Rapid isolation of yeast genomic DNA: Bust n' Grab

BACKGROUND: Mutagenesis of yeast artificial chromosomes (YACs) often requires analysis of large numbers of yeast clones to obtain correctly targeted mutants. Conventional ways to isolate yeast genomic DNA utilize either glass beads or enzymatic digestion to disrupt yeast cell wall. Using small glass beads is messy, whereas enzymatic digestion of the cells is expensive when many samples need to be analyzed. We sought to develop an easier and faster protocol than the existing methods for obtaining yeast genomic DNA from liquid cultures or colonies on plates. RESULTS: Repeated freeze-thawing of cells in a lysis buffer was used to disrupt the cells and release genomic DNA. Cell lysis was followed by extraction with chloroform and ethanol precipitation of DNA. Two hundred ng – 3 μg of genomic DNA could be isolated from a 1.5 ml overnight liquid culture or from a large colony. Samples were either resuspended directly in a restriction enzyme/RNase coctail mixture for Southern blot hybridization or used for several PCR reactions. We demonstrated the utility of this method by showing an analysis of yeast clones containing a mutagenized human β-globin locus YAC. CONCLUSION: An efficient, inexpensive method for obtaining yeast genomic DNA from liquid cultures or directly from colonies was developed. This protocol circumvents the use of enzymes or glass beads, and therefore is cheaper and easier to perform when processing large numbers of samples

ECONOMIC IMPACTS ON THE ILLINOIS ECONOMY OF ALTERNATIVE DAIRY PRODUCTION SYSTEMS

Dairy in Illinois has declined in farm numbers, cows, and value of dairy product. Alternative dairy systems (intensive grazing, traditional, and a concentrated feeding system) were evaluated for their potential to sustain dairy in Illinois. The economic impact of each system on the Illinois economy was evaluated using IMPLAN.Livestock Production/Industries,

PUBLIC PERCEPTIONS REGARDING GROWTH OF THE DAIRY INDUSTRY IN ILLINOIS

Community opposition to dairies has altered location decisions by milk producers. Our objective was to identify residents' perceptions towards dairy by individual and community characteristics. A mail survey of residents of dairy counties and non-dairy counties was conducted. Dairy county residents were more willing to live close to a dairy.Livestock Production/Industries,

The Muscle Ankyrin Repeat Proteins CARP, Ankrd2, and DARP Are Not Essential for Normal Cardiac Development and Function at Basal Conditions and in Response to Pressure Overload

Ankrd1/CARP, Ankrd2/Arpp, and Ankrd23/DARP belong to a family of stress inducible ankyrin repeat proteins expressed in striated muscle (MARPs). The MARPs are homologous in structure and localized in the nucleus where they negatively regulate gene expression as well as in the sarcomeric I-band, where they are thought to be involved in mechanosensing. Together with their strong induction during cardiac disease and the identification of causative Ankrd1 gene mutations in cardiomyopathy patients, this suggests their important roles in cardiac development, function, and disease. To determine the functional role of MARPs in vivo, we studied knockout (KO) mice of each of the three family members. Single KO mice were viable and had no apparent cardiac phenotype. We therefore hypothesized that the three highly homologous MARP proteins may have redundant functions in the heart and studied double and triple MARP KO mice. Unexpectedly, MARP triple KO mice were viable and had normal cardiac function both at basal levels and in response to mechanical pressure overload induced by transverse aortic constriction as assessed by echocardiography and hemodynamic studies. Thus, CARP, Ankrd2, and DARP are not essential for normal cardiac development and function at basal conditions and in response to mechanical pressure overload

Malware Type Recognition and Cyber Situational Awareness

Current technologies for computer network and host defense do not provide suitable information to support strategic and tactical decision making processes. Although pattern-based malware detection is an active research area, the additional context of the type of malware can improve cyber situational awareness. This additional context is an indicator of threat capability thus allowing organizations to assess information losses and focus response actions appropriately. Malware Type Recognition (MaTR) is a research initiative extending detection technologies to provide the additional context of malware types using only static heuristics. Test results with MaTR demonstrate over a 99% accurate detection rate and 59% test accuracy in malware typing

Malware Target Recognition via Static Heuristics

Organizations increasingly rely on the confidentiality, integrity and availability of their information and communications technologies to conduct effective business operations while maintaining their competitive edge. Exploitation of these networks via the introduction of undetected malware ultimately degrades their competitive edge, while taking advantage of limited network visibility and the high cost of analyzing massive numbers of programs. This article introduces the novel Malware Target Recognition (MaTR) system which combines the decision tree machine learning algorithm with static heuristic features for malware detection. By focusing on contextually important static heuristic features, this research demonstrates superior detection results. Experimental results on large sample datasets demonstrate near ideal malware detection performance (99.9+% accuracy) with low false positive (8.73e-4) and false negative rates (8.03e-4) at the same point on the performance curve. Test results against a set of publicly unknown malware, including potential advanced competitor tools, show MaTR’s superior detection rate (99%) versus the union of detections from three commercial antivirus products (60%). The resulting model is a fine granularity sensor with potential to dramatically augment cyberspace situation awareness

Application of Dynamic System Identification to Timber Beams - part I

In this first part of a two-part paper, development of a method of dynamic system identification for timber beams is presented with an analytical verification of the method using a finite-element model. A method of global nondestructive evaluation for identifying local damage and decay in timber beams is investigated in this paper. Experimental modal analysis is used in conjunction with a previously developed damage localization algorithm. The damage localization algorithm utilizes changes in modal strain energy between the mode shapes of a calibrated model, representing the undamaged state of the beam of interest, and the experimentally obtained mode shapes for a timber beam. Analytical evaluations were performed to demonstrate and verify the use of this method of global nondestructive evaluation for the localization of damage or decay in timber beams. In a companion paper, experimental laboratory tests are presented that verify the use of dynamic system identification to locate damage within timber beams

Transgenic Expression of Human LAMA5 Suppresses Murine Lama5 mRNA and Laminin α5 Protein Deposition

Laminin α5 is required for kidney glomerular basement membrane (GBM) assembly, and mice with targeted deletions of the Lama5 gene fail to form glomeruli. As a tool to begin to understand factors regulating the expression of the LAMA5 gene, we generated transgenic mice carrying the human LAMA5 locus in a bacterial artificial chromosome. These mice deposited human laminin α5 protein into basement membranes in heart, liver, spleen and kidney. Here, we characterized two lines of transgenics; Line 13 expressed ∼6 times more LAMA5 than Line 25. Mice from both lines were healthy, and kidney function and morphology were normal. Examination of developing glomeruli from fetal LAMA5 transgenics showed that the human transgene was expressed at the correct stage of glomerular development, and deposited into the nascent GBM simultaneously with mouse laminin α5. Expression of human LAMA5 did not affect the timing of the mouse laminin α1–α5 isoform switch, or that for mouse laminin β1–β2. Immunoelectron microscopy showed that human laminin α5 originated in both glomerular endothelial cells and podocytes, known to be origins for mouse laminin α5 normally. Notably, in neonatal transgenics expressing the highest levels of human LAMA5, there was a striking reduction of mouse laminin α5 protein in kidney basement membranes compared to wildtype, and significantly lower levels of mouse Lama5 mRNA. This suggests the presence in kidney of a laminin expression monitor, which may be important for regulating the overall production of basement membrane protein