SIAL: A simple image analysis library for wet-lab scientists.
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ABSTRACT:
SUBMITTER: Tyrpak DR
PROVIDER: S-EPMC8373214 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:COMPARE Food Ring Trial - wet lab
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Project description:BACKGROUND: Despite the large volume of genome sequencing data produced by next-generation sequencing technologies and the highly sophisticated software dedicated to handling these types of data, gaps are commonly found in draft genome assemblies. The existence of gaps compromises our ability to take full advantage of the genome data. This study aims to identify a practical approach for biologists to complete their own genome assemblies using commonly available tools and resources. RESULTS: A pipeline was developed to assemble complete genomes primarily from the next generation sequencing (NGS) data. The input of the pipeline is paired-end Illumina sequence reads, and the output is a high quality complete genome sequence. The pipeline alternates the employment of computational and biological methods in seven steps. It combines the strengths of de novo assembly, reference-based assembly, customized programming, public databases utilization, and wet lab experimentation. The application of the pipeline is demonstrated by the completion of a bacterial genome, Thermotoga sp. strain RQ7, a hydrogen-producing strain. CONCLUSIONS: The developed pipeline provides an example of effective integration of computational and biological principles. It highlights the complementary roles that in silico and wet lab methodologies play in bioinformatical studies. The constituting principles and methods are applicable to similar studies on both prokaryotic and eukaryotic genomes.
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Project description:Humanized monoclonal antibodies (mAbs) are among the most promising modern therapeutics, but defined engineering strategies are still not available. Antibody humanization often leads to a loss of affinity, as it is the case for our model antibody Ab2/3H6 (PDB entry 3BQU). Identifying appropriate back-to-mouse mutations is needed to restore binding affinity, but highly challenging. In order to get more insight, we have applied molecular dynamics simulations and correlated them to antibody binding and expression in wet lab experiments. In this study, we discuss six mAb variants and investigate a tyrosine conglomeration, an isopolar substitution and the improvement of antibody binding towards wildtype affinity. In the 3D structure of the mouse wildtype, residue R94h is surrounded by three tyrosines which form a so-called 'tyrosine cage'. We demonstrate that the tyrosine cage has a supporting function for the CDRh3 loop conformation. The isopolar substitution is not able to mimic the function appropriately. Finally, we show that additional light chain mutations can restore binding to wildtype-comparable level, and also improve the expression of the mAb significantly. We conclude that the variable light chain of Ab2/3H6 is of underestimated importance for the interaction with its antigen mAb 2F5.
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Project description:IntroductionWe undertook a systematic review of the use of wet lab (animal and cadaveric) simulation models in urological training, with an aim to establishing a level of evidence (LoE) for studies and level of recommendation (LoR) for models, as well as evaluating types of validation.MethodsMedline, EMBASE, and Cochrane databases were searched for English-language studies using search terms including a combination of "surgery," "surgical training," and "medical education." These results were combined with "wet lab," "animal model," "cadaveric," and "in-vivo." Studies were then assigned a LoE and LoR if appropriate as per the education-modified Oxford Centre for Evidence-Based Medicine classification.ResultsA total of 43 articles met the inclusion criteria. There was a mean of 23.1 (±19.2) participants per study with a median of 20. Overall, the studies were largely of low quality, with 90.7% of studies being lower than LoE 2a (n=26 for LoE 2b and n=13 for LoE 3). The majority (72.1%, n=31) of studies were in animal models and 27.9% (n=12) were in cadaveric models.ConclusionsSimulation in urological education is becoming more prevalent in the literature, however, there is a focus on animal rather than cadaveric simulation, possibly due to cost and ethical considerations. Studies are also predominately of a low LoE; higher LoEs, especially randomized controlled studies, are needed.
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Project description:The varietal authentication of wines is fundamental for assessing wine quality, and it is part of its compositional profiling. The availability of historical, cultural and chemical composition information is extremely important for quality evaluation. DNA-based techniques are a powerful tool for proving the varietal composition of a wine. SSR-amplification of genomic residual Vitis vinifera DNA, namely Wine DNA Fingerprinting (WDF) is able to produce strong, analytical evidence concerning the monovarietal nature of a wine, and for blended wines by generating the probability of the presence/absence of a certain variety, all in association with a dedicated bioinformatics elaboration of genotypes associated with possible varietal candidates. Together with WDF we could exploit Bioinformatics techniques, due to the number of grape genomes grown. In this paper, the use of WDF and the development of a bioinformatics tool for allelic data validation, retrieved from the amplification of 7 to 10 SSRs markers in the Vitis vinifera genome, are reported. The wines were chosen based on increasing complexity; from monovarietal, experimental ones, to commercial monovarietals, to blended commercial wines. The results demonstrate that WDF, after calculation of different distance matrices and Neighbor-Joining input data, followed by Principal Component Analysis (PCA) can effectively describe the varietal nature of wines. In the unknown blended wines the WDF profiles were compared to possible varietal candidates (Merlot, Pinot Noir, Cabernet Sauvignon and Zinfandel), and the output graphs show the most probable varieties used in the blend as closeness to the tested wine. This pioneering work should be meant as to favor in perspective the multidisciplinary building-up of on-line databanks and bioinformatics toolkits on wine. The paper concludes with a discussion on an integrated decision support system based on bioinformatics, chemistry and cultural data to assess wine quality.
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Project description:We report here that a dense liquid formed by spontaneous condensation, also known as simple coacervation, of a single mussel foot protein-3S-mimicking peptide exhibits properties critical for underwater adhesion. A structurally homogeneous coacervate is deposited on underwater surfaces as micrometer-thick layers, and, after compression, displays orders of magnitude higher underwater adhesion at 2 N m-1 than that reported from thin films of the most adhesive mussel-foot-derived peptides or their synthetic mimics. The increase in adhesion efficiency does not require nor rely on post-deposition curing or chemical processing, but rather represents an intrinsic physical property of the single-component coacervate. Its wet adhesive and rheological properties correlate with significant dehydration, tight peptide packing and restriction in peptide mobility. We suggest that such dense coacervate liquids represent an essential adaptation for the initial priming stages of mussel adhesive deposition, and provide a hitherto untapped design principle for synthetic underwater adhesives.
| S-EPMC5744669 | biostudies-literature
Project description:IntroductionStudies have shown that structured cataract surgery training curricula are beneficial for resident surgeons-in-training, yet nearly one-third of US training programs do not have one, and public dissemination of said curricula are lacking.MethodsWe created a microsurgical simulation center and accompanying structured training curriculum. Weekly lectures focused on the steps of cataract surgery, variations on technique, and complications. Each didactic was followed by a 1.5- to 2-hour time block with faculty supervision in the wet lab. Finally, to demonstrate proficiency, residents submitted a recorded video illustrating their competency within 1 week of the lecture. We reviewed videos and provided written feedback via a standardized form. Curriculum effectiveness was evaluated through formative feedback on the course itself and complication rates for resident-performed cataract surgery before and after implementation of the curriculum.ResultsThe course was implemented in 4 consecutive academic years, allowing time for nine junior residents to participate in the course at least once before operating as a senior. The incidence of posterior capsule tears for senior residents decreased from 3.07% in the 4 years preceding curriculum implementation to 1.13% for the senior residents who completed the course at least once as juniors (p = .0571). Supervised wet lab sessions and submitted videos allowed faculty to identify surgically struggling residents early.DiscussionImplementation of a cataract surgery training curriculum for junior ophthalmology residents provides a safe and effective environment to practice surgical techniques. Such a curriculum may decrease the complication rates of beginner surgeons.
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Project description:mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGFβ pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival.
2012-03-08 | GSE16476 | GEO