The Importance of Proposed Changes in the “Common Rule” for ­Clinical and Translational Researchers

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/88061/1/j.1752-8062.2011.00352.x.pd

Small scale DNA preps for Neurospora crassa

Molecular biology experiments often require preparation of small amounts of DNA from many samples. This abbreviated DNA isolation method yields an average of 0.6 micrograms of genomic DNA that is suitable for Southern analysis or PCR. Starting with fresh mycelium, 20 to 40 samples can be processed in approximately two hours. Better yields (about 5 micrograms) may be obtained by suspending approximately 100 microliters of ground lyophilized mycelium in 500 microliters of isolation buffer and following the protocol starting from step 4. Spin refers to centrifugation of samples at 14,000 rpm in a microcentrifuge

Flume testing of underwater seep detection using temperature sensing on or just below the surface of sand or gravel sediments

Temperature anomalies can identify locations of seeps of groundwater into surface waters. However, the method’s sensitivity to details such as thermometer burial depth, sediment material, seep velocity, and surface water current are largely unknown. We report on a series of laboratory flume experiments in which controlled seeps under variable sediment texture, surface currents, burial depth, and temperature differentials were imposed. The focus of the study is temperature effects at the sediment surface to a few centimeters below the sediment surface, as these locations are of particular interest when using fiber-optic distributed temperature sensors (DTS). The data demonstrate: (1) without surface water flow, seep-related thermal anomalies were apparent in all cases, i.e., the method is feasible in such cases; (2) probe burial is helpful for fine sediment although not effective with coarse bed sediment, i.e., the method is strongly sensitive to sediment properties; (3) placing a thin rubber sheet over an unburied thermal probe increases detection of seeps in some circumstances, but not in others, and is generally not as robust as probe burial; and (4) local surface flow velocity, details of probe position and depth, and seepage velocity all influence observed temperature anomalies, limiting the opportunity to quantify seepage velocity, particularly with unburied temperature sensors. Overall, these findings suggest optimal installation would be at a well-defined depth within fine sediment, that installation in gravel and coarser sediment is not suited to the method if there are any significant surface currents, and that more data would be required to obtain accurate estimates of seepage velocity, though a single sensor may be sufficient to identify the location of seepage.Keywords: Temperature, Gravel, Sand, Flow, Sediment, Seepag

Active-distributed temperature sensing to continuously quantify vertical flow in boreholes

We show how a distributed borehole flowmeter can be created from armored Fiber Optic cables with the Active-Distributed Temperature Sensing (A-DTS) method. The principle is that in a flowing fluid, the difference in temperature between a heated and unheated cable is a function of the fluid velocity. We outline the physical basis of the methodology and report on the deployment of a prototype A-DTS flowmeter in a fractured rock aquifer. With this design, an increase in flow velocity from 0.01 to 0.3 m s−1 elicited a 2.5°C cooling effect. It is envisaged that with further development this method will have applications where point measurements of borehole vertical flow do not fully capture combined spatiotemporal dynamics

A simple plating assay for aneuploidy in sexual progeny of Neurospora crassa, and a new allele of mei-1.

We developed a simple ascospore plating assay for aneuploidy, based on identifying disomic progeny that inherit two independently selectable mtr alleles. We validated the assay using a known meiotic mutant, mei-2. We used this assay to demonstrate that elevated frequencies of aneuploidy previously reported to be associated with reduced DNA methylation were not, in fact, due to the methylation deficiencies. A new allele of the mei-1 gene was responsible for some of the high aneuploidy

Use of a bacterial hygromycin B resistance gene as a dominant selectable marker in Neurospora crassa transformation

Dominant transformation markers allow maximum flexibility in the choice of transformation recipients

A method for finding the genetic map position of cloned DNA fragments

A method for finding the genetic map position of cloned DNA fragment

One-Liners

One-Liners from P.T. Borgia, J. Irelan and E.U. Selker, and B.C. Turner and A. Fairfiel

Probabilistic classification of acute myocardial infarction from multiple cardiac markers

Logistic regression and Gaussian mixture model (GMM) classifiers have been trained to estimate the probability of acute myocardial infarction (AMI) in patients based upon the concentrations of a panel of cardiac markers. The panel consists of two new markers, fatty acid binding protein (FABP) and glycogen phosphorylase BB (GPBB), in addition to the traditional cardiac troponin I (cTnI), creatine kinase MB (CKMB) and myoglobin. The effect of using principal component analysis (PCA) and Fisher discriminant analysis (FDA) to preprocess the marker concentrations was also investigated. The need for classifiers to give an accurate estimate of the probability of AMI is argued and three categories of performance measure are described, namely discriminatory ability, sharpness, and reliability. Numerical performance measures for each category are given and applied. The optimum classifier, based solely upon the samples take on admission, was the logistic regression classifier using FDA preprocessing. This gave an accuracy of 0.85 (95% confidence interval: 0.78–0.91) and a normalised Brier score of 0.89. When samples at both admission and a further time, 1–6 h later, were included, the performance increased significantly, showing that logistic regression classifiers can indeed use the information from the five cardiac markers to accurately and reliably estimate the probability AMI