72 research outputs found
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
Preoperative Metabolic Syndrome Is Predictive of Significant Gastric Cancer Mortality after Gastrectomy: The Fujian Prospective Investigation of Cancer (FIESTA) Study
Metabolic syndrome (MetS) has been shown to be associated with an increased risk of gastric cancer. However, the impact of MetS on gastric cancer mortality remains largely unknown. Here, we prospectively examined the prediction of preoperative MetS for gastric cancer mortality by analyzing a subset of data from the ongoing Fujian prospective investigation of cancer (FIESTA) study. This study was conducted among 3012 patients with gastric cancer who received radical gastrectomy between 2000 and 2010. The latest follow-up was completed in 2015. Blood/tissue specimens, demographic and clinicopathologic characteristics were collected at baseline. During 15-year follow-up, 1331 of 3012 patients died of gastric cancer. The median survival time (MST) of patients with MetS was 31.3 months, which was significantly shorter than that of MetS-free patients (157.1 months). The coexistence of MetS before surgery was associated with a 2.3-fold increased risk for gastric cancer mortality (P < 0.001). The multivariate-adjusted hazard ratios (HRs) were increased with invasion depth T1/T2 (HR = 2.78, P < 0.001), regional lymph node metastasis N0 (HR = 2.65, P < 0.001), positive distant metastasis (HR = 2.53, P < 0.001), TNM stage I/II (HR = 3.00, P < 0.001), intestinal type (HR = 2.96, P < 0.001), negative tumor embolus (HR = 2.34, P < 0.001), and tumor size ≤4.5 cm (HR = 2.49, P < 0.001). Further survival tree analysis confirmed the top splitting role of TNM stage, followed by MetS or hyperglycemia with remarkable discrimination ability. In this large cohort study, preoperative MetS, especially hyperglycemia, was predictive of significant gastric cancer mortality in patients with radical gastrectomy, especially for early stage of gastric cancer
Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length
Through alternative polyadenylation, human mRNAs acquire longer or shorter 30 untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To under- stand the dynamics of polyadenylation site usage, we performed transcriptome-wide mapping of both binding sites of 30 end processing factors CPSF- 160, CPSF-100, CPSF-73, CPSF-30, Fip1, CstF-64, CstF-64t, CF Im25, CF Im59, and CF Im68 and 30 end processing sites in HEK293 cells. We found that although binding sites of these factors generally cluster around the poly(A) sites most frequently used in cleavage, CstF-64/CstF-64t and CFIm proteins have much higher positional specificity compared to CPSF components. Knockdown of CF Im68 induced a systematic use of proximal polyade- nylation sites, indicating that changes in relative abundance of a single 30 end processing factor can modulate the length of 30 untranslated regions across the transcriptome and suggesting a mechanism behind the previously observed increase in tumor cell invasiveness upon CF Im68 knockdown
Adaptation of Staphylococcus aureus to ruminant and equine hosts involves SaPI-carried variants of von Willebrand factor-binding protein
Staphylococci adapt specifically to various animal hosts by genetically determined mechanisms that are not well understood. One such adaptation involves the ability to coagulate host plasma, by which strains isolated from ruminants or horses can be differentiated from closely related human strains. Here, we report first that this differential coagulation activity is due to animal-specific alleles of the von Willebrand factor-binding protein (vWbp) gene, vwb, and second that these vwb alleles are carried by highly mobile pathogenicity islands, SaPIs. Although all Staphylococcus aureus possess chromosomal vwb as well as coagulase (coa) genes, neither confers species-specific coagulation activity; however, the SaPI-coded vWbps possess a unique N-terminal region specific for the activation of ruminant and equine prothrombin. vWbp-encoding SaPIs are widely distributed among S. aureus strains infecting ruminant or equine hosts, and we have identified and characterized four of these, SaPIbov4, SaPIbov5, SaPIeq1 and SaPIov2, which encode vWbpSbo4, vWbpSbo5, vWbpSeq1 and vWbpSov2 respectively. Moreover, the SaPI-carried vwb genes are regulated differently from the chromosomal vwb genes of the same strains. We suggest that the SaPI-encoded vWbps may represent an important host adaptation mechanism for S. aureus pathogenicity, and therefore that acquisition of vWbp-encoding SaPIs may be determinative for animal specificity
Impaired cue identification and intention retrieval underlie prospective memory deficits in patients with first-episode schizophrenia
Objective: Schizophrenia is associated with impairment in prospective memory, the ability to remember to carry out an intended action in the future. It has been established that cue identification (detection of the cue event signaling that an intended action should be performed) and intention retrieval (retrieval of an intention from long-term memory following the recognition of a prospective cue) are two important processes underlying prospective memory. The purpose of this study was to examine prospective memory deficit and underlying cognitive processes in patients with first-episode schizophrenia.</p
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