Comparison of amphibian whole-cell and cell-free activity towards different transferrins.
Ontology highlight
ABSTRACT:
SUBMITTER: James GT
PROVIDER: S-EPMC1164205 | biostudies-other | 1976 Oct
REPOSITORIES: biostudies-other
Similar Datasets
Project description:1. Transferrin-bound iron was released by a cell-free solution prepared from Rana catesbeiana immature erythrocytes, showing that cellular integrity is not necessarily a requirement for this process as previously thought. 2. The biological molecule(s) involved in the removal of iron from transferrin is relatively small.
| S-EPMC1165544 | biostudies-other
Project description:Despite rapid advances over the last decade, synthetic biology lacks the predictive tools needed to enable rational design. Unlike established engineering disciplines, the engineering of synthetic gene circuits still relies heavily on experimental trial-and-error, a time-consuming and inefficient process that slows down the biological design cycle. This reliance on experimental tuning is because current modeling approaches are unable to make reliable predictions about the in vivo behavior of synthetic circuits. A major reason for this lack of predictability is that current models view circuits in isolation, ignoring the vast number of complex cellular processes that impinge on the dynamics of the synthetic circuit and vice versa. To address this problem, we present a modeling approach for the design of synthetic circuits in the context of cellular networks. Using the recently published whole-cell model of Mycoplasma genitalium, we examined the effect of adding genes into the host genome. We also investigated how codon usage correlates with gene expression and find agreement with existing experimental results. Finally, we successfully implemented a synthetic Goodwin oscillator in the whole-cell model. We provide an updated software framework for the whole-cell model that lays the foundation for the integration of whole-cell models with synthetic gene circuit models. This software framework is made freely available to the community to enable future extensions. We envision that this approach will be critical to transforming the field of synthetic biology into a rational and predictive engineering discipline.
| S-EPMC3695969 | biostudies-other
Project description:Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnosis, prognosis and monitoring treatment of disease. However, a sensitive and specific whole-genome sequencing (WGS) method is required to identify novel genetic variations (i.e., SNVs, CNVs and INDELS) on ccfDNA that can be used as clinical biomarkers. In this article, five WGS methods were compared: ThruPLEX Plasma-seq, QIAseq cfDNA All-in-One, NEXTFLEX Cell Free DNA-seq, Accel-NGS 2 S PCR FREE DNA and Accel-NGS 2 S PLUS DNA. The Accel PCR-free kit did not produce enough material for sequencing. The other kits had significant common number of SNVs, INDELs and CNVs and showed similar results for SNVs and CNVs. The detection of variants and genomic signatures depends more upon the type of plasma sample rather than the WGS method used. Accel detected several variants not observed by the other kits. ThruPLEX seemed to identify more low-abundant SNVs and SNV signatures were similar to signatures observed with the QIAseq kit. Accel and NEXTFLEX had similar CNV and SNV signatures. These results demonstrate the importance of establishing a standardized workflow for identifying non-invasive candidate biomarkers. Moreover, the combination of variants discovered in ccfDNA using WGS has the potential to identify enrichment pathways, while the analysis of signatures could identify new subgroups of patients.
| S-EPMC7148341 | biostudies-literature
Project description:Although the fast-growing metagenomic next-generation sequencing (mNGS) has been used in diagnosing infectious diseases, low detection rate of mNGS in detecting pathogens with low loads limits its extensive application. In this study, 130 patients with suspected pulmonary infections were enrolled, from whom bronchoalveolar lavage fluid (BALF) samples were collected. The conventional tests and mNGS of cell-free DNA (cfDNA) and whole-cell DNA (wcDNA) using BALF were simultaneously performed. mNGS of cfDNA showed higher detection rate (91.5%) and total coincidence rate (73.8%) than mNGS of wcDNA (83.1% and 63.9%) and conventional methods (26.9% and 30.8%). A total of 70 microbes were detected by mNGS of cfDNA, and most of them (60) were also identified by mNGS of wcDNA. The 31.8% (21/66) of fungi, 38.6% (27/70) of viruses, and 26.7% (8/30) of intracellular microbes can be only detected by mNGS of cfDNA, much higher than those [19.7% (13/66), 14.3% (10/70), and 6.7% (2/30)] only detected by mNGS of wcDNA. After in-depth analysis on these microbes with low loads set by reads per million (RPM), we found that more RPM and fungi/viruses/intracellular microbes were detected by mNGS of cfDNA than by mNGS of wcDNA. Besides, the abilities of mNGS using both cfDNA and wcDNA to detect microbes with high loads were similar. We highlighted the advantage of mNGS using cfDNA in detecting fungi, viruses, and intracellular microbes with low loads, and suggested that mNGS of cfDNA could be considered as the first choice for diagnosing pulmonary infections.
| S-EPMC9684712 | biostudies-literature
Project description:A keystone in protection work is accurate and thorough the monitoring of amphibian species, and the currently applied conventional survey methods are invasive, time-consuming, and dependent on expert knowledge. Research suggests that eDNA metabarcoding is a precise and cost-efficient method that could supplement the currently applied methods. The present study assessed the efficiency of conventional survey methods and eDNA metabarcoding in terms of species richness, the average number of detected species per site, the relative frequency of species occurrence, and the similarity of applied methods. The study found eDNA metabarcoding surveys to detect Lissotriton vulgaris (smooth newt), Triturus cristatus (great crested newt), Rana arvalis (moor frog), Rana temporaria (common frog), and Bufo bufo (common toad), as well as an average of 0.9 species per site, reflecting the species composition at the time of sampling in mid-July 2020. In addition to the species mentioned above, the conventional survey detected Epidalea calamita (natterjack toad) and an average of 1.7 species per site, reflecting the species composition at the time of sampling in early June 2020. The similarity between the methods applied in the present study was 27%, thus indicating a large number of unique observations of both eDNA metabarcoding and conventional surveys. The differences in detection can most likely be explained by the time of sampling, which was conducted a month apart. eDNA metabarcoding was efficient in detecting multiple amphibian species and produced unique observations that were not detected using conventional survey methods. Applying eDNA techniques as a supplement will most likely produce important knowledge on species distribution and presence, as well as enable more frequent monitoring due to cost efficiency and disturbance.
| S-EPMC8944553 | biostudies-literature
Project description:OBJECTIVE:Eating whole grains (WG) is recommended for health, but multiple conflicting definitions exist for identifying whole grain (WG) products, limiting the ability of consumers and organizations to select such products. We investigated how five recommended WG criteria relate to healthfulness and price of grain products. DESIGN:We categorized grain products by different WG criteria including: the industry-sponsored Whole Grain stamp (WG-Stamp); WG as the first ingredient (WG-first); WG as the first ingredient without added sugars (WG-first-no-added-sugars); the word ‘whole’ before any grain in the ingredients (‘whole’-anywhere); and a content of total carbohydrate to fibre of ?10:1 (10:1-ratio). We investigated associations of each criterion with health-related characteristics including fibre, sugars, sodium, energy, trans-fats and price. SETTING:Two major grocery store chains. SUBJECTS:Five hundred and forty-five grain products. RESULTS:Each WG criterion identified products with higher fibre than products considered non-WG; the 10:1-ratio exhibited the largest differences (+3·15 g/serving, P < 0·0001). Products achieving the 10:1-ratio also contained lower sugar (?1·28 g/serving, P = 0·01), sodium (?15·4 mg/serving, P = 0·04) and likelihood of trans-fats (OR = 0·14, P < 0·0001), without energy differences. WG-first-no-added-sugars performed similarly, but identified many fewer products as WG and also not a lower likelihood of containing trans-fats. The WG-Stamp, WG-first and ‘whole’-anywhere criteria identified products with a lower likelihood of trans-fats, but also significantly more sugars and energy (P < 0·05 each). Products meeting the WG-Stamp or 10:1-ratio criterion were more expensive than products that did not (+$US 0·04/serving, P = 0·009 and +$US 0·05/serving, P = 0·003, respectively). CONCLUSIONS:Among proposed WG criteria, the 10:1-ratio identified the most healthful WG products. Other criteria performed less well, including the industry-supported WG-Stamp which identified products with higher fibre and lower trans-fats, but also higher sugars and energy. These findings inform efforts by consumers, organizations and policy makers to identify healthful WG products.
| S-EPMC4486284 | biostudies-literature
Project description:Actigraphic measurements are an important part of research in different disciplines, yet the procedure of determining activity values is unexpectedly not standardized in the literature. Although the measured raw acceleration signal can be diversely processed, and then the activity values can be calculated by different activity calculation methods, the documentations of them are generally incomplete or vary by manufacturer. These numerous activity metrics may require different types of preprocessing of the acceleration signal. For example, digital filtering of the acceleration signals can have various parameters; moreover, both the filter and the activity metrics can also be applied per axis or on the magnitudes of the acceleration vector. Level crossing-based activity metrics also depend on threshold level values, yet the determination of their exact values is unclear as well. Due to the serious inconsistency of determining activity values, we created a detailed and comprehensive comparison of the different available activity calculation procedures because, up to the present, it was lacking in the literature. We assessed the different methods by analysing the triaxial acceleration signals measured during a 10-day movement of 42 subjects. We calculated 148 different activity signals for each subject's movement using the combinations of various types of preprocessing and 7 different activity metrics applied on both axial and magnitude data. We determined the strength of the linear relationship between the metrics by correlation analysis, while we also examined the effects of the preprocessing steps. Moreover, we established that the standard deviation of the data series can be used as an appropriate, adaptive and generalized threshold level for the level intersection-based metrics. On the basis of these results, our work also serves as a general guide on how to proceed if one wants to determine activity from the raw acceleration data. All of the analysed raw acceleration signals are also publicly available.
| S-EPMC8691611 | biostudies-literature
Project description:An element essential for PCR detection of microbial agents in many sample types is the extraction step, designed to purify nucleic acids. Despite the importance of this step, yields have not been extensively compared across methods to determine whether the method used contributes to quantitative differences and the lack of commutability seen with existing clinical methods. This may in part explain why plasma and blood viral load assays have proven difficult to standardize. Also, studies have identified small DNA fragments of <200?bp in plasma (cell-free DNA [cfDNA]), which may include significant quantities of viral DNA. Our study evaluated extraction yields for 11 commercially available extraction methods, including 4 new methods designed to isolate cfDNA. Solutions of DNA fragments with sizes ranging from 50 to 1,500?bp were extracted, and then the eluates were tested by droplet digital PCR to determine the DNA fragment yield for each method. The results demonstrated a wide range of extraction yields across the variety of methods/instruments used, with the 50- and 100-bp fragment sizes showing especially inconsistent quantitative results and poor yields of less than 20%. Slightly higher, more consistent yields were seen with 2 of the 4 circulating cell-free extraction kits. These results demonstrate a significant need for further evaluation of nucleic acid yields across the variety of extraction platforms and highlight the poor extraction yields of small DNA fragments by existing methods. Further work is necessary to determine the impact of this inconsistency across instruments and the relevance of the low yields for smaller DNA fragments in clinical virology testing.
| S-EPMC6258844 | biostudies-literature
Project description:Epigenetic mechanisms, including DNA methylation, that underlie neuropsychiatric conditions have become a promising area of research. Most commonly used DNA sources in such studies are peripheral (whole) blood (WB), saliva (SL), and lymphoblastoid cell lines (LCLs); thus, the question of the consistency of DNA methylation patterns in those cells is of particular interest. To investigate this question we performed comparative analyses of methylation patterns in WB, SL, and LCLs derived from the same individuals, using Illumina HumanMethylation27 BeadChip arrays. Our results showed that DNA methylation patterns in SL are relatively consistent with those in WB, whereas the patterns in LCLs are similarly distinct from both WB and SL. The results indicated that due to multiple random and directed changes in DNA methylation throughout cell culturing, LCLs are not a reliable source of DNA for epigenetic studies and should be used with caution when investigating epigenetic mechanisms underlying biological processes.
| S-EPMC3577999 | biostudies-other
Project description:We demonstrated a unique optofluidic lab-on-a-chip device that can measure optically encoded forward scattering signals. From the design of the spatial pattern, we can measure the position and velocity of each cell in the flow and generate a 2-D cell distribution plot over the cross section of the channel. Moreover, we have demonstrated that the cell distribution is highly sensitive to its size and stiffness. The latter is an important biomarker for cell classification and our method offers a simple and unequivocal method to classify cells by their size and stiffness. We have proved the concept using live and fixed HeLa cells. Due to the stiffness and size difference of neutrophils compared to other types of white blood cells, we have demonstrated detection of neutrophils from other blood cells. Finally, we have performed the test using 5 ?L of human blood. In a greatly simplified blood preparation process, skipping the usual steps of anticoagulation, centrifuge, antibody labelling or staining, filtering, etc., we have demonstrated that our device and detection principle can count neutrophils in whole human blood. Our system is compact, inexpensive and simple to fabricate and operate, having a commodity laser diode and a Si PIN photoreceiver as the main pieces of hardware. Although the results are still preliminary, the studies indicate that this optofluidic device holds promise to be a point-of-care and home care device to measure neutrophil concentration, which is the key indicator of the immune functions for cancer patients undergoing chemotherapy.
| S-EPMC3472004 | biostudies-literature