Polymerase chain reaction

Utility of clinical metagenomics in complex infections: Cryptococcal meningitis complicated by Nocardia brain abscess

Nocardia farcinica brain abscess (BA) is a rare yet life-threatening infection of the central nervous system (CNS) that predominantly affects immunocompromised patients. Its nonspecific symptoms often lead to delayed diagnosis and poor outcomes. Early diagnosis and precise treatment are essential to improve the prognosis of patients. We report the rare case of a 75-year-old man with IgG4-related disease undergoing long-term methylprednisolone therapy who presented with a N. farcinica brain abscess. The patient initially presented with cryptococcal meningitis but exhibited persistent symptoms despite standard antifungal treatment. Follow-up neuroimaging revealed new intracranial abscess formations. Metagenomic next-generation sequencing (mNGS) of brain tissue and cerebrospinal fluid (CSF) identified abundant N. farcinica-specific sequences, confirming a concurrent Nocardia brain abscess complicating the cryptococcal infection. The patient's condition gradually improved with timely antibiotic treatment and is currently in recovery. This case underscores the heightened risk of sequential opportunistic infections in immunocompromised individuals and exemplifies the clinical value of mNGS in detecting rare infectious diseases. We further conducted a systematic review of patients with Nocardia central nervous system infections confirmed by mNGS, analyzing their clinical presentations, laboratory parameters, therapeutic regimens, and prognostic outcomes. In summary, our study demonstrates that mNGS offers significant diagnostic advantages compared to conventional microbiological methods for uncommon infections. These findings provide clinically actionable, evidence-based guidance for the diagnosis and management of Nocardia brain abscesses.

Graphene-mediated surface enhanced Raman spectroscopy for DNA Detection&hybridization: Breakthroughs and challenges

In response to the growing demand for advanced DNA research, the need for refined scientific methodologies has become increasingly evident. This review provides a comprehensive synthesis of recent advancements in the application of graphene-mediated Surface Enhanced Raman Spectroscopy (G-SERS) for DNA detection and hybridization, highlighting its significant potential in biomedical fields particularly gene detection and emphasizing its crucial role in advancing genetic research. More importantly, it emphasizes the pivotal role of Au and Ag nanoparticles, with varying shapes and sizes, in enhancing signal intensity and improving analytical performance, highlighting the significant contributions of G-SERS in enhancing both the sensitivity and selectivity of DNA analysis. Furthermore, our review explores innovative hybrid approaches that integrate SERS with Quartz Crystal Microbalance (QCM) and Atomic Force Microscopy (AFM), marking a transformative shift in analytical capabilities. Overall, this review offers valuable insights into the evolving landscape of DNA analysis technologies, paving the way for future advancements in genetic research.

Periodontal Pathogens Correlate with Rheumatoid Arthritis Disease Parameters: A Systematic Review Based on Clinical Studies

Background: Numerous studies have found higher levels of autoantibodies including anti citrullinated protein antibodies (ACPAs), anti-cyclic citrullinated peptides (aCCP), or rheumatoid factor (RF) against periodontal microorganisms in rheumatoid arthritis (RA). Objective: To evaluate the correlation between periodontal bacteria and RA disease parameters. Methods: We utilized PubMed, Scopus, ScienceDirect, and manual search databases up until March 2024 using PRISMA 2020 guidelines. The data were obtained from microbiological assays by RT-PCR/qPCR, sequencing, and serological testing of disease parameters (ACPA, aCCP, and RF) utilizing ELISA method. Results: A total of 1514 documents were discovered based on the inclusion criteria. Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Prevotella_9 were associated with elevated levels of ACPA/aCCP and RF in RA with periodontitis. A positive correlation was found between Peptococcus simiae, Aminipila butyrica, Leptotrichia spp., Leptotrichia wadei, and Neisseria bacilliformis with ACPA, and Treponema sp. canine oral taxon 087 with RF. Conclusions: This study found that several oral microorganisms correlate with elevated ACPA/aCCP and RF in RA with periodontitis. Future studies of the oral microbiome and the molecular mechanisms are anticipated to discover new therapies and diagnostic methods for periodontitis and RA.

Development of Quantitative Real-Time PCR Tests for the Identification of Biting Midge Species and Clades (Diptera: Ceratopogonidae) of the Obsoletus Group (Subgenus Avaritia), Including Important Viral Vectors in Europe

Species of the widespread Obsoletus Complex (Culicoides subgenus Avarita Fox, 1955) have been implicated as potential key vectors during the bluetongue and Schmallenberg epidemics in Central Europe in 2006 and 2012. Although extensive efforts have been made to clarify vector-pathogen relationships, one of the most important steps in this process-correct species identification-remains difficult, due to the presence of isomorphic species within the Obsoletus Group. To overcome the difficulties in morphological species identification, several PCR tests were developed. With the aim of developing a high-throughput PCR, capable of differentiating all putative vector species and newly described haplotypes of the subgenus Avaritia present in Europe, a dataset of 4407 published sequences of the mitochondrial (mt) cytochrome c oxidase subunit I (COI) was used to develop specific primers and probes, which can either be applied in a singleplex PCR or in different multiplex PCR approaches. The real-time PCR achieved very high diagnostic sensitivity (100%) and specificity (91.7%) and reliably detected the three clades of C. obsoletus sensu stricto (s.s.) in a pool of specimens. Thus, the new real-time PCR approach will provide an excellent tool for large-scale monitoring, which could improve the understanding of the biology, geographical distribution, and habitat preference of European biting midge species involved in the transmission of bluetongue, Schmallenberg, and epizootic hemorrhagic disease viruses.

Reduction of background-triggered amplification in lesion-induced DNA amplification (LIDA)

Lesion-induced DNA amplification (LIDA) enables isothermal amplification of nucleic acids, and the only enzyme required is T4 DNA ligase. However, the application of LIDA for the amplification of trace amounts of nucleic acids has been hindered by the observed background-triggered amplification in the absence of the initial target due to a pseudo-blunt end ligation reaction of two of the primers. In this work, we have tested three approaches to minimize the background-triggered amplification: increasing and decreasing the concentration of salts such as NaCl and MgCl2, respectively, and increasing the concentration of ATP. All these optimizations sharply decreased the background-triggered amplification. Employing the most favourable buffer condition of 2.5 mM MgCl2 where the target-initiated amplification was least affected while reducing the background-triggered process enabled us to achieve a detection range of 14 nM-140 aM with an approximate limit of detection of 680 aM, which is five orders of magnitude more sensitive than using our standard amplification conditions. This optimization of the salt and co-factor concentrations to decrease the background and enhance the sensitivity of LIDA has demonstrated LIDA's potential for application in clinical diagnostics.

Viruses of parasites: A roadmap toward diagnostic and therapeutic development

With few preventive and therapeutic solutions available, parasites remain associated with devastating health, social and economic consequences, especially in impoverished communities in tropical areas. The discovery that parasites host viruses, and that these parasite viruses can contribute to diseases, has triggered a paradigm shift in thought and action, whereby parasite viruses are being assessed as targets for diagnostic, therapeutic and preventive interventions. This review lays out critical steps needed to discover and characterize viruses of parasites, highlighting challenges and identifying opportunities through examples of virus discoveries that fill the gap in our incomplete understanding of parasite pathogenicity.

Reverse-Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) for Viral Detection - A Case Study

An assay and protocol framework are provided for utilizing reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP) at the point-of-care for diagnosing and monitoring a hypothetical zoonotic viral outbreak in a resource-limited area. This manuscript utilizes a previously published decision tree algorithm to determine an appropriate molecular diagnostic point-of-care test that can effectively address the outbreak presented in the hypothetical case study. © 2025 Wiley Periodicals LLC.

Impact of Resveratrol Supplementation on Human Sirtuin 1: A Grading of Recommendations Assessment, Development and Evaluation-Assessed Systematic Review and Dose-Response Meta-Analysis of Randomized Controlled Trials

BACKGROUND

Resveratrol, a natural polyphenol compound, possesses anti-aging, antitumor, and vascular protective properties. These attributes are believed to stem from its influence on Sirtuin 1 (Sirt1), a member of the human Sirtuin family and a nicotinamide adenine dinucleotide-dependent histone deacetylase.

OBJECTIVE

The aim of this study was to quantitatively investigate the impact of resveratrol supplementation on Sirt1 levels in adults by conducting a systematic review and meta-analysis of randomized controlled trials (RCTs) involving resveratrol supplementation.

METHODS

This Grading of Recommendations Assessment, Development and Evaluation-assessed systematic review involved a comprehensive search of PubMed, Embase, MEDLINE, Scopus, Web of Science, Cochrane Central Register of Controlled Trials, and Google Scholar databases using related keywords and was conducted from March 14, 2024, to April 15, 2024, to identify all RCTs investigating resveratrol's effects on Sirt1. Effect sizes were quantified as mean differences (MDs) or standardized mean differences (SMDs), with standard deviations of outcomes. An overall effect estimate was derived using a random-effects model when 2 or more studies reported similar outcomes. Statistical heterogeneity was assessed through the calculation of I2 statistics. In addition, a dose-response analysis was performed to assess potential dose-response relationships. Risk of bias was assessed using the Cochrane risk-of-bias tool for RCTs (RoB 2). Publication bias was evaluated using Begg's test and a meta-regression using the year of publication as a moderator.

RESULTS

Eleven RCTs examining the effects of resveratrol on Sirt1 gene expression (4 RCTs), protein expression (5 RCTs), and serum levels (3 RCTs) were included in the meta-analysis. The results showed no significant impact of resveratrol on Sirt1 gene expression (SMD = 0.05; 95% CI -0.24 to 0.344; P = .73), protein expression (SMD = 0.3; 95% CI -0.15 to 0.77; P = .18), or serum levels (MD = -0.04; 95% CI -0.235 to 0.16; P = .7). However, subgroup analyses suggested a significant increase in Sirt1 gene expression in studies with an intervention duration of <12 weeks and evaluating blood tissue. Furthermore, the impact of resveratrol on Sirt1 appeared to be influenced by the dosage regimen, with a significant effect for intervention duration.

CONCLUSIONS

Study results indicate that resveratrol supplementation does not significantly influence human Sirt1 based on the overall meta-analysis. However, the dose-response analysis suggests that the effect of resveratrol on Sirt1 depends on the dosage regimen.

Genetic Profiling of Acute and Chronic Leukemia via Next-Generation Sequencing: Current Insights and Future Perspectives

Leukemia is a heterogeneous group of hematologic malignancies characterized by distinct genetic and molecular abnormalities. Advancements in genomic technologies have significantly transformed the diagnosis, prognosis, and treatment strategies for leukemia. Among these, next-generation sequencing (NGS) has emerged as a powerful tool, enabling high-resolution genomic profiling that surpasses conventional diagnostic approaches. By providing comprehensive insights into genetic mutations, clonal evolution, and resistance mechanisms, NGS has revolutionized precision medicine in leukemia management. Despite its transformative potential, the clinical integration of NGS presents challenges, including data interpretation complexities, standardization issues, and cost considerations. However, continuous advancements in sequencing platforms and bioinformatics pipelines are enhancing the reliability and accessibility of NGS in routine clinical practice. The expanding role of NGS in leukemia is paving the way for improved risk stratification, targeted therapies, and real-time disease monitoring, ultimately leading to better patient outcomes. This review highlights the impact of NGS on leukemia research and clinical applications, discussing its advantages over traditional diagnostic techniques, key sequencing approaches, and emerging challenges. As precision oncology continues to evolve, NGS is expected to play an increasingly central role in the diagnosis and management of leukemia, driving innovations in personalized medicine and therapeutic interventions.

Multiplex Real-Time Polymerase Chain Reaction and Recombinase Polymerase Amplification: Methods for Quick and Cost-Effective Detection of Vancomycin-Resistant Enterococci (VRE)

Background/Objectives: Vancomycin-resistant enterococci (VRE) are one of the leading causes of antibiotic-resistant infections in the hospital setting worldwide, and this has become a major issue, because most patients infected with this strain are difficult to treat. Multiplex real-time polymerase chain reaction (RT PCR) is an advantageous technique that can amplify multiple targets in a single reaction, and can be used to quickly detect specific targets in VRE within two hours, starting from suspected colonies of bacterial cultures, without sample preparation. Methods: In this study, we selected the glycopeptide/vancomycin resistance genes that are most common in clinical settings, vanA and vanB, in combination with the species markers ddl_faecium and ddl_faecalis for the most common VRE species-Enterococcus faecium and Enterococcus faecalis. Results: DNA from forty clinical VRE strains was prepared using a fast and economic heat lysis method, and a multiplex real-time PCR assay was optimized and carried out subsequently. The results were in concordance with the results from recombinase polymerase amplification (RPA) of the same VRE samples. Conclusions: Multiplex RT PCR and RPA for VRE detection proffers a second method for the confirmation of vancomycin resistance, and it can be developed as a fast screening assay for patients before admission into high-risk settings.

Detection and quantification of lactoferrin: Innovations, applications, and challenges

Lactoferrin (LF), is an 80 kDa glycoprotein with diverse bio-functions in the human body. It is involved in host defense, tumor growth inhibition, anti-inflammatory and enzymatic activity, and demonstrates antioxidant, antimicrobial, antiviral, and antiparasitic properties. As part of the transferrin family, LF is recognized as an iron-binding glycoprotein. Reliable analytical methods are crucial for ensuring consumer safety and enhancing food production through hazard analysis and good manufacturing practices. This review details recent advancements in analytical methods, offering an in-depth look at their primary applications for LF detection. The article underscores the advantages and disadvantages of common analytical techniques, such as conventional and modern methods. Additionally, it explores developments in biosensors related to detection mechanisms, including the use of nanomaterials as signal probes and carriers for loading signal probes; also addressing sensitivity and performance evaluation. Finally, it considers the challenges and potential opportunities in the advancement of biosensors for LF detection.

Genetic and molecular profiling in Merkel Cell Carcinoma: Focus on MCPyV oncoproteins and emerging diagnostic techniques

Merkel Cell Carcinoma (MCC) is an uncommon yet highly malignant form of skin cancer, frequently linked to the Merkel cell polyomavirus (MCPyV). This review comprehensively covers data from year 2000 to 2024, employing keywords such as MCC, MCPyV Oncoproteins, Immunohistochemistry, Southern Blot, Western Blot, Polymerase Chain Reaction (PCR), Digital Droplet PCR (ddPCR), Next-Generation Sequencing (NGS), and In Situ Hybridization (ISH). The search engines utilized were Google, PubMed Central, Scopus, and other journal databases like ScienceDirect. This review is essential for researchers and the broader medical community as it consolidates two decades of research on the genetic and molecular profiling of MCC, particularly focusing on MCPyV's role in its pathogenesis. It highlights the diagnostic advancements and therapeutic potential of targeting viral oncoproteins and provides insights into the development of both in vivo and in vitro models for better understanding MCC. The findings emphasize the significance of early detection, molecular diagnostics, and personalized treatment approaches, aiming to improve outcomes for patients with this malignant malignancy.

Polymerase Chain Reaction: A Toolbox for Molecular Discovery

Polymerase chain reaction (PCR), a revolutionary molecular tool, has transformed genetic studies by facilitating rapid DNA amplification. The PCR process relies on several key components: a DNA template or cDNA, two primers, Taq polymerase, nucleotides, and a buffer. These elements collectively facilitate the amplification process, which comprises three stages: denaturation, annealing, and extension. These stages are repeated in cycles to exponentially amplify the target DNA sequence. Furthermore, the power of PCR lies in its ability to generate exponential copies of target DNA in a remarkably short period. Moreover, various PCR techniques are available, encompassing traditional approaches like quantitative PCR, reverse transcription PCR, and nested PCR, as well as innovative methods such as extreme PCR, inverse PCR, and touchdown PCR. These techniques are extensively utilized in molecular, biological, and medical research laboratories for both research and diagnostic applications. This review explores a comprehensive overview of PCR, covering its history, underlying principles, and diverse applications in diagnostics, research, and drug development.

Toxocara canis infections in mice: from subtle to severe consequences in 100 weeks

Toxocara canis is a widespread parasite of canids with a wide range of paratenic hosts, but also one of the overlooked agents causing nervous system infections of humans. Previous experimental infections of mice demonstrated the impact of high infection doses of larvae on neurobehavioral disorders and pathological changes. In contrast to previous studies, we aimed to investigate the long-term (up to 100 weeks) impact of low- to high-dose infection in mice. We focused on their physical condition, motor skills, and the accompanying pathologies in the brain. Three groups of BALB/c mice were infected with 10, 100, and 1000 T. canis larvae/mouse and specific anti-T. canis excretory-secretory antigens immunoglobulin G antibody response, general condition, and motor skills were tested in defined intervals within 100 weeks after infection. The number of larvae in selected organs was assessed and the pathological changes in the brain were studied histologically. As a result, subtle to severe impairments in general condition and motor skills were detected, with generally earlier onsets occurring the higher the infection dose was. The specific immunoglobulin G antibody levels corresponding to the infection dose were detected in all infected groups. Necrosis, cellular infiltrations, and foamy cells developed in moderate- and high-infection dose mice, in contrast with hemorrhages detected in all groups. This study demonstrated the long-term negative impact of T. canis infection on the paratenic host, particularly at moderate and high infectious doses. Although pathological changes in the brain were observed even in low-infection dose mice, their physical and motor condition was comparable to the control group.

Peritonitis After Endometrial Cytology in a Woman With Hydrosalpinx Caused by Chronic Chlamydia trachomatis Infection

Some women infected with Chlamydia trachomatis (CT) are asymptomatic, while others experience lower abdominal discomfort when the inflammatory process extends to the fallopian tubes. Without treatment, salpingitis can progress to pelvic peritonitis and subsequently, peritonitis in the upper abdomen, a condition known as Fitz-Hugh-Curtis syndrome, in some cases. A nucleic acid amplification assay is required for diagnosing CT infection. However, this assay may yield a negative result even in the presence of CT infection. This report presents a case of a 45-year-old woman with a history of hydrosalpinx and no history of lower abdominal pain who underwent endometrial cytology at a local gynecology clinic because of irregular bleeding. The following day, she developed peritonitis. A nucleic acid amplification assay for CT yielded a negative result at the onset of peritonitis. Hence, the patient received tazobactam/piperacillin as a treatment option. However, this drug was ineffective. Subsequently, the patient was found to be positive for serum CT IgG and IgA antibodies. Her peritonitis could have developed as a result of endometrial cytology performed in the presence of a chronic CT infection in the uterus; through this procedure, CT-infected endometrial cells may have spread into the abdominal cavity via the fallopian tubes. Nevertheless, the addition of minocycline hydrochloride markedly improved the symptoms of peritonitis. This case shows that when dealing with chronic CT infections in the female internal genitalia, the standard nucleic acid amplification testing screening test for CT might not be entirely effective in detecting the infection. Additionally, it is important to recognize that in cases of chronic CT infection of the uterus that involved genital bleeding, examining the uterine cavity could lead to peritonitis in a short timeframe.

A Narrative Review of Molecular, Immunohistochemical and In-Situ Techniques in Dermatopathology

Skin disorders pose a significant health burden globally, affecting millions of individuals across diverse demographics. Advancements in molecular techniques have revolutionised our understanding of the underlying mechanisms of skin disorders, offering insights into their pathogenesis, diagnosis, and potential targeted treatment. Furthermore, the integration of molecular diagnostics into clinical practice has enhanced the accuracy of skin disorder diagnoses. Polymerase chain reaction (PCR), next-generation sequencing (NGS), and other molecular assays have allowed for the detection of infectious agents, assessment of genetic mutations, and profile gene expression patterns with unequalled precision. These techniques have proven instrumental in distinguishing between subtypes of skin cancers, aiding treatment strategies and prognostic assessments. Moreover, molecular profiling is increasingly guiding the selection of therapeutic agents, ensuring a personalised and effective approach to managing skin disorders. The application of PCR has revolutionised the field by enabling the identification of microbial DNA (i.e., Mycobacterium tuberculosis and Epstein-Barr Virus) in skin infections and detecting specific genetic mutations associated with dermatological disorders (e.g., BRAF). DNA sequencing technologies, such as next-generation sequencing, have facilitated the elucidation of genetic variations and mutations in skin diseases (i.e., bullous disorders), paving the way for personalised treatment approaches. Gene expression profiling techniques, such as microarrays and RNA sequencing, have provided insights into dysregulated pathways and molecular signatures associated with conditions ranging from inflammatory skin disorders to cutaneous malignancies. Immunohistochemistry and fluorescence in situ hybridization have proven invaluable in determining protein expression patterns and detecting chromosomal abnormalities, respectively, aiding in the characterization of skin lesions in conjunction with the molecular data. Proteomic studies have contributed to understanding the intricate protein networks involved in dermatological conditions (i.e., psoriasis), while epigenetic analyses have shed light on the role of epigenetic modifications in gene regulation within skin cancer (i.e., Malignant Melanoma). Together, these molecular techniques have laid the groundwork for targeted therapies and precision medicine in dermatology, with implications for improved diagnostics and treatment outcomes. This review focuses on the routinely employed molecular techniques within dermatopathology, with a focus on cutaneous malignancies, autoimmune diseases, infectious diseases, and neonatal screening which can be implemented in the diagnosis and contribute to improved patient care.

Molecular methods in cancer diagnostics: a short review

BACKGROUND

One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required.

OBJECTIVE

In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer.

METHODS

We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria.

RESULTS

The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes.

LIMITATION

The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field.

CONCLUSION

After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.

Fast and Economic Microarray-Based Detection of Species-, Resistance-, and Virulence-Associated Genes in Clinical Strains of Vancomycin-Resistant Enterococci (VRE)

Today, there is a continuous worldwide battle against antimicrobial resistance (AMR) and that includes vancomycin-resistant enterococci (VRE). Methods that can adequately and quickly detect transmission chains in outbreaks are needed to trace and manage this problem fast and cost-effectively. In this study, DNA-microarray-based technology was developed for this purpose. It commenced with the bioinformatic design of specific oligonucleotide sequences to obtain amplification primers and hybridization probes. Microarrays were manufactured using these synthesized oligonucleotides. A highly parallel and stringent labeling and hybridization protocol was developed and employed using isolated genomic DNA from previously sequenced (referenced) clinical VRE strains for optimal sensitivity and specificity. Microarray results showed the detection of virulence, resistance, and species-specific genes in the VRE strains. Theoretical predictions of the microarray results were also derived from the sequences of the same VRE strain and were compared to array results while optimizing protocols until the microarray result and theoretical predictions were a match. The study concludes that DNA microarray technology can be used to quickly, accurately, and economically detect specifically and massively parallel target genes in enterococci.

Feasibility of implementing RPA coupled with CRISPR-Cas12a (RPA-Cas12a) for Hepatozoon canis detection in dogs

Hepatozoonosis, caused by the protozoan Hepatozoon canis, is a prevalent blood disease affecting owned and stray dogs and cats. The prevalence of these parasites among companion animals in Thailand remains poorly understood. Diagnosing the old-world form of the disease is challenging due to the wide range of nonspecific clinical signs and the reliance on finding low levels of Hepatozoon gamonts in blood smears for conventional diagnosis. PCR demonstrates high specificity and sensitivity but it requires sophisticated instrumentation. Therefore, we established recombinase polymerase amplification (RPA) coupled with Cas12a for H. canis detection based on 18S rRNA. Our findings showed that RPA-Cas12a using gRNA_H was highly specific to H. canis, without yielding positives for other pathogen species including Babesia species. Even in cases of co-infection, RPA-Cas12a only detected positives in samples containing H. canis. This approach detected minimal amounts of H. canis18S rRNA-harboring plasmid at 10 copies per reaction, whereas plasmid-spiked canine blood enabled detection at a minimal amount of 100 copies per reaction. The performance of RPA-Cas12a was validated by comparing it with quantitative PCR-high resolution melting analysis (qPCR-HRM) and sequencing based on 35 canine blood samples. RPA-Cas12a demonstrated precision and accuracy values of 94 % and 90 %, respectively comparable to qPCR-HRM. Overall, these results indicate that RPA-Cas12a serves as a promising tool for H. canis detection as indicated by comparable performance to qPCR-HRM and is suitable for implementation in small animal hospitals or clinics due to its minimal resource requirements, thereby contributing to effective diagnosis and treatment for infected dogs.

Traditional approaches and recent tools for studying inflammasome activity

Inflammasomes play a major role in the immune response to infection, development of autoimmune disease, and control of cancer. Western blots were originally used in the early 2000s to characterize inflammasome activation. Since then, a panoply of techniques has been developed to characterize and visualize inflammasome activation in cells, tissues, and animals. This review article describes the most common techniques used by researchers in the inflammasome field and proposes that cell-specific characterization of inflammasome activation in tissues or animals may soon be commonly reported.

A sensitive one-pot ROA assay for rapid miRNA detection

MicroRNAs (miRNAs) and short RNA fragments (18-25 nt) are crucial biomarkers in biological research and disease diagnostics. However, their accurate and rapid detection remains a challenge, largely due to their low abundance, short length, and sequence similarities. In this study, we report on a highly sensitive, one-step RNA O-circle amplification (ROA) assay for rapid and accurate miRNA detection. The ROA assay commences with the hybridization of a circular probe with the test RNA, followed by a linear rolling circle amplification (RCA) using dUTP. This amplification process is facilitated by U-nick reactions, which lead to an exponential amplification for readout. Under optimized conditions, assays can be completed within an hour, producing an amplification yield up to the microgram level, with a detection limit as low as 0.15 fmol (6 pM). Notably, the ROA assay requires only one step, and the results can be easily read visually, making it user-friendly. This ROA assay has proven effective in detecting various miRNAs and phage ssRNA. Overall, the ROA assay offers a user-friendly, rapid, and accurate solution for miRNA detection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-024-00140-0.

Evaluating Immunologic and Illness Outcomes of SARS-CoV-2 Infection in Vaccinated and Unvaccinated Children Aged ≥ 5 Years, in a Multisite Longitudinal Cohort

Hybrid immunity, as a result of infection and vaccination to SARS-CoV-2, has been well studied in adults but limited evidence is available in children. We evaluated the antibody responses to primary SARS-CoV-2 infection among vaccinated and unvaccinated children aged ≥ 5 years.

METHODS

A longitudinal cohort study of children aged ≥ 5 was conducted during August 2021-August 2022, at sites in Arizona, Texas, Utah, and Florida. Children submitted weekly nasal swabs for PCR testing and provided sera 14-59 days after PCR-confirmed SARS-CoV-2 infection. Antibodies were measured by ELISA against the receptor-binding domain (RBD) and S2 domain of ancestral Spike (WA1), in addition to Omicron (BA.2) RBD, following infection in children, with and without prior monovalent ancestral mRNA COVID-19 vaccination.

RESULTS

Among the 257 participants aged 5 to 18 years, 166 (65%) had received at least two mRNA COVID-19 vaccine doses ≥ 14 days prior to infection. Of these, 53 occurred during Delta predominance, with 37 (70%) unvaccinated at the time of infection. The remaining 204 infections occurred during Omicron predominance, with 53 (26%) participants unvaccinated. After adjusting for weight, age, symptomatic infection, and gender, significantly higher mean RBD AUC values were observed among the vaccinated group compared to the unvaccinated group for both WA1 and Omicron (p < 0.0001). A smaller percentage of vaccinated children reported fever during illness, with 55 (33%) reporting fever compared to 44 (48%) unvaccinated children reporting fever (p = 0.021).

CONCLUSIONS

Children with vaccine-induced immunity at the time of SARS-CoV-2 infection had higher antibody levels during convalescence and experienced less fever compared to unvaccinated children during infection.

The Performance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Virus Using the Colorimetric Reverse-Transcription Loop Mediated Isothermal Amplification (RT-LAMP) Method in Saliva Specimens of Suspected COVID-19 Patients

Introduction

Corona Virus Disease-19 (COVID-19) is a disease caused by Severe-Acute-Respiratory-Syndrome-Coronavirus-2 (SARS-CoV-2). The most reliable and widely accepted method for diagnosing this infection, despite facing various challenges, is the Reverse Transcription Polymerase Chain Reaction (RT-PCR) method, which utilizes nasopharyngeal swab sample. Reverse-transcription loop mediated isothermal amplification (RT-LAMP) is a simpler nucleic acid amplification method compared to the RT-PCR method. This method has several advantages, including: of amplification at constant temperature, faster results, and potentially greater examination capacity.

Purpose

This study aimed to compare the validity of the RT-LAMP method using saliva specimens with that of the RT-PCR method using nasopharyngeal smears.

Methods

This was an analytical observational study with a cross-sectional design. The participants were inpatients in the COVID-19 special isolation building of Hasan Sadikin General Hospital, Indonesia with a probable (clinical symptoms of covid, but not confirm NAAT examination) or confirmed diagnosis of COVID-19 from September 2021 to February 2022. The inclusion criteria are COVID-19 patients with symptoms, adult subjects, and composite mentions. Patients who were unable to secrete saliva were also excluded.

Results

In total, 118 specimens were collected. The validity test results of the saliva specimens using the RT-LAMP method showed sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), of 65.5%, 100%, 100%, and 75%, respectively. The results increased in subjects treated between 3 and 7 days after symptom onset ie 73.2%, 100%, 100%, and 82.3%, respectively.

Conclusion

The very strong specificity accompanied by good sensitivity and NPV in the group of subjects treated 3-7 days after the onset of symptoms indicates that the RT-LAMP method using saliva specimens can be an efficient and reliable alternative tool in detecting the SARS-CoV-2 virus.

Navigating the CRISPR/Cas Landscape for Enhanced Diagnosis and Treatment of Wilson's Disease

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system continues to evolve, thereby enabling more precise detection and repair of mutagenesis. The development of CRISPR/Cas-based diagnosis holds promise for high-throughput, cost-effective, and portable nucleic acid screening and genetic disease diagnosis. In addition, advancements in transportation strategies such as adeno-associated virus (AAV), lentiviral vectors, nanoparticles, and virus-like vectors (VLPs) offer synergistic insights for gene therapeutics in vivo. Wilson's disease (WD), a copper metabolism disorder, is primarily caused by mutations in the ATPase copper transporting beta (ATP7B) gene. The condition is associated with the accumulation of copper in the body, leading to irreversible damage to various organs, including the liver, nervous system, kidneys, and eyes. However, the heterogeneous nature and individualized presentation of physical and neurological symptoms in WD patients pose significant challenges to accurate diagnosis. Furthermore, patients must consume copper-chelating medication throughout their lifetime. Herein, we provide a detailed description of WD and review the application of novel CRISPR-based strategies for its diagnosis and treatment, along with the challenges that need to be overcome.

A Mini-Review of Diagnostic Methods for the Antigen and Antibody Detection of Rocky Mountain and Brazilian Spotted Fever

Rocky Mountain or Brazilian spotted fever, caused by Rickettsia rickettsii, is a fulminant, seasonal, and neglected disease that occurs in focal points of North America and South America. Its rapid detection is essential for the better prognosis and survival rate of infected individuals. However, disease diagnosis still faces challenges as the accuracy of many of the available laboratory tests fluctuates. This review aimed to analyze methods for antibody or antigen detection, their gaps, and their evolution over time. A search was conducted to find all studies in the Pubmed database that described the antibody or antigen detection of R. rickettsii infections. Initially, a total of 403 articles were screened. Of these articles, only 17 fulfilled the pre-established inclusion criteria and were selected. Among the different methods applied, the IFA technique was the one most frequently found in the studies. However, it presented varied results such as a low specificity when using the indirect method. Other techniques, such as ELISA and immunohistochemistry, were also found, although in smaller numbers and with their own limitations. Although some studies showed promising results, there is a pressing need to find new techniques to develop a rapid and effective diagnosis of R. rickettssi infection.

Organic Electrochemical Transistors for Biomarker Detections

The improvement of living standards and the advancement of medical technology have led to an increased focus on health among individuals. Detections of biomarkers are feasible approaches to obtaining information about health status, disease progression, and response to treatment of an individual. In recent years, organic electrochemical transistors (OECTs) have demonstrated high electrical performances and effectiveness in detecting various types of biomarkers. This review provides an overview of the working principles of OECTs and their performance in detecting multiple types of biomarkers, with a focus on the recent advances and representative applications of OECTs in wearable and implantable biomarker detections, and provides a perspective for the future development of OECT-based biomarker sensors.

New insight in molecular detection of Mycobacterium tuberculosis

Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogenic bacterium that has claimed millions of lives since the Middle Ages. According to the World Health Organization's report, tuberculosis ranks among the ten deadliest diseases worldwide. The presence of an extensive array of genes and diverse proteins within the cellular structure of this bacterium has provided us with a potent tool for diagnosis. While the culture method remains the gold standard for tuberculosis diagnosis, it is possible that molecular diagnostic methods, emphasis on the identification of mutation genes (e.g., rpoB and gyrA) and single nucleotide polymorphisms, could offer a safe and reliable alternative. Over the past few decades, as our understanding of molecular genetics has expanded, methods have been developed based on gene expansion and detection. These methods typically commence with DNA amplification through nucleic acid targeted techniques such as polymerase chain reaction. Various molecular compounds and diverse approaches have been employed in molecular assays. In this review, we endeavor to provide an overview of molecular assays for the diagnosis of tuberculosis with their properties (utilization, challenges, and functions). The ultimate goal is to explore the potential of replacing traditional bacterial methods with these advanced molecular diagnostic techniques.

PACRAT: pathogen detection with aptamer-observed cascaded recombinase polymerase amplification-in vitro transcription

The SARS-CoV-2 pandemic underscored the need for early, rapid, and widespread pathogen detection tests that are readily accessible. Many existing rapid isothermal detection methods use the recombinase polymerase amplification (RPA), which exhibits polymerase chain reaction (PCR)-like sensitivity, specificity, and even higher speed. However, coupling RPA to other enzymatic reactions has proven difficult. For the first time, we demonstrate that with tuning of buffer conditions and optimization of reagent concentrations, RPA can be cascaded into an in vitro transcription reaction, enabling detection using fluorescent aptamers in a one-pot reaction. We show that this reaction, which we term PACRAT (pathogen detection with aptamer-observed cascaded recombinase polymerase amplification-in vitro transcription) can be used to detect SARS-CoV-2 RNA with single-copy detection limits, Escherichia coli with single-cell detection limits, and 10-min detection times. Further demonstrating the utility of our one-pot, cascaded amplification system, we show PACRAT can be used for multiplexed detection of the pathogens SARS-CoV-2 and E. coli, along with multiplexed detection of two variants of SARS-CoV-2.

Using QUASR-PCR as a field-based genotyping assay for a tick acaricide resistance marker

A novel, turnkey, field-based workflow was developed and validated using Rhipicephalus microplus DNA as a template to detect the presence of the voltage-gated sodium channel kdr mutation. The field-based compatible workflow comprises manual sample homogenization for DNA extraction, PCR amplification of the targets in a closed tube, and end-point detection of the PCR products. An R. microplus species-specific assay was also included to confirm species identity and ensure the validity of the kdr mutation assay. The assays were sensitive and specific to the targets, and the workflow resulted in a turnaround time of approximately 1 h at a low cost. The novel combination of PCR with closed-tube and end-point fluorescent detection allows for easy conversion of existing conventional lab-based PCR assays into field-based detection assays. The incorporation of custom-designed 3D-printed components in the workflow provides easy adaptability and modification of the components for diverse nucleic acid detection workflows.

Bacteriophage-based bioassays: an expected paradigm shift in microbial diagnostics

Bacteriophages, as abundant and specific agents, hold significant promise as a solution to combat the growing threat of antimicrobial resistance. Their unique ability to selectively lyse bacterial cells without harming humans makes them a compelling alternative to traditional antibiotics and point-of-care diagnostics. The article reviews the current landscape of diagnostic technologies, identify gaps and highlight emerging possibilities demonstrates a comprehensive approach to advancing clinical diagnosis of microbial pathogens and covers an overview of existing phage-based bioassays. Overall, the provided data in this review effectively communicates the potential of bacteriophages in transforming therapeutic and diagnostic paradigms, offering a holistic perspective on the benefits and opportunities they present in combating microbial infections and enhancing public health.

Molecular diagnosis of human toxoplasmosis: the state of the art

Toxoplasma gondii (T. gondii) is an obligate intracellular apicomplexan protozoan that causes toxoplasmosis. Approximately one-third of the world's population is currently T. gondii-seropositive. Although most infections are symptomless, a few can produce retinal lesions and, in immunocompromised persons or when congenitally contracted, can progress to life-threatening central nervous system disseminated infections. Therefore, quick, and precise diagnosis is a must. Molecular techniques nowadays play a crucial role in toxoplasmosis diagnosis, particularly in immunocompromised patients or congenital toxoplasmosis. This review aimed to detail recent advancements in molecular diagnostics of T. gondii infections. The terms "Toxoplasmosis," "Molecular diagnostics," "PCR," "qPCR," "B1," and "rep529" were used to search the English-language literature. In developed nations, conventional PCR (PCR) and nested PCR have been supplanted by quantitative PCR (qPCR), although they are still widely employed in poor nations. The diagnosis of toxoplasmosis has been revolutionized by the emergence of molecular diagnostics. Unfortunately, there is still substantial interlaboratory variability. There is an immediate need for standardization to increase the comparability of results between laboratories and clinical trials.

Graphical abstract

A graphical abstract highlighting the summary of Toxoplasma molecular diagnostics, created using Biorender.com.

Molecular pathways and therapeutic strategies in dermatofibrosarcoma protuberans (DFSP): unravelling the tumor's genetic landscape

Dermatofibrosarcoma Protuberans (DFSP) is a rare soft tissue sarcoma distinguished by its infiltrative growth pattern and recurrence potential. Understanding the molecular characteristics of DFSP is essential for enhancing its diagnosis, prognosis, and treatment strategies. The paper provides an overview of DFSP, highlighting the significance of its molecular understanding. The gene expression profiling has uncovered unique molecular signatures in DFSP, highlighting its heterogeneity and potential therapeutic targets. The Platelet-Derived Growth Factor Receptors (PDGFRs) and Fibroblast Growth Factor Receptors (FGFRs) signaling pathways play essential roles in the progression and development of DFSP. The abnormal activation of these pathways presents opportunities for therapeutic interventions. Several emerging therapies, i.e., immunotherapies, immunomodulatory strategies, and immune checkpoint inhibitors, offer promising alternatives to surgical resection. In DFSP management, combination strategies, including rational combination therapies, aim to exploit the synergistic effects and overcome resistance. The article consisting future perspectives and challenges includes the discovery of prognostic and predictive biomarkers to improve risk stratification and treatment selection. Preclinical models, such as Patient-derived xenografts (PDX) and genetically engineered mouse models, help study the biology of DFSP and evaluate therapeutic interventions. The manuscript also covers small-molecule inhibitors, clinical trials, immune checkpoint inhibitors for DFSP treatment, combination therapies, rational therapies, and resistance mechanisms, which are unique and not broadly covered in recent pieces of literature. See also the graphical abstract(Fig. 1).

Collagen peptides affect collagen synthesis and the expression of collagen, elastin, and versican genes in cultured human dermal fibroblasts

Background

Collagen is one of the major proteins of the skin and it is particularly important for its strength and resilience. Skin aging is a natural process that is characterized by the decrease and fragmentation of collagen in the dermis. Oral supplementation with collagen peptides has been clinically shown to have a positive effect on the skin condition. However, the mechanisms of aging-related changes synthesized by cells exposed to collagen are currently not well understood. Therefore, in this in vitro study, the mechanisms associated with collagen, elastin, and versican in human dermal fibroblasts were investigated after exposure to collagen peptides.

Methods

The effects of different concentrations of collagen peptides on cell viability and metabolism were analyzed. For gene expression analysis, human dermal fibroblasts were treated with collagen peptides. This was then followed by RNA extraction and DNA synthesis. Gene expressions of collagen type 1 (COL1A1), elastin (ELN), and versican (VCAN) were quantified by quantitative reverse transcription polymerase chain reaction (RT-qPCR). In addition, collagen levels were analyzed by confocal scanning laser microscopy using immunostaining.

Results

Collagen peptides tested in the study increased the expression of the relevant COL1A1, ELN, and VCAN genes in human dermal fibroblasts (p < 0.005). Furthermore, confocal microscopy showed increased collagen expression in the dermal fibroblast culture after treatment with the collagen peptides (p < 0.005).

Conclusion

These data provide cell-based evidence for the beneficial effects of exposure to collagen peptides on the skin's collagen content and on the molecules that provide firmness and elasticity. This may support the hypothesis that collagen peptides are important for maintaining extracellular matrix (ECM) structure and skin regeneration.

The buzz about honey-based biosurveys

Approximately 1.8 million metric tonnes of honey are produced globally every year. The key source behind this output, the honey bee (Apis mellifera), works tirelessly to create the delicious condiment that is consumed worldwide. The honey that finds its way into jars on store shelves contains a myriad of information about its biogeographical origins, such as the bees that produced it, the botanical constituents, and traces of other organisms or pathogens that have come in contact with the product or its producer. With the ongoing threat of honey bee decline and overall global biodiversity loss, access to ecological information has become an key factor in preventing the loss of species. This review delves into the various molecular techniques developed to characterize the collective DNA harnessed within honey samples, and how it can be used to elucidate the ecological interactions between honey bees and the environment. We also explore how these DNA-based methods can be used for large-scale biogeographical studies through the environmental DNA collected by foraging honey bees. Further development of these techniques can assist in the conservation of biodiversity by detecting ecosystem perturbations, with the potential to be expanded towards other critical flying pollinators.

Nitrite-dependent anaerobic methane oxidation (N-DAMO) in global aquatic environments: A review

The vast majority of processes in the carbon and nitrogen cycles are driven by microorganisms. The nitrite-dependent anaerobic oxidation of methane (N-DAMO) process links carbon and nitrogen cycles, offering a novel approach for the simultaneous reduction of methane emissions and nitrite pollution. However, there is currently no comprehensive summary of the current status of the N-DAMO process in natural aquatic environments. Therefore, our study aims to fill this knowledge gap by conducting a comprehensive review of the global research trends in N-DAMO processes in various aquatic environments (excluding artificial bioreactors). Our review mainly focused on molecular identification, global study sites, and their interactions with other elemental cycling processes. Furthermore, we performed a data integration analysis to unveil the effects of key environmental factors on the abundance of N-DAMO bacteria and the rate of N-DAMO process. By combining the findings from the literature review and data integration analysis, we proposed future research perspectives on N-DAMO processes in global aquatic environments. Our overarching goal is to advance the understanding of the N-DAMO process and its role in synergistically reducing carbon emissions and removing nitrogen. By doing so, we aim to make a significant contribution to the timely achievement of China's carbon peak and carbon neutrality targets.

Change in Diagnosis of Helicobacter pylori Infection in the Treatment-Failure Era

Helicobacter pylori (H. pylori) infection is a prevalent global health issue, associated with several gastrointestinal disorders, including gastritis, peptic ulcers, and gastric cancer. The landscape of H. pylori treatment has evolved over the years, with increasing challenges due to antibiotic resistance and treatment failure. Traditional diagnostic methods, such as the urea breath test, stool antigen test, and endoscopy with biopsy, are commonly used in clinical practice. However, the emergence of antibiotic-resistant strains has led to a decline in treatment efficacy, necessitating a re-evaluation of common diagnostic tools. This narrative review aims to explore the possible changes in the diagnostic approach of H. pylori infection in the era of treatment failure. Molecular techniques, including polymerase chain reaction and whole genome sequencing, which have high sensitivity and specificity, allow the detection of genes associated with antibiotic resistance. On the other hand, culture isolation and a phenotypic antibiogram could be used in the diagnostic routine, although H. pylori is a fastidious bacterium. However, new molecular approaches are promising tools for detecting the pathogen and its resistance genes. In this regard, more real-life studies are needed to reveal new diagnostic tools suitable for identifying multidrug-resistant H. pylori strains and for outlining proper treatment.

Real-Time Monitoring of a Nucleic Acid Amplification Reaction Using a Mass Sensor Based on a Quartz-Crystal Microbalance

Nucleic acid amplification reactions such as polymerase chain reaction (PCR), which uses a DNA polymerase to amplify individual double-stranded DNA fragments, are a useful technique for visualizing the presence of specific genomes. Although the fluorescent labeling method is mainly used with DNA amplification, other detection methods should be considered for further improvements, such as miniaturization and cost reduction, of reaction-monitoring devices. In this study, the quartz-crystal microbalance (QCM) method, which can measure nanogram-order masses, was applied for the real-time detection of DNA fragments in a solution with nucleic acids. This was combined with an isothermal nucleic acid amplification reaction based on the recombinase polymerase amplification (RPA) method, which allowed DNA amplification at a constant temperature. When the DNA amplification reaction was initiated on a QCM sensor plate with an immobilized primer DNA strand, a significant increase in mass was observed compared to when the primer DNA was not immobilized. QCM was shown to be sufficiently sensitive for the in situ detection of amplified DNA fragments. Combining a portable QCM device and RPA offers a sensitive point-of-care method for detecting nucleic acids.

A machine vision-assisted Argonaute-mediated fluorescence biosensor for the detection of viable Salmonella in food without convoluted DNA extraction and amplification procedures

The precise identification viable pathogens hold paramount significance in the prevention of foodborne diseases outbreaks. In this study, we integrated machine vision and learning with single microsphere to develop a phage and Clostridium butyricum Argonaute (CbAgo)-mediated fluorescence biosensor for detecting viable Salmonella typhimurium (S. typhimurium) without convoluted DNA extraction and amplification procedures. Phage and lysis buffer was utilized to capture and lyse viable S. typhimurium, respectively. Subsequently, CbAgo can cleave the bacterial DNA to obtain target DNA that guides a newly targeted cleavage of fluorescent probes. After that, the resulting fluorescent signal accumulates on the streptavidin-modified single microsphere. The overall detection process is then analyzed and interpreted by machine vision and learning algorithms, achieving highly sensitive detection of S. typhimurium with a limit of detection at 40.5 CFU/mL and a linear range of 50-107 CFU/mL. Furthermore, the proposed biosensor demonstrates standard recovery rates and coefficients of variation at 93.22% - 106.02% and 1.47% - 12.75%, respectively. This biosensor exhibits exceptional sensitivity and selectivity, presenting a promising method for the rapid and effective detection of foodborne pathogens. ENVIRONMENTAL IMPLICATION: Bacterial pathogens exist widely in the environment and seriously threaten the safety of human life. In this study, we developed a phage and Clostridium butyricum Argonaute-mediated fluorescence biosensor for the detection of viable Salmonella typhimurium in environmental water and food samples. Compared with other Salmonella detection methods, this method does not need complex DNA extraction and amplification steps, which reduces the use of chemical reagents and experimental consumables in classic DNA extraction kit methods.

COVID-19: An overview on possible transmission ways, sampling matrices and diagnosis

COVID-19 is an RNA virus belonging to the SARS family of viruses and includes a wide range of symptoms along with effects on other body organs in addition to the respiratory system. The high speed of transmission, severe complications, and high death rate caused scientists to focus on this disease. Today, many different investigation types are performed on COVID-19 from various points of view in the literature. This review summarizes most of them to provide a useful guideline for researchers in this field. After a general introduction, this review is divided into three parts. In the first one, various transmission ways COVID-19 are classified and explained in detail. The second part reviews the used biological samples for the detection of virus and the final section describes the various methods reported for the diagnosis of COVID-19 in various biological matrices.

A review of CRISPR-Cas and PCR-based methods for the detection of animal species in the food chain-current challenges and future prospects

Regular testing and systematic investigation play a vital role to ensure product safety. Until now, the existing food authentication techniques have been based on proteins, lipids, and nucleic acid-based assays. Among various deoxyribonucleic acid (DNA)-based methods, the recently developed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based bio-sensing is an innovative and fast-expanding technology. The CRISPR/Cas-9 is known as Clustered Regularly Interspaced Short Palindromic Repeats due to the flexibility and simplicity of the CRISPR/Cas9 site-specific editing tool has been applied in many biological research areas such as Gene therapy, cell line development, discovering mechanisms of disease, and drug discovery. Nowadays, the CRISPR-Cas system has also been introduced into food authentication via detecting DNA barcodes of poultry and livestock both in processed and unprocessed food samples. This review documents various DNA based approaches, in an accessible format. Future CRISPR technologies are forecast while challenges are outlined.

Rapid detection of viable microbes with 5-cyano-2,3-di-(p-tolyl)tetrazolium chloride and 5(6)-carboxyfluorescein diacetate using a fibre fluorescence spectroscopy system

AIMS

To assess the efficacy of two commercially available viability dyes, 5-cyano-2,3-di-(p-tolyl)tetrazolium chloride (CTC) and 5(6)-carboxyfluorescein diacetate (CFDA), in reporting on viable cell concentration and species using an all-fibre fluorometer.

METHODS AND RESULTS

Four bacterial species (two Gram-positive and two Gram-negative) commonly associated with food poisoning or food spoilage (Escherichia coli, Salmonella enterica, Staphylococcus aureus, and Bacillus cereus) were stained with CTC or CFDA and the fibre fluorometer was used to collect full fluorescence emission spectra. A good correlation between concentration and fluorescence intensity was found for Gram-negative bacteria between 107 and 108 colony-forming units (CFU) ml-1. There was no correlation with concentration for Gram-positive bacteria; however, the information in the CTC and CFDA spectra shows the potential to distinguish Gram-negative cells from Gram-positive cells, although it may simply reflect the overall bacterial metabolic activity under staining conditions from this study.

CONCLUSIONS

The limit of detection (LoD) is too high in the dip-probe approach for analysis; however, the development of an approach measuring the fluorescence of single cells may improve this limitation. The development of new bacteria-specific fluorogenic dyes may also address this limitation. The ability to differentiate bacteria using these dyes may add value to measurements made to enumerate bacteria using CTC and CFDA.

Isothermal amplification-based microfluidic devices for detecting foodborne pathogens: a review

The gold standard for nucleic acid amplification-based diagnosis is the polymerase chain reaction (PCR). The PCR recognizes the targets such as foodborne pathogens by amplifying their specific genes. The integration of nucleic acid amplification-based assays on microfluidic platforms represents a highly promising solution for convenient, cheap, and effective control of foodborne pathogens. However, the application of the PCR is limited to on-site detection because the method requires sophisticated equipment for temperature control, which makes it complicated for microfluidic integration. Alternatively, isothermal amplification methods are promising tools for integrating microfluidic platforms for on-site detection of foodborne pathogens. This review summarized advances in isothermal amplification-based microfluidic devices for detecting foodborne pathogens. Different nucleic acid extraction approaches and the integration of these approaches in microfluidic platforms were first reviewed. Microfluidic platforms integrated with three common isothermal amplification methods including loop-mediated isothermal amplification, recombinase polymerase amplification, and recombinase-aided amplification were then described and discussed.

The Superior Effect of Radiofrequency With Targeted Ultrasound for Facial Rejuvenation by Inducing Hyaluronic Acid Synthesis: A Pilot Preclinical Study

Background

The level of dermal hyaluronic acid (HA) can be depleted by 75% at age 70. HA provides dermal hydration, volume, and thickness, making it a major component of the extracellular matrix. Restoration of dermal and epidermal HA can be achieved by combining radiofrequency (RF) energy and targeted ultrasound (TUS). The monopolar RF generates heat, with the TUS stimulating HA production. The heat induces a regenerative response in the skin, increasing the fibroblast activity and producing various extracellular matrix compounds, including HA.

Objectives

To investigate the effect of the simultaneous application of RF + TUS or RF + US on the stimulation of HA production.

Methods

Twelve animals underwent 4 treatments. Six were treated with transcutaneous RF + TUS and 6 with the combination RF + US. The opposite untreated side served as a control. Punch biopsies of the skin were taken at baseline, immediately posttreatment, 1 month, and 2 months posttreatment. The tissue was evaluated with real-time quantitative polymerase chain reaction (RT-qPCR), matrix-assisted laser desorption (MALDI) and time of flight (TOF), and confocal microscopy.

Results

The RT-qPCR focused on assessing the production of has1 and has2, enzymes responsible for HA synthesis. RT-qPCR results of the RF + TUS group revealed a +98% and +45% increase in hyaluronic synthetase (HAS) 1 and HAS2 production after the treatments, respectively. The MALDI-TOF revealed a +224% increase in measured HA 2 months after the treatments. The changes were also visible in the confocal microscopy. The control group showed no significant (P > .05) results in either of the evaluation methods.

Conclusions

Concurrent application of RF and TUS significantly enhances the natural regenerative processes in skin tissue.

Level of Evidence 5

Au/Pt@ZIF-90 Nanoenzyme Capsule-Based "Explosive" Signal Amplifier for "All-in-Tube" POCT

The sensitive, convenient, and visual detection of low-concentration disease markers in biological samples has always been a priority in disease diagnosis. However, existing research has been problematic due to complex operation and unsatisfactory sensitivity. Consequently, an "explosive" signal amplification platform based on Au/Pt@ZIF-90 was developed for sensitive visual detection of disease markers. In this study, a controllable and explosively released Au/Pt nanoparticles (NPs) "nanoenzyme capsule" was prepared by encapsulating Au/Pt NPs with excellent peroxidase activity in ZIF-90. This was achieved by adjusting the particle size of ZIF-90 and the encapsulation amount of Au/Pt NPs. Using the prepared capsules as the signal output module and aptamer as the target recognition module, an "All-in-Tube" portable point-of-care (POC) platform was constructed by integrating the Au/Pt@ZIF-90/filter paper and TMB/strips into an Eppendorf (EP) tube. By utilizing specific competitive binding of targets to aptamers, the platform enabled the sensitive and convenient measurement of small molecular disease markers. Taking adenosine as the proof of concept, the portable detection achieved excellent sensitivity. Moreover, the platform can achieve universal detection of various targets by varying the aptamer sequence. This signal amplification strategy provides a design pattern for the detection of low-concentration targets in biological samples and holds significant potential in the fields of disease diagnosis and environmental monitoring.

From Clinical Suspicion to Diagnosis: A Review of Diagnostic Approaches and Challenges in Fungal Keratitis

Fungal keratitis is a relatively rare yet severe ocular infection that can lead to profound vision impairment and even permanent vision loss. Rapid and accurate diagnosis plays a crucial role in the effective management of the disease. A patient's history establishes the initial clinical suspicion since it can provide valuable clues to potential predisposing factors and sources of fungal exposure. Regarding the evaluation of the observed symptoms, they are not exclusive to fungal keratitis, but their timeline can aid in distinguishing fungal keratitis from other conditions. Thorough clinical examination of the affected eye with a slit-lamp microscope guides diagnosis because some clinical features are valuable predictors of fungal keratitis. Definitive diagnosis is established through appropriate microbiological investigations. Direct microscopic examination of corneal scrapings or biopsy specimens can assist in the presumptive diagnosis of fungal keratitis, but culture remains the gold standard for diagnosing fungal keratitis. Advanced molecular techniques such as PCR and MALDI-ToF MS are explored for their rapid and sensitive diagnostic capabilities. Non-invasive techniques like in vivo confocal microscopy (IVCM) and optical coherence tomography (OCT) are useful for real-time imaging. Every diagnostic technique has both advantages and drawbacks. Also, the selection of a diagnostic approach can depend on various factors, including the specific clinical context, the availability of resources, and the proficiency of healthcare personnel.

A comprehensive review on anticancer evaluation techniques

The development of effective anticancer strategies and the improvement of our understanding of cancer need analytical tools. Utilizing a variety of analytical approaches while investigating anti-cancer medicines gives us a thorough understanding of the traits and mechanisms concerned to cancer cells, which enables us to develop potent treatments to combat them. The importance of anticancer research may be attributed to various analytical techniques that contributes to the identification of therapeutic targets and the assessment of medication efficacy, which are crucial things in expanding our understanding of cancer biology. The study looks at methods that are often used in cancer research, including cell viability assays, clonogenic assay, flow cytometry, 2D electrophoresis, microarray, immunofluorescence, western blot caspase activation assay, bioinformatics, etc. The fundamentals, applications, and how each technique analytical advances our understanding of cancer are briefly reviewed.

Aeromonas spp. in drinking water and food: Occurrence, virulence potential and antimicrobial resistance

Aeromonas sp. is a Gram-negative, non-spore-forming, rod-shaped, oxidase-positive, facultative anaerobic bacterium and a natural contaminant found in aquatic environments. Some species can invade, colonize, and damage host cells due to the presence of virulence factors, such as flagella, elastase, hemolysins, aerolysins, adhesins, enterotoxins, phospholipases and lipases, that lead to pathogenic activities. Consequently, can cause many health disorders that range from gastrointestinal problems, enteric infections, and ulcers to hemorrhagic septicemia. Aeromonas has been isolated and identified from a variety of sources, including drinking water and ready-to-eat foods (fish, meat, fresh vegetables, dairy products, and others). Some species of this opportunistic pathogen are resistant to several commercial antibiotics, including some used as a last resort for treatment, which represents a major challenge in the clinical segment. Antimicrobial resistance can be attributed to the indiscriminate use of antibiotics by society in aquaculture and horticulture. In addition, antibiotic resistance is attributed to plasmid transfer between microorganisms and horizontal gene transfer. This review aimed to (i) verify the occurrence of Aeromonas species in water and food intended for human consumption; (ii) identify the methods used to detect Aeromonas species; (iii) report on the virulence genes carried by different species; and (iv) report on the antimicrobial resistance of this genus in the last 5 years of research. Additionally, we present the existence of Aeromonas spp. resistant to antimicrobials in food and drinking water represents a potential threat to public health.

Diagnosis and management of malaria in the intensive care unit

Malaria is responsible for approximately three-quarters of a million deaths in humans globally each year. Most of the morbidity and mortality reported are from Sub-Saharan Africa and Asia, where the disease is endemic. In non-endemic areas, malaria is the most common cause of imported infection and is associated with significant mortality despite recent advancements and investments in elimination programs. Severe malaria often requires intensive care unit admission and can be complicated by cerebral malaria, respiratory distress, acute kidney injury, bleeding complications, and co-infection. Intensive care management includes prompt diagnosis and early initiation of effective antimalarial therapy, recognition of complications, and appropriate supportive care. However, the lack of diagnostic capacities due to limited advances in equipment, personnel, and infrastructure presents a challenge to the effective diagnosis and management of malaria. This article reviews the clinical classification, diagnosis, and management of malaria as relevant to critical care clinicians, highlighting the role of diagnostic capacity, treatment options, and supportive care.

Variant allele frequency: a decision-making tool in precision oncology?

Precision oncology requires additional predictive biomarkers for targeted therapy selection. Variant allele frequency (VAF), measuring the proportion of variant alleles within a genomic locus, provides insights into tumor clonality in somatic genomic testing, yielding a strong rationale for targeting dominant cancer cell populations. The prognostic and predictive roles of VAF have been evaluated across different studies. Yet, the absence of validated VAF thresholds and a lack of standardization between sequencing assays currently hampers its clinical utility. Therefore, analytical and clinical validation must be further examined. This Review summarizes the evidence regarding the use of VAF as a predictive biomarker and discusses challenges and opportunities for its clinical implementation as a decision-making tool for targeted therapy selection.

A Self-Regenerating Artificial Cell, that is One Step Closer to Living Cells: Challenges and Perspectives

Controllable, self-regenerating artificial cells (SRACs) can be a vital advancement in the field of synthetic biology, which seeks to create living cells by recombining various biological molecules in the lab. This represents, more importantly, the first step on a long journey toward creating reproductive cells from rather fragmentary biochemical mimics. However, it is still a difficult task to replicate the complex processes involved in cell regeneration, such as genetic material replication and cell membrane division, in artificially created spaces. This review highlights recent advances in the field of controllable, SRACs and the strategies to achieve the goal of creating such cells. Self-regenerating cells start by replicating DNA and transferring it to a location where proteins can be synthesized. Functional but essential proteins must be synthesized for sustained energy generation and survival needs and function in the same liposomal space. Finally, self-division and repeated cycling lead to autonomous, self-regenerating cells. The pursuit of controllable, SRACs will enable authors to make bold advances in understanding life at the cellular level, ultimately providing an opportunity to use this knowledge to understand the nature of life.