Greg Hampikian

A magnetic shape memory micropump: contact-free, and compatible with PCR and human DNA profiling

Magnetic shape memory (MSM) Ni–Mn–Ga elements are relatively new materials with a variety of remarkable properties. They respond to changes in magnetic fields by elongating and shortening up to 6%. We have constructed a micropump which consists principally of a single component, the MSM element. The pump can be driven by the rotation of a diametrically magnetized cylindrical magnet or by an electrical rotation of the magnetic field; it is reversible, and can be effectively operated by hand without any electrical power. The MSM element does not inhibit the polymerase chain reaction. We demonstrate that it is compatible with forensic applications and show that it does not inhibit human DNA profiling. This novel pump is suitable for lab-on-a-chip applications that require microfluidics.

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

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.

Dockomatic - automated ligand creation and docking

BackgroundThe 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.ResultsDockoMatic 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.ConclusionsDockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

Morphologic and Molecular Description of Metopus fuscus Kahl from North America and New rDNA Sequences from Seven Metopids (Armophorea, Metopidae)

Most species in the large ciliate genus Metopus Claparède & Lachmann, 1858 lack detailed descriptions based on modern morphologic and molecular methods. This lack of data for the vast majority of species hampers application of a morphospecies approach to the taxonomy of Metopus and other armophorids. In this report we redescribe the large species, Metopus fuscusKahl, 1927 based on in vivo observation, silver impregnation, scanning electron microscopy, and single-cell 18S rDNA sequencing of a freshwater North American (Idaho) population. Metopus fuscus invariably has a perinuclear envelope of endosymbiotic bacteria not found in other species. Unlike the original description of a single row of coarse granules between ciliary rows, the Idaho population has five loose rows of small interkinetal granules. We discuss the possible importance of this character in metopids. We also provide a phylogenetic analysis including seven other new metopid 18S rDNA sequences: Brachonella spiralis, B. galeata, Metopus laminarius, M. setosus, M. striatus, M. violaceus, Palmarella lata. Metopus fuscus and M. setosus form a fully supported clade, challenging previous morphospecies groupings. We discuss some ambiguities of armophorid morphologic terminology in the earlier literature. Our phylogenetic analysis of Idaho metopids indicates that the genera Metopus and Brachonella are both nonmonophyletic.

Morphology and Phylogeny of a New Woodruffiid Ciliate, Etoschophrya inornata sp. n. (Ciliophora, Colpodea, Platyophryida), with an Account on Evolution of Platyophryids

Bourland, W. A., Hampikian, G. & Vďačný, P. (2012). Morphology and phylogeny of a new woodruffiid ciliate, Etoschophrya inornata sp. n. (Ciliophora, Colpodea, Platyophryida), with an account on evolution of platyophryids. —Zoologica Scripta, 41, 400–416.

Y-STR variation in the Basque diaspora in the Western USA: evolutionary and forensic perspectives

Individuals of Basque origin migrated in large numbers to the Western USA in the second half of the nineteenth century, and the flow continued with less intensity during the last century. The European source population, that of the Basque Country, has long been a cultural and geographical isolate. Previous studies have demonstrated that Y-STR frequencies of Basques are different from those of other Spanish and European populations [1]. The Basque diaspora in the Western USA is a recent migration, but the founder effect and the incorporation of new American Y chromosomes into the paternal genetic pool of the Basque diaspora could have influenced its genetic structure and could thus have practical implications for forensic genetics. To check for genetic substructure among the European source and Basque diaspora populations and determine the most suitable population database for the Basque diaspora in the Western USA, we have analysed the haplotype distribution of 17 Y-STRs in both populations. We have found that the Basque diaspora in the Western USA largely conserve the Y chromosome lineage characteristic of the autochthonous European Basque population with no statistically significant differences. This implies that a common 17 Y-STR Basque population database could be used to calculate identification or kinship parameters regardless of whether the Basque individuals are from the European Basque Country or from the Basque diaspora in the Western USA.

Nullomer Derived Anticancer Peptides (NulloPs): Differential Lethal Effects on Normal and Cancer Cells in vitro

We demonstrate the first use of the nullomer (absent sequences) approach to drug discovery and development. Nullomers are the shortest absent sequences determined in a species, or group of species. By identifying the shortest absent peptide sequences from the NCBI databases, we screened several potential anti-cancer peptides. In order to improve cell penetration and solubility we added short poly arginine tails (5Rs), and initially solubilized the peptides in 1M trehalose. The results for one of the absent sequences 9R (RRRRRNWMWC), and its scrambled version 9S1R (RRRRRWCMNW) are reported here. We refer to these peptides derived from nullomers as PolyArgNulloPs. A control PolyArgNulloP, 124R (RRRRRWFMHW), was also included. The lethal effects of 9R and 9S1R are mediated by mitochondrial impairment as demonstrated by increased ROS production, ATP depletion, cell growth inhibition, and ultimately cell death. These effects increase over time for cancer cells with a concomitant drop in IC-50 for breast and prostate cancer cells. This is in sharp contrast to the effects in normal cells, which show a decreased sensitivity to the NulloPs over time.

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

ABSTRACT. 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.

Mitochondrial DNA analysis of an immigrant basque population: Loss of diversity due to founder effects

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 Tajimas D and Fus 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.

Morphology and Phylogeny of Bryophryoides ocellatus N. G., N. Sp. (Ciliophora, Colpodea) from In Situ Soil Percolates of Idaho, U.S.A.

We describe the morphology and 18S rDNA phylogeny of Bryophryoides ocellatus n. g., n. sp., a bryophryid ciliate inhabiting in situ soil percolates from Idaho, U.S.A. The new genus is distinguished from other bryophryid genera by a combination of the following features: (1) kreyellid (irregularly meshed) silverline pattern, (2) polymorphic adoral organelles in the preoral suture, (3) absence of vestibular kineties. In phylogenetic analyses, Bryophryoides ocellatus is most closely related to Bryophrya gemmea. The 18S rDNA sequence pairwise distance of 2% between these genera, while similar to that between many colpodidan species, exceeds that between some colpodidan genera (e.g. Mykophagophrys and Pseudoplatyophrya, 1.1%), further supporting establishment of the new genus. Topology hypothesis testing strongly supports the monophyly of the Colpodida including the bryophryids. Despite weak nodal support, tests of topology constraints narrowly reject the non-monophyly of the sequenced Bryophryidae (Bryophrya+Bryophryoides+Notoxoma). Likewise, the monophyletic origin of the sequenced Bryophryidae is indicated in the phylogenetic networks though with low support.