaccination and thus prevent HIV-1 acquisition.