Simple and accurate methods for quantifying deformation, disruption, and development in biological tissues.
Ontology highlight
ABSTRACT:
SUBMITTER: Boyle JJ
PROVIDER: S-EPMC4191098 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Quantifying the amount of carbon dioxide (CO2) in seawater is an essential component of ocean acidification research; however, equipment for measuring CO2 directly can be costly and involve complex, bulky apparatus. Consequently, other parameters of the carbonate system, such as pH and total alkalinity (AT), are often measured and used to calculate the partial pressure of CO2 (pCO2) in seawater, especially in biological CO2-manipulation studies, including large ecological experiments and those conducted at field sites. Here we compare four methods of pCO2 determination that have been used in biological ocean acidification experiments: 1) Versatile INstrument for the Determination of Total inorganic carbon and titration Alkalinity (VINDTA) measurement of dissolved inorganic carbon (CT) and AT, 2) spectrophotometric measurement of pHT and AT, 3) electrode measurement of pHNBS and AT, and 4) the direct measurement of CO2 using a portable CO2 equilibrator with a non-dispersive infrared (NDIR) gas analyser. In this study, we found these four methods can produce very similar pCO2 estimates, and the three methods often suited to field-based application (spectrophotometric pHT, electrode pHNBS and CO2 equilibrator) produced estimated measurement uncertainties of 3.5-4.6% for pCO2. Importantly, we are not advocating the replacement of established methods to measure seawater carbonate chemistry, particularly for high-accuracy quantification of carbonate parameters in seawater such as open ocean chemistry, for real-time measures of ocean change, nor for the measurement of small changes in seawater pCO2. However, for biological CO2-manipulation experiments measuring differences of over 100 ?atm pCO2 among treatments, we find the four methods described here can produce similar results with careful use.
| S-EPMC5619781 | biostudies-literature
Project description:We present Smart-Seq2 Rolling Circle to Concatemeric Consensus (Smar2C2) for the identification and quantification of transcription start sites. Smar2C2 allows for the identification of upwards of 70 million unique transcription start sites from a single sample with as little as 40 pg of RNA input.
2022-10-04 | GSE197144 | GEO
Project description:Expanded use of reduced complexity approaches in epidemiology and environmental justice investigations motivates detailed evaluation of these modeling approaches. Chemical transport models (CTMs) remain the most complete representation of atmospheric processes but are limited in applications that require large numbers of runs, such as those that evaluate individual impacts from large numbers of sources. This limitation motivates comparisons between modern CTM-derived techniques and intentionally simpler alternatives. We model population-weighted PM2.5 source impacts from each of greater than 1100 coal power plants operating in the United States in 2006 and 2011 using three approaches: (1) adjoint PM2.5 sensitivities calculated by the GEOS-Chem CTM; (2) a wind field-based Lagrangian model called HyADS; and (3) a simple calculation based on emissions and inverse source-receptor distance. Annual individual power plants' nationwide population-weighted PM2.5 source impacts calculated by HyADS and the inverse distance approach have normalized mean errors between 20 and 28% and root mean square error ranges between 0.0003 and 0.0005 µg m-3 compared with adjoint sensitivities. Reduced complexity approaches are most similar to the GEOS-Chem adjoint sensitivities nearby and downwind of sources, with degrading performance farther from and upwind of sources particularly when wind fields are not accounted for.
| S-EPMC7494583 | biostudies-literature
Project description:We developed a theoretical framework to prove the existence and quantify the Waddington landscape as well as chreode-biological paths for development and differentiation. The cells can have states with the higher probability ones giving the different cell types. Different cell types correspond to different basins of attractions of the probability landscape. We study how the cells develop from undifferentiated cells to differentiated cells from landscape perspectives. We quantified the Waddington landscape through construction of underlying probability landscape for cell development. We show the developmental process proceeds as moving from undifferentiated to the differentiated basins of attractions. The barrier height of the basins of attractions correlates with the escape time that determines the stability of cell types. We show that the developmental process can be quantitatively described and uncovered by the biological paths on the quantified Waddington landscape from undifferentiated to the differentiated cells. We found the dynamics of the developmental process is controlled by a combination of the gradient and curl force on the landscape. The biological paths often do not follow the steepest descent path on the landscape. The landscape framework also quantifies the possibility of reverse differentiation process such as cell reprogramming from differentiated cells back to the original stem cell. We show that the biological path of reverse differentiation is irreversible and different from the one for differentiation process. We found that the developmental process described by the underlying landscape and the associated biological paths is relatively stable and robust against the influences of environmental perturbations.
| S-EPMC3100956 | biostudies-literature
Project description:Computed tomography remains strongly underused in plant sciences despite its high potential in delivering detailed 3D phenotypical information because of the low X-ray absorption of most plant tissues. Existing protocols to study soft tissues display poor performance, especially when compared to those used on animals. More efficient protocols to study plant material are therefore needed. Flowers of Arabidopsis thaliana and Marcgravia caudata were immersed in a selection of contrasting agents used to treat samples for transmission electron microscopy. Grayscale values for floral tissues and background were measured as a function of time. Contrast was quantified via a contrast index. The thick buds of Marcgravia were scanned to determine which contrasting agents best penetrate thick tissues. The highest contrast increase with cytoplasm-rich tissues was obtained with phosphotungstate, whereas osmium tetroxide and bismuth tatrate displayed the highest contrast increase with vacuolated tissues. Phosphotungstate also displayed the best sample penetration. Furthermore, infiltration with phosphotungstate allowed imaging of all plants parts at a high resolution of 3 µm, which approaches the maximum resolution of our equipment: 1.5 µm. The high affinity of phosphotungstate for vasculature, cytoplasm-rich tissue, and pollen causes these tissues to absorb more X-rays than the surrounding tissues, which, in turn, makes these tissues appear brighter on the scan data. Tissues with different brightness can then be virtually dissected from each other by selecting the bracket of grayscale to be visualized. Promising directions for the future include in silico phenotyping and developmental studies of plant inner parts (e.g., ovules, vasculature, pollen, and cell nuclei) via virtual dissection as well as correlations of quantitative phenotypes with omics datasets. Therefore, this work represents a crucial improvement of previous methods, allowing new directions of research to be undertaken in areas ranging from morphology to systems biology.
| S-EPMC3785515 | biostudies-literature
Project description:Ovule development is one of the most important processes in the reproductive development of higher plants and is a determinant of seed quality and quantity. Phytohormones play key roles in this process since loss-of-function mutants in hormone signaling show defective ovule phenotypes and reduced fertility. However, it is difficult to distinguish the direct effects of hormones on ovule development because it is parts of reproductive development and the defective phenotypes would be the indirect effects following the defective vegetative development. The treatment of hormones is a direct method to investigate the hormonal regulation of ovule development, but ovule is embedded inside several layers of floral organs, and traditional methods for hormone (or inhibitor) treatments have various limitations. We have developed simple methods to apply treatments to the flowers in a living plant, where an inflorescence apex is immersed into a solution in an inverted tube. We have also developed a specific system to culture and treat excised flowers/pistils. These procedures will be useful for research on the hormonal regulation of ovule development. We provide examples of how treatments with brassinosteroids (BR) and BR biosynthesis inhibitor. We cultured and treated plant materials using our newly developed methods, and observed the morphology of wild type ovules and fluorescence signals in a marker line to monitor the progress of ovule development. The results demonstrate BR promotes ovule development and our new methods are efficient and repeatable.
| S-EPMC6015908 | biostudies-literature
Project description:Lithium metal-based batteries are attractive energy storage devices because of high energy density. However, uncontrolled dendrite growth and virtually infinite volume change, which cause performance fading and safety concerns, have limited their applications. Here, we demonstrate that a composite lithium metal electrode with an ion-conducting mesoscale skeleton can improve electrochemical performance by locally reducing the current density. In addition, the potential for short-circuiting is largely alleviated due to side deposition of mossy lithium on the three-dimensional electroactive surface of the composite electrode. Moreover, the electrode volume only slightly changes with the support of a rigid and stable scaffold. Therefore, this mesoscale composite electrode can cycle stably for 200 cycles with low polarization under a high areal current density up to 5 mA/cm2. Most attractively, the proposed fabrication process, which only involves simple mechanical deformation, is scalable and cost effective, providing a new strategy for developing high performance and long lifespan lithium anodes.
| S-EPMC6420310 | biostudies-literature
Project description:Microsatellite instability (MSI) testing is important for the classification of Lynch syndrome, as a prognostic marker and as a guide for adjuvant chemotherapy in colorectal cancer (CRC). The gold standard for determining MSI status has traditionally been fluorescent multiplex polymerase chain reaction (PCR) and capillary gel electrophoresis (CGE). However, its use in the clinical setting has diminished and has been replaced by immunohistochemical (IHC) detection of loss of mismatch repair protein expression due to practicability and cost. The aim of this study was to develop a simple, cost-effective and accurate MSI assay based on CGE. After amplification of microsatellites by polymerase chain reaction (PCR) using the National Cancer Institute (NCI) panel (BAT 25, BAT26, D5S346, D2S123, D17S250) of MSI markers, parallel CGE was utilized to classify colorectal cancers as MSI-H, MSI-L and MSS using the 5200 Fragment Analyzer System. Cell lines and patient cancer specimens were tested. DNA from 56 formalin-fixed paraffin-embedded cancer specimens and matched normal tissue were extracted and CGE was performed. An automated computational algorithm for MSI status determination was also developed. Using the fragment analyser, MSI status was found to be 100% concordant with the known MSI status of cell lines and was 86% and 87% concordant with immunohistochemistry (IHC) from patient cancer specimens using traditional assessment and our MSI scoring system, respectively, for MSI determination. The misclassification rate was mainly attributed to IHC, with only one (1.8%) sampling error attributed to CGE testing. CGE was also able to distinguish MSI-L from MSI-H and MSS, which is not possible with IHC. An MSI score based on total allelic variability that can accurately determine MSI status was also successfully developed. A significant reduction in cost compared with traditional fluorescent multiplex PCR and CGE was achieved with this technique. A simple, cost-effective and reliable method of determining MSI status and an MSI scoring system based on an automatic computational algorithm to determine MSI status, as well as degree of allelic instability in colorectal cancer, has been developed using the 5200 Fragment Analyzer System.
| S-EPMC8227602 | biostudies-literature
Project description:BackgroundComparative, functional, and developmental studies of animal morphology require accurate visualization of three-dimensional structures, but few widely applicable methods exist for non-destructive whole-volume imaging of animal tissues. Quantitative studies in particular require accurately aligned and calibrated volume images of animal structures. X-ray microtomography (microCT) has the potential to produce quantitative 3D images of small biological samples, but its widespread use for non-mineralized tissues has been limited by the low x-ray contrast of soft tissues. Although osmium staining and a few other techniques have been used for contrast enhancement, generally useful methods for microCT imaging for comparative morphology are still lacking.ResultsSeveral very simple and versatile staining methods are presented for microCT imaging of animal soft tissues, along with advice on tissue fixation and sample preparation. The stains, based on inorganic iodine and phosphotungstic acid, are easier to handle and much less toxic than osmium, and they produce high-contrast x-ray images of a wide variety of soft tissues. The breadth of possible applications is illustrated with a few microCT images of model and non-model animals, including volume and section images of vertebrates, embryos, insects, and other invertebrates. Each image dataset contains x-ray absorbance values for every point in the imaged volume, and objects as small as individual muscle fibers and single blood cells can be resolved in their original locations and orientations within the sample.ConclusionWith very simple contrast staining, microCT imaging can produce quantitative, high-resolution, high-contrast volume images of animal soft tissues, without destroying the specimens and with possibilities of combining with other preparation and imaging methods. Such images are expected to be useful in comparative, developmental, functional, and quantitative studies of morphology.
| S-EPMC2717911 | biostudies-literature
Project description:ObjectiveTo evaluate siMS score and siMS risk score, novel continuous metabolic syndrome scores as methods for quantification of metabolic status and risk.Materials and methodsDeveloped siMS score was calculated using formula: siMS score = 2*Waist/Height + Gly/5.6 + Tg/1.7 + TAsystolic/130-HDL/1.02 or 1.28 (for male or female subjects, respectively). siMS risk score was calculated using formula: siMS risk score = siMS score * age/45 or 50 (for male or female subjects, respectively) * family history of cardio/cerebro-vascular events (event = 1.2, no event = 1). A sample of 528 obese and non-obese participants was used to validate siMS score and siMS risk score. Scores calculated as sum of z-scores (each component of metabolic syndrome regressed with age and gender) and sum of scores derived from principal component analysis (PCA) were used for evaluation of siMS score. Variants were made by replacing glucose with HOMA in calculations. Framingham score was used for evaluation of siMS risk score.ResultsCorrelation between siMS score with sum of z-scores and weighted sum of factors of PCA was high (r = 0.866 and r = 0.822, respectively). Correlation between siMS risk score and log transformed Framingham score was medium to high for age groups 18+,30+ and 35+ (0.835, 0.707 and 0.667, respectively).ConclusionssiMS score and siMS risk score showed high correlation with more complex scores. Demonstrated accuracy together with superior simplicity and the ability to evaluate and follow-up individual patients makes siMS and siMS risk scores very convenient for use in clinical practice and research as well.
| S-EPMC4706421 | biostudies-literature