Relevant principal factors affecting the reproducibility of insect primary culture.
Ontology highlight
ABSTRACT:
SUBMITTER: Ogata N
PROVIDER: S-EPMC5486689 | biostudies-literature | 2017 Jun
REPOSITORIES: biostudies-literature
Publications
Relevant principal factors affecting the reproducibility of insect primary culture.
Ogata Norichika N Iwabuchi Kikuo K
In vitro cellular & developmental biology. Animal 20170222 6
The primary culture of insect cells often suffers from problems with poor reproducibility in the quality of the final cell preparations. The cellular composition of the explants (cell number and cell types), surgical methods (surgical duration and surgical isolation), and physiological and genetic differences between donors may be critical factors affecting the reproducibility of culture. However, little is known about where biological variation (interindividual differences between donors) ends ...[more]
Similar Datasets
Project description:RNA interference-based screening is a powerful new genomic technology that addresses gene function en masse. To evaluate factors influencing hit list composition and reproducibility, the authors performed 2 identically designed small interfering RNA (siRNA)-based, whole-genome screens for host factors supporting yellow fever virus infection. These screens represent 2 separate experiments completed 5 months apart and allow the direct assessment of the reproducibility of a given siRNA technology when performed in the same environment. Candidate hit lists generated by sum rank, median absolute deviation, z-score, and strictly standardized mean difference were compared within and between whole-genome screens. Application of these analysis methodologies within a single screening data set using a fixed threshold equivalent to a p-value < or = 0.001 resulted in hit lists ranging from 82 to 1140 members and highlighted the tremendous impact analysis methodology has on hit list composition. Intra- and interscreen reproducibility was significantly influenced by the analysis methodology and ranged from 32% to 99%. This study also highlighted the power of testing at least 2 independent siRNAs for each gene product in primary screens. To facilitate validation, the authors conclude by suggesting methods to reduce false discovery at the primary screening stage. In this study, they present the first comprehensive comparison of multiple analysis strategies and demonstrate the impact of the analysis methodology on the composition of the "hit list." Therefore, they propose that the entire data set derived from functional genome-scale screens, especially if publicly funded, should be made available as is done with data derived from gene expression and genome-wide association studies.
| S-EPMC3149892 | biostudies-literature
Project description:Primary cutaneous aspergillosis (PCA) is an uncommon infection of the skin. There is a paucity of organized literature regarding this entity in regard to patient characteristics, associated Aspergillus species, and treatment modalities on outcome (disease recurrence, disease dissemination, and mortality).We reviewed all published reports of PCA from 1967 to 2015. Cases were deemed eligible if they included the following: patient baseline characteristics (age, sex, underlying condition), evidence of proven or probable PCA, primary treatment strategy, and outcome.We identified 130 eligible cases reported from 1967 to 2015. The patients were predominantly male (63.8%) with a mean age of 30.4?±?22.1 years. Rates of PCA recurrence, dissemination, and mortality were 10.8%, 18.5%, and 31.5%, respectively. In half of the cases, there was an association with a foreign body. Seven different Aspergillus species were reported to cause PCA. Systemic antifungal therapy without surgery was the most common form of therapy (60% of cases). Disease dissemination was more common in patients with underlying systemic conditions and occurred on average 41.4 days after PCA diagnosis (range of 3-120 days). In a multivariate linear regression model of mortality including only patients with immunosuppressive conditions, dissemination and human immunodeficiency virus/acquired immune deficiency syndrome were statistically significantly associated with increased mortality.Nearly one-third of patients with PCA die with the disease. Dissemination and host status are critical in patient outcome.
| S-EPMC4937894 | biostudies-other
Project description:Background:Predicting discharge destination following total joint arthroplasty (TJA) is important, as discharge destination has major implications for post-operative costs, clinical outcomes, and readmissions. Few studies have looked at factors affecting discharge destination for patients following primary simultaneous bilateral total joint arthroplasty. Questions/Purposes:The purpose of this study was to describe clinical and social factors that relate to a discharge to home versus rehabilitation facility (RF) for patients after primary simultaneous bilateral total hip arthroplasty (PSBTHA) or primary simultaneous bilateral total knee arthroplasty (PSBTKA). Methods:The inclusion criteria for this retrospective cohort study were all patients after PSBTHA or PSBTKA at a metropolitan orthopedic specialty hospital between February 1, 2016, and March 31, 2018. Exclusion criteria were revisions, differing weight-bearing status, bed-rest orders, and non-standard hip precautions. Social and clinical demographic data were collected. Multiple regression analysis was conducted to determine which factors related most to discharge plan. Results:Of 253 PSBTHA patients, 153 were discharged home and 100 to an RF. Regression analysis found a posterolateral approach to be the only significant factor associated with an RF discharge. Of 619 PSBTKA patients, 136 were discharged home and 483 to RF. Increased body mass index and older age increased the likelihood of discharge to an RF. Patients with an adductor-only nerve block were more likely to be sent to RF. Conclusion:These findings shed light on the variables that contribute to discharge destination after PSBTHA and PSBTKA. Such information allows for safe pre-operative discharge planning and assists with discharge to the appropriate level of patient care. Future studies might investigate the effect of surgeon experience, surgical technique, and pre-operative discussion with a physical therapist on the discharge disposition of patients undergoing bilateral total joint arthroplasty.
| S-EPMC6778168 | biostudies-literature
Project description:Experimental infections of insects with arboviruses are performed to achieve a variety of objectives but principally to draw inferences about the potential role of field populations in transmission or to explore the molecular basis of vector-pathogen interactions. The design of such studies determines both their reproducibility and the extent to which their results can be extrapolated to natural environments, and is constrained by the resources available. We discuss recent findings regarding the effects of nutrition, the microbiome, co-infecting agents and feeding methods on the outcome of such experiments, and identify resource-efficient ways to increase their relevance and reproducibility, including the development of community standards for reporting such studies and better standards for cell line and colony authentication.
| S-EPMC6299244 | biostudies-other
Project description:Objective:To provide a standardized protocol for the measurement of cervical strain elastography, present its reproducibility, and analyze baseline clinical factors affecting the measurement of elastographic parameters. Methods:This study was performed by the Korean Research Group of Cervical Elastography. We enrolled pregnant women according to our study protocol. After measuring the cervical length, elastography was performed using the E-Cervix™ quantification tool to measure the strain of the cervix using intrinsic compression. We evaluated 5 elastographic parameters, namely, the strain of the internal os of the cervix (IOS), strain of the external os of the cervix (EOS), ratio of the strain of IOS and EOS, elasticity contrast index, and hardness ratio. For baseline clinical factors, we examined the maternal body mass index, blood pressure, heart rate, uterine artery Doppler indices, and fetal presentation. Results:We established a specific protocol for the measurement of cervical elastography using the E cervix program. For all elastographic parameters, the intra-observer intraclass correlation coefficient (ICC) ranged from 0.633 to 0.723 for single measures and from 0.838 to 0.887 for average measures, and the inter-observer ICC ranged from 0.814 to 0.977 for single measures and from 0.901 to 0.988 for average measures. Regression analysis showed that the measurement of the elastographic parameter was not affected by baseline clinical factors. Conclusion:We present a standardized protocol for the measurement of cervical elastography using intrinsic compression. According to this protocol, reproducibility was acceptable and the measurement of elastographic parameters was not affected by the baseline clinical factors studied.
| S-EPMC6962587 | biostudies-literature
Project description:Type 2 diabetes is impacting millions of people globally; however, many future cases can be prevented through lifestyle changes and interventions. Primary care is an important setting for diabetes prevention, for at-risk populations, because it is a patient's primary point of contact with the health care system and professionals can provide lifestyle counselling and support, as well as monitoring health outcomes. These are all essential elements for diabetes prevention for at-risk adults.To understand the factors related to the delivery and uptake of type 2 diabetes prevention interventions within primary care in higher income countries.For this narrative systematic review, we combined qualitative and quantitative studies of diabetes prevention within a primary care setting for patients at-risk of developing the condition. We used an iterative approach for evidence collection, which included using several databases (MEDLINE, Embase, Pysch info, BNI, SSCI, CINAHL, ASSIA), where we combined diabetes terms with primary care terms. Narrative and thematic synthesis were utilised to identify the prominent themes emerging from the data.A database of 6646 records was screened by the research team, and 18 papers were included. Three major themes were identified in this review. The first theme of context and setting of diabetes progression includes the risk and progression of diabetes, primary care as a setting, and where the responsibility for change is thought to lie. This review also found mixed views on the value of preventative services within primary care. The second theme focused on the various patient factors associated with diabetes prevention such as a patient's motivation to modify their current lifestyle, perceptions and knowledge (or lack thereof) of the impacts of diabetes, lack of follow-up in healthcare settings, and trust in healthcare professionals. The third theme was centred on professional factors impacting on diabetes prevention which included workload, time constraints, resources, self-efficacy and knowledge as well as professionals' perception of patient motivations towards change.This review explored the factors influencing diabetes prevention in primary care, and identified the context of prevention, as well as patient and professional factors related to preventative services being offered in primary care. This systematic review complements previous reviews of real-world settings by exploring the significant factors in prevention, and the findings are relevant to academics, policymakers, patients and practitioners interested in understanding the factors associated with the delivery and uptake of diabetes prevention interventions.
| S-EPMC5439678 | biostudies-literature
Project description:In times of spreading multidrug-resistant bacteria, species identification and decontamination of cell cultures can be challenging. Here, we describe a mobile cell culture contaminant with "black dot"-like microscopic appearance in newly established irreplaceable hybridoma cell lines and its identification. Using 16S rRNA gene sequencing, species-specific PCRs, whole genome sequencing (WGS), and MALDI-TOF mass spectrometry, the contaminant was identified as the ubiquitous environmental and clinically relevant Gram-negative bacterium Ralstonia insidiosa (R. insidiosa), a strong biofilm producer. Further characterizations by transmission electron microscopy (TEM) and biochemical API test were not conclusive. Whole genome sequencing of our R. insidiosa isolate revealed numerous drug-resistance determinants. Genome-wide comparison to other Ralstonia species could not unambiguously designate our isolate to R. insidiosa (<95% average nucleotide identity) suggesting a potential novel species or subspecies, closely related to R. insidiosa and R. pickettii. After determining the antibiotic susceptibility profile, the hybridoma cell culture was successfully decontaminated with ciprofloxacin without affecting antibody production.
| S-EPMC7603027 | biostudies-literature
Project description:BackgroundThe large airway epithelial barrier provides one of the first lines of defense against respiratory viruses, including SARS-CoV-2 that causes COVID-19. Substantial inter-individual variability in individual disease courses is hypothesized to be partially mediated by the differential regulation of the genes that interact with the SARS-CoV-2 virus or are involved in the subsequent host response. Here, we comprehensively investigated non-genetic and genetic factors influencing COVID-19-relevant bronchial epithelial gene expression.MethodsWe analyzed RNA-sequencing data from bronchial epithelial brushings obtained from uninfected individuals. We related ACE2 gene expression to host and environmental factors in the SPIROMICS cohort of smokers with and without chronic obstructive pulmonary disease (COPD) and replicated these associations in two asthma cohorts, SARP and MAST. To identify airway biology beyond ACE2 binding that may contribute to increased susceptibility, we used gene set enrichment analyses to determine if gene expression changes indicative of a suppressed airway immune response observed early in SARS-CoV-2 infection are also observed in association with host factors. To identify host genetic variants affecting COVID-19 susceptibility in SPIROMICS, we performed expression quantitative trait (eQTL) mapping and investigated the phenotypic associations of the eQTL variants.ResultsWe found that ACE2 expression was higher in relation to active smoking, obesity, and hypertension that are known risk factors of COVID-19 severity, while an association with interferon-related inflammation was driven by the truncated, non-binding ACE2 isoform. We discovered that expression patterns of a suppressed airway immune response to early SARS-CoV-2 infection, compared to other viruses, are similar to patterns associated with obesity, hypertension, and cardiovascular disease, which may thus contribute to a COVID-19-susceptible airway environment. eQTL mapping identified regulatory variants for genes implicated in COVID-19, some of which had pheWAS evidence for their potential role in respiratory infections.ConclusionsThese data provide evidence that clinically relevant variation in the expression of COVID-19-related genes is associated with host factors, environmental exposures, and likely host genetic variation.
| S-EPMC8059115 | biostudies-literature
Project description:Optimization of experimental conditions is critical in ensuring robust experimental reproducibility. Through detailed metabolomic analysis we found that cell culture conditions significantly impacted on glutaminase (GLS1) sensitivity resulting in variable sensitivity and irreproducibility in data. Baseline metabolite profiling highlighted that untreated cells underwent significant changes in metabolic status. Both the extracellular levels of glutamine and lactate and the intracellular levels of multiple metabolites changed drastically during the assay. We show that these changes compromise the robustness of the assay and make it difficult to reproduce. We discuss the implications of the cells' metabolic environment when studying the effects of perturbations to cell function by any type of inhibitor. We then devised 'metabolically rationalized standard' assay conditions, in which glutaminase-1 inhibition reduced glutamine metabolism differently in both cell lines assayed, and decreased the proliferation of one of them. The adoption of optimized conditions such as the ones described here should lead to an improvement in reproducibility and help eliminate false negatives as well as false positives in these assays.
| S-EPMC5813001 | biostudies-literature
Project description:A well-organized education program improved the patients' knowledge about their disease, inhaler technique and quality of life in asthma and chronic obstructive pulmonary disease (COPD) patients. The effectiveness of the education program can be evaluated by assessing patients' satisfaction with the education program as well. In this study, we compared the patients' satisfaction with education program between COPD and asthma patients.A total of 284 asthma and COPD patients were enrolled. Three educational visits were conducted at 2-week intervals. On the first visit, we taught the patients about their diseases and the proper inhaler technique. On the second visit, non-pharmacologic treatments and action plans for acute exacerbation were introduced. On the final appointment, we summarized the educational concepts covered in the two prior visits. After the education program, the patients were assessed for their quality of life, knowledge of chronic airways disease, and satisfaction with the education program, using a structured questionnaire.After the education program, 99.3% of the asthma patients knew much more about their disease and 96.8% agreed that education from the hospital is needed. For COPD patients, 94.8% felt more informed about their disease and 95.7% agreed that education from the hospital is needed. However, 17.1% of asthma patients and 13.5% of COPD patients disagreed to paying an additional fee for the education program. Finally, the knowledge improvement was linked to patient satisfaction with the education program.The improvement in self-knowledge about their disease was linked to their satisfaction with the education program. However, costs associated with the program could limit its accessibility to the patients. The patient education program is a self-management intervention to improve the lives of patients with asthma and COPD. Thus, a policy to reduce the economic burden of the patients should be considered to disseminate the education program in primary care clinics.
| S-EPMC5543003 | biostudies-other