Molecular Discrimination Research Articles

Examining the Relationship between Aptamer Complexity and Molecular Discrimination of a Low-Epitope Target

Examining the Relationship between Aptamer Complexity and Molecular Discrimination of a Low-Epitope Target

Van der Waals interactions between nonpolar alkyl chains and polar oxide surfaces prevent catalyst deactivation in aldehyde gas sensing

Catalysis-based electrical sensing of volatile organic compounds on metal oxide surfaces is a powerful method for molecular discrimination. However, catalyst deactivation caused by the poisoning of catalytic sites by analytes and/or catalyzed products remains a challenge. This study highlights the underestimated role of van der Waals interactions between hydrophobic aliphatic alkyl chains and hydrophilic ZnO surfaces in mitigating catalyst deactivation during aliphatic aldehyde sensing. By immobilizing octadecylphosphonic acid (ODPA) on ZnO nanowire sensors, recovery times for nonanal detection are significantly reduced without compromising sensitivity. Temperature-programmed measurements demonstrate a reduction in desorption temperature of carboxylates on ODPA-modified ZnO to below 150 °C, whereas carboxylates on bare ZnO remain above 300 °C, indicating a significant decrease in catalyst deactivation. Density functional theory calculations reveal that accumulated van der Waals interactions between alkyl chains and ZnO surfaces significantly contributed to adsorption molecular kinetics. IR spectroscopy using deuterated self-assembled monolayers (SAMs) reveals conformational changes of alkyl chains within the SAMs caused by aldehyde adsorption, supporting the suggested adsorption kinetics. A model is proposed based on the dynamic surface-covering by alkyl chains destabilizes catalytically oxidized carboxylic acids.

Matings Between Individuals with Similar Major Histocompatibility Complex (MHC) Improve Offspring Survival in the Rainbow Trout (Oncorhynchus mykiss)

The major histocompatibility complex (MHC) consists of genes involved in immune response and molecular discrimination between self and non-self. MHC genes are the most polymorphic in vertebrates. The origin and maintenance of polymorphism in MHC genes in populations is still unresolved. Mechanisms such as sexual selection and heterozygote advantage have been suggested as explanations for this high variability. In this study, a farmed population of rainbow trout (Oncorhynchus mykiss) characterized by the presence of specific MHC class IIB gene haplotypes at a frequency higher (30%) than that expected from random matings was investigated. Therefore, it was hypothesized that disassortative matings occur with an adaptive advantage for females, resulting in improved reproductive performance when mated with individuals with similar MHC haplotypes. Genetic analyses of the breeders were performed to define the MHC haplotypes and to perform specific matings. The effect of mating was evaluated by analyzing the survival rate of the offspring at various stages of incubation until swim-up. The reproductive performance of the offspring derived from specimens with similar haplotypes showed a better survival trend during the first life stages and reduced malformations. The results obtained are in contrast with the heterozygous advantage theory, therefore it was hypothesized, as for other salmonid species, the presence of a positive selection towards locally adapted MHC genes that promotes reproduction between genetically similar individuals.

Rapid extraction of trace benzene by a crown-ether-based metal-organic framework

ABSTRACT Due to almost identical boiling points of benzene and cyclohexane, the extraction of trace benzene from cyclohexane is currently performed via the energy-intensive extractive distillation method. Their adsorptive separation by porous materials is hampered by their similar dimensions. Metal-organic frameworks (MOFs) with versatile pore environments are capable of molecular discrimination, but the separation of trace substrates in liquid-phase remains extremely challenging. Herein, we report a robust MOF (NKU-300) with triangular channels decorated with crown ether that can discriminate trace benzene from cyclohexane, exhibiting an unprecedented selectivity of 8615(10) for the mixture of benzene/cyclohexane (v/v = 1/1000). Remarkably, NKU-300 demonstrates exceptional selectivities for the extraction of benzene from cyclohexane over a wide range of concentrations of 0.1%–50% with ultrafast sorption kinetics and excellent stability. Single-crystal X-ray diffraction and computational modelling reveal that multiple supramolecular interactions cooperatively immobilise benzene molecules in the triangular channel, enabling superior separation performance. This study will promote the application of advanced sorbents with tailored binding sites for challenging industrial separations.

Case Study: Contribution of Extended Sequencing and Phylogeographic Analysis in the Investigation of Measles Outbreaks in Tunisia in 2019.

Despite the availability of an effective vaccine for several decades, the measles virus continues to spread worldwide. From 2018 to 2019, several countries experienced large measles outbreaks with genotype B3, including Tunisia. We analyzed 66 samples collected from serologically confirmed measles cases during this outbreak. Fifty-five percent were aged less than 12 months and had not received a measles vaccine. Phylogenetic analysis using the 450 nucleoprotein (N450) window revealed that all strains belonged to genotype B3, with five different variants identified. The N450 sequence of the predominant one, which circulated all through the epidemic period, was identical to the named strain MVs/Kabul.AFG/20.14/3. For better molecular discrimination, the amplification and sequencing of 1018 nucleotides in the non-coding region between the M and F genes (MF-NCRs) revealed higher variability with at least nine clusters. A phylogeographic study using Bayesian methods suggested the Governorate of Kasserine (on the borders of Algeria) as the introduction point with a TMRCA (Time to Most Recent Common Ancestor) for the 2019 sequences estimated around October 2018. These findings emphasize the crucial role of advanced molecular investigations in tracing measles transmission pathways which, together with good vaccine coverage, will help the final success of the global measles elimination program.

Tri-functional carbon membrane for one-step uptake of low-concentration hydrogen to high purity

The uptake of hydrogen (H2) from natural gas pipelines (CH4) through membrane separation technology is an efficient avenue of obtaining H2 resources. Carbon membranes have the potential to be an attractive option for energy-efficient gas separations in the next generation of membranes due to their precise molecular discrimination ability and easy scalability. Here, we report a carbon membrane composed of a mesoporous substrate, seed layer and sieving layer, achieving a one-step uptake with 55.3 × 10-9 mol·m−2·s−1 Pa−1 permeance and a separation factor for H2/CH4 of 359.1 by feeding hydrogen (20 vol%). As revealed by the kinetic diffusion experiment, H2 is transported in mesoporous substrate via Knudsen flow, differing from the transition flow taken by CH4, thus H2 diffusion rates exceed CH4 by an order of magnitude, which substantially increased H2 purity from 20 vol% to higher purity as gas mixtures passed through the substrate. Then, the H2 passed through the seed layer and sieving layer, resulting in a final H2 purity of ∼ 99 vol%, a sharp increase from the initial low concentration. This carbon membrane integrates three functions of capture, pre-separation and purification into one material and provides a new solution for the uptake of H2 from CH4.

Study of the population genetic structure of Opisthorchis-like eggs in northern Thailand using mitochondrial genes.

Opisthorchis-like eggs are a public health problem in northern and northeastern Thailand. However, the genetic epidemiology and structure of these parasites in northern Thailand are unknown. Thus, this study investigated their population genetic structure using cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) nucleotide sequences. A study was conducted in the hill tribe regions of Chiang Mai Province, northern Thailand. Internal transcribed spacer 2 polymerase chain reaction and restriction fragment length polymorphism were used to distinguish 205 positive feces samples for Opisthorchis-like eggs. The results showed that the prevalence of O. viverrini and Haplorchis taichui was 10.5% and 38.2%, respectively, and the co-infection rate was 37.2%. To determine the genetic structure of O. viverrini and H. taichui using cox1 and nad1 genes, genetic analysis was performed using 30 randomly chosen fecal samples for Opisthorchis-like eggs. Pairwise FST analysis indicated that O. viverrini and H. taichui displayed nonsignificant genetic differentiation within Chiang Mai Province and between interpopulations from different geographic areas. Moreover, within the intrapopulation in Chiang Mai Province,cox1 presented higher gene flow than nad1 in O. viverrini, while nad1 demonstrated higher gene flow than cox1 in H. taichui. The neutrality tests based on Fu's Fs indicated population expansion and selective sweep from bottleneck or hitchhiking in O. viverrini and H. taichui populations, supported by haplotype network patterns. Phylogenetic tree analysis based on cox1 and nad1 revealed the monophyly of O. viverrini and H. taichui and genetic relationships with other isolates collected from Thailand, Lao People's Democratic Republic (PDR), and Vietnam. This study investigated the molecular discrimination and genetic structure of Opisthorchis-like eggs in northern Thailand. The genetic information derived from this study could be associated with the background, molecular epidemiology, and disease severity of these parasites.

Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases.

Intestinal lavage fluid (IVF) containing the mucosa-associated microbiota instead of fecal samples was used to study the gut microbiota using different omics approaches. Focusing on the 63 IVF samples collected from healthy and hepatitis B virus-liver disease (HBV-LD), a question is prompted whether omics features could be extracted to distinguish these samples. The IVF-related microbiota derived from the omics data was classified into two enterotype sets, whereas the genomics-based enterotypes were poorly overlapped with the proteomics-based one in either distribution of microbiota or of IVFs. There is lack of molecular features in these enterotypes to specifically recognize healthy or HBV-LD. Running machine learning against the omics data sought the appropriate models to discriminate the healthy and HBV-LD IVFs based on selected genes or proteins. Although a single omics dataset is basically workable in such discrimination, integration of the two datasets enhances discrimination efficiency. The protein features with higher frequencies in the models are further compared between healthy and HBV-LD based on their abundance, bringing about three potential protein biomarkers. This study highlights that integration of metaomics data is beneficial for a molecular discriminator of healthy and HBV-LD, and reveals the IVF samples are valuable for microbiome in a small cohort.

Stereoisomers Are Not Machine Learning's Best Friends.

This study addresses the challenge of accurately identifying stereoisomers in cheminformatics, which originates from our objective to apply machine learning to predict the association constant between cyclodextrin and a guest. Identifying stereoisomers is indeed crucial for machine learning applications. Current tools offer various molecular descriptors, including their textual representation as Isomeric SMILES that can distinguish stereoisomers. However, such representation is text-based and does not have a fixed size, so a conversion is needed to make it usable to machine learning approaches. Word embedding techniques can be used to solve this problem. Mol2vec, a word embedding approach for molecules, offers such a conversion. Unfortunately, it cannot distinguish between stereoisomers due to its inability to capture the spatial configuration of molecular structures. This study proposes several approaches that use word embedding techniques to handle molecular discrimination using stereochemical information on molecules or considering Isomeric SMILES notation as a text in Natural Language Processing. Our aim is to generate a distinct vector for each unique molecule, correctly identifying stereoisomer information in cheminformatics. The proposed approaches are then compared to our original machine learning task: predicting the association constant between cyclodextrin and a guest molecule.

Prevalence and Molecular Discrimination of the Neglected Hydatidosis in Camels and Humans, Egypt

Prevalence and Molecular Discrimination of the Neglected Hydatidosis in Camels and Humans, Egypt

Molecular authentication and discrimination between banana shrimp and Pacific white shrimp by duplex PCR-lateral flow dipstick (dPCR-LFD) system

Banana shrimp is easily substituted by Pacific white shrimp due to its relatively similar morphology and appearance. The duplex PCR-lateral flow dipstick (dPCR-LFD) system was developed to authenticate these two species based on the mitochondrial cytochrome b (Cytb) gene. Two pairs of species-specific primers were designed for dPCR amplification. The specificity was also tested toward nine marine species. The sensitivity of the method was also evaluated at the DNA range of 0.02 %-60 % of adulterated Pacific white shrimp DNA in DNA from banana shrimp. Several types of cooked samples under various conditions were also tested. The developed dPCR-LFD system could specifically differentiate banana shrimp from Pacific white shrimp. No cross-amplification was observed in the specificity test. The sensitivity test showed the detection limit of 0.02 % (0.01 ng) of Pacific white shrimp DNA. The cooking processes including boiling, frying, and steaming did not show any effect on the efficiency of the dPCR-LFD system. This technique could be therefore implemented for the authentication of banana shrimp and Pacific white shrimp products as well as further use for other seafood frauds.

Adulteration detection of Gastrodia elata Blume and its commercial products using chloroplast DNA marker-based species-specific PCR assays

Gastrodia elata Blume has been recognized as a precious herbal medicine for thousands years due to its abundant bioactive ingredients and health-promoting features. The inadvertent or intentional adulteration of G. elata poses a severe crisis for consumers and significantly disrupts the market order. Therefore, accurate discrimination of G. elata from its adulterants is crucial to ensure its therapeutic effects and protect consumers’ interests. In this study, two species-specific PCR assays for molecular discrimination of G. elata from its five adulterants were established by targeting the chloroplast rps12 and clpP regions, respectively. Both of the assays can reliably identify as little as 0.1 % of deliberate adulteration with a detection threshold of only 0.01 ng of template DNA, and the assays are effective in detecting adulteration within G. elata as well as its commercial extracts. The present study provide a highly sensitive and reliable method for ascertaining the authenticity of G. elata and its commercial products, and the methodology can be employed in the authenticity and adulteration detection of other herbal products.

Molecular Discrimination for Two Anadenanthera Species of Seasonally Dry Tropical Forest Remnants in Brazil

Anadenanthera colubrina (Acol) and Anadenanthera peregrina (Aper) (Fabaceae) are two species popularly known as “angicos” that occur in seasonally dry tropical forest (SDTR) remnants in Brazil. Since many of the morphological characteristics of Anadenanthera species are superimposed and species-specific characteristics are difficult to observe, their identification is complex. Therefore, in this research, a set of ISSR (Inter-Simple Sequence Repeat Polymorphic DNA) molecular markers was standardized, aiming to characterize A. colubrina and A. peregrina species and study the genetic diversity of three populations of each species located within a fragmented landscape in São Paulo State, southeastern Brazil. Seven ISSR markers (UBC 2, 820, 851, 858, 864, 866, and 886) that show polymorphism for both species were used. The Bayesian cluster, PCoA and dendrogram analysis show that the total sample divides into two groups corresponding to each species. Also, a genetic divergence (Gst = 0.143) and a high number of migrants per generation (Nm = 3.0) were detected between them. The Acol populations showed significantly higher values for mean genetic diversity (h = 0.30) than Aper (h = 0.25) (p < 0.05). The ISSR marker UBC2250bp showed species-specific electrophoretic fingerprints for both species. The molecular tools generated herein support the conservation of Anadenanthera sp. and the restoration of vegetation where the species naturally occurs.

Cis-Trans and Length-Selective Molecular Discrimination of Halogenated Organic Compounds by a Crystalline Hybrid Macrocyclic Arene.

The development of adsorbents with robust molecular discrimination capabilities for halogenated organic compounds (HOCs) holds significant importance due to their potential in adsorptive separation and mitigation of associated health risks. In this study, we report a molecular discrimination behavior based on crystalline hybrid macrocyclic arene H, offering precise capture of cis-trans isomers and length-selective separation of HOCs. The activated H crystals (Hα) demonstrate exceptional discrimination and separation performance by selectively capturing trans-1,2-dichloroethylene (trans-DCE) from cis/trans-isomer mixtures with a high selectivity of 98.8%. Evidenced by single-crystal X-ray diffraction and density functional theory (DFT) calculations, this high adsorption selectivity arises from the formation of more stable complex crystals between H and the preferred guest trans-DCE. Moreover, Hα exhibits the ability to selectively trap size-matched 1,2-dibromoethane (DBE) from mixtures of alkylene dibromides with varying alkane-chain lengths, although their capture and separation are recognized to be difficult as a consequence of low-polarity bonds. The solid-state transformations between guest-free and guest-containing Hα crystals indicate their recyclability, showcasing promising prospects for potential applications.

Molecular discrimination of G1 and G3 genotypes of Echinococcus granulosus sensu stricto obtained from human, cattle, and sheep using the mitochondrial NADH dehydrogenase subunit 5 marker

Cystic echinococcosis (CE) is a common zoonotic disease caused by the larval form of Echinococcus granulosus sensu lato. This study determined the genotype and haplotype differences using the NADH dehydrogenase subunit 5 gene in hydatid cyst samples. Human (n = 12), cattle (n = 28), and sheep (n = 31) hydatid cyst isolates were included. Seventy-one genomic DNA samples were successfully extracted, and a 759 bp mitochondrial NADH dehydrogenase subunit 5 gene fragment was amplified by PCR. Following the sequence analysis, E. granulosus sensu stricto isolates were identified as G1 (n = 61) and G3 (n = 10). A total of 23 haplotypes were obtained from the 71 E. granulosus s.s. G1 and G3 samples. The main haplotype was Hap01 (60.56 %), which consisted of the G1 genotype. The second largest haplotype was Hap04, which consisted entirely of the G3 genotype. Hap14 acted as a bridge between the G1 and G3 genotypes. This study identifies G1 as the dominant genotype in humans and farm animals in Turkey. High haplotype and nucleotide diversity in genotypes were observed. Additionally, this is the first report on the phylogeography and gene flow models of the E. granulosus s.s. population in Turkey using the NADH dehydrogenase subunit 5 gene, the best marker distinguishing between G1 and G3 genotypes.

Sub-micro porous thin polymer membranes for discriminating H2 and CO2

Polymeric membranes with high permeance and remarkable selectivity for simultaneous H2 purification and CO2 capture under industry-relevant conditions are absent. Herein, sub-micro pores with precise molecular sieving capability are created in ultra-thin (13–30 nm) polymer membranes via controllable transformation of amine-linked polymer (ALP) films into benzimidazole-and-amine-linked polymer (BIALP) layers. The BIALP membranes exhibit stable unprecedented H2/CO2 selectivity of 120 with a H2 permeance of 315 GPU. Furthermore, high pressure (up to 11 bar) and thermal (up to 300 °C) resistance is delivered. This work provides a concept on designing porous polymeric membranes for precise molecular discrimination.

Identifying LasR Quorum Sensors with Improved Signal Specificity by Mapping the Sequence-Function Landscape.

Programmable intercellular signaling using components of naturally occurring quorum sensing can allow for coordinated functions to be engineered in microbial consortia. LuxR-type transcriptional regulators are widely used for this purpose and are activated by homoserine lactone (HSL) signals. However, they often suffer from imperfect molecular discrimination of structurally similar HSLs, causing misregulation within engineered consortia containing multiple HSL signals. Here, we studied one such example, the regulator LasR from Pseudomonas aeruginosa. We elucidated its sequence-function relationship for ligand specificity using targeted protein engineering and multiplexed high-throughput biosensor screening. A pooled combinatorial saturation mutagenesis library (9,486 LasR DNA sequences) was created by mutating six residues in LasR's β5 sheet with single, double, or triple amino acid substitutions. Sort-seq assays were performed in parallel using cognate and noncognate HSLs to quantify each corresponding sensor's response to each HSL signal, which identified hundreds of highly specific variants. Sensor variants identified were individually assayed and exhibited up to 60.6-fold (p = 0.0013) improved relative activation by the cognate signal compared to the wildtype. Interestingly, we uncovered prevalent mutational epistasis and previously unidentified residues contributing to signal specificity. The resulting sensors with negligible signal crosstalk could be broadly applied to engineer bacteria consortia.

MicroRNA Expression Profiling-Potential Molecular Discrimination of Papillary Thyroid Carcinoma Subtypes.

In this cross-sectional study, total RNA was extracted from paraffin-embedded tissues of 43 patients, 17 with an infiltrative follicular variant of PTC (iFVPTC) and 26 with a conventional variant of PTC (cPTC). Nine miRNAs were evaluated using qRT-PCR technology and specific miRNA assays. We found specific patterns for cPTC and iFVPTC, such as miRNA altered in both types of tumours (miR-146b-5p, miR-181a-5p, miR-221-3p, miR-21-5p and miR-222-3p) and two miRNAs significantly expressed only in cPTC (miR-20b-5p, miR-21-5p). The iFVPTC group presented strong and moderate correlations between miRNA expression and clinical data. miR-221-3p, miR-195-5p, miR-181-5p, miR-146b-5p and miR-222 were correlated with age, tumour size (TS) or lymph node metastases (N), while only miR-20b-5p, miR-195-5p and miR-181-5p were correlated with TS, N and age in the cPTC group. The present study allowed the identification of a signature of two miRNAs to confirm miRNA differences between the two histological subtypes of TC. Our results provide advances in the molecular diagnosis of TC and could help to improve the diagnostic performance of already existing molecular classifiers.

Molecular Discrimination and Phylogenetic Relationships of Physalis Species Based on ITS2 and rbcL DNA Barcode Sequence

Plants of the genus Physalis are of economic interest because of their fleshy edible fruits with high nutritional value. Some species have high medicinal value with a long history of ethno-medicinal use to treat diverse diseases. There is therefore a need to correctly discriminate the different species of Physalis for proper utilization. Although most Physalis species have unique morphologies, their vegetative stages are identical, making it difficult to accurately identify them based on morphological characteristics. DNA barcoding has the potential to discriminate species accurately. In this study, ribulose bisphosphate carboxylase large (rbcL) and internal transcribed spacer 2 (ITS2) regions were used to discriminate Physalis species and to reveal their phylogenetic relationships and genetic diversity. Physalis plant samples were collected from seven counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. Genomic DNA was isolated from leaf samples of 64 Physalis accessions and used for PCR amplification and the sequencing of rbcL and ITS2 barcode regions. The discriminatory ability of the barcodes was based on BLASTn comparison, phylogenetic reconstruction and cluster analysis, and the determination of inter- and intra-specific distances. The nucleotide polymorphism, genetic diversity and distance of the identified Physalis species were determined using DnaSP and MEGA 11.0 software. Species discrimination was more robust using ITS2 sequences. The species identified and discriminated by ITS2 sequences were Physalis purpurea, Physalis peruviana and Physalis cordata. The rbcL sequences were only able to identify Physalis to the genus level. There was high interspecific and low intraspecific divergence within the identified Physalis species based on ITS2 sequences. The ITS2 barcode is an ideal DNA barcode for use in the discrimination of species, as well as in genetic diversity studies of Physalis accessions in Kenya.

Development of a sensitive and user-friendly allele-specific PCR assay for adulteration detection of spices

Spice adulteration not only seriously interferes with their flavoring functions but also leads to life-threatening poisoning for consumers. To overcome the limitations of traditional methods in spice adulteration detection, a multiplex allele-specific PCR system was developed for molecular discrimination of four commonly used spices, Foeniculum vulgare Mill., Zanthoxylum bungeanum Maxim., Illicium verum Hook.f., and Syzygium aromaticum (L.) Merr. & L.M.Perry, from their corresponding adulterants based on chloroplast SNP markers. The developed assay, eliminating the obstacles of DNA sequencing and false negative results, can detect 0.1% of spice adulteration down to 0.01 ng level of genomic DNA with absolute allelic specificity and favorable efficiency. Based on the results, a standard operating procedure for using multiplex allele-specific PCR for spice adulteration detection was established. Therefore, the present study provided a simple, reliable, and sensitive molecular method for adulteration detection of spices.