Minimal Risk Of Contamination Research Articles

MAGs-centric crack: how long will, spore-positive Frankia and most Protofrankia, microsymbionts remain recalcitrant to axenic growth?

Nearly 50 years after the ground-breaking isolation of the primary Comptonia peregrina microsymbiont under axenic conditions, efforts to isolate a substantial number of Protofrankia and Frankia strains continue with enduring challenges and complexities. This study aimed to streamline genomic insights through comparative and predictive tools to extract traits crucial for isolating specific Frankia in axenic conditions. Pangenome analysis unveiled significant genetic diversity, suggesting untapped potential for cultivation strategies. Shared metabolic strategies in cellular components, central metabolic pathways, and resource acquisition traits offered promising avenues for cultivation. Ecological trait extraction indicated that most uncultured strains exhibit no apparent barriers to axenic growth. Despite ongoing challenges, potential caveats, and errors that could bias predictive analyses, this study provides a nuanced perspective. It highlights potential breakthroughs and guides refined cultivation strategies for these yet-uncultured strains. We advocate for tailored media formulations enriched with simple carbon sources in aerobic environments, with atmospheric nitrogen optionally sufficient to minimize contamination risks. Temperature adjustments should align with strain preferences—28–29°C for Frankia and 32–35°C for Protofrankia—while maintaining an alkaline pH. Given potential extended incubation periods (predicted doubling times ranging from 3.26 to 9.60 days, possibly up to 21.98 days), patience and rigorous contamination monitoring are crucial for optimizing cultivation conditions.

Assessment of risk intensity in the triffa plain aquifer: Integration of hazard quantification, land use analysis, dynamic vulnerability GCITF, and DRASTIC method

This study aims to assess the level of groundwater pollution risk in the Triffa Plain, stemming from various pollution sources, with a specific focus on agricultural intensification and excessive pesticide use. Data were collected from ABHM (the Moulouya Hydraulic Basin Agency) and ORMVAM (Regional Office of Moulouya Agricultural Development), and a field visit was conducted in July 2023. The study utilized two main methodologies for mapping risk intensity: the COST 620 action and overlaying vulnerability maps with the land use (LU) factor. Vulnerability maps were generated using the original DRASTIC method and the new dynamic vulnerability assessment method, GCITF.The research approach involved comparing the COST 620 risk index (Ri) and the land use risk index (LU) to identify the most suitable method for the study area. Due to challenges in inventorying various point sources of pollution, the study focused on mapping the primary sources of pollution (diffuse, point, and linear). The key findings indicate that the predominant pollution intensity in the region is high, covering 60.66% of the total surface area. These results closely align with those obtained using the European COST 620 approach and the spatial distribution of nitrates. The study demonstrates the reliability of integrating the GCITF method in assessing groundwater contamination risk, highlighting the significant negative impacts of agricultural activities on the Triffa Plain aquifer, primarily due to uncontrolled pesticide and fertilizer use and point sources of pollution.This study suggests that implementing targeted technical solutions for specific pollution sources is crucial for reducing contamination in the Triffa Plain. These pollution risk intensity maps can assist planners and decision-makers in understanding the origin of pollution and identifying necessary actions to minimize contamination risk, contributing to better groundwater management and protection in the region.

A bacteriophage-based validation of a personal protective equipment doffing procedure to be used with high-consequence pathogens.

To determine if the high-level personal protective equipment used in the treatment of high-consequence infectious diseases is effective at stopping the spread of pathogens to healthcare personnel (HCP) while doffing. Personal protective equipment (PPE) is fundamental to the safety of HCPs. HCPs treating patients with high-consequence infectious diseases use several layers of PPE, forming complex protective ensembles. With high-containment PPE, step-by-step procedures are often used for donning and doffing to minimize contamination risk to the HCP, but these procedures are rarely empirically validated and instead rely on following infection prevention best practices. A doffing protocol video for a high-containment PPE ensemble was evaluated to determine potential contamination pathways. These potential pathways were tested using fluorescence and genetically marked bacteriophages. The experiments revealed existing protocols permit contamination pathways allowing for transmission of bacteriophages to HCPs. Updates to the doffing protocols were generated based on the discovered contamination pathways. This updated doffing protocol eliminated the movement of viable bacteriophages from the outside of the PPE to the skin of the HCP. Our results illustrate the need for quantitative, scientific investigations of infection prevention practices, such as doffing PPE.

Urinary bladder catheterisation of female pigs: Influence of bladder content and Escherichia coli urinary tract infection on procedural outcome.

Catheterisation of the urinary bladder is needed in many types of human disease models in pigs. Based on our extensive experience with the pig as an infection model, we here demonstrate an approach of catheterising domestic pigs (40 attempts) and Göttingen minipigs (10 attempts) using a blinded method, that is, without speculums or videoscopes to visualise the urethral opening. The procedure was tested on control animals and pigs with experimental Escherichia coli urinary tract infection (UTI) to assess the potential influence of this condition on procedural outcome. Lastly, we performed cystoscopy in three animals to visualise the route to the urethra and to localise potential anatomical obstacles. All domestic pigs were catheterised successfully in an average of 2 minutes and 23 seconds, and this was not influenced by UTI (p = 0.06) or bladder urine content at the time of catheterisation (p = 0.32). All Göttingen minipigs were successfully catheterised in an average of 4 minutes and 27 seconds. We conclude that blinded catheterisation is a fast and reliable approach that can be performed in pigs with or without UTI with minimal risk of trauma or contamination.

Novel Protocol for the Preparation of Porcine Bone Marrow Primary Cell Culture for African Swine Fever Virus Isolation.

Isolation of African swine fever virus (ASFV) is a critical step towards the identification, titration, characterization, and even modification of the virus. Therefore, it is important to identify a suitable cell line that supports the efficient replication of ASFV for these purposes. This should be achieved even when starting with a low virus load, as in the case of isolating the virus from field samples. This article presents a detailed protocol on the preparation of porcine bone marrow primary (PBMP) cell culture, which has a high sensitivity towards ASFV, resulting in high viral yields with a minimal risk of bacterial contamination.

Abstract 764: Automated walk away NGS sample preparation for constructing in-line molecular barcoded RNA libraries from Fresh Frozen and FFPE samples

Abstract RNA-Seq is a revolutionary technology for transcriptome analysis, which has been used to quantify transcript levels, confirm gene annotation, identify novel transcripts, splice variants, and fusion detection. Traditionally, the usefulness of RNA-Seq has been limited by pre-analytical (sample availability, low integrity, tumor heterogeneity, complex protocols) and analytical factors (small mRNA fraction, high read duplicate rate), which can lead to higher costs, longer turnaround times, and false negative results. We have developed and automated a streamlined workflow for construction of highly complex RNA Libraries from fresh frozen and FFPE samples that addresses these concerns. We use target enrichment by bait selection with FFPE-derived samples, where rRNA depletion is found to be inconsistent and poly(A) enrichment cannot be used due to degradation of the source material. A fully automated protocol using pre-aliquoted reagents, has been optimized on the Magnis NGS Prep System for a wide range of RNA inputs (10-200 ng), various sample types (Intact and FFPE total RNA) and equipped with 192 Unique Dual sample Indices (UDI) to minimize the effects of possible index hopping and contamination. Addition of in-line molecular barcodes incorporated at the ligation step helps differentiate fragmentation from PCR duplicates, which increases the total number of reads available for further analysis (gene expression and fusion detection). With minimal risk of contamination, this automated protocol delivers up to eight target-enriched NGS Illumina sequencing-ready cDNA libraries from total RNA input per run in about 12 hours without the need of any user intervention. Both catalog and custom probes can be utilized, and PCR cycles can easily be adjusted from the touchscreen to optimize the library yields. For Research Use Only. Not for use in Diagnostic procedures. Citation Format: Saharnaz Bigdeli, Bahram Arezi, Jan Godoski, Denise Rhodes, Ryan Aguilar, Karen William, Bernd Buehler, Ji Zhu, Ronda Allen. Automated walk away NGS sample preparation for constructing in-line molecular barcoded RNA libraries from Fresh Frozen and FFPE samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 764.

Fondaparinux Sodium: Recent Advances in the Management of Thrombosis.

Fondaparinux sodium is a chemically synthesized selective factor Xa inhibitor approved for the prevention and treatment of venous thromboembolic events, that is, deep vein thrombosis, pulmonary embolism, and superficial vein thrombosis, in acutely ill (including those affected by COVID-19 or cancer patients) and those undergoing surgeries. Since its approval in 2002, the efficacy and safety of fondaparinux is well demonstrated by many clinical studies, establishing the value of fondaparinux in clinical practice. Some of the advantages with fondaparinux are its chemical nature of synthesis, minimal risk of contamination, 100% absolute bioavailability subcutaneously, instant onset of action, a long half-life, direct renal excretion, fewer adverse reactions when compared with direct oral anticoagulants, and being an ideal alternative in conditions where oral anticoagulants are not approved for use or in patients intolerant to low molecular weight heparins (LMWH). In the last decade, the real-world use of fondaparinux has been explored in other conditions such as acute coronary syndromes, bariatric surgery, in patients developing vaccine-induced immune thrombotic thrombocytopenia (VITT) and in pregnant women with heparin-induced thrombocytopenia (HIT), or those intolerant to LMWH. The emerging data from these studies have culminated in recent updates in the guidelines that recommend the use of fondaparinux under various conditions. This paper aims to review the recent data and the subsequent updates in the recommendations of various guidelines on the use of fondaparinux sodium.

Waste heat recovery solution based on a heat pipe heat exchanger for the aluminium die casting industry

An analysis of the end use of energy in the EU reveals that industry is one of the three dominant categories, which accounts for 26.1% of the final end use of energy. In the case of the aluminium industry, approximately 70% of energy consumption is due to heat and thermal processes, highlighting a vast potential for waste heat recovery technologies. Within the aluminium die casting industry, liquid aluminium is cast, formed, cooled, and further processed within a thermal heat process, which includes three sub-processes: solubilising, quenching, and ageing. In the case presented, a thermal heat process is the second most energy intensive process within the factory, and the ageing heat treatment furnace accounts for 15% of the thermal heat process. The thermal heat treatment generates a significant amount of waste heat. The recovery of that waste heat, with minimal risk of cross contamination between streams and reduced chance of equipment failure, has been achieved via the use of a heat pipe heat exchanger (HPHE). The HPHE has been designed, manufactured, and installed in the solution furnace exhaust stack. The HPHE was designed to recover up to 88.6 kW in steady state operating conditions at 400 °C. The return on investment has been evaluated at 35 months with an expected CO2 emissions reduction of 86 tCO2/year when best engineering practices are applied. Furthermore, a theoretical modelling tool to predict the thermal performance of the HPHE was developed and validated within a ±20% deviation from the experimental results. This paper further presents the development of the theoretical model to allow a characterisation of HPHE technology and will act as a guideline for the design of HPHEs within the aluminium industry.

A study on the impact of harvesting operations on the mineral oil contamination of olive oils

During the 2020–21 olive oil campaign, the contribution of harvesting operations to mineral oil saturated (MOSH) and aromatic hydrocarbon (MOAH) contamination was studied. Oils extracted from hand-picked olives (15 different olive groves) generally had background MOSH (<2.7 mg/kg), and no quantifiable MOAH. In 40% of the cases, an important contamination increase was observed after harvesting operations. Except for one sample (325.8 and 111.0 mg/kg of MOSH and MOAH, respectively), other samples reached 4.3–33.7 mg/kg of MOSH and 1.1–11.3 mg/kg of MOAH. Accidental leaks of lubricants and/or contact with lubricated mechanical parts, were identified as important sources of contamination. Chromatographic traces obtained by on-line high-performance liquid chromatography (HPLC)-gas chromatography (GC)-flame ionization detection (FID) allowed for source identification. A comprehensive two-dimensional gas chromatographic platform (GC × GC) with parallel FID/MS detection was implemented for confirmation and to attempt the characterization of the contaminations. Good harvesting practices are suggested to minimize contamination risks.

Microplastics throughout a tap water supply network

AbstractThe aim of the present study was to evaluate the presence of microplastics in drinking water along a large distribution water supply network. Tap water was collected in situ at sampling cabinets using an in‐line sampling procedure that provided a representative sample with minimal risk of external contamination and avoided the transportation of large volumes to the laboratory. Microplastics &gt; 50 μm were analysed via Fourier transform infrared spectroscopy (FTIR). Microplastics were detected in 38% of samples with a mean concentration of 0.01 microplastics per litre and polymers identified were polypropylene (PP), polyester (PES) and polyamide (PA). Detection of polytetrafluoroethylene (PTFE) and silicone particles were associated to the maintenance of cabinets. This study contributes to increase the knowledge regarding the presence and behaviour of microplastics throughout a large drinking water supply network providing water to 3 000 000 inhabitants. Results indicate that the pipes and the supply network not release microplastics into the drinking water.

Emergency response to stormwater contamination: A framework for containment and treatment

This paper presents a Stormwater Emergency Response Framework (SERF) for use in the containment and treatment of stormwater runoff following a hazardous material release. The framework consists of four high level process steps and a decision tree. These resources are intended to assist stormwater managers in fulfilling their emergency response responsibilities within the United States' National Incident Management System. Robust hydraulic and watershed modeling may take weeks to months to develop for a contaminated site, whereas decisions made in the initial hours can have a significant impact on limiting contamination spread. Many web resources are publicly available to assist responders in visualizing stormwater runoff flow paths. A case study provided in this paper also demonstrates how simple calculations may be utilized to estimate peak flows and storage volumes necessary to respond to precipitation events immediately. These calculations are useful for decision makers’ allocation of containment and treatment resources within the impacted area. This includes where to deploy available resources to minimize contamination risks to downstream communities and where supplemental resources from outside partners are urgently needed.

Pacemaker implantation in a COVID-19 patient. Balancing the patient's needs and the team's risk of exposure.

COVID-19 patients may have cardiovascular complications requiring invasive treatment. Pacemaker implantation procedure may be challenging because of the necessity of personal protective equipment use. We report pacemaker implantation in a 78-year-old man with severe bilateral COVID-19 interstitial pneumonia, a second degree 2:1 atrioventricular block, and concomitant aortic stenosis.

The Radiological Images and the Diagnostic of COVID-19

The gold-standard method to identify the presence of COVID-19 is the RT-PCR. However, the imaging diagnostic has been requested when there is suspicion of disease’s presence and/or the inflammatory phase of the disease begins. Ths artices described the most common manifestations and patterns of lung abnormality on computed X-Ray (CXR), computer tomography (CT) and Ultrasound of the chest in COVID-19. Notwithstanding the RT-PCR is the gold-standard diagnostic method for COVID-19, the CT has been shown an essential tool to identify pneumonia and the complications of COVID-19 in a patient. This review article aimed to summarize the radiological findings of COVID-19 researches for the following three principal areas: (1) radiological performance in the detection of COVID-19; (2) radiological role in the diagnosis of COVID-19; and (3) radiological function in the monitoring of COVID-19. We searched the articles in the main database (PubMed/Medline, Elsevier Science Direct, Scopus, Isi Web of Science, Embase, Exerpta Medica, UptoDate, Lilacs, Novel Coronavirus Resource Directory from Elsevier), in the high-impact international scientific Journals (Scimago Journal and Country Rank - SJR - and Journal Citation Reports - JCR), such as The Lancet, Science, Nature, The New England Journal of Medicine, Physiological Reviews, Journal of the American Medical Association, Plos One, Journal of Clinical Investigation, and in the data from Center for Disease Control (CDC), National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID) and World Health Organization (WHO). We prior selected meta-analysis, systematic reviews, article reviews and original articles in this order. We reviewed 121 articles and used 57 for this paper from March to May 2020, using the terms coronavirus, SARS-CoV-2, novel coronavirus, Wuhan coronavirus, severe acute respiratory syndrome, 2019-nCoV, 2019 novel coronavirus, n-CoV-2, covid, n-Sars-2, COVID-19, corona virus, coronaviruses, diagnostic, radiology, imaging, computed tomography, chest, CT, X-Ray, with the tools MeSH (Medical Subject Headings), AND, OR, and characters [,“,; /., to ensure the best review topics. We concluded that the imaging method to detect the features of COVID-19 plays an important role in the diagnosis and follow up of the patient with COVID-19 pneumonia. Despite CT has a better sensitivity when compared to CRX and ultrasound, the portable CRX and portable ultrasound could be a new tool with minimal risk of contamination and with good sensitivity.

A single mutation increases heavy-chain heterodimer assembly of bispecific antibodies by inducing structural disorder in one homodimer species

We previously reported efficient heavy-chain assembly of heterodimeric bispecific antibodies by exchanging the interdomain protein interface of the human IgG1 CH3 dimer with the protein interface of the constant α and β domains of the human T-cell receptor, a technology known as bispecific engagement by antibodies based on the T-cell receptor (BEAT). Efficient heterodimerization in mammalian cell transient transfections was observed, but levels were influenced by the nature of the binding arms, particularly in the Fab-scFv-Fc format. In this study, we report a single amino acid change that significantly and consistently improved the heterodimerization rate of this format (≥95%) by inducing partial disorder in one homodimer species without affecting the heterodimer. Correct folding and assembly of the heterodimer were confirmed by the high-resolution (1.88–1.98 Å) crystal structure presented here. Thermal stability and 1-anilinonaphthalene-8-sulfonic acid–binding experiments, comparing original BEAT, mutated BEAT, and “knobs-into-holes” interfaces, suggested a cooperative assembly process of heavy chains in heterodimers. The observed gain in stability of the interfaces could be classified in the following rank order: mutated BEAT > original BEAT > knobs-into-holes. We therefore propose that the superior cooperativity found in BEAT interfaces is the key driver of their greater performance. Furthermore, we show how the mutated BEAT interface can be exploited for the routine preparation of drug candidates, with minimal risk of homodimer contamination using a single Protein A chromatography step.

DNA identification of human remains in Disaster Victim Identification (DVI): An efficient sampling method for muscle, bone, bone marrow and teeth

In disaster victim identification (DVI), DNA profiling is considered to be one of the most reliable and efficient means to identify bodies or separated body parts. This requires a post mortem DNA sample, and an ante mortem DNA sample of the presumed victim or their biological relative(s). Usually the collection of an adequate ante mortem sample is technically simple, but the acquisition of a good quality post mortem sample under unfavourable DVI circumstances is complicated due to the variable degree of preservation of the human remains and the high risk of DNA (cross) contamination. This paper provides the community with an efficient method to collect post-mortem DNA samples from muscle, bone, bone marrow and teeth, with a minimal risk of contamination. Our method has been applied in a recent, challenging DVI operation (i.e. the identification of the 298 victims of the MH17 airplane crash in 2014). 98,2% of the collected PM samples provided the DVI team with highly informative DNA genotyping results without the risk of contamination and consequent mistyping the victim’s DNA. Moreover, the method is easy, cheap and quick. This paper provides the DVI community with a step-wise instructions with recommendations for the type of tissue to be sampled and the site of excision (preferably the upper leg). Although initially designed for DVI purposes, the method is also suited for the identification of individual victims.

A study about the young consumers' consumption behaviors of street foods.

As in almost every country in the world, street foods are frequently used in Turkey. To determine the preferences for these foods, a questionnaire was given to 847 individuals constituted by randomly selected high school and university students. Of the participants, 43.4% were male and 56.6% were female; the majority of them were between 19 and 22 years of age. It was found that 40.1% of the young people ate street food 2-3 times per week, whereas 23.3% were found to eat it every day. Turkish bagels, döner, boiled corn in a cup and toast are most preferred street foods. A statistically significant negative correlations were found between consumption preference scores and education, gender, and age. Although consumers know that street foods can cause contamination with microorganisms, that sellers do not pay attention to hygiene, and that these foods are raw or not cooked well, they prefer because of their cheapness, deliciousness, variety and fast service. Street foods are widely consumed in Turkish young students and because of preventing food poisoning, they should be educated about food hygiene and safety. Also, educating vendors in personal hygiene and good manufacture practice can minimize contamination risk.

Scrubbing technique for needleless connectors to minimize contamination risk

This study aimed to investigate the appropriate scrubbing technique for needleless connectors to minimize contamination risk. To demonstrate a highly effective scrubbing technique to physically eliminate bacteria, needleless connectors were contaminated with Geobacillus stearothermophilus spores and then scrubbed. The study showed that the highest bacterial elimination rate was achieved by scrubbing an access port in a straight line with an alcohol cotton swab, applying a force that was almost equal to an arterial compression haemostasis to the access port, and repeating this procedure once using a new alcohol cotton swab.

Genotyping of KRAS Mutational Status by the In-Check Lab-on-Chip Platform.

The KRAS oncogene is involved in the pathogenesis of several types of cancer, particularly colorectal cancer (CRC). The most frequent mutations in this gene are associated with poor survival, increased tumor aggressiveness and resistance to therapy with anti-epidermal growth factor receptor (EGFR) antibodies. For this reason, KRAS mutation testing has become increasingly common in clinical practice for personalized cancer treatments of CRC patients. Detection methods for KRAS mutations are currently expensive, laborious, time-consuming and often lack of diagnostic sensitivity and specificity. In this study, we describe the development of a Lab-on-Chip assay for genotyping of KRAS mutational status. This assay, based on the In-Check platform, integrates microfluidic handling, a multiplex polymerase chain reaction (PCR) and a low-density microarray. This integrated sample-to-result system enables the detection of KRAS point mutations, including those occurring in codons 12 and 13 of exon 2, 59 and 61 of exon 3, 117 and 146 of exon 4. Thanks to its miniaturization, automation, rapid analysis, minimal risk of sample contamination, increased accuracy and reproducibility of results, this Lab-on-Chip platform may offer immediate opportunities to simplify KRAS genotyping into clinical routine.

Hydrophobic Sand Is a Non-Toxic Method of Urine Collection, Appropriate for Urinary Metal Analysis in the Rat.

Hydrophobic sand is a relatively new method of urine collection in the rodent, comparable to the established method using a metabolic cage. Urine samples are often used in rodent research, especially for biomarkers of health changes after internal contamination from embedded metals, such as in a model of a military shrapnel wound. However, little research has been done on the potential interference of hydrophobic sand with urine metal concentrations either by contamination from the sand particulate, or adsorption of metals from the urine. We compare urine collected from rats using the metabolic cage method and the hydrophobic sand method for differences in metal concentration of common urinary metals, and examine physical properties of the sand material for potential sources of contamination. We found minimal risk of internal contamination of the rat by hydrophobic sand, and no interference of the sand with several common metals of interest (cobalt, strontium, copper, and manganese), although we advise caution in studies of aluminum in urine.

Automation of library preparation using Illumina ForenSeq kit for routine sequencing of casework samples

Massively Parallel Sequencing (MPS) technologies are called upon to play a major role in forensic genomics in the next few years. However, library preparation protocols contain numerous steps which can complexify casework analysis in routine. Implementation of a MPS analytical workflow, in a casework laboratory, requires automation to guarantee a full sample tracking and to minimize contamination risks. In this study, we present the development and validation of a fully automated workflow using Illumina ForenSeq DNA signature Prep Kit on a NGS STARlet HID Illumina platform. Automation greatly helps with library preparation reproducibility and significantly reduces hands-on time. We are confident that automation of MPS technologies will enhance forensic laboratory to adopt these powerful analytical tools determinant for the future of the forensic genomics field.