It's Worth a Shot

The presentation contained information about the virus, how it spreads, the vaccine, who should and should not take it, when it is recommended to be taken, how it invokes an immune response on a cellular level, and what role protein synthesis plays in the vaccine. Students and their partners were given one of seven viruses to research: measles, mumps, rubella, influenza, hepatitis B, rabies, or COVID-19. Students researched the disease and its vaccine type using credible sources, such as the Centers for Disease Control and Prevention (CDC), the World Health Organization (WHO), Johns Hopkins University, etc. Students answered the following questions: * How does the virus spread? * What are the symptoms of the virus? * How common is the virus? (statistical number) * What does the virus look like? (include picture with antigens shown) * When is the vaccine recommended by the CDC? * How often does the booster for the vaccine need to be taken? * Who should not receive the vaccine? * How does the vaccine work on a cellular level? (Be specific about the type of vaccine and how it invokes an immune response) * What role does protein synthesis play in the vaccine? * What is the vaccine efficacy or effectiveness? * Does the vaccine do any of the following: * Change the host cell's DNA? * Give the person the disease?

Viral vector vaccines: efforts to develop vaccines against emerging infectious diseases

Vaccines are one of the most effective means of preventing viral infections. Since Edward Jenner invented the world's first vaccine in 1796, against smallpox, various types of vaccine have been developed, including inactivated vaccines, attenuated live vaccines, recombinant protein vaccines, viral vector vaccines and nucleic acid vaccines. Viral vector vaccines and nucleic acid vaccines （mRNA vaccines and DNA vaccines） have been developed most recently. In these vaccines, genes encoding viral proteins that serve as antigens are introduced into the body. The viral vector is an excellent vaccine delivery system that efficiently delivers antigen genes to target cells, and has been utilized for vaccine development against a variety of emerging infectious diseases, including AIDS, malaria, Ebola hemorrhagic fever, dengue fever, and most recently COVID-19. Here, we provide an overview of viral vector vaccines and discuss recent efforts to develop vaccines against emerging infectious diseases.Alternate :抄録ウイルス性感染症を予防するうえで、ワクチンは最も有効な手段の一つである。1976年、エドワード・ジェンナーが世界初のワクチンである種痘を発明して以来、さまざまなウイルス性感染症に対して、不活化ワクチン、弱毒生ワクチン、組換えタンパクワクチン、ウイルスベクターワクチン、核酸ワクチンなど、多様なプラットフォームに基づくワクチン開発が進められてきた。本稿では、数あるワクチンプラットフォームの中から、ウイルスベクターワクチンに着目して、いくつかの例をあげて概説するとともに、近年、国際的な問題となっている新興感染症に対するワクチン開発などの取り組みについても述べる。

RESPECTUFUL CLOSURE OF A CEnR DNA INTEGRITY STUDY

OBJECTIVES/GOALS: Methods for recruitment and retention of participants in research have been extensively discussed, but procedures to end studies in a way that is respectful to participants and keeps them engaged are seldom described. We relate the procedures to close a study focused on genomic DNA damage and DNA repair capacity in a longitudinal population sample. METHODS/STUDY POPULATION: Data collection, which included the provision of 30 ml blood sample along with a health status survey and anthropometric measurements, was discontinued earlier than anticipated during the fourth of a five-year Community Engaged Research (CEnR) study focused on residents of historically marginalized, low wealth communities. In collaboration with the project's Community Advisory Board, we devised a strategy to inform study participants of the study closure, which included: 1) attempts at one-on-one contact via phone, 2) provision of a study closure packet, 3) periodic mailing of study updates through study year five, 4) sustained interaction with participants through invitations to participate in additional research projects. RESULTS/ANTICIPATED RESULTS: Among 149 participants (65% female, 99% of African American descent), 106 (71%) have been reached by phone. The communication included: 1) expressions of gratitude for their participation;2) explanation of study findings to date;and 3) assurance that data analysis continued. Among those reached, 96% agreed to ongoing communication and 97% agreed to be contacted about future studies. We continue procedures to reach the remaining 43 participants. Over the study closure period, two qualitative studies offered opportunities for participants to join in focus groups (FG). The first one queried perceptions of community-based research. The response rate was 66% among 65 persons invited. The second study, focused on COVID-19 knowledge and invited 39 individuals with 24 scheduled to participate (62% response rate). DISCUSSION/SIGNIFICANCE: Translational research views the participant as an active partner. Study closure offers an opportunity to foster a long-lasting participant-research institution partnership, while also promoting participants' broad engagement and familiarity with research. Respectful research closure is an important step in CEnR.

Adapting the GACT-X Aligner to Accelerate Minimap2 in an FPGA Cloud Instance

Featured ApplicationFast long-read assembly to reference in AWS cloud FPGA instances.In genomic analysis, long reads are an emerging type of data processed by assembly algorithms to recover the complete genome sample. They are, on average, one or two orders of magnitude longer than short reads from the previous generation, which provides important advantages in information quality. However, longer sequences bring new challenges to computer processing, undermining the performance of assembly algorithms developed for short reads. This issue is amplified by the exponential growth of genetic data generation and by the slowdown of transistor technology progress, illustrated by Moore's Law. Minimap2 is the current state-of-the-art long-read assembler and takes dozens of CPU hours to assemble a human genome with clinical standard coverage. One of its bottlenecks, the alignment stage, has not been successfully accelerated on FPGAs in the literature. GACT-X is an alignment algorithm developed for FPGA implementation, suitable for any size input sequence. In this work, GACT-X was adapted to work as the aligner of Minimap2, and these are integrated and implemented in an FPGA cloud platform. The measurements for accuracy and speed-up are presented for three different datasets in different combinations of numbers of kernels and threads. The integrated solution's performance limitations due to data transfer are also analyzed and discussed.

Multi-Strain Human Papillomavirus (HPV) Vaccine Innovation via Computational Study: A Mini Review

Human papillomavirus (HPV) is a small and non-enveloped deoxyribonucleic acid (DNA) virus that infected mucosal cells. This viral genome is composed of early and late genes. Late (L) encodes the L1 and L2 proteins. The structural protein L1 is located outside the virion. It contributes to the viral attachment mechanism;hence it becomes the target for multi-strain vaccine design. This review aims to discuss the potency of conserved L1 HPV region and the innovation of multi-strain vaccines for prevention strategies of HPV infection. Bioinformatics methods in vaccine design applied for identification of conserved sequences from databases, epitopes map, antigenicity test, prediction of similarity, and autoimmune level. The multi-strain vaccine innovation initiated in this review has more benefits compared to previous vaccines based on the level of vaccine coverage via conserved regions, potential of immune cell epitopes, antigenic properties, and possibility of autoimmune when produced. Therefore, the multi-strain HPV vaccines are predicted to be more effective than previous vaccines, including bivalent or quadrivalent. In conclusion, the strategy for expanding the prevention of HPV infection could be carried out by developing a new multi-strain-based vaccine by using conserved regions in L1 capsid from all virus strains to increase the protection.

Adoption of a Clinical Assessment Service in Hepatology

P49 Table 1The impact of the clinical assessment service on the hepatology outpatient service2020 % Total ‘New appts 190 100% Total pts seen 134 71% Total DNAs 56 29% Total pts seen 134 100% Of pts seen & F/Up 113 84% Of pts seen & D/C’d 21 16% Total DNAs 56 100% DNA & Reschedule 33 59% DNA & D/C’d 23 41% 2022 % Total ‘New’ appts 181 100% Total pts seen 141 78% Total DNAs 40 22% Total pts seen 141 100% Of pts seen & F/Up 100 71% Of pts seen & D/C’d 41 29% Total DNAs 40 100% DNA & Reschedule 25 62.5% DNA & D/C’d 15 37.5% Since CAS has been introduced there have been several positive outcomes: in 2021, 18% of the referrals were appropriately repatriated to primary care with advice;30% of the referrals were managed without needing a face-to-face appointment;the waiting time reduced from 8 weeks to 5 weeks for a clinical review, and from 16 weeks to 15 weeks for a follow-up appointment;from 2020 to 2022 the proportion of patients discharged after the first clinical review has increased from 16% to 29%;specialist treatment is instigated more quickly;patients can be discharged following their first face-to-face visit as all information is to hand, it has eliminated unnecessary follow-up and has resulted in a clear and concise pathway to refer the patients into the service, with the diagnostic tests being performed at an earlier stage In summary CAS was introduced as an urgent service response to COVID-19 but we have identified key benefits and intend to continue it.

Advancing the Science of Vaccine Safety: Introduction to the International Network of Special Immunisation Services: An International Journal of Medical Toxicology and Drug Experience

Introduction: Vaccines are vital tools to control epidemic and pandemic diseases, such as COVID-19, demonstrating safety and effectiveness. However, rare adverse events of special interest (AESIs) following vaccination arise with every new emerging pathogen vaccine program. The mechanisms underlying AESIs such as myopericarditis following COVID-19 mRNA vaccines are not known. Adversomics, a set of technologies that measure the inventory of molecules (e.g., DNA, RNAs, proteins, inflamatory mediators) in a given sample collected during and after an adverse reaction, has potential to uncover the etiologies of AESIs. The International Network of Special Immunization Services (INSIS) brings together vaccine safety, public health, and systems biology experts in middleand high-income countries to investigate the causes of, and identify strategies to mitigate AESIs following vaccination (insisvaccine.org). Objective: INSIS aims apply an 'adversomics' approach to identify molecular signatures and biomarker risk factors associated with AESIs to inform vaccine development and risk-benefit of assessment of vaccines for pandemic and epidemic diseases, with scalability to respond to new safety signals anywhere in the world. Methods: INSIS-led studies will employ a case-control design. Wellcharacterized cases with AESIs post-vaccination, starting with thrombosis with thrombocytopenia syndrome (TTS) following COVID-19 viral vector vaccines and myopericarditis following COVID-19 mRNA vaccines, will be matched to controls. Brighton Collaboration case definitions and harmonized protocols will be employed to collect detailed clinical data and serial blood samples suitable for adversomics (e.g., transcriptomics, proteomics, metabolomics, flow-based immunophenotyping) analysis. A central database and centralized sample processing at INSIS-affiliated multi-OMICs labs will ensure internal validity. Integration of clinical and biological data will enable comparisons of analyte levels and immune responses within groups over time and between cases and controls. Global collaboration across five continents will ensure adequate sample size. Results: The INSIS approach and its reach as a global network will enable characterization of molecular signatures and biomarkers associated with post-vaccination AESIs. Conclusion: INSIS-led studies will provide insight into pathways triggered in these AESIs and susceptible populations to inform vaccine development strategies to reduce the potential to trigger pathways involved in AESIs, risk-benefit assessment, and personalized vaccination strategies. Through global collaboration, INSIS aims to reduce the potential for AESIs in the COVID-19 pandemic and beyond.

Pfizer-BioNTech COVID-19 Vaccine Associated Risk of Olfactory Hallucinations-Signal Review: An International Journal of Medical Toxicology and Drug Experience

Introduction: Pfizer-BioNTech Covid-19 vaccine is highly purified single-stranded messenger RNA (mRNA) produced using a cell-free in vitro transcription from the corresponding DNA templates indicated for preventing coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1]. Olfactory hallucination is a condition in which a person perceives odors that aren't present. Some might notice the odor in just one nostril, while others have it in both [2]. Objective: The purpose of this review is to assess the risk of olfactory hallucinations from the Pfizer-BioNTech Covid-19 vaccine and, if necessary, make regulatory recommendations. Methods: The Signal Detection (SD) team at SFDA performed a signal review using the National Pharmacovigilance Center (NPC) database and World WHO database, VigiBase, with literature screening to retrieve all related information to assess the causality between olfactory hallucinations and Pfizer-BioNTech Covid-19 vaccine use. The search was conducted on January 4th, 2022. The disproportionality of the observed and the expected reporting rates for drug/adverse drug reaction pair was estimated using an information component (IC), a tool developed by WHO-UMC to measure the reporting ratio. Positive IC reflects higher statistical association, while negative values indicate less statistical association. Results: Local Cases: The SD team at SFDA has searched the NPC database for individual case safety reports (ICSR) reporting olfactory hallucinations in association with the Pfizer-BioNTech COVID-19 vaccine. The search resulted in one ISCR and, on the basis of WHO-UMC causality assessment criteria, olfactory hallucinations were considered probably associated with the vaccine. Global Cases: A search was conducted in the WHO database (Vigibase) to retrieve all reported cases using a signal detection tool (Vigilyze) [3]. The search yielded 59 ICSRs. The signal detection team applied the WHO-UMC causality assessment tool on cases with a completeness score of (0.8) and above (n = 13). 11 cases were found supportive of the association, with 10 being probable and one being possible. Literature: Late November 2021, a case report of a 57-year-old woman seeking medical care after complaining of "smelling smoke" after receiving her second dose of the vaccine was published [4]. Datamining: The results of (IC = 1.9) revealed a positive statistical association for the vaccine/ADR combination. Conclusion: The weighted cumulative evidence identified from local and global cases is sufficient to suggest a causal association between the Pfizer-BioNTech COVID-19 vaccine and olfactory hallucinations. While a more thorough review of safety data is needed to confirm the risk, health care professionals should be aware of the risk that could happen after vaccination.

Oral-Systemic Health and Disorders: Latest Advances on Oral–Gut–Lung Microbiome Axis

In particular, the bi-directional communication network, also known as the gut lung axis connecting the intestinal and pulmonary microbiota, is considered responsible for the massively increased bacterial load in the cecum after acute lung injury, causing alterations in airway microbiota and its transitory translocation into the bloodstream toward the bowel [7,8]. [...]subjects with chronic obstructive pulmonary disease often show intestinal hyper-permeability and a high prevalence of IBD [9]. Both mechanisms would underlie the association between periodontitis and inflammatory and degenerative diseases, such as atherosclerosis, Alzheimer’s disease, age-related macular degeneration [22], chronic inflammatory bowel disease [23], and solid neoplasms, such as colorectal carcinoma [24]. [...]intestinal microbes could, due to mucosal barrier impairment, translocate to the liver through the biliary tract and the portal vein, and oral dysbiosis could exacerbate chronic liver diseases, likely modulating the gut ecosystem through the oral–gut axis, on the one side, and may reflect the intestinal dysbiotic ecosystem, affected in turn by hepatic diseases, on the other side [12,25]. Furthermore, mainly the upper but also the lower airways of healthy individuals frequently harbor oral anaerobes, including Prevotella and Veillonella species, probably secondary to continuing microaspiration by contiguity. [...]detecting oral bacterial DNA in the lower airways in healthy subjects could represent the traces of aspirated oral bacteria either not eliminated through physiological clearance or living in dynamic equilibrium with host defensive responses by promoting mucosal immunity of the Th17/neutrophilic phenotype and suppressing innate immunity. Whether bacteria from the oral microbiome regulate responses to pulmonary pathogens and whether they interfere in inflammatory lung disease pathogenesis [26] is still under study. [...]a growing body of evidence highlights that gut and oral dysbioses, interconnected with the local microbial and inflammatory environment of the lung, liver, and other organs, are crucially implied in a multitude of diseases also involving distant organs.

Handheld, Low-Cost, Aptamer-Based Sensing Device for Rapid SARS-CoV-2 RNA Detection Using Novelly Synthesized Gold Nanoparticles.

The development of a cost-efficient device to rapidly detect pandemic viruses is paramount. Hence, an innovative and scalable synthesis of metal nanoparticles followed by its usage for rapid detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been reported in this work. The simple synthesis of metal nanoparticles utilizing tin as a solid-state reusable reducing agent is used for the SARS-CoV-2 ribonucleic acid (RNA) detection. Moreover, the solid-state reduction process occurs faster and leads to the enhanced formation of silver and gold nanoparticles (AuNPs) with voltage. By adding tin as a solid-state reducing agent with the precursor, the nanoparticles are formed within 30 s. This synthesis method can be easily scaled up for a commercially viable process to obtain different-sized metal nanoparticles. This is the first disclosure of the usage of tin as a reusable solid-state reducing agent for metal nanoparticle synthesis. An electronic device, consisting of AuNPs functionalized with a deoxyribonucleic acid (DNA)-based aptamer, can detect SARS-CoV-2 RNA in less than 5 min. With an increase in SARS-CoV-2 variants, such as Delta and Omicron, the detection device could be used for identifying the nucleic acids of the COVID-19 variants by modifying the aptamer sequence. The reported work overcomes the drawbacks of complex instrumentation, trained labor, and increased turnaround time.

‘Time to invest in genomics’ in poorer countries – WHO

Speed read Genomics has been crucial in COVID-19 response, driving research But many poor countries lack access to the technology First WHO Science Council report makes recommendations to address barriers The World Health Organization (WHO) has issued an urgent call to accelerate access to genomics, especially in resource-poor countries, in a report that examines technology gaps and opportunities. Genomics is the branch of science that uses methods from biochemistry, genetics, and molecular biology to understand and use biological information in DNA and RNA to benefit medicine and public health — but the technology can also be used in agricultural research. While genomics technology is driving some of the most ground-breaking research in medical science, including COVID-19 vaccine research and development, its full potential is yet to be realised globally, especially in low- and middle-income countries (LMICs), according to the WHO Science Council’s inaugural report.

In Silico Study and Excito-Repellent Activity of Vitex negundo L. Essential Oil against Anopheles gambiae

(1) Background: Essential oil from Vitex negundo is known to have repellent and insecticidal properties toward the Anopheles gambiae and this is linked to its monoterpene and sesquiterpene content. In this work, an effort is made to delineate the constitution of V. negundo essential oil (VNEO) and their interaction with odorant-binding proteins (OBPs) of A. gambiae and hence access its repellent efficiency as cost-effective and safer malaria vector control alternatives. (2) Methods: Anopheles species authentication was performed by genomic DNA analysis and was subjected to behavioral analysis. GC-MS profiling was used to identify individual components of VNEO. Anopheles OBPs were obtained from the RCSB protein data bank and used for docking studies. Determination of ligand efficiency metrics and QSAR studies were performed using Hyper Chem Professional 8.0.3, and molecular dynamics simulations were performed using the Desmond module. (3) Results: GC-MS analysis of VNEO showed 28 compounds (monoterpenes, 80.16%;sesquiterpenes, 7.63%;and unknown constituents, 10.88%). The ligand efficiency metrics of all four ligands against the OBP 7 were within acceptable ranges. β-selinene (−12.2 kcal/mol), β-caryophellene (−9.5 kcal/mol), sulcatone (−10.9 kcal/mol), and α-ylangene (−9.3 kcal/mol) showed the strongest binding affinities for the target proteins. The most stable hydrophobic interactions were observed between β-selinene (Phe111 and Phe120), Sulcatone (Phe54 and Phe120), and α-ylangene (Phe111), while only sulcatone (Tyr49) presented H-bond interactions in the simulated environment. (4) Conclusions: Sulcatone and β-caryophyllene presented the best log p values, 6.45 and 5.20, respectively. These lead phytocompounds can be used in their purest as repellent supplement or as a natural anti-mosquito agent in product formulations.

Association of Single Nucleotide Polymorphisms with COVID19 Severity in Malaysia

Introduction: Coronavirus disease 2019 (COVID-19) has brought countless infections and deaths worldwide. COVID-19 patients demonstrated a great diversity in clinical manifestation and disease severity, but factors for these diversions are yet to be determined. Genetic variations such as the single nucleotide polymorphisms (SNPs) might be responsible for COVID-19 severity. Methods: Genomic DNA was extracted from the peripheral blood of 215 recovered COVID-19 patients with different disease severities (asymptomatic, mild, and severe). Their personal information such as gender, age, BMI, and comorbidities was recorded. Global Screening Array (GSA) was performed to search for SNPs linked with the COVID-19 severity. Potential SNPs were further genotyped using real-time PCR for validation, and their risk association was assessed. Results: Hypertension and obesity were the most prevalent comorbidities in severe COVID-19 patients. The GSA showed three potential SNPs (rs923147, rs409017, and rs17062791) that were significantly associated with COVID-19 severity. Further analyses on these SNPs revealed that male, older (>60 years), and overweight subjects who carried an A allele in the rs923147 were protective against severe COVID-19. In contrast, male patients who inherited a G allele had an increased risk of severe COVID-19. For the rs409017 SNP, the presence of an A allele significantly increased the risk of subjects developing severe COVID-19. Besides, obese patients who carried a T allele in the rs17062791 SNP had a significantly lower risk of developing mild symptoms. Conclusion: This study suggests SNPs' potential role that is linked with the COVID-19 severity. These data are useful in predicting the disease severity of COVID-19 patients.

The Complete History of the Black Death, 2nd edn ( Woodbridge: The Boydell Press, 2021 ), pp. 1058, £ 143, hardback, ISBN: 9781783275168

[...]it is impossible to master everything in such a considerable mass of documentation on a global scale (covering Europe, Africa, the Middle East and Asia): this poses a real challenge, according to the author’s own introduction! With J.F.D. Shrewsbury on the Bubonic plague in the British Isles (1971), or the documentary trails produced by Philip Ziegler (1969) or Rosemary Horrox (1994), David Herlihy (1965–91), Élisabeth Carpentier (1963) and M. Livi Bacci for Italy (1978), Marie-Hélène Congourdeau for the Byzantine territory (1988–98) or Michael Dols (1974–82) and Mohammed Melhaoui (Paris, 2005, not cited) for the Arabic world (Egypt and North Africa) provide a base of capital data. The main purpose is to trace the outbreak and spread of the pandemic: its origin, its modes of diffusion, the epidemic progress, in order to better understand the epidemiological mechanism, its nature, and to evaluate its incidence of lethality and mortality. While the first evidence from the genetic examination of dental pulp dates the origins of the plague back to around 5,100–4,900 years ago in Sweden (p. 98), the emergence of research in palaeobiology, in particular on DNA (Hinnebusch, 2002–17, Bos, Holmes, Callaway, in Nature, 2011, Wagner, Lancet, 2014), has provided a very supportive context for knowledge renewal: a ‘molecular history’ (McCormick, 2007) is open!

An Overview of Microbial Source Tracking Using Host-Specific Genetic Markers to Identify Origins of Fecal Contamination in Different Water Environments

Fecal contamination of water constitutes a serious health risk to humans and environmental ecosystems. This is mainly due to the fact that fecal material carries a variety of enteropathogens, which can enter and circulate in water bodies through fecal pollution. In this respect, the prompt identification of the polluting source(s) is pivotal to guiding appropriate target-specific remediation actions. Notably, microbial source tracking (MST) is widely applied to determine the host origin(s) contributing to fecal water pollution through the identification of zoogenic and/or anthropogenic sources of fecal environmental DNA (eDNA). A wide array of host-associated molecular markers have been developed and exploited for polluting source attribution in various aquatic ecosystems. This review is intended to provide the most up-to-date overview of genetic marker-based MST studies carried out in different water types, such as freshwaters (including surface and groundwaters) and seawaters (from coasts, beaches, lagoons, and estuaries), as well as drinking water systems. Focusing on the latest scientific progress/achievements, this work aims to gain updated knowledge on the applicability and robustness of using MST for water quality surveillance. Moreover, it also provides a future perspective on advancing MST applications for environmental research.

Every fifth published metagenome is not available to science

Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high–impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions—a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.

Never Cared for What They Do: High Structural Stability of Guanine-Quadruplexes in the Presence of Strand-Break Damage

DNA integrity is an important factor that assures genome stability and, more generally, the viability of cells and organisms. In the presence of DNA damage, the normal cell cycle is perturbed when cells activate their repair processes. Although efficient, the repair system is not always able to ensure complete restoration of gene integrity. In these cases, mutations not only may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold that induces apoptosis and programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiation are the most toxic due to the inherent difficultly of repair, which may lead to genomic instability. In this article we show, by using classical molecular simulation techniques, that compared to canonical double-helical B-DNA, guanine-quadruplex (G4) arrangements show remarkable structural stability, even in the presence of two strand breaks. Since G4-DNA is recognized for its regulatory roles in cell senescence and gene expression, including oncogenes, this stability may be related to an evolutionary cellular response aimed at minimizing the effects of ionizing radiation.

A Propidium Monoazide (PMAxx)-Droplet Digital PCR (ddPCR) for the Detection of Viable Burkholderia cepacia Complex in Nuclease-Free Water and Antiseptics

Pharmaceutical products contaminated with Burkholderia cepacia complex (BCC) strains constitute a serious health issue for susceptible individuals. New detection methods to distinguish DNA from viable cells are required to ensure pharmaceutical product quality and safety. In this study, we have assessed a droplet digital PCR (ddPCR) with a variant propidium monoazide (PMAxx) for selective detection of live/dead BCC cells in autoclaved nuclease-free water after 365 days, in 0.001% chlorhexidine gluconate (CHX), and in 0.005% benzalkonium chloride (BZK) solutions after 184 days. Using 10 μM PMAxx and 5 min light exposure, a proportion of dead BCC was quantified by ddPCR. The detection limit of culture-based method was 104 CFU/mL, equivalent to 9.7 pg/μL for B. cenocepacia J2315, while that of ddPCR was 9.7 fg/μL. The true positive rate from nuclease-free water and CHX using PMAxx-ddPCR assay was 60.0% and 38.3%, respectively, compared to 85.0% and 74.6% without PMAxx (p < 0.05), respectively. However, in BZK-treated cells, no difference in the detection rate was observed between the ddPCR assay on samples treated with PMAxx (67.1%) and without PMAxx (63.3%). This study shows that the PMAxx-ddPCR assay provides a better tool for selective detection of live BCC cells in non-sterile pharmaceutical products.

edna2021: The fourth annual meeting of The eDNA Society “Species distributions, and beyond”

The eDNA Society was founded in Japan in 2018 to develop eDNA science as a discipline that contributes to the human well‐being and the sustainable use of ecosystems. Since then, the society has expanded attracting a wide variety of people from international universities, research institutes, consultant companies, and local/national governments. Here we report edna2021, the fourth annual meeting of The eDNA Society, which was held mainly online on November 20–21, 2021. We had c.a. 500 participants in total, from at least 15 countries. In the meeting, we discussed not only the technical aspects of environmental DNA but also its potential for various applications including its combinations with environmental RNA, sediment core samples, population genetic analyses, etc.

Infectious Disease Alert Updates

Even a group of relatively young, healthier adults with COVID-19 (with a mean age of 42 years), who were followed in the outpatient setting, experienced a surprising frequency (39%) of residual complaints at seven to nine months following their acute infection.1 These included fatigue (20.7%), loss of taste and/or smell (16.8%), dyspnea (11.7%), headaches (10%), difficulty concentrating (5.9%), insomnia (5.7%), and memory loss (5.6%). [...]COVID-19 occurred, and public health funding for sexually transmitted disease (STD) clinics and contact tracing was diverted. Based on early reports, it is estimated that we are going to see a 100% increase in syphilis cases from 2020 to 2021;and some authors predict an explosion of STDs in the next five years — the result of a nightmarish storm of diminished public health funding and lots of people “sheltering” for COVID-19 but apparently not for sex. * What’s the problem? Transmission may occur in the absence of visible disease. * These authors examined the frequency of Treponema pallidum (TP) deoxyribonucleic acid (DNA) detected by real-time polymerase chain reaction (PCR) (targeting the polA gene) in blood, pharyngeal and anal specimens, and urine (as a proxy for urethra) as a marker of infectivity.