Greg Hampikian

The Y-STR Genetic Diversity of an Idaho Basque Population, with Comparison to European Basques and US Caucasians

Josu Zubizarreta et al. — Thu, 05 Jan 2012 15:21:05 PST

Fifty unrelated Basque males from southwest Idaho were typed for the 17 Y-STR loci in the Yfiler multiplex kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385a/b). A total of 42 haplotypes were identified, with no more than two individuals sharing a single haplotype. The haplotype diversity (HD) was 0.9935, and gene diversity (D) over loci was 0.457 ± 0.137. The Idaho Basque population was compared to the source population from the Basque autonomous region of Northern Spain and Southern France, as well as a US Caucasian population. The haplotype diversity for the immigrant Basque sample is within 0.4% of the haplotype diversity of the European Basques (0.9903); thus the power of discrimination is similar for each population. The Idaho Basque population has less diversity in 9 out of 16 loci (considering DYS385a/b together) and 3% less diversity across all loci, compared to the European Basque population. A multi-dimensional scaling analysis (MDS) was created using pairwise R_ST values to compare the Idaho Basques to other populations. Based upon R_ST and F_ST measures, no significant differentiation was found between the Idaho and source European Basque population.

Exit to Freedom

Greg Hampikian et al. — Mon, 05 Dec 2011 16:59:30 PST

This is the first-ever personal account of a wrongful conviction overturned by DNA evidence. "With God as my witness, I have been falsely accused of these crimes. I did not commit them. I'm an innocent man." In 1983 Calvin C. Johnson Jr. spoke these words to a judge who later handed down a life sentence for rape and related crimes. Johnson spent sixteen years behind bars before he was freed in 1999 after DNA testing conclusively proved him not guilty. "Exit to Freedom" is the unforgettable story of Johnson's unrelenting quest for justice against incredible odds and under circumstances that threatened to shred his dignity and hope. As Johnson recalls his trial and long journey toward freedom through five Georgia prisons, he speaks candidly about everything from his middle-class childhood in Atlanta to the reasons he became a rape suspect to the steadfast support of his family. However disturbed readers may become by this portrait of a justice system undermined by its own cynicism, Johnson feels no bitterness toward his accusers. In a book that offers many lessons about freedom, that may be the most important one of all.

A Prototype Continuous Flow Polymerase Chain Reaction LTCC Device

Korey Moeller et al. — Fri, 02 Dec 2011 13:30:58 PST

There is a growing need for remote biological sensing in both laboratory and harsh field environments. Sensing and detection of biological entities such as anthrax, Ebola and other micro-organisms of interest involves sampling of the environment, amplification, analysis and identification of the target DNA. A key component of such a sensor is a low cost, portable, reusable, continuous flow polymerase chain reaction (PCR) thermal cycler. Fabrication with low temperature co-fired ceramics (LTCC) can provide a reusable low cost device capable of operating in a wide range of environments The design and manufacture of a prototype continuous flow micro-fluidic PCR device using low temperature co-fired ceramic is presented. Initial modeling of flow characteristics and heat transfer was carried out in SolidWorks™. The prototype device employs resistance heaters below the channels, buried and surface thermocouples for temperature monitoring, and air gaps for thermal isolation.

Subjectivity and Bias in Forensic DNA Mixture Interpretation

Itiel E. Dror et al. — Fri, 02 Dec 2011 13:30:55 PST

The objectivity of forensic science decision making has received increased attention and scrutiny. However, there are only a few published studies experimentally addressing the potential for contextual bias. Because of the esteem of DNA evidence, it is important to study and assess the impact of subjectivity and bias on DNA mixture interpretation. The study reported here presents empirical data suggesting that DNA mixture interpretation is subjective. When 17 North American expert DNA examiners were asked for their interpretation of data from an adjudicated criminal case in that jurisdiction, they produced inconsistent interpretations. Furthermore, the majority of 'context free' experts disagreed with the laboratory's pre-trial conclusions, suggesting that the extraneous context of the criminal case may have influenced the interpretation of the DNA evidence, thereby showing a biasing effect of contextual information in DNA mixture interpretation.

A Simple Method to Tune the Gross Antibacterial Activity of Cellulosic Biomaterials

Lambrini Adamopoulos et al. — Fri, 02 Dec 2011 13:30:52 PST

A very preliminary approach for grossly tuning the antibacterial activity of cellulosic fibers has been developed and its preliminary findings are described herein. The approach is universal for cellulosic-based substrates and first involves a physico-chemical adsorption phenomenon between fatty acid methyl esters (FAMEs) and cellulose. The cellulose biomaterials were in the form of disks 2 cm in diameter that were subjected to standard agar growth plates containing a gamut of gram positive and gram negative bacteria. Zones of inhibition were measured around the biomaterials which displayed a broad spectrum of antibacterial activity. This activity could be tuned simply by grossly changing the surface area of the cellulosic surface topology as indicated by the surface fibrillation of the microfibrils and hence the bioactive availability of the fatty acids. Thus, the potential application of these materials in the biomedical field appears promising.

The Genetics of Innocence: Analysis of 194 U.S. DNA Exonerations

Greg Hampikian et al. — Thu, 15 Sep 2011 08:21:21 PDT

This new analysis of 194 DNA exonerations, representing 171 criminal events, examines the types of evidence and DNA testing that have been used to free the victims of wrongful conviction. The types of DNA testing used to free the innocent parallels the growth of these techniques in forensic science. Short tandem repeat (STR) analysis now prevails (70%), though Y-STR analysis (16%) and mitochondrial testing (10%) are still used when STR analysis is not feasible, and the recently developed mini-STRs have been used for exonerations since 2008 (2.6%). The types of exculpatory evidence included intimate swabs (65%), clothing (53%), hair (13%), fingernail evidence (5%), cigarettes (3%), and other evidence. The most common factor associated with wrongful convictions was misidentification (75%), including misidentification by the victim (65%). False confessions (including admissions and pleas) were obtained in 30% of the cases, and informant testimony (including jailhouse and government informants) was used in 22% of the false convictions. Several types of invalid forensic science testimony were used to wrongfully convict in the 146 trials where transcripts or reliable forensic science data were available for analysis. Invalid testimony included serology (38%), hair comparison (22%), fingerprint comparison (2%), and bite mark comparison (3%). In 43% of the exonerations, the true perpetrator of the crime was identified through postconviction testing.

Mitochondrial DNA Analysis of an Immigrant Basque Population: Loss of Diversity Due to Founder Effects

Michael C. Davis et al. — Wed, 29 Jun 2011 12:36:26 PDT

The Basques have a well-documented history of migration and settlement in the Americas, and they often retain cultural identity across generations. Numerous genetic studies have been carried out on European Basques; thus, immigrant Basques are an ideal population for investigating the genetic consequences of a recent human migration event. We have sampled 53 unrelated individuals with Basque ancestry in Boise, Idaho and determined the mitochondrial DNA (mtDNA) sequence variation of the first and second hypervariable regions. Thirty-six mtDNA haplotypes were detected in our sample. We found evidence of genetic changes consistent with founder effects, which is compatible with the known history of migration. Compared with the European Basque population, the immigrant Basques are significantly different in terms of haplogroup frequency distribution and diversity. They have a lower measure of weighted intralineage mean pairwise diversity (WIMP) and greater genetic distance from other European populations. These data indicate that this immigrant Basque population has experienced a reduction in genetic diversity compared with the putative source population. However, this loss of diversity is not detectable using indices of demographic history such as Tajima’s D and Fu’s F. This study represents the first description of mtDNA diversity in an immigrant Basque population, and our findings indicate that founder effects accompanying this relatively recent migration event have shaped the genetic diversity of this population.

Ribonucleotide and Ribonucleoside Determination by Ambient Pressure Ion Mobility Spectrometry

Abu B. Kanu et al. — Wed, 29 Jun 2011 12:36:16 PDT

Detection limits and reduced mobilities for 12 ribonucleotides and 4 ribonucleosides were measured by ambient pressure electrospray ionization–ion mobility spectrometry (ESI–IMS). With the instrument used in this study it was possible to separate some of these compounds within mixtures. Detection limits reported for ribonucleotides and ribonucleosides ranged from 15 to 300 pmol and the reduced mobilities ranged from 41 to 56 suggesting that ambient pressure ESI–IMS may be used for their rapid and sensitive separation and detection. This report demonstrates that it was possible to use ion mobility spectrometry (IMS) to obtain a spectrum for the separation of nucleotides and nucleosides in less than 1 min. The application holds great promise for nucleotide analysis in the area of separating DNA fragments in genome sequencing and also for forensics DNA typing examinations used for the identification of blood stains in crime scenes and paternity testing.

Morphology, Morphometrics, and Molecular Characterization of Bryophrya gemmea n. sp. (Ciliophora, Colpodea): Implications for the Phylogeny and Evolutionary Scenario for the Formation of Oral Ciliature in the Order Colpodida

William A. Bourland et al. — Thu, 26 May 2011 14:22:30 PDT

We studied the morphology, morphometry, resting, and reproductive cysts, as well as the molecular phylogeny of Bryophrya gemmea n. sp., a colpodid ciliate that was discovered in ephemeral puddles in Idaho, northwest United States. This new species is distinguished from congeners by the irregularly pentagonal adoral organelles, four to five vestibular kineties, the single micronucleus, and one to three rows of brightly refractive protuberant interkinetal cortical granules to the right of the preoral suture. Resting cysts have two distinct membranes and an outer mucous coat. As typical for most colpodids, reproduction occurs in division cysts but details of ontogenesis are unknown. The 18S rRNA gene sequence shows only weak support for the phylogenetic relationship between Bryophrya and the bryophryid genus Notoxoma previously inferred from morphologic characters. Further, our molecular phylogenies classify bryophryids rather basal within the order Colpodida, not supporting ordinal status suggested by morphologists. Based on molecular data and morphologic characters, the colpodid genus Ilsiella is removed from the family Marynidae and placed in a new family, Ilsiellidae. Considering the molecular data, an evolutionary scenario for the formation of colpodid oral structures from a cyrtolophosidid ancestor through a bryophryid intermediate is proposed.

Phenotypic and Cytologic Studies of Lymphoid Cells and Monocytes in Primary Culture of Porcine Bone Marrow During Infection of African Swine Fever Virus

E. M. Karalova et al. — Mon, 23 May 2011 14:44:45 PDT

We have modeled in vitro infection of African swine fever virus (ASFV) in primary unstimulated cells of the porcine bone marrow and have studied the phenotypical cytophotometry. Monocytes and large-sized lymphocytes completely vanished in 72 h of infection which is result of high sensitivity of those cells to ASFV. We describe DNA synthesis in monocytes at 24 h post infection. Cytophotometry of the uninfected cells revealed the few number of atypical lymphocytes and lymphoblasts after 72 h of cultivation; whereas in viral infected cultures, atypical cells appeared in large quantity (about 14%) with 24 h. Most of atypical lymphocytes and lymphoblasts had altered nucleus, and only a small number of atypical cells had additional nucleus. The cytophotometry of main and additional nuclei showed that DNA content didn’t exceed diploid standard which indicates that the additional nuclei were consequence of fragmentation of nuclei in lymphocytes.

DockoMatic - Automated Ligand Creation and Docking

Casey W. Bullock et al. — Tue, 19 Apr 2011 13:43:49 PDT

Background: The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions.

Results: DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations.

Conclusions: DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

Exit to Freedom

Calvin C. Johnson, Jr. et al. — Fri, 16 Jan 2009 14:43:53 PST

"This is the first-ever personal account of a wrongful conviction overturned by DNA evidence. "With God as my witness, I have been falsely accused of these crimes. I did not commit them. I'm an innocent man." In 1983 Calvin C. Johnson Jr. spoke these words to a judge who later handed down a life sentence for rape and related crimes. Johnson spent sixteen years behind bars before he was freed in 1999 after DNA testing conclusively proved him not guilty. "Exit to Freedom" is the unforgettable story of Johnson's unrelenting quest for justice against incredible odds and under circumstances that threatened to shred his dignity and hope. As Johnson recalls his trial and long journey toward freedom through five Georgia prisons, he speaks candidly about everything from his middle-class childhood in Atlanta to the reasons he became a rape suspect to the steadfast support of his family. However disturbed readers may become by this portrait of a justice system undermined by its own cynicism, Johnson feels no bitterness toward his accusers. In a book that offers many lessons about freedom, that may be the most important one of all."