Dynamic analysis of capillary electrophoresis data using real-time neural networks

Machine learning applications in forensic DNA profiling: A critical review

Machine learning (ML) is a range of powerful computational algorithms capable of generating predictive models via intelligent autonomous analysis of relatively large and often unstructured data. ML has become an integral part of our daily lives with a plethora of applications, including web, business, automotive industry, clinical diagnostics, scientific research, and more recently, forensic science. In the field of forensic DNA, the manual analysis of complex data can be challenging, time-consuming, and error-prone. The integration of novel ML-based methods may aid in streamlining this process while maintaining the high accuracy and reproducibility required for forensic tools. Due to the relative novelty of such applications, the forensic community is largely unaware of ML capabilities and limitations. Furthermore, computer science and ML professionals are often unfamiliar with the forensic science field and its specific requirements. This manuscript offers a brief introduction to the capabilities of machine learning methods and their applications in the context of forensic DNA analysis and offers a critical review of the current literature in this rapidly developing field.

Optimizing Analytical Thresholds for Low-Template DNA Analysis: Insights from Multi-Laboratory Negative Controls

When analyzing challenging samples, such as low-template DNA, analysts aim to maximize information while minimizing noise, often by adjusting the analytical threshold (AT) for optimal results. A potential approach involves calculating the AT based on the baseline signal distribution in electrophoresis results. This study investigates the impact of reagent kits, testing quarters, environmental conditions, and amplification cycles on baseline signals using historical records and experimental data on low-template DNA. Variations in these aspects contribute to differences in baseline signal patterns. Analysts should remain vigilant regarding routine instrument maintenance and reagent replacement, as these may affect baseline signals. Prompt analysis of baseline status and tailored adjustments to ATs under specific laboratory conditions are advised. A comparative analysis of published methods for calculating the optimal AT from a negative signal distribution highlighted the efficiency of utilizing baseline signals to enhance forensic genetic analysis, with the exception of extremely low-template samples and high-amplification cycles. Moreover, a user-friendly program for real-time analysis was developed, enabling prompt adjustments to ATs based on negative control profiles. In conclusion, this study provides insights into baseline signals, aiming to enhance genetic analysis accuracy across diverse laboratories. Practical recommendations are offered for optimizing ATs in forensic DNA analysis.

Characterization of sulfonated phthalocyanines by mass spectrometry and capillary electrophoresis

We report the characterization of sulfonated phthalocyanines using capillary electrophoresis and mass spectrometry. Derivatives investigated included the copper, cobalt, zinc and metal-free sulfonated phthalocyanines. In general, sulfonated phthalocyanines were found as aggregates in capillary electrophoresis separations, even at low concentration. Separations were much better at pH 9.0 than at pH 2.5. The addition of β-cyclodextrin did not alter the electropherograms significantly. The electropherograms of commercially available copper phthalocyanine-3,4',4″,4‴-tetrasulfonic acid and 4,4',4″,4‴-tetrasulfonic acid were very different, consistent with the latter compound having a structure that is not fully sulfonated. Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) were used to characterize the sulfonated phthalocyanines. In general, MALDI gave better results than ESI. Mass spectral evidence was obtained for a pentasulfonated species of both the metal-free phthalocyanine and zinc phthalocyanine when these species were made by sulfonation of the metal-free phthalocyanine (followed by zinc insertion in the latter case). Sulfonated tetraphenylporphyrin derivatives were used as standards for mass spectrometry and to estimate the effect of net charge on the capillary electrophoresis migration time for sulfonated tetrapyrroles. Clean separation of the sulfonated tetraphenylporphyrin derivatives [5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS4), 5,10,15-tris(4-sulfonatophenyl)-20-phenylporphyrin (TPPS3) and 5,10-bis(4-sulfonatophenyl)-15,20-diphenylporphyrin (TPPS2a)] was observed by capillary electrophoresis.

Sulfonated naphthyl porphyrins as agents against HIV-1

Sulfonated 5,10,15,20-tetra(1-naphthyl)porphyrin (T1NapS) and 5,10,15,20-tetra(2-naphthyl)porphyrin (T2NapS) and their copper and iron chelates show activity against the human immunodeficiency virus (HIV-1). The porphyrins were prepared by sulfonation of the parent structures with sulfuric acid. More highly sulfonated structures were prepared by sulfonation for longer times. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry showed species with as many as eight sulfonates. Some of the mass spectral peaks for the copper chelates were consistent with loss of water, apparently from intramolecular sulfone formation between two adjacent naphthalene rings that took place during copper insertion. The compounds could be separated using capillary electrophoresis; addition of beta- or gamma-cyclodextrin gave substantially better separation of the components. Activity against HIV was evaluated using an epithelial HeLa-CD4-CCR5 cell line; EC50 values for HIV-1 IIIB and HIV-1 JR-FL ranged from 1 to 15 microg/ml. The compounds exhibit low toxicity for human epithelial cells and have potential as microbicides which might be used to provide protection against sexual transmission of HIV.

Electromigration dispersion in capillary zone electrophoresis. Experimental validation of use of the Haarhoff-Van der Linde function

This paper provides experimental validation of the use of the Haarhoff-Van der Linde (HVL) peak fitting function to fit experimental capillary zone electrophoresis (CZE) electropherograms. The test mixtures were composed of paraquat over a five order of magnitude concentration range (1.2 microM to 120 mM) and 4-aminopyridine at constant concentration (0.53 mM) as internal standard. Peak descriptors and electrophoresis parameters were extracted reliably by a Gaussian function from 4 to 40 microM; by the HVL function from 120 microM to 4 mM; and by a triangular function from 4 to 120 mM. The HVL function can be used where there is significant peak asymmetry due to electromigration distortion (EMD) and the Gaussian contribution toward the peak variance is greater than 25%. The peak centre (a1) and the Gaussian variance (a2) of the paraquat peak are shown to be independent of concentration. Diffusion coefficients obtained from a2 for both analytes were found to be in good agreement with their theoretical values. For all peaks where the distortion coefficient (a3) can be extracted, this parameter is shown to be directly proportional to the sample loading, as predicted by EMD theory. For the 4-aminopyridinium ion, mobilities calculated from a3 and measured independently are in excellent agreement. These results show that the HVL function accurately describes the two major processes, diffusion and EMD. contributing to the variance during a CZE separation.

Electrokinetic chromatography

The important features of electrokinetic chromatography are critically reviewed. Special emphasis is given to systems using micelles as pseudostationary phase. Short and comprehensive overviews are given on the subjects of separation, comparison with capillary electrochromatography, on-line coupling with mass spectrometry, and developments that are expected in the future. A greater coverage on the subject of improvement of detection sensitivity, specifically by on-line concentration was also contributed.