DNA Sequence Research Articles

G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients

G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients

Unveiling a novel GJB2 dominant K22T mutation in a Chinese family with hearing loss.

Hearing loss constitutes one of the most prevalent conditions within the field of otolaryngology. Recent investigations have revealed that mutations in deafness-associated genes, including point mutations and variations in DNA sequences, can cause hearing impairments. With the ethology of deafness remaining unclear for a substantial portion of the affected population, further screenings for pathogenic mutations are imperative to unveil the underlying mechanisms. On this study, by using next-generation sequencing, we examine 129 commonly implicated deafness-related genes in a Chinese family with hearing loss, revealing a novel heterozygous dominant mutation in the GJB2 gene (GJB2: c.65T>G: p. Lys22Thr). This mutation consistently occurs in affected family members but is not detected in unaffected individuals, strongly suggesting its causative role in hearing loss. Structural analysis indicates potential disruption to the Cx26 gap junction channel's hydrogen bond and electrostatic interactions, aligning with predictions from the PolyPhen and SIFT algorithms. In conclusion, our study provides conclusive evidence that the identified heterozygous GJB2 mutation (GJB2: c.65T>G: p. Lys22Thr), specifically the K22T alteration, is the primary determinant of the family's deafness. This contribution enhances our understanding of the interplay between common deafness-associated genes and hearing loss, offering valuable insights for diagnostic guidance and the formulation of therapeutic strategies for this condition.

MulTFBS: A Spatial-Temporal Network with Multichannels for Predicting Transcription Factor Binding Sites.

Revealing the mechanisms that influence transcription factor binding specificity is the key to understanding gene regulation. In previous studies, DNA double helix structure and one-hot embedding have been used successfully to design computational methods for predicting transcription factor binding sites (TFBSs). However, DNA sequence as a kind of biological language, the method of word embedding representation in natural language processing, has not been considered properly in TFBS prediction models. In our work, we integrate different types of features of DNA sequence to design a multichanneled deep learning framework, namely MulTFBS, in which independent one-hot encoding, word embedding encoding, which can incorporate contextual information and extract the global features of the sequences, and double helix three-dimensional structural features have been trained in different channels. To extract sequence high-level information effectively, in our deep learning framework, we select the spatial-temporal network by combining convolutional neural networks and bidirectional long short-term memory networks with attention mechanism. Compared with six state-of-the-art methods on 66 universal protein-binding microarray data sets of different transcription factors, MulTFBS performs best on all data sets in the regression tasks, with the average R2 of 0.698 and the average PCC of 0.833, which are 5.4% and 3.2% higher, respectively, than the suboptimal method CRPTS. In addition, we evaluate the classification performance of MulTFBS for distinguishing bound or unbound regions on TF ChIP-seq data. The results show that our framework also performs well in the TFBS classification tasks.

Prevalence and genetic diversity of azole-resistant Malassezia pachydermatis isolates from canine otitis and dermatitis: a two-year study.

Despite previous reports on the emergence of Malassezia pachydermatis strains with decreased susceptibility to azoles, there is limited information on the actual prevalence and genetic diversity of azole-resistant isolates of this yeast species. We assessed the prevalence of azole resistance in M. pachydermatis isolates from cases of dog otitis or skin disease attended in a veterinary teaching hospital during a 2-year period and analyzed the ERG11 (encoding a lanosterol 14-α demethylase, the primary target of azoles) and whole genome sequence diversity of a group of isolates that displayed reduced azole susceptibility. Susceptibility testing of 89M. pachydermatis isolates from 54 clinical episodes (1-6 isolates/episode) revealed low minimum inhibitory concentrations (MICs) to most azoles and other antifungals, but 11 isolates from six different episodes (i.e., 12.4% of isolates and 11.1% of episodes) had decreased susceptibility to multiple azoles (fluconazole, itraconazole, ketoconazole, posaconazole, ravuconazole, and/or voriconazole). ERG11 sequencing of these 11 azole-resistant isolates identified eight DNA sequence profiles, most of which contained amino acid substitutions also found in some azole-susceptible isolates. Analysis of whole genome sequencing (WGS) results revealed that the azole-resistant isolates from a same episode of otitis, or even different episodes affecting a same animal, were more genetically related to each other than to isolates from other dogs. In conclusion, our results confirmed the remarkable ERG11 sequence variability in M. pachydermatis isolates of animal origin observed in previous studies and demonstrate the value of WGS for disentangling the epidemiology of this yeast species.

Zinc Oxide:Gold Nanoparticles (ZnO:Au NPs) Exhibited Antifungal Efficacy Against Aspergillus niger and Aspergillus candidus

AbstractFungal pathogens are a major health issue that threatens the era of antifungal drugs commonly used in the treatment of infections. An effective approach of biosynthetic nanoparticles can be used as antifungal agents owing to their intrinsic features such as their simplicity, non-toxic, and physicochemical properties. Therefore, this study was aimed to molecularly ascertain Aspergillus species known to cause aspergillosis and investigate the potency of zinc oxide:gold nanoparticles (ZnO:Au NPs) against the fungal pathogens. Two Aspergillus strains retrieved with potato dextrose agar (PDA) culture media from commercial food products in South Africa were molecularly identified using calmodulin (CaM) gene region. DNA sequence phylogeny of the gene showed that the strains were A. niger and A. candidus. ZnO:Au (1%) NPs were synthesised and characterised using X-ray diffraction (XRD), scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS). Two distinct peak plasmon bands for ZnO and ZnO:Au NPs were 390 nm and 565 nm, respectively. FE-SEM images demonstrated the presence of Au on the surface of ZnO nanoparticles in the ZnO:Au nanocomposites. The ZnO:Au NPs antifungal activity of 10 µg/mL and 50 µg/mL concentrations were evaluated against the two Aspergillus spp. ZnO:Au NPs at 50 µg/mL exhibited a maximum antifungal activity against A. candidus and A. niger, with zones of inhibition (ZoI) of 31.2 ± 0.15 mm and 25.0 ± 0.06, respectively. When the ZoI was observed by SEM, major morphological damages on the conidia were observed for both strains, indicating that the antifungal activity may have been enhanced by the ZnO:Au NPs. Therefore, due to these outstanding properties, ZnO:Au NPs can be utilised as potential antifungal agents to inhibit the proliferation of fungal pathogens.

Genome-wide association study reveals candidate genes critical for skin pigmentation in common carp (Cyprinus carpio) strains including koi

The differentiation and variation of body color in fish is an important component of biological evolution and phylogenetic research, and is influenced by several factors such as heredity, nutrition, physiological hormones and rearing conditions, with heredity being the most critical factor. An improved comprehension of the genetic regulation in different carp populations will facilitate future applications of precision breeding and pigment cell development-related genes editing. In this study, we used restriction site-associated DNA sequencing (2d-RAD) to determine the distribution characteristics of single nucleotide polymorphisms (SNPs) in eight common carp strains including six koi strains, i.e., Kohaku (Hb), Taisho (Dz), Showa (Zh), Golden (Hj), Matsukawabake (Sch) and Five-color (Ws), and two genetically improved breeding strains, i.e., FFRC No. 2 strain (Fr) and red FFRC strain (Hfr), and then SNP markers to resolve genetic information on the population structure and skin color formation of these strains. We found that most individuals of eight strains were clearly divided into eight clades. Genetic diversity within Fr, Sch and Ws is relatively high, while it is low within Dz, Hb and Hfr. A comparison between the populations revealed that Hfr and Ws have the highest degree of genetic differences, while Hb and Dz have the lowest. The GWAS analysis for two strategies identified several SNPs that are significantly related to skin color variation and affect melanin synthesis (ephrinb2, slc22a23, herc2, ephb2), carotenoid metabolism (oca2, bcmo1, bco2) and circadian rhythm(cipc). To summarize, our study provides some information on the genetic structure and diversity of Japanese koi and Chinese FFRC carp. Furthermore, based on the data obtained on relevant genes related to skin color differentiation and pigmentation, it can provide a theoretical basis for the subsequent integration of dominant traits and precision breeding in carps.

Distribution and genetic diversity of cobitid species in Iran (Teleostei: Cobitidae)

Several species of Cobitis have been reported within Iran, but only four are recognized as valid. The geographical distribution and genetic diversity of these species are not well-known. Two new populations of C. saniae and C. avicennae were reported herein based on their morphological and phylogenetic characters from the Mahabad River, a tributary of the Urmia Lake basin, and the Razavar River, a tributary of the Karkheh drainage, respectively. The genetic diversity and genetic structure of populations of C. saniae, C. avicennae, and C. faridpaki were analysed using the DNA sequences of the mitochondrial COI gene. COI sequences from various watersheds in Iran, Azerbaijan, and Georgia were used. A moderate to high level haplotype diversity and low nucleotide diversity were found in most of the populations of all three species. The AMOVA test and pairwise FST comparison revealed significant genetic structure and genetic distance between the Urmia Lake basin and other C. saniae populations. The results highlight the importance of conserving these species and their habitats, particularly in the Urmia Lake basin, where significant genetic differentiation was observed.

Cisplatin-activated and hemoglobin-mediated injectable hydrogel system for antitumor chemodynamic and chemotherapy

Low specificity and hypoxia-induced drug resistance are significant challenges in traditional cancer treatment. To enhance the anticancer efficacy, an injectable hydrogel system is developed through the formation of dynamic covalent bonds in hyaluronic acid, allowing for localized controlled release of drugs. This system also utilizes double-stranded DNA sequences for the intercalation delivery of the chemotherapeutic drug, enabling a multifaceted approach to therapy. Cisplatin not only serves as a chemotherapy drug but also acts as a catalyst for chemodynamic therapy (CDT) to initiate CDT cascades by creating hydrogen peroxide for the Fenton reaction. Hemoglobin, enclosed in PLGA nanoparticles, provides ferrous ions that react with hydrogen peroxide in an acidic environment, yielding hydroxyl radicals that induce cancer cell death. Additionally, oxygen released from hemoglobin mitigates hypoxia-induced chemoresistance, bolstering overall anticancer efficacy. Results demonstrate the shear-thinning properties and injectability of the hydrogel. Cisplatin elevates intracellular hydrogen peroxide levels in tumor cells, while hemoglobin efficiently releases ferrous ions and generates reactive oxygen species (ROS) in the presence of hydrogen peroxide. In in vitro and in vivo study, the combinational use of chemo- and chemodynamic therapies achieves a synergistic anticancer effect on combating glioblastoma. In summary, our CDT-based hydrogel, activated by endogenous cues and mediated by chemo drugs, spontaneously produces ROS and ameliorates the adverse tumor microenvironment with rational and selective antitumor strategies.

CRISPR/Cas9 gene targeting plus nanopore DNA sequencing with the plasmid pBR322 in the classroom.

Both nanopore-based DNA sequencing and CRISPR/Cas-based gene editing represent groundbreaking innovations in molecular biology and genomics, offering unprecedented insights into and tools for working with genetic information. For students, reading, editing, and even writing DNA will be part of their everyday life. We have developed a laboratory procedure that includes (i) the biosynthesis of a guide RNA for, (ii) targeting Cas9 to specifically linearize the pBR322 plasmid, and (iii) the identification of the cutting site through nanopore DNA sequencing. The protocol is intentionally kept simple and requires neither living organisms nor biosafety laboratories. We divided the experimental procedures into separate activities to facilitate customization. Assuming access to a well-equipped molecular biology laboratory, an initial investment of approximately $2,700 is necessary. The material costs for each experiment group amount to around $130. Furthermore, we have developed a freely accessible website (https://dnalesen.hs-mittweida.de) for sequence read analysis and visualization, lowering the required computational skills to a minimum. For those with strong computational skills, we provide instructions for terminal-based data processing. With the presented activities, we aim to provide a hands-on experiment that engages students in modern molecular genetics and motivates them to discuss potential implications. The complete experiment can be accomplished within half a day and has been successfully implemented by us at high schools, in teacher training, and at universities. Our tip is to combine CRISPR/Cas gene targeting with nanopore-based DNA sequencing. As a tool, we provide a website that facilitates sequence data analysis and visualization.

Fundamentals for predicting transcriptional regulations from DNA sequence patterns.

Cell-type-specific regulatory elements, cataloged through extensive experiments and bioinformatics in large-scale consortiums, have enabled enrichment analyses of genetic associations that primarily utilize positional information of the regulatory elements. These analyses have identified cell types and pathways genetically associated with human complex traits. However, our understanding of detailed allelic effects on these elements' activities and on-off states remains incomplete, hampering the interpretation of human genetic study results. This review introduces machine learning methods to learn sequence-dependent transcriptional regulation mechanisms from DNA sequences for predicting such allelic effects (not associations). We provide a concise history of machine-learning-based approaches, the requirements, and the key computational processes, focusing on primers in machine learning. Convolution and self-attention, pivotal in modern deep-learning models, are explained through geometrical interpretations using dot products. This facilitates understanding of the concept and why these have been used for machine learning for DNA sequences. These will inspire further research in this genetics and genomics field.

Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India

BackgroundCurrent clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India.Results903 smMIPs were designed to target exon and exon–intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood.ConclusionWe developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.

Which Cyclaneusma minus morphotypes are responsible for needle cast of Pinus spp. in Slovakia?

AbstractCyclaneusma needle cast (CNC) is a needle disease which caused deterioration of vitality and reduction in the growth of pines. The disease is caused by the ascomycetous fungus Cyclaneusma minus, which has two well-described morphotypes; C. minus simile and C. minus verum. The distribution and host range of C. minus simile and verum was determined from needle samples and isolates collected throughout Slovakia from 2014 to 2020. Samples from 111 localities, 11 pine host species and 245 trees collected in different types of planting were analysed. It was found, that both morphotypes are present, but C. minus verum is predominantly responsible for CNC in urban and forest plantings in Slovakia. C. minus verum was positively detected in more than 88% of collected samples, whereas C. minus simile was only in four samples from three localities. Morphotype-specific primers were sufficiently sensitive even for new pine-host species. The host range of C. minus simile and C. minus verum was enriched worldwide. C. minus verum was observed in nine host species, whereas C. minus simile was identified only in one. Cyclaneusma niveum was also recorded and its presence was confirmed through DNA sequencing.

Antigen escape as a shared mechanism of resistance to BCMA-directed therapies in multiple myeloma

B-cell maturation antigen (BCMA)-targeting therapeutics have dramatically improved outcomes in relapsed/refractory multiple myeloma (RRMM). However, whether the mechanisms of resistance between these therapies are shared and how the identification of such mechanisms before therapy initiation could refine clinical decision-making remains undefined. We analyzed outcomes for 72 RRMM patients treated with teclistamab, a CD3 x BCMA bispecific antibody (BsAb), 42% (30/72) of whom had prior BCMA-directed therapy exposure. Malignant plasma cell BCMA expression was present in all BCMA therapy-naïve patients. Prior therapy-mediated loss of plasma cell BCMA expression before teclistamab treatment, measured by immunohistochemistry, was observed in 3 patients, none of whom responded to teclistamab, and one of whom also did not respond to ciltacabtagene autoleucel. Whole exome sequencing of tumor DNA from one patient revealed biallelic loss of TNFRSF17 following treatment with belantamab mafodotin. Low-to-undetectable peripheral blood soluble BCMA levels correlated with the absence of BCMA expression by bone marrow plasma cells. Thus, although rare, loss of BCMA expression following TNFRSF17 gene deletions can occur following any BCMA-directed therapy and prevents response to subsequent anti-BCMA-directed treatments, underscoring the importance of verifying the presence of a target antigen.

Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant

Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatment plant in Trieste (Italy) were used to determine the bacterial biodiversity. Wastewater samples were collected directly from the untreated sewage to obtain a true representation of the microbiological community present in the plant. Different samplers and collection media provide an indication of the different grades of biodiversity, with condensation growth tubes and DNA/RNA shieldTM capturing the richer bacterial genera. Overall, in terms of relative abundance, the air samples have a lower number of bacterial genera (64 OTUs) than the wastewater ones (75 OTUs). Using the metabarcoding approach to aerosol samples, we provide the first preliminary step toward the understanding of a significant diversity between different air sampling systems, enabling the scientific community to orient research towards the most informative sampling strategy.

Columnar Cell Thyroid Carcinoma: A Heterogeneous Entity Demonstrating Overlap Between Papillary Thyroid Carcinoma and Follicular Neoplasms.

Columnar cell papillary thyroid carcinoma (CC-PTC) is a morphologic subtype of papillary thyroid carcinoma with a variable prognosis. It is characterized by neoplastic thyroid follicular-derived cells with pseudostratified columnar morphology arranged in papillary or follicular structures with supranuclear or subnuclear vacuoles. The molecular profile of this subtype has only recently come under scrutiny, with mixed results. The aim of this study is to further explore the morphologic, immunohistochemical, and genetic profile of CC-PTC, as well as to correlate these features with clinical outcomes. CC-PTC cases were identified from 3 institutions. Immunohistochemistry (ER, CDX2) and molecular testing (DNA and RNA sequencing) were performed. Clinicopathologic parameters and patient outcomes were recorded. Twelve cases (2006-2023) were identified, all in adults (age 45-91). Two presented with disease outside the thyroid gland (neck and mediastinum) and two presented with distant metastasis. Four were high-grade differentiated thyroid carcinomas (necrosis or mitoses), one of which died of disease. Four were noninvasive or minimally invasive, one of which locally recurred. Three patients had lymph node metastases. ER and CDX2 were positive in 73% and 50%, respectively. Pathogenic mutations were found in TERT promoter (n = 3), RAS (n = 2), ATM, NOTCH1, APC, and ESR1, along with cases bearing AGK::BRAF fusion (n = 1), BRAF VE1 expression (n = 1), and NF2 loss (n = 1). This study represents the largest molecularly defined cohort of non-oncocytic thyroid carcinomas with columnar cell morphology. These tumors represent a genetically and behaviorally heterogeneous group of neoplasms, some of which have RAS-like or follicular neoplasm-like genetics, some of which have BRAF-p.V600E-like or classic papillary thyroid carcinoma-like genetics, and some of which remain unclear. Noninvasive or minimally invasive tumors showed an indolent course compared to those with angioinvasion, gross extrathyroidal growth, or high-grade morphology. Consideration could be given to reclassification of this neoplasm outside of the subtyping of papillary thyroid carcinoma in light of its genetic diversity, distinct morphology, and clinical behavior more closely aligned with follicular thyroid neoplasms.

Shotgun metagenomic investigation of foodborne pathogens and antimicrobial resistance genes in artisanal fermented meat products from the Mediterranean area

In this pilot study, we compared the metagenomic profiles of different types of artisanal fermented meat products collected in Italy, Greece, Portugal, and Morocco to investigate their taxonomic profile, also in relation to the presence of foodborne pathogens and antimicrobial resistance genes. In addition, technical replicates of the same biological sample were tested to estimate the reproducibility of shotgun metagenomics. The taxonomic analysis showed a high level of variability between different fermented meat products at both the phylum and genus levels. Staphylococcus aureus was identified with the highest abundance in Italian fermented meat; Escherichia coli in fermented meat from Morocco; Salmonella enterica in fermented meat from Greece; Klebsiella pneumoniae and Yersinia enterocolitica in fermented meat from Portugal. The fungi Aspergillus, Neosartoria, Emericella, Penicillum and Debaryomyces showed a negative correlation with Lactococcus, Enterococcus, Streptococcus, Leuconostoc and Lactobacillus. The resistome analysis indicated that genes conferring resistance to aminoglycoside, macrolide, and tetracycline were widely spread in all the samples. Our results showed that the reproducibility between technical replicates tested by shotgun metagenomic was very high under the same conditions of analysis (either DNA extraction, library preparation, sequencing analysis, and bioinformatic analysis), considering both the degree of overlapping and the pairwise correlation.

The potential of tailed amplicons for SARS-CoV-2 detection in Nucleic Acid Lateral Flow Assays.

Nucleic Acid Lateral Flow Assays (NALFAs) are a promising solution for the point-of-care detection of viruses like SARS-CoV-2. However, they show some drawbacks, such as the great dependency on the use of antibodies and the need for post-amplification protocols that enable the preparation of amplicons for effective readings, as well as low sensitivity. Here, we developed amplicons of a specific SARS-CoV-2 gene tailed with single-strand DNA (ssDNA) sequences to hybridize with DNA probes immobilized on the NALFA strips, thus overcoming the aforementioned problems. Results have shown that tailed primers have not compromised the amplification efficiency and allowed the correct detection of the amplicons in the lateral flow strip. This approach has presented a limit of detection (LOD) of 25 RNA copies /reaction mix (1 copy/μL) and the test of cross-reactivity with other related viruses has not shown any cross-reactivity. Twenty clinical samples were evaluated by NALFA and simultaneously compared with the gold standard RT-qPCR protocol, originating equal results. Although the number of clinical specimens tested being relatively small, this indicates a sensitivity and specificity both of 100%. In short, an alternative NALFA was successfully implemented, rendering an accurate route for SARS-CoV-2 diagnosis, compatible with low-resource settings.

Rapid and Sensitive Detection of Verticillium dahliae from Soil Using LAMP-CRISPR/Cas12a Technology

Cotton Verticillium wilt is mainly caused by the fungus Verticillium dahliae, which threatens the production of cotton. Its pathogen can survive in the soil for several years in the form of microsclerotia, making it a destructive soil-borne disease. The accurate, sensitive, and rapid detection of V. dahliae from complex soil samples is of great significance for the early warning and management of cotton Verticillium wilt. In this study, we combined the loop-mediated isothermal amplification (LAMP) with CRISPR/Cas12a technology to develop an accurate, sensitive, and rapid detection method for V. dahliae. Initially, LAMP primers and CRISPR RNA (crRNA) were designed based on a specific DNA sequence of V. dahliae, which was validated using several closely related Verticillium spp. The lower detection limit of the LAMP-CRISPR/Cas12a combined with the fluorescent visualization detection system is approximately ~10 fg/μL genomic DNA per reaction. When combined with crude DNA-extraction methods, it is possible to detect as few as two microsclerotia per gram of soil, with the total detection process taking less than 90 min. Furthermore, to improve the method’s user and field friendliness, the field detection results were visualized using lateral flow strips (LFS). The LAMP-CRISPR/Cas12a-LFS system has a lower detection limit of ~1 fg/μL genomic DNA of the V. dahliae, and when combined with the field crude DNA-extraction method, it can detect as few as six microsclerotia per gram of soil, with the total detection process taking less than 2 h. In summary, this study expands the application of LAMP-CRISPR/Cas12a nucleic acid detection in V. dahliae and will contribute to the development of field-deployable diagnostic productions.

A potentiostat readout array for nanopore-based DNA sequencing

A potentiostat readout array for nanopore-based DNA sequencing

Epigenetic and gene therapy in human and veterinary medicine.

Gene therapy is a focus of interest in both human and veterinary medicine, especially in recent years due to the potential applications of CRISPR/Cas9 technology. Another relatively new approach is that of epigenetic therapy, which involves an intervention based on epigenetic marks, including DNA methylation, histone post-translational modifications, and post-transcription modifications of distinct RNAs. The epigenome results from enzymatic reactions, which regulate gene expression without altering DNA sequences. In contrast to conventional CRISP/Cas9 techniques, the recently established methodology of epigenetic editing mediated by the CRISPR/dCas9 system is designed to target specific genes without causing DNA breaks. Both natural epigenetic processes and epigenetic editing regulate gene expression and thereby contribute to maintaining the balance between physiological functions and pathophysiological states. From this perspective, knowledge of specific epigenetic marks has immense potential in both human and veterinary medicine. For instance, the use of epigenetic drugs (chemical compounds with therapeutic potential affecting the epigenome) seems to be promising for the treatment of cancer, metabolic, and infectious diseases. Also, there is evidence that an epigenetic diet (nutrition-like factors affecting epigenome) should be considered as part of a healthy lifestyle and could contribute to the prevention of pathophysiological processes. In summary, epigenetic-based approaches in human and veterinary medicine have increasing significance in targeting aberrant gene expression associated with various diseases. In this case, CRISPR/dCas9, epigenetic targeting, and some epigenetic nutrition factors could contribute to reversing an abnormal epigenetic landscape to a healthy physiological state.