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

A novel hand-assisted laparoscopic versus conventional laparoscopic right hemicolectomy for right colon cancer: study protocol for a randomized controlled trial

Abstract Background Although conventional laparoscopic and hand-assisted laparoscopic surgery for colorectal cancer is widely used today, there remain many technical challenges especially for right colon cancer in obese patients. Herein, we develop a novel hand-assisted laparoscopic surgery (HALS) with complete mesocolic excision (CME), D3 lymphadenectomy, and a total “no-touch” isolation technique (HALS-CME) in right hemicolectomy to overcome these issues. According to previous clinic practice, this novel procedure is not only feasible and safe but has several technical merits. However, the feasibility, short-term minimally invasive virtues, long-term oncological superiority, and potential total “no-touch” isolation technique benefits of HALS-CME should be confirmed by a prospective randomized controlled trial. Methods/design This is a single-center, open-label, noninferiority, randomized controlled trial. Eligible participants will be randomly assigned to the HALS-CME group or to the laparoscopic surgery with CME, D3 lymphadenectomy, and total “no-touch” isolation technique (LAP-CME) group, or to conventional laparoscopic surgery with CME and D3 lymphadenectomy (cLAP) group at a 1:1:1 ratio using a centralized randomization list. Primary endpoints include safety, efficacy, and being oncologically clear, and 3-year disease-free, progression-free, and overall survival. Second endpoints include operative outcomes (operation time, blood loss, and incision length), pathologic evaluation (grading the plane of surgery, length of proximal and distal resection margins, distance between the tumor and the central arterial high tie, distance between the nearest bowel wall and the same high tie, area of mesentery resected, width of the chain of lymph-adipose tissue, length of the central lymph-adipose chain, number of harvested lymph nodes), and postoperative outcomes (pain intensity, postoperative inflammatory and immune responses, postoperative recovery). Discussion This trial will provide valuable clinical evidence for the feasibility, safety, and potential total “no-touch” isolation technique benefits of HALS-CME for right hemicolectomy. The hypothesis is that HALS-CME is feasible for the radical D3 resection of right colon cancer and offers short-term safety and long-term oncological superiority compared with conventional laparoscopic surgery. Trial registration ClinicalTrials.gov, NCT02625272 . Registered on 8 December 2015

A low-cost, disposable card for rapid polymerase chain reaction

A low-cost, disposable card for rapid polymerase chain reaction (PCR) was developed in this work. Commercially available, adhesive-coated aluminum foils and polypropylene films were laminated with structured polycarbonate films to form microreactors in a card format. Ice valves [1] were employed to seal the reaction chambers during thermal cycling and a Peltier-based thermal cycler was configured for rapid thermal cycling and ice valve actuation. Numerical modeling was conducted to optimize the design of the PCR reactor and investigate the thermal gradient in the reaction chamber in the direction of sample thickness. The PCR reactor was experimentally characterized by using thin foil thermocouples and validated by a successful amplification of 10 copy of E. coli tuf gene in 27 min.close151

Impact of <i>XRCC2</i> Arg188His Polymorphism on Cancer Susceptibility: A Meta-Analysis

<div><p>Background</p><p>Association between the single nucleotide polymorphism rs3218536 (known as Arg188His) located in the X-ray repair cross complementing group 2 (<i>XRCC2</i>) gene and cancer susceptibility has been widely investigated. However, results thus far have remained controversial. A meta-analysis was performed to identify the impact of this polymorphism on cancer susceptibility.</p><p>Methods</p><p>PubMed and Embase databases were searched systematically until September 7, 2013 to obtain all the records evaluating the association between the <i>XRCC2</i> Arg188His polymorphism and the risk of all types of cancers. We used the odds ratio (OR) as measure of effect, and pooled the data in a Mantel-Haenszel weighed random-effects meta-analysis to provide a summary estimate of the impact of this polymorphism on breast cancer, ovarian cancer and other cancers. All the analyses were carried out in STATA 12.0.</p><p>Results</p><p>With 30868 cases and 38656 controls, a total of 45 case-control studies from 26 publications were eventually included in our meta-analysis. No significant association was observed between the <i>XRCC2</i> Arg188His polymorphism and breast cancer susceptibility (dominant model: OR = 0.94, 95%CI = 0.86–1.04, P = 0.232). However, a significant impact of this polymorphism was detected on decreased ovarian cancer risk (dominant model: OR = 0.83, 95%CI = 0.73–0.95, P = 0.007). In addition, we found this polymorphism was associated with increased upper aerodigestive tract (UADT) cancer susceptibility (dominant model: OR = 1.51, 95%CI = 1.04–2.20, P = 0.032).</p><p>Conclusion</p><p>The Arg188His polymorphism might play different roles in carcinogenesis of various cancer types. Current evidence did not suggest that this polymorphism was directly associated with breast cancer susceptibility. However, this polymorphism might contribute to decreased gynecological cancer risk and increased UADT cancer risk. More preclinical and epidemiological studies were still imperative for further evaluation.</p></div

Forest plot for the subgroup analysis of gynecological cancer (dominant model: Arg/His+His/His vs. Arg/Arg).

<p>Significant association was detected between the <i>XRCC2</i> Arg188His polymorphism and decreased risk for ovarian cancer and cervical cancer.</p

Stratified analysis of the <i>XRCC2</i> Arg188His polymorphism on cancer susceptibility.

<p>*Subgroup analysis.</p><p>**Number of studies included.</p><p>P: P-value of association test, <i>P_h</i>: P-value of Q-test for heterogeneity test; NA: not available.</p

Forest plot for the association of the <i>XRCC2</i> Arg188His polymorphism with breast cancer risk (dominant model: His/His + Arg/His vs. Arg/Arg).

<p>No significant association was observed between the Arg188His polymorphism and susceptibility of breast cancer.</p

Forest plot for the association between the <i>XRCC2</i> Arg188His polymorphism and UADT cancer risk (dominant model: Arg/His+ His/His vs. Arg/Arg).

<p>Significant association was observed between this polymorphism and increased risk for UADT cancer.</p

Sensitivity analysis on the association between the <i>XRCC2</i> Arg188His polymorphism and susceptibility of breast cancer (dominant model: Arg/His+His/His vs. Arg/Arg).

<p>No statistically different results were obtained by excluding every single study in sequence.</p