Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Temporal-spatial characteristics and path analysis of maritime cyclones in Guangdong coastal areas in the South China Sea

This study was conducted to analyze the maritime cyclone characteristics in Guangdong coast in the years of 1949 to 2016, including inter-annual variation, the intensity of tropical cyclones, generating location and time, and path direction. The temporal-spatial characteristics were also studied. Results show there were 183 tropical cyclones landed in Guangdong coast in the past 68 years, with an average of 2.7 each year, which more than 60 percent were a typhoon. Most of the tropical cyclones were generated in the northwest Pacific, spanning from April to December. The path directions were mainly north, northwest, and west. The strengths of the tropical cyclones were reduced from central Guangdong coast to the east and the west sides, and the section of Zhanjiang city to Shenzhen city was the most vulnerable to tropical cyclones. Tropical cyclones that generated in the South China Sea tend to attack the west of the Guangdong coast, while the ones that produced in the northwest Pacific tend to attack the east of the Guangdong coast. In the study area, the tropical cyclones frequently occurred from July to September and became strongest in September. There are a most common landing section and path direction for each month. Finally, based on the statistical data and research results, the tropical cyclone paths in Guangdong coast were preliminarily analyzed

Survival and Growth of Residual Trees in a Variable Retention Harvest Experiment in a Boreal Mixedwood Forest

Long-term sustainability of forest resources is in question given wide-spread use of conventional clear-cut silviculture. In response, variable retention (VR) harvest has been increasingly promoted as a landscape-based approach to enhance sustainability by maintaining biodiversity and other ecosystem functions in managed forests. Although the success of the VR approach depends on post-harvest stand dynamics, little is known about growth and mortality of residual trees after harvest and how such trees respond to interactions between amount of retention and tree or site level covariates. We use data from three censuses distributed over a 10-year period of the main merchantable species to study the effects of retention level (i.e., percent of trees retained), mixedwood cover type, tree species, and three tree or terrain covariates (tree stem diameter, percent live crown, and soil wetness) on survival and growth of residual trees in a retention harvest experiment in NW Alberta, Canada. Both mortality and growth of residual trees were negatively related to retention levels. During the first five-year period after harvest, effects of retention levels on mortality were more evident for white spruce (Picea glauca) than for Populus spp., but effects on growth were weaker for white spruce. Tree mortality decreased through time following VR harvest for all species and in most cover types, while trends in tree growth varied by species. During the second five-year period after harvest, growth of residual Populus spp. had decreased from high levels observed in the first period. In contrast, growth of residual white spruce was greater in the second five-year period than in the first period. After the original harvest, re-entry of stands for additional harvest focused mainly on hardwoods may be economically rewarding and ecologically justified, depending on the overall objectives for retention. The positive effect of increased retention level on tree survival was strongest for trees with larger diameter and longer crowns. Thus, retention patches are a management option to protect large trees and trees with greater crown length when retaining such trees is a management goal

Challenges in estimating forest biomass: use of allometric equations for three boreal tree species

Regionally-fitted allometric equations for individual trees and root-to-shoot ratio values are normally used to estimate local above- and belowground forest biomass, respectively. However, uncertainties arising from such applications are poorly understood. We developed both above- and belowground biomass equations using destructive sampling for three dominant upland boreal tree species in northwestern Alberta, Canada. Compared to our equations, the diameter-based national equations derived for use across Canada underestimated aboveground biomass for Picea glauca, but gave reasonable estimates for Populus balsamifera and P. tremuloides. The national equations based on both tree diameter and height overestimated aboveground biomass for the Populus species, but underestimated it for Picea glauca in our study area. The root-to-shoot ratio approach proposed by IPCC overestimated belowground biomass by 16â 41% depending on forest cover type in comparison to our values estimated directly on site, with the greatest bias in deciduous-dominated stands. When the general allometric equations for aboveground and the root-to-shoot ratio for belowground biomass were combined to estimate stand biomass, overestimation could be as high as 18% in our study area. Our study supports development of improved regional allometric equations for more accurate local-scale estimations. Incorporating intraspecific variation of important traits like tree taper may be especially helpful.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

The regulatory role of hepatoma-derived growth factor as an angiogenic factor in the eye

Hepatoma-derived growth factor (HDGF) is a mitogen that promotes endothelial proliferation and neuronal survival. Using a unique technology of ligandomics, we recently identified HDGF as a retinal endothelial binding protein. The purpose of this study is to examine the role of HDGF in regulating ocular vasculature and the expression of HDGF in the retina. HDGF expression in the retinal was analyzed with western blot and immunohistochemistry. Angiogenic activity was investigated in human retinal microvascular endothelial cells (HRMVECs) with in vitro endothelial proliferation, migration, and permeability assays. In vivo angiogenic activity was quantified with a corneal pocket assay. The Evans blue assay and western blot using anti-mouse albumin were performed to detect the capacity of HDGF to induce retinal vascular leakage. Immunohistochemistry revealed that HDGF is expressed in the retina with a distinct pattern. HDGF was detected in retinal ganglion cells and the inner nuclear layer but not in the inner plexiform layer, suggesting that HDGF is expressed in the nucleus, but not in the cytoplasm, of retinal neurons. In contrast to family member HDGF-related protein 3 (HRP-3) that has no expression in photoreceptors, HDGF is also present in the outer nuclear layer and the inner and outer segments of photoreceptors. This suggests that HDGF is expressed in the nucleus as well as the cytoplasm of photoreceptors. In vitro functional assays showed that HDGF induced the proliferation, migration, and permeability of HRMVECs. Corneal pocket assay indicated that HDGF directly stimulated angiogenesis in vivo. Intravitreal injection of HDGF significantly induced retinal vascular leakage. These results suggest that HDGF is an angiogenic factor that regulates retinal vasculature in physiologic and pathological conditions. Identification of HDGF by ligandomics and its independent characterization in this study also support the validity of this new technology for systematic identification of cellular ligands, including angiogenic factors

Additional file 9 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Additional file 9. Figure S6: ctDNA testing, LDCT scans, and disease-related events of patients during follow-up periods. . Swimmer plot illustrating the first positive ctDNA testing, the last negative LDCT scans, and pathological events of patients that experienced recurrence or deceased. B). The original and adjusted time intervals between the first positive ctDNA testing and final LDCT scans that detected disease recurrence. Abbreviations: LDCT – low-dose computed tomography, LUAD – lung adenocarcinoma, LUSC - lung squamous-cell carcinoma

Additional file 13 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Additional file 13. Supplementary results

Additional file 3 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Additional file 3. Table S3: Performance of three strategies