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Koch S.L.,Federal Bureau of Investigation Laboratory | Michaud A.L.,National Laboratory Center | Mikell C.E.,Federal Bureau of Investigation Laboratory
Journal of Forensic Sciences | Year: 2013

Although it has been generally accepted within the forensic hair community that decompositional changes in the form of an identifiable banding pattern can occur in the root area of hairs after death, little detailed information with regard to this phenomenon is known (e.g., rates at which this occurs and conditions that cause this banding). Hairs were collected daily from bodies placed in water, an air-conditioned environment, an enclosed vehicle, on the surface of the ground, and buried at the University of Tennessee Forensic Anthropology Center. The hairs were examined microscopically and the level of change documented for each environment. The onset of the banding was observed to have been delayed in water, air-conditioning, and cold weather and was hastened by warm weather and within the vehicle. This study provides validation that decomposition does produce varying effects on hair at the proximal portion of a hair root, including a dark band. © 2012 American Academy of Forensic Sciences.

Adamowicz M.S.,University of New Haven | Stasulli D.M.,University of New Haven | Sobestanovich E.M.,University of New Haven | Bille T.W.,National Laboratory Center
PLoS ONE | Year: 2014

Samples for forensic DNA analysis are often collected from a wide variety of objects using cotton or nylon tipped swabs. Testing has shown that significant quantities of DNA are retained on the swab, however, and subsequently lost. When processing evidentiary samples, the recovery of the maximum amount of available DNA is critical, potentially dictating whether a usable profile can be derived from a piece of evidence or not. The QIAamp DNA Investigator extraction kit was used with its recommended protocol for swabs (one hour incubation at 56°C) as a baseline. Results indicate that over 50% of the recoverable DNA may be retained on the cotton swab tip, or otherwise lost, for both blood and buccal cell samples when using this protocol. The protocol's incubation time and temperature were altered, as was incubating while shaking or stationary to test for increases in recovery efficiency. An additional step was then tested that included periodic re-suspension of the swab tip in the extraction buffer during incubation. Aliquots of liquid blood or a buccal cell suspension were deposited and dried on cotton swabs and compared with swab-less controls. The concentration of DNA in each extract was quantified and STR analysis was performed to assess the quality of the extracted DNA. Stationary incubations and those performed at 65°C did not result in significant gains in DNA yield. Samples incubated for 24 hours yielded less DNA. Increased yields were observed with three and 18 hour incubation periods. Increases in DNA yields were also observed using a swab re-suspension method for both cell types. The swab re-suspension method yielded an average two-fold increase in recovered DNA yield with buccal cells and an average three-fold increase with blood cells. These findings demonstrate that more of the DNA collected on swabs can be recovered with specific protocol alterations. © 2014, Public Library of Science. All rights reserved.

Bille T.,National Laboratory Center | Bright J.-A.,ESR | Buckleton J.,ESR
Journal of Forensic Sciences | Year: 2013

Mixed DNA profiles are being encountered more frequently as laboratories analyze increasing amounts of touch evidence. If it is determined that an individual could be a possible contributor to the mixture, it is necessary to perform a statistical analysis to allow an assignment of weight to the evidence. Currently, the combined probability of inclusion (CPI) and the likelihood ratio (LR) are the most commonly used methods to perform the statistical analysis. A third method, random match probability (RMP), is available. This article compares the advantages and disadvantages of the CPI and LR methods to the RMP method. We demonstrate that although the LR method is still considered the most powerful of the binary methods, the RMP and LR methods make similar use of the observed data such as peak height, assumed number of contributors, and known contributors where the CPI calculation tends to waste information and be less informative. © 2013 American Academy of Forensic Sciences.

News Article | April 6, 2016
Site: www.scientificcomputing.com

Over the past decade, University of Chicago professor and INCITE investigator Benoît Roux has made great strides in biochemistry using Argonne Leadership Computing Facility resources. One of his recent discoveries fills in essential information inaccessible to experimentalists, and potentially crucial to new therapeutic drug design. “Molecular machines,” composed of protein components, consume energy in order to perform specific biological functions. The concerted actions of the proteins trigger many of the critical activities that occur in living cells. However, like any machine, the components can break (through various mutations) and then the proteins fail to perform their functions correctly. It is known that malfunctioning proteins can result in a host of diseases, but pinpointing when and how a malfunction occurs is a significant challenge. Usually, very few functional states of molecular machines are determined by experimentalists working in wet laboratories. Therefore, more structure-function information is needed to develop an understanding of disease processes and to design novel therapeutic agents. The research team of Benoît Roux, a professor in the University of Chicago’s Department of Biochemistry and Molecular Biology and a senior scientist in the U.S. Department of Energy’s (DOE) Argonne National Laboratory Center for Nanoscale Materials, relies on an integrative approach to discover and define the basic mechanisms of biomolecular systems — an approach that relies on theory, modeling and running large-scale simulations on some of the fastest open-science supercomputers in the world. Computers have already changed the landscape of biology in considerable ways; modeling and simulation tools are routinely used to fill in knowledge gaps from experiments, and they are used to help design and define research studies. Petascale supercomputing provides a window into something else entirely: the ability to calculate all the interactions occurring between the atoms and molecules in a biomolecular system, such as a molecular machine, and visualize the motion that emerges. Roux’s team recently concluded a three-year Innovative and Novel Computational Impact on Theory and Experiment (INCITE) project at the Argonne Leadership Computing Facility (ALCF), a DOE Office of Science User Facility, to understand how P-type ATPase ion pumps — an important class of membrane transport proteins — operate. Over the past decade, Roux and his collaborators, Avisek Das, Mikolai Fajer, and Yilin Meng, have been developing new computational approaches to simulate virtual models of biomolecular systems with an unprecedented accuracy. The team exploits state-of-the-art developments in molecular dynamics (MD) and protein modeling. The MD simulation approach, frequently used in computational physics and chemistry, calculates the motions of all the atoms in a given molecular system over time — information that’s impossible to access experimentally. In biology, large-scale MD simulations provide a perspective to understand how a biologically important molecular machine functions. For several years, Roux’s research has been focused on membrane proteins, which control the bidirectional flow of material and information in a cell. Now, in a major breakthrough, he and his team have described the complete transport cycle in atomic detail of a large calcium pump called Sarco/endoplasmic reticulum calcium ATPase, or SERCA, which plays an important role in normal muscle contraction. This membrane protein uses the energy from ATP hydrolysis to transport calcium ions against their concentration gradient and, importantly, its malfunction causes cardiac and skeletal muscle diseases. Roux and his team wanted to understand how SERCA functions in a membrane, so he set out to build a complete atomistic picture of the pump in action. Das, a postdoctoral research fellow in Roux’s lab, did that by obtaining all the transition pathways for the entire ion transport cycle using an approach called the string method — essentially capturing a “molecular movie” of the transport process, frame-by-frame, of how different protein components and parts within the proteins communicated with each other. This achievement has yielded an unprecedented level of detail about the pump’s mechanism, which can now be exploited by experimentalists to further probe this important system. A membrane protein, like all protein molecules, consists of a long chain of amino acids. Once fully formed, it folds into a highly specific conformation that enables it to perform its biological function. Membrane proteins change shape and go through many conformational “states” to perform their functions. “From a scientific standpoint, membrane proteins, such as the calcium pump, are very interesting because they undergo complex changes in their three-dimensional conformations,” said Roux. “Ultimately, a better understanding may have a great impact on human health.” Experimentalists understand the structural details of proteins’ stable conformational states, but very little about the process by which a protein changes from one conformational state to another. “Only computer simulation can explore the interactions that occur during these structural transitions,” said Roux. Intermediate conformations along these transitions could potentially provide the essential information needed for the discovery of novel therapeutic agent design. (Drugs are essentially molecules that counteract the effect of bad mutations to help recover the normal functions of the protein.) Because membrane proteins regulate many aspects of cell physiology, they can serve as possible diagnostic tools or therapeutic targets. Roux and his team are trying to obtain detailed knowledge about all of the relevant conformational states that occur during the transport cycle of SERCA. In years one and two of his study, Roux’s team identified two of the conformation transition pathways needed to describe SERCA’s transport cycle. Last year, the project shifted focus to the three remaining pathways. As is the case for much of the domain science research being conducted on DOE leadership supercomputer systems today, biomolecular science relies on advances in methodology, as well as in software and hardware technologies. The usefulness of Roux’s simulations hinges on the accuracy of the modeling parameters and on the efficiency of the MD algorithm enabling the adequate sampling of motions. Computational science teams can spend years refining their application code to do what they need it to do, which is often to simulate a particular physical phenomenon at the necessary space and time scales. Code advancements can push the simulation capabilities and take advantage of the machine’s features, such as high processor counts or advanced chips, to evolve the system for longer and longer periods of time. Roux and his team used a premier MD simulation code, called NAMD, that combines two advanced algorithms — the swarm-of-trajectory string method and multi-dimensional umbrella sampling. NAMD, which was first developed at the University of Illinois at Urbana-Champaign by Klaus Schulten and Laxmikant Kale, is a program used to carry out classical simulations of biomolecular systems. It is based on the Charm++ parallel programming system and runtime library, which provides infrastructure for implementing highly scalable parallel applications. When combined with a machine-specific communication library (such as PAMI, available on the Blue Gene/Q), the string method can achieve extreme scalability on leadership-class supercomputers. ALCF staff provided maintenance and support for NAMD software and helped to coordinate and monitor the jobs running on Mira, ALCF’s 10-petaflops IBM Blue Gene/Q. ALCF computational scientist Wei Jiang has been actively collaborating with Roux’s team since 2012, as part of Mira’s Early Science Program. Jiang worked with IBM’s system software team on early stage porting and optimization of NAMD on the Blue Gene/Q architecture. He is also one of the core developers of NAMD’s multiple copy algorithm, which is the foundation for multiple INCITE projects that use NAMD. Jiang, who has a background in computational biology, considers the recent work a significant breakthrough. “Only in the third year of the project did we begin to see real progress,” said Jiang. “The first and second year of an INCITE project is often accumulated experience.” The computations Roux and his team ran for this breakthrough work will serve as a roadmap for simulating and visualizing the basic mechanisms of biomolecular systems going forward. By studying experimentally well-characterized systems of increasing size and complexity within a unified theoretical framework, Roux’s approach offers a new route for addressing fundamental biological questions. Roux’s team can be considered to be among the bleeding-edge users of the ALCF, the recipient of a steady succession of INCITE awards on Blue Gene systems since 2008, and whose work on supercomputing resources at Argonne dates back to the laboratory’s Blue Gene/L, which the Mathematics and Computer Science Division installed in 2005 for evaluation. When ALCF’s next-generation system Theta arrives later this year, Roux’s team will again be among the early science users. This research is supported by DOE’s Office of Science. Computing time at the ALCF was allocated through DOE’s Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program. Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy's Office of Science. The U.S. Department of Energy's Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time.

Diegoli T.M.,413 Research Blvd | Farr M.,National Laboratory Center | Cromartie C.,National Laboratory Center | Cromartie C.,FBI Laboratory | And 3 more authors.
Forensic Science International: Genetics | Year: 2012

Damage to the DNA molecule can occur through exposure to environmental conditions such as ultraviolet light, heat and humidity. Forensic samples are particularly prone to such damage due to their prolonged exposure after deposition at crime scenes or mass disasters. Current methods for typing such samples rely heavily on the intact DNA template, and can be adversely affected by damage that is present. Proposed solutions center around increased access to the smaller remaining fragments and/or increased sensitivity. However, all rely on the polymerase chain reaction to copy the starting material; the required polymerase can be impeded by certain types of damage such as dimer-formation after ultraviolet light exposure, resulting in stochastic effects that can complicate interpretation. In vitro repair of such damage offers the ability to generate high quality profiles using traditional methods without changes to the current amplification reagents or conditions. Typically, repair reactions required large quantities of starting material and a separate repair reaction. Forensic samples, however, usually consist of small quantities, and quality control measures necessitate laboratory procedures that minimize sample manipulation. Here, an optimized protocol for forensic application of the PreCR™ Repair Mix to current typing methods is demonstrated for samples damaged by ultraviolet light exposure. © 2011 Published by Elsevier Ireland Ltd.

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