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Prague, Czech Republic

DNA Laboratory

Prague, Czech Republic
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Stevens E.,University College London | Carss K.J.,Wellcome Trust Sanger Institute | Cirak S.,University College London | Foley A.R.,University College London | And 23 more authors.
American Journal of Human Genetics | Year: 2013

Mutations in several known or putative glycosyltransferases cause glycosylation defects in α-dystroglycan (α-DG), an integral component of the dystrophin glycoprotein complex. The hypoglycosylation reduces the ability of α-DG to bind laminin and other extracellular matrix ligands and is responsible for the pathogenesis of an inherited subset of muscular dystrophies known as the dystroglycanopathies. By exome and Sanger sequencing we identified two individuals affected by a dystroglycanopathy with mutations in β-1,3-N-acetylgalactosaminyltransferase 2 (B3GALNT2). B3GALNT2 transfers N-acetyl galactosamine (GalNAc) in a β-1,3 linkage to N-acetyl glucosamine (GlcNAc). A subsequent study of a separate cohort of individuals identified recessive mutations in four additional cases that were all affected by dystroglycanopathy with structural brain involvement. We show that functional dystroglycan glycosylation was reduced in the fibroblasts and muscle (when available) of these individuals via flow cytometry, immunoblotting, and immunocytochemistry. B3GALNT2 localized to the endoplasmic reticulum, and this localization was perturbed by some of the missense mutations identified. Moreover, knockdown of b3galnt2 in zebrafish recapitulated the human congenital muscular dystrophy phenotype with reduced motility, brain abnormalities, and disordered muscle fibers with evidence of damage to both the myosepta and the sarcolemma. Functional dystroglycan glycosylation was also reduced in the b3galnt2 knockdown zebrafish embryos. Together these results demonstrate a role for B3GALNT2 in the glycosylation of α-DG and show that B3GALNT2 mutations can cause dystroglycanopathy with muscle and brain involvement. © 2013 The American Society of Human Genetics.

News Article | March 16, 2016
Site: www.labdesignnews.com

A third tour has been added to the Laboratory Design Conference agenda. The conference will be held April 25-27 in Houston, Texas. . Sign up to tour the Harris County Forensics facility (Existing DNA Laboratory and New Building): In January 2013, the Harris County Institute of Forensic Sciences opened its 15,000 sq. ft., state-of-the-art Forensics Genetics Laboratory within a renovated train bay of Houston’s historic Nabisco cookie plant, today known as the Texas Medical Center’s John P. McGovern Campus.  The location of the laboratory in the TMC campus allows for close collaboration with other renowned medical and research science faculties. The Institute’s Forensic Genetics Laboratory received a Certificate of Recognition for Excellence in Construction from the Texas Building Branch of the Associated General Contractors. The project consisted of 17,000 sq. ft. designed for Serology Labs, Extraction Labs, Evidence Receiving/Storage, and administrative space for the laboratory. Vaughn Construction is serving as the construction manager-at-risk, with Johnston L.L.C. as the architect. The new, 140,000 sq. ft. Main Campus of the Harris County Institute of Forensic Sciences is currently being constructed on a 3.2-acre site directly across from its existing location. The comprehensive planning process for the building, which will house both the Medical Examiner and Crime Laboratory services for Harris County, began in 2007 and incorporated experts from business, medical, laboratory and scientific fields. The resulting design culminates in an integrated use of space flowing seamlessly between clinical, laboratory, administrative, public and teaching/training areas. Consideration was also given to the exterior design of the facility to ensure it complements the aesthetics of neighboring institutions located on the Texas Medical Center Campus. The new Forensic Center is expected to be completed in 2017. Vaughn Construction is serving as the construction manager-at-risk, with Page/ as the architect. The other facilities offered as part of the Laboratory Design Conference's tour package are Brockman Hall for Physics at Rice University, and Texas Medical Center. Click here for more information about these facilities . Tours of exemplary lab facilities, including those to which attendees would not otherwise have access, are an integral part of the overall   experience. Breakfast and round-trip transportation from the hotel to these sites will be provided.

Korn M.,DNA Laboratory | Korn M.,University of Konstanz | Rabet N.,University Pierre and Marie Curie | Ghate H.V.,Modern College | And 2 more authors.
Molecular Phylogenetics and Evolution | Year: 2013

We used a combined analysis of one nuclear (28S rDNA) and three mitochondrial markers (COI, 12S rDNA, 16S rDNA) to infer the molecular phylogeny of the Notostraca, represented by samples from the six continents that are inhabited by this group of branchiopod crustaceans. Our results confirm the monophyly of both extant notostracan genera Triops and Lepidurus with good support in model based and maximum parsimony analyses. We used branchiopod fossils as a calibration to infer divergence times among notostracan lineages and accounted for rate heterogeneity among lineages by applying relaxed-clock models. Our divergence date estimates indicate an initial diversification into the genera Triops and Lepidurus in the Mesozoic, most likely at a minimum age of 152.3-233.5. Ma, i.e., in the Triassic or Jurassic. Implications for the interpretation of fossils and the evolution of notostracan morphology are discussed. We further use the divergence date estimates to formulate a biogeographic hypothesis that explains distributions of extant lineages predominantly by overland dispersal routes.We identified an additional hitherto unrecognised highly diverged lineage within Lepidurus apus lubbocki and three additional previously unknown major lineages within Triops. Within T. granarius we found deep differentiation, with representatives distributed among three major phylogenetic lineages. One of these major lineages comprises T. cancriformis, the T. mauritanicus species group and two hitherto unrecognised T. granarius lineages. Samples that were morphologically identified as T. granarius diverged from the most basal nodes within this major lineage, and divergence dates suggested an approximate age of 23.7-49.6. Ma for T. cancriformis, indicating the need for a taxonomic revision of Triassic and Permian fossils that are currently attributed to the extant T. cancriformis. We thus elevate T. cancriformis minor to full species status as Triops minor Trusheim, 1938 and include in this species the additional Upper Triassic samples that were attributed to T. cancriformis. We further elevate T. cancriformis permiensis to full species status as Triops permiensis Gand et al., 1997. © 2013 Elsevier Inc.

Barth M.B.,Martin Luther University of Halle Wittenberg | Barth M.B.,DNA Laboratory | Moritz R.F.A.,Martin Luther University of Halle Wittenberg | Moritz R.F.A.,University of Pretoria | Kraus F.B.,Martin Luther University of Halle Wittenberg
PLoS ONE | Year: 2014

The unique nomadic life-history pattern of army ants (army ant adaptive syndrome), including obligate colony fission and strongly male-biased sex-ratios, makes army ants prone to heavily reduced effective population sizes (Ne). Excessive multiple mating by queens (polyandry) has been suggested to compensate these negative effects by increasing genetic variance in colonies and populations. However, the combined effects and evolutionary consequences of polyandry and army ant life history on genetic colony and population structure have only been studied in a few selected species. Here we provide new genetic data on paternity frequencies, colony structure and paternity skew for the five Neotropical army ants Eciton mexicanum, E. vagans, Labidus coecus, L. praedator and Nomamyrmex esenbeckii ; and compare those data among a total of nine army ant species (including literature data). The number of effective matings per queen ranged from about 6 up to 25 in our tested species, and we show that such extreme polyandry is in two ways highly adaptive. First, given the detected low intracolonial relatedness and population differentiation extreme polyandry may counteract inbreeding and low N e. Second, as indicated by a negative correlation of paternity frequency and paternity skew, queens maximize intracolonial genotypic variance by increasingly equalizing paternity shares with higher numbers of sires. Thus, extreme polyandry is not only an integral part of the army ant syndrome, but generally adaptive in social insects by improving genetic variance, even at the high end spectrum of mating frequencies. © 2014 Barth et al.

Karija Vlahovic M.,DNA Laboratory | Kubat M.,DNA Laboratory
Legal Medicine | Year: 2012

This paper describes the automated purification of DNA extracted from human bones using Maxwell® 16 bench top instrument. Analysis of nuclear short tandem repeats (STR) is invaluable in identification of human remains exhumed from mass graves in Croatia. Up to today 4683 skeletal remains have been recovered and for 897 human remains identity has not been determined. DNA has been extracted from 70% of all unidentified samples. For more than 90% of the samples nuclear STR profiles have been obtained using either organic phenol/chloroform method or silica-column purification for the extraction of DNA from bones or teeth. In order to evaluate a Maxwell® 16 DNA extraction performance 40 bone samples with different stage of decomposition were analyzed. The efficacy of manual silica based extraction and an automated purification was compared. The DNA yield per gram of starting material, removal of inhibitors and the quality of resulting STR profiles of the Maxwell extracts from duplicate amplifications were evaluated. The results show that Maxwell 16 platform can be used instead of manual DNA extraction procedures. © 2012 Elsevier Ireland Ltd.

Balamurugan K.,University of Southern Mississippi | Duncan G.,DNA Laboratory
Legal Medicine | Year: 2012

We have analyzed 17 Y-chromosomal STR loci in a population sample of 69 unrelated male individuals of the Rwanda-Hutu population from East Central Africa using an AmpF. lSTR® Yfiler™ PCR amplification kit. A total of 62 unique haplotypes were identified among the 69 individuals studied. The haplotype diversity was found to be 0.9970 for this population. The gene diversity ranged from 0.1130 (DYS392) to 0.7722 (DYS385). Comparison of populations in this study with twenty-five other national and global populations using Principal Co-ordinate Analysis (PCA) and phylogenetic molecular analysis using a genetic distance matrix indicates a delineation of all the African populations from other unrelated populations. The results of population pair-wise Fst p values indicate statistically significant differentiation of the Rwandan population when compared with 25 other global populations including four African populations (p= 0.0000). Analysis of Molecular Variance (AMOVA) of the Rwanda population with four other African populations indicated a 93% variance within populations and 7% variance among the five populations. A data base search of the 62 haplotypes yielded only one non-African haplotype match, suggesting these haplotypes are unique to the African continent. © 2011 Elsevier Ireland Ltd.

Madi T.,Florida International University | Balamurugan K.,University of Southern Mississippi | Bombardi R.,University of Southern Mississippi | Duncan G.,DNA Laboratory | Mccord B.,Florida International University
Electrophoresis | Year: 2012

The goal of this study is to explore the application of epigenetic markers in the identification of biofluids that are commonly found at the crime scene. A series of genetic loci were examined in order to define epigenetic markers that display differential methylation patterns between blood, saliva, semen, and epithelial tissue. Among the different loci tested, we have identified a panel of markers, C20orf117, ZC3H12D, BCAS4, and FGF7, that can be used in the determination of these four tissue types. Since methylation modifications occur at cytosine bases that are immediately followed by guanine bases (CpG sites), methylation levels were measured at CpG sites spanning each marker. Up to 11 samples of each tissue type were collected and subjected to bisulfite modification to convert unmethylated CpG-associated cytosine bases to thymine bases. The bisulfite modified DNA was then amplified via nested PCR using a primer set of which one primer was biotin labeled. Biotinylated PCR products were in turn analyzed and the methylation level at each CpG site was quantitated by pyrosequencing. The percent methylation values at each CpG site were determined and averaged for each tissue type. The results indicated significant methylation differences between the tissue types. The methylation patterns at the ZC3H12D and FGF7 loci differentiated sperm from blood, saliva, and epithelial cells. The C20orf117 locus differentiated blood from sperm, saliva, and epithelial cells and saliva was differentiated from blood, sperm, and epithelial cells at a fourth locus, BCAS4. The results of this study demonstrate the applicability of epigenetic markers as a novel tool for the determination of biofluids using bisulfite modification and pyrosequencing. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

We used three molecular markers to investigate populations of Triops granarius from a study area in western Morocco that had a north-south span of approx. 434 km, the most distant populations situated at more than 470 km distance from each other. Previous studies had already investigated two Triops granarius populations from this region and revealed their affiliation to the major phylogenetic lineage that includes Triops cancriformis. By contrast, based on the geographic position of the type locality and the morphology of the type, Triops granarius s.s. likely belongs to a clade that forms the sister group to American and Australian Triops, i.e. including Triops longicaudatus and Triops australiensis. In the present study a second, hitherto unknown phylogenetic lineage was discovered among Moroccan populations of Tr iops granarius s.l. Our phylogenetic analyses show that both Moroccan lineages of Triops granarius s.l. represent a pair of genetically and morphologically well differentiated sister species that should be separated from Triops granarius. We therefore formally describe them as two new species, Triops maximus sp. nov. and Triops multifidus sp. nov. The early larval stages of both species show a peculiar morphology with 10 to 15 setae on the exopodite of the 2nd antenna. The number of these setae was generally thought to span five to seven in Notostraca. Despite the fact that the antennal setae form a central part of the main locomotory organ in early instars, we found their number to vary by up to two between body-sides of single individuals. Copyright © 2016 Magnolia Press.

Bright J.-A.,ESR Ltd | Bright J.-A.,University of Auckland | Neville S.,DNA Laboratory | Curran J.M.,University of Auckland | Buckleton J.S.,ESR Ltd
Australian Journal of Forensic Sciences | Year: 2014

In this paper, the variability of peak heights for mixed DNA profiles separated on two different models of a capillary electrophoresis instrument is examined. The Applied Biosystems 3500xl instrument produces larger peaks than the 3130xl instrument. If the relative difference in peak heights between the two instruments was a constant factor then all relative heights should be preserved. However, if that factor differed, say, for small versus large peaks then relative heights would change. The effect of peak height and dye on the relative difference in peak height between injections of the same amplicon on a 3500xl and 3130xl instrument for a series of mixed DNA profiles using the Promega PowerPlex 21 multiplex is described. The ratio of peak heights between instrument models resulted in values up to four times higher on the 3500 compared with the 3130. The magnitude of this difference was shown to be dependent on the dye but not on the peak heights themselves. Relative parameters stutter, heterozygote balance, and mixture proportion were very similar between the two instrument models, indicating that the interpretation guidelines developed on one machine are likely to be transportable to different capillary electrophoresis instrument models and different machines of the same model. © 2013 Australian Academy of Forensic Sciences.

Researchers identified and named a new genus of horned praying mantis, naming it Alangularis for its angled wings. Credit: Rick Wherley A scientist from The Cleveland Museum of Natural History led research that revised the horned praying mantis group and traced the evolution of its distinctive camouflage features. Dr. Gavin Svenson and his colleagues identified a new genus and new tribe of praying mantis and discovered that disruptive camouflage evolved twice within the group. The second, more recent, occasion occurred after the re-evolution of a special leg lobe that disguises the body profile to help the insect hide from predators. The research was published Nov. 16, 2015 online in the journal Systematic Entomology. Svenson and the team studied the origins of 16 features that provide disruptive crypsis for the Central and South American horned praying mantises of the subfamily Vatinae, all of which contribute to their camouflage strategy. These features include a head process or horn and leafy looking lobes on the legs. The team analyzed 33 species and nearly 400 specimens from Museum collections in the United States, South America and Europe as well as insects Svenson recently sampled from South America. "Praying mantises depend on camouflage to avoid predators, but we have known little about the patterns of how body structures contributing to crypsis evolved," said Dr. Gavin Svenson, curator of invertebrate zoology at The Cleveland Museum of Natural History and lead author of the study. "We discovered that two mantis lineages evolved structural camouflage millions of years apart in very similar ways. This not only suggests that re-evolution occurred, but demonstrates that the developmental mechanisms controlling cryptic features may be more ancient than the camouflaged mantises themselves." The research revealed that leafy lobes on the middle and hind legs evolved during the first origin of the horned mantises. Afterward, one lineage invested in a camouflage strategy and began to accumulate other leg lobes, an extended head process or horn, and even lobes on the abdomen, while the other lost these early evolved leg lobes and relied only on coloration to blend in with vegetation. However, a second, smaller lineage of mantises within this color camouflaged group began to gain disruptive cryptic features about 20 million years later after the re-evolution of those same early originating leg lobes. This second shift to a strategy of disruptive camouflage appears to have followed a remarkably similar path as the first through the accumulation of leg lobes in the same positions, as well as a similar extended head process or horn. Researchers suggested that the second origin of disruptive camouflage was most likely controlled by genetic and developmental mechanisms that were already present. Essentially, the capability to evolve camouflage was already in the genetic toolkit of the lineage and those features re-emerged when it was advantageous for survival. According to Svenson, since many other, more distantly related, mantis groups have disruptive camouflage, it may have evolved very early in praying mantises and is mostly a matter of being turned on or off in a variety of ways. The scientists used DNA sequence data generated in the Cleveland Museum of Natural History's DNA Laboratory and studied morphological features to reclassify the group. The newly identified genus, Alangularis, recognizes a unique and colorful species of praying mantis that was incorrectly included within another genus. The new genus name translates to "angled wings," which reflects its acute wing tips. The new tribe, Heterovatini, was established to include two genera that share many characteristics with the rest of Vatinae, but retain no disruptive cryptic features other than the shared leg lobes. "Finding that camouflage evolved twice in the horned mantises was surprising," said Svenson. "But even more amazing is how alike the two distantly related camouflaged groups really are and what that means for camouflage evolution in mantises as a whole." Svenson's research is focused on the evolutionary patterns of relationship, distribution and complex features of praying mantises. His current research project aims to align new sources of relationship evidence (DNA sequence data) with morphology and other features to create a new and accurate classification system for praying mantises that reflects true evolutionary relationships. Explore further: Octopuses focus on key features for successful camouflage More information: GAVIN J. SVENSON et al. Re-evolution of a morphological precursor of crypsis investment in the newly revised horned praying mantises (Insecta, Mantodea, Vatinae), Systematic Entomology (2015). DOI: 10.1111/syen.12151

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