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Genome Sequence of a Proteus mirabilis Strain Isolated from the Salivary Glands of Larval Lucilia sericata.

Recent Research Articles from UNTHSC - Sat, 07/30/2016 - 06:32

Genome Sequence of a Proteus mirabilis Strain Isolated from the Salivary Glands of Larval Lucilia sericata.

Genome Announc. 2016;4(4)

Authors: Yuan Y, Zhang Y, Fu S, Crippen TL, Visi DK, Benbow ME, Allen MS, Tomberlin JK, Sze SH, Tarone AM

Abstract
We announce a draft genome sequence of a Proteus mirabilis strain derived from Lucilia sericata salivary glands. This strain is demonstrated to attract and induce oviposition by L. sericata, a common blow fly important to medicine, agriculture, and forensics. The genome sequence will help dissect interkingdom communication between the species.

PMID: 27469950 [PubMed]

Tip110: Physical properties, primary structure, and biological functions.

Recent Research Articles from UNTHSC - Fri, 07/29/2016 - 06:31
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Tip110: Physical properties, primary structure, and biological functions.

Life Sci. 2016 Mar 15;149:79-95

Authors: Whitmill A, Timani KA, Liu Y, He JJ

Abstract
HIV-1 Tat-interacting protein of 110kDa (Tip110), also referred to as squamous cell carcinoma antigen recognized by T cells 3 (Sart3), p110 or p110(nrb), was initially identified as a cDNA clone (KIAA0156) without annotated functions. Over the past twenty years, several functions have been attributed to this protein. The proposed biological functions include roles for Tip110 in pre-mRNA splicing, gene transcription, stem cell biology, and development. Dysregulation of Tip110 is also a contributing factor in the development of cancer and other human diseases. It is clear that our understanding of this protein is rapidly evolving. In this review, we aimed to provide a summary of all the existing literature on this gene/protein and its proposed biological functions.

PMID: 26896687 [PubMed - indexed for MEDLINE]

MIEN1 drives breast tumor cell migration by regulating cytoskeletal-focal adhesion dynamics.

Recent Research Articles from UNTHSC - Thu, 07/28/2016 - 06:31

MIEN1 drives breast tumor cell migration by regulating cytoskeletal-focal adhesion dynamics.

Oncotarget. 2016 Jul 23;

Authors: Kpetemey M, Chaudhary P, Van Treuren T, Vishwanatha JK

Abstract
Migration and invasion enhancer 1 (MIEN1) is an important regulator of cell migration and invasion. MIEN1 overexpression represents an oncogenic event that promotes tumor cell dissemination and metastasis. The underlying mechanism by which MIEN1 regulates migration and invasion has yet to be deciphered. Here, we demonstrate that MIEN1 acts as a cytoskeletal-signaling adapter protein to drive breast cancer cell migration. MIEN1 localization is concentrated underneath the actin-enriched protrusive structures of the migrating breast cancer cells. Depletion of MIEN1 led to the loss of actin-protrusive structures whereas the over-expression of MIEN1 resulted in rich and thick membrane extensions. Knockdown of MIEN1 also decreased the cell-substratum adhesion, suggesting a role for MIEN1 in actin cytoskeletal dynamics. Our results show that MIEN1 supports the transition of G-actin to F-actin polymerization and stabilizes F-actin polymers. Additionally, MIEN1 promotes cellular adhesion and actin dynamics by inducing phosphorylation of FAK at Tyr-925 and reducing phosphorylation of cofilin at Ser-3, which results in breast cancer cell migration. Collectively, our data show that MIEN1 plays an essential role in maintaining the plasticity of the dynamic membrane-associated actin cytoskeleton, which leads to an increase in cell motility. Hence, targeting MIEN1 might represent a promising means to prevent breast tumor metastasis.

PMID: 27462783 [PubMed - as supplied by publisher]

Function of Ubiquitin (Ub) Specific Protease 15 (USP15) in HIV-1 Replication and Viral Protein Degradation.

Recent Research Articles from UNTHSC - Thu, 07/28/2016 - 06:31

Function of Ubiquitin (Ub) Specific Protease 15 (USP15) in HIV-1 Replication and Viral Protein Degradation.

Virus Res. 2016 Jul 23;

Authors: Pyeon D, Timani KA, Gulraiz F, Park IW

Abstract
HIV-1 Nef is necessary and may be sufficient for HIV-1-associated AIDS pathogenicity, in that knockout of Nef alone can protect HIV-infected patients from AIDS. We therefore investigated the feasibility of physical knockout of Nef, using the host ubiquitin proteasome system in HIV-1-infected cells. Our co-immunoprecipitation analysis demonstrated that Nef interacted with ubiquitin specific protease 15 (USP15), and that USP15, which is known to stabilize cellular proteins, degraded Nef. Nef could also cause decay of USP15, although Nef-mediated degradation of USP15 was weaker than USP15-mediated Nef degradation. Direct interaction between Nef and USP15 was essential for the observed reciprocal decay of the proteins. Further, USP15 degraded not only Nef but also HIV-1 structural protein, Gag, thereby substantially inhibiting HIV-1 replication. However, Gag did not degrade USP15, indicating that the Nef and USP15 complex, in distinction to other viral proteins, play an integral role in coordinating viral protein degradation and hence HIV-1 replication. Moreover, Nef and USP15 globally suppressed ubiquitylation of cellular proteins, indicating that these proteins are major determinants for the stability of cellular as well as viral proteins. Taken together, these data indicate that Nef and USP15 are vital in regulating degradation of viral and cellular proteins and thus HIV-1 replication, and specific degradation of viral, not cellular proteins, by USP15 points to USP15 as a candidate therapeutic agent to combat AIDS by eliminating viral proteins from the infected cells via USP15-mediated proteosomal degradation.

PMID: 27460547 [PubMed - as supplied by publisher]

Identification and Characterization of Novel Matrix-Derived Bioactive Peptides: A Role for Collagenase from Santyl® Ointment in Post-Debridement Wound Healing?

Recent Research Articles from UNTHSC - Thu, 07/28/2016 - 06:31
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Identification and Characterization of Novel Matrix-Derived Bioactive Peptides: A Role for Collagenase from Santyl® Ointment in Post-Debridement Wound Healing?

PLoS One. 2016;11(7):e0159598

Authors: Sheets AR, Demidova-Rice TN, Shi L, Ronfard V, Grover KV, Herman IM

Abstract
Debridement, the removal of diseased, nonviable tissue, is critical for clinicians to readily assess wound status and prepare the wound bed for advanced therapeutics or downstream active healing. Removing necrotic slough and eschar through surgical or mechanical methods is less specific and may be painful for patients. Enzymatic debridement agents, such as Clostridial collagenase, selectively and painlessly degrade devitalized tissue. In addition to its debriding activities, highly-purified Clostridial collagenase actively promotes healing, and our past studies reveal that extracellular matrices digested with this enzyme yield peptides that activate cellular migratory, proliferative and angiogenic responses to injury in vitro, and promote wound closure in vivo. Intriguingly, while collagenase Santyl® ointment, a sterile preparation containing Clostridial collagenases and other non-specific proteases, is a well-accepted enzymatic debridement agent, its role as an active healing entity has never been established. Based on our previous studies of pure Clostridial collagenase, we now ask whether the mixture of enzymes contained within Santyl® produces matrix-derived peptides that promote cellular injury responses in vitro and stimulate wound closure in vivo. Here, we identify novel collagen fragments, along with collagen-associated peptides derived from thrombospondin-1, multimerin-1, fibronectin, TGFβ-induced protein ig-h3 and tenascin-C, generated from Santyl® collagenase-digested human dermal capillary endothelial and fibroblastic matrices, which increase cell proliferation and angiogenic remodeling in vitro by 50-100% over controls. Using an established model of impaired healing, we further demonstrate a specific dose of collagenase from Santyl® ointment, as well as the newly-identified and chemically-synthesized ECM-derived peptides significantly increase wound re-epithelialization by 60-100% over saline-treated controls. These results not only confirm and extend our earlier studies using purified collagenase- and matrix-derived peptides to stimulate healing in vitro and in vivo, but these Santyl®-generated, matrix-derived peptides may also represent exciting new opportunities for creating advanced wound healing therapies that are enabled by enzymatic debridement and potentially go beyond debridement.

PMID: 27459729 [PubMed - in process]

Introduction to special issue on Advances in blood-based biomarkers of Alzheimer's disease.

Recent Research Articles from UNTHSC - Thu, 07/28/2016 - 06:31
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Introduction to special issue on Advances in blood-based biomarkers of Alzheimer's disease.

Alzheimers Dement (Amst). 2016;3:110-2

Authors: O'Bryant SE

PMID: 27453933 [PubMed]

A blood screening test for Alzheimer's disease.

Recent Research Articles from UNTHSC - Thu, 07/28/2016 - 06:31
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A blood screening test for Alzheimer's disease.

Alzheimers Dement (Amst). 2016;3:83-90

Authors: O'Bryant SE, Edwards M, Johnson L, Hall J, Villarreal AE, Britton GB, Quiceno M, Cullum CM, Graff-Radford NR

Abstract
INTRODUCTION: This study combined data across four independent cohorts to examine the positive and negative predictive values of an Alzheimer's disease (AD) blood test if implemented in primary care.
METHODS: Blood samples from 1329 subjects from multiple independent, multiethnic, community-based, and clinic-based cohorts were analyzed. A "locked-down" referent group of 1128 samples was generated with 201 samples randomly selected for validation purposes. Random forest analyses were used to create the AD blood screen. Positive (PPV) and negative (NPV) predictive values were calculated.
RESULTS: In detecting AD, PPV was 0.81, and NPV was 0.95 while using the full AD blood test. When detecting mild cognitive impairment, PPV and NPV were 0.74 and 0.93, respectively. Preliminary analyses were conducted to detect any "neurodegenerative disease". The full 21-protein AD blood test yielded a PPV of 0.85 and NPV of 0.94.
DISCUSSION: The present study creates the first-ever multiethnic referent sample that spans community-based and clinic-based populations for implementation of an AD blood screen.

PMID: 27453929 [PubMed]

Neural Control of Blood Pressure in Chronic Intermittent Hypoxia.

Recent Research Articles from UNTHSC - Thu, 07/28/2016 - 06:31
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Neural Control of Blood Pressure in Chronic Intermittent Hypoxia.

Curr Hypertens Rep. 2016 Mar;18(3):19

Authors: Shell B, Faulk K, Cunningham JT

Abstract
Sleep apnea (SA) is increasing in prevalence and is commonly comorbid with hypertension. Chronic intermittent hypoxia is used to model the arterial hypoxemia seen in SA, and through this paradigm, the mechanisms that underlie SA-induced hypertension are becoming clear. Cyclic hypoxic exposure during sleep chronically stimulates the carotid chemoreflexes, inducing sensory long-term facilitation, and drives sympathetic outflow from the hindbrain. The elevated sympathetic tone drives hypertension and renal sympathetic activity to the kidneys resulting in increased plasma renin activity and eventually angiotensin II (Ang II) peripherally. Upon waking, when respiration is normalized, the sympathetic activity does not diminish. This is partially because of adaptations leading to overactivation of the hindbrain regions controlling sympathetic outflow such as the nucleus tractus solitarius (NTS), and rostral ventrolateral medulla (RVLM). The sustained sympathetic activity is also due to enhanced synaptic signaling from the forebrain through the paraventricular nucleus (PVN). During the waking hours, when the chemoreceptors are not exposed to hypoxia, the forebrain circumventricular organs (CVOs) are stimulated by peripherally circulating Ang II from the elevated plasma renin activity. The CVOs and median preoptic nucleus chronically activate the PVN due to the Ang II signaling. All together, this leads to elevated nocturnal mean arterial pressure (MAP) as a response to hypoxemia, as well as inappropriately elevated diurnal MAP in response to maladaptations.

PMID: 26838032 [PubMed - indexed for MEDLINE]

Glycosyltransferase ST6GAL1 contributes to the regulation of pluripotency in human pluripotent stem cells.

Recent Research Articles from UNTHSC - Thu, 07/28/2016 - 06:31
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Glycosyltransferase ST6GAL1 contributes to the regulation of pluripotency in human pluripotent stem cells.

Sci Rep. 2015;5:13317

Authors: Wang YC, Stein JW, Lynch CL, Tran HT, Lee CY, Coleman R, Hatch A, Antontsev VG, Chy HS, O'Brien CM, Murthy SK, Laslett AL, Peterson SE, Loring JF

Abstract
Many studies have suggested the significance of glycosyltransferase-mediated macromolecule glycosylation in the regulation of pluripotent states in human pluripotent stem cells (hPSCs). Here, we observed that the sialyltransferase ST6GAL1 was preferentially expressed in undifferentiated hPSCs compared to non-pluripotent cells. A lectin which preferentially recognizes α-2,6 sialylated galactosides showed strong binding reactivity with undifferentiated hPSCs and their glycoproteins, and did so to a much lesser extent with differentiated cells. In addition, downregulation of ST6GAL1 in undifferentiated hPSCs led to a decrease in POU5F1 (also known as OCT4) protein and significantly altered the expression of many genes that orchestrate cell morphogenesis during differentiation. The induction of cellular pluripotency in somatic cells was substantially impeded by the shRNA-mediated suppression of ST6GAL1, partially through interference with the expression of endogenous POU5F1 and SOX2. Targeting ST6GAL1 activity with a sialyltransferase inhibitor during cell reprogramming resulted in a dose-dependent reduction in the generation of human induced pluripotent stem cells (hiPSCs). Collectively, our data indicate that ST6GAL1 plays an important role in the regulation of pluripotency and differentiation in hPSCs, and the pluripotent state in human cells can be modulated using pharmacological tools to target sialyltransferase activity.

PMID: 26304831 [PubMed - indexed for MEDLINE]

Allele frequencies for 15 autosomal STR loci and haplotype data for 17 Y-STR loci in a population from Belize.

Recent Research Articles from UNTHSC - Thu, 07/28/2016 - 06:31
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Allele frequencies for 15 autosomal STR loci and haplotype data for 17 Y-STR loci in a population from Belize.

Int J Legal Med. 2015 Nov;129(6):1217-8

Authors: Flores S, Sun J, King J, Eisenberg A, Budowle B

Abstract
Allele frequencies for 15 autosomal STR loci (N = 290) and haplotype data for 17 Y-STR loci (N = 157) were determined for an admixed population from Belize. There were no detectable departures from Hardy-Weinberg equilibrium expectations at any autosomal STR loci except for the D8S1179 locus (p = 0.002). The combined power of discrimination (PD) and combined power of exclusion (PE) were greater than 0.99999999 and 0.99999951, respectively. In addition, a total of 144 distinct Y-STR haplotypes were observed with 133 Y-STR haplotypes observed only once. The most common Y-STR haplotype was observed three times for two separate haplotypes. The various analyses of these forensically relevant STR loci showed that these markers are informative in the Belize population for forensic and parentage testing applications.

PMID: 25193820 [PubMed - indexed for MEDLINE]

The many faces of the trabecular meshwork cell.

Recent Research Articles from UNTHSC - Sun, 07/24/2016 - 22:32
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The many faces of the trabecular meshwork cell.

Exp Eye Res. 2016 Jul 18;

Authors: Stamer WD, Clark AF

Abstract
With the combined purpose of facilitating useful vision over a lifetime, a number of ocular cells have evolved specialized features not found elsewhere in the body. The trabecular meshwork (TM) cell at the irido-corneal angle, which is a key regulator of intraocular pressure, is no exception. Examination of cells in culture isolated from the human TM has shown that they are unique in many ways, displaying characteristic features of several different cell types. Thus, these neural crest derived cells display expression patterns and behaviors typical of endothelia, fibroblasts, smooth muscle and macrophages, owing to the multiple roles and two distinct environments where they operate to maintain intraocular pressure homeostasis. In most individuals, TM cells function normally over a lifetime in the face of persistent stressors, including phagocytic, oxidative, mechanical and metabolic stresses. Study of TM cells isolated from ocular hypertensive eyes has shown a compromised ability to perform their daily duties. This review highlights the many responsibilities of the TM cell and its challenges, progress in our understanding of TM biology over the past 30 years, as well as discusses unanswered questions about TM dysfunction that results in IOP dysregulation and glaucoma.

PMID: 27443500 [PubMed - as supplied by publisher]

Are positive allosteric modulators of α7 nAChRs clinically safe?

Recent Research Articles from UNTHSC - Sun, 07/24/2016 - 22:32
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Are positive allosteric modulators of α7 nAChRs clinically safe?

J Neurochem. 2016 Jan;136(2):217-9

Authors: Uteshev V

PMID: 26182952 [PubMed - indexed for MEDLINE]

What's New in Musculoskeletal Infection: Update on Biofilms.

Recent Research Articles from UNTHSC - Fri, 07/22/2016 - 06:30

What's New in Musculoskeletal Infection: Update on Biofilms.

J Bone Joint Surg Am. 2016 Jul 20;98(14):1226-34

Authors: Nana A, Nelson SB, McLaren A, Chen AF

PMID: 27440572 [PubMed - in process]

The efficacy of novel anatomical sites for the assessment of muscle oxygenation during central hypovolemia.

Recent Research Articles from UNTHSC - Fri, 07/22/2016 - 06:30

The efficacy of novel anatomical sites for the assessment of muscle oxygenation during central hypovolemia.

Exp Biol Med (Maywood). 2016 Jul 19;

Authors: Sprick JD, Soller BR, Rickards CA

Abstract
Muscle tissue oxygenation (SmO2) can track central blood volume loss associated with hemorrhage. Traditional peripheral measurement sites (e.g., forearm) may not be practical due to excessive movement or injury (e.g., amputation). The aim of this study was to evaluate the efficacy of three novel anatomical sites for the assessment of SmO2 under progressive central hypovolemia. 10 male volunteers were exposed to stepwise prone lower body negative pressure to decrease central blood volume, while SmO2 was assessed at four sites-the traditional site of the flexor carpi ulnaris (ARM), and three novel sites not previously investigated during lower body negative pressure, the deltoid, latissimus dorsi, and trapezius. SmO2 at the novel sites was compared to the ARM sensor and to stroke volume responses. A reduction in SmO2 was detected by the ARM sensor at the first level of lower body negative pressure (-15 mmHg; P = 0.007), and at -30 (the deltoid), -45 (latissimus dorsi), and -60 mmHg lower body negative pressure (trapezius) at the novel sites (P ≤ 0.04). SmO2 responses at all novel sites were correlated with responses at the ARM (R ≥ 0.89), and tracked the reduction in stroke volume (R ≥ 0.87); the latissimus dorsi site exhibited the strongest linear correlations (R ≥ 0.96). Of the novel sensor sites, the latissimus dorsi exhibited the strongest linear associations with SmO2 at the ARM, and with reductions in central blood volume. These findings have important implications for detection of hemorrhage in austere environments (e.g., combat) when use of a peripheral sensor may not be ideal, and may facilitate incorporation of these sensors into uniforms.

PMID: 27439541 [PubMed - as supplied by publisher]

Stem geometry changes initial femoral fixation stability of a revised press-fit hip prosthesis: A finite element study.

Recent Research Articles from UNTHSC - Wed, 07/20/2016 - 15:30
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Stem geometry changes initial femoral fixation stability of a revised press-fit hip prosthesis: A finite element study.

Technol Health Care. 2016 Jul 8;

Authors: Russell RD, Huo MH, Rodrigues DC, Kosmopoulos V

Abstract
BACKGROUND: Stable femoral fixation during uncemented total hip arthroplasty is critical to allow for subsequent osseointegration of the prosthesis. Varying stem designs provide surgeons with multiple options to gain femoral fixation.
OBJECTIVE: The purpose of this study was to compare the initial fixation stability of cylindrical and tapered stem implants using two different underreaming techniques (press-fit conditions) for revision total hip arthroplasty (THA).
METHODS: A finite element femur model was created from three-dimensional computed tomography images simulating a trabecular bone defect commonly observed in revision THA. Two 18-mm generic femoral hip implants were modeled using the same geometry, differing only in that one had a cylindrical stem and the other had a 2 degree tapered stem. Surgery was simulated using a 0.05-mm and 0.01-mm press-fit and tested with a physiologically relevant loading protocol.
RESULTS: Mean contact pressure was influenced more by the surgical technique than by the stem geometry. The 0.05-mm press-fit condition resulted in the highest contact pressures for both the cylindrical (27.35 MPa) and tapered (20.99 MPa) stems. Changing the press-fit to 0.01-mm greatly decreased the contact pressure by 79.8% and 78.5% for the cylindrical (5.53 MPa) and tapered (4.52 MPa) models, respectively. The cylindrical stem geometry consistently showed less relative micromotion at all the cross-sections sampled as compared to the tapered stem regardless of press-fit condition.
CONCLUSIONS: This finite element analysis study demonstrates that tapered stem results in lower average contact pressure and greater micromotion at the implant-bone interface than a cylindrical stem geometry. More studies are needed to establish how these different stem geometries perform in such non-ideal conditions encountered in revision THA cases where less bone stock is available.

PMID: 27434281 [PubMed - as supplied by publisher]

Mycobacterium Tuberculosis Infection, Immigration Status, and Diagnostic Discordance: A Comparison of Tuberculin Skin Test and QuantiFERON-TB Gold In-Tube Test Among Immigrants to the U.S.

Recent Research Articles from UNTHSC - Wed, 07/20/2016 - 15:30
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Mycobacterium Tuberculosis Infection, Immigration Status, and Diagnostic Discordance: A Comparison of Tuberculin Skin Test and QuantiFERON-TB Gold In-Tube Test Among Immigrants to the U.S.

Public Health Rep. 2016 Mar-Apr;131(2):303-10

Authors: Wilson FA, Miller TL, Stimpson JP

Abstract
OBJECTIVE: We used a recent source of nationally representative population data on tuberculosis (TB) infection to characterize concordance between the tuberculin skin test (TST) and the QuantiFERON-TB Gold In-Tube (QFT-GIT) blood test for immigrants in the United States.
METHODS: We used TB screening data from the 2011-2012 National Health and Nutrition Examination Survey to examine concordance between the TST and QFT-GIT--an interferon-gamma release assay (IGRA) blood test--for 7,097 U.S. natives, naturalized citizens, and noncitizens.
RESULTS: Consistent with prior findings, one in five immigrants in the survey was identified with latent TB infection (LTBI), a rate 14 times higher than for U.S. natives. We also found higher rates of discordant TST/IGRA results among immigrants than among U.S. natives. Unadjusted discordance between TST and IGRA was 3% among U.S. natives (weighted N=5,684,274 of 191,179,213) but ranged up to 19% for noncitizens (weighted N=3,722,960 of 19,377,147). Adjusting for age, sex, and race/ethnicity, noncitizens had more than nine times the odds of having a positive TST result but negative QFT-GIT result compared with U.S. natives.
CONCLUSIONS: Our findings suggest that whether and how either of these tests should be deployed is highly context sensitive. Significant discordance in test results when used among immigrants raises the possibility of missed opportunities for harm reduction in this already at-risk population. However, we found little distinction between the tests in terms of diagnostic outcome when used in a U.S. native population, suggesting little benefit to the adoption and use of the QFT-GIT test in place of TST on the basis of test performance alone for this population.

PMID: 26957665 [PubMed - indexed for MEDLINE]

The effects of metal ion PCR inhibitors on results obtained with the Quantifiler(®) Human DNA Quantification Kit.

Recent Research Articles from UNTHSC - Tue, 07/19/2016 - 18:30
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The effects of metal ion PCR inhibitors on results obtained with the Quantifiler(®) Human DNA Quantification Kit.

Forensic Sci Int Genet. 2015 Nov;19:180-9

Authors: Combs LG, Warren JE, Huynh V, Castaneda J, Golden TD, Roby RK

Abstract
Forensic DNA samples may include the presence of PCR inhibitors, even after extraction and purification. Studies have demonstrated that metal ions, co-purified at specific concentrations, inhibit DNA amplifications. Metal ions are endogenous to sample types, such as bone, and can be introduced from environmental sources. In order to examine the effect of metal ions as PCR inhibitors during quantitative real-time PCR, 2800 M DNA was treated with 0.0025-18.750 mM concentrations of aluminum, calcium, copper, iron, nickel, and lead. DNA samples, both untreated and metal-treated, were quantified using the Quantifiler(®) Human DNA Quantification Kit. Quantification cycle (Cq) values for the Quantifiler(®) Human DNA and internal PCR control (IPC) assays were measured and the estimated concentrations of human DNA were obtained. Comparisons were conducted between metal-treated and control DNA samples to determine the accuracy of the quantification estimates and to test the efficacy of the IPC inhibition detection. This kit is most resistant to the presence of calcium as compared to all metals tested; the maximum concentration tested does not affect the amplification of the IPC or quantification of the sample. This kit is most sensitive to the presence of aluminum; concentrations greater than 0.0750 mM negatively affected the quantification, although the IPC assay accurately assessed the presence of PCR inhibition. The Quantifiler(®) Human DNA Quantification Kit accurately quantifies human DNA in the presence of 0.5000 mM copper, iron, nickel, and lead; however, the IPC does not indicate the presence of PCR inhibition at this concentration of these metals. Unexpectedly, estimates of DNA quantity in samples treated with 18.750 mM copper yielded values in excess of the actual concentration of DNA in the samples; fluorescence spectroscopy experiments indicated this increase was not a direct interaction between the copper metal and 6-FAM dye used to label the probe that targets human DNA in the Quantifiler(®) kit. Evidence of inhibition was observed for the human-specific assay at a lower metal concentration than detected by the IPC, for all metals examined except calcium. These results strongly suggest that determination of a "true negative" sample should not be based solely on the failure of the IPC to indicate the presence of a PCR inhibitor and indicate that amplification of all samples should be attempted, regardless of the quantification results.

PMID: 26240969 [PubMed - indexed for MEDLINE]

An evaluation of the PowerSeq™ Auto System: A multiplex short tandem repeat marker kit compatible with massively parallel sequencing.

Recent Research Articles from UNTHSC - Tue, 07/19/2016 - 18:30
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An evaluation of the PowerSeq™ Auto System: A multiplex short tandem repeat marker kit compatible with massively parallel sequencing.

Forensic Sci Int Genet. 2015 Nov;19:172-9

Authors: Zeng X, King J, Hermanson S, Patel J, Storts DR, Budowle B

Abstract
Capillary electrophoresis (CE) and multiplex amplification with fluorescent tagging have been routinely used for STR typing in forensic genetics. However, CE-based methods restrict the number of markers that can be multiplexed simultaneously and cannot detect any intra-repeat variations within STRs. Several studies already have indicated that massively parallel sequencing (MPS) may be another potential technology for STR typing. In this study, the prototype PowerSeq(™) Auto System (Promega) containing the 23 STR loci and amelogenin was evaluated using Illumina MiSeq. Results showed that single source complete profiles could be obtained using as little as 62 pg of input DNA. The reproducibility study showed that the profiles generated were consistent among multiple typing experiments for a given individual. The mixture study indicated that partial STR profiles of the minor contributor could be detected up to 19:1 mixture. The mock forensic casework study showed that full or partial profiles could be obtained from different types of single source and mixture samples. These studies indicate that the PowerSeq Auto System and the Illumina MiSeq can generate concordant results with current CE-based methods. In addition, MPS-based systems can facilitate mixture deconvolution with the detection of intra-repeat variations within length-based STR alleles.

PMID: 26240968 [PubMed - indexed for MEDLINE]

Native American population data based on the Globalfiler(®) autosomal STR loci.

Recent Research Articles from UNTHSC - Sun, 07/17/2016 - 06:38

Native American population data based on the Globalfiler(®) autosomal STR loci.

Forensic Sci Int Genet. 2016 Jun 27;

Authors: Ng J, Oldt RF, McCulloh KL, Weise JA, Viray J, Budowle B, Smith DG, Kanthaswamy S

Abstract
Native American population data are limited and thus impact computing accurate statistical parameters for forensic investigations. Thus, additional information should be generated from geographically representative tribes in North America, particularly from those that are not included in existing population databases for forensic use. The Globafiler(®) PCR Amplification kit was used to produce STR genotypic data for 533 individuals who represent 31 Native American tribal populations derived from eight geographically diverse regions in North America. Population genetic estimates from 21 autosomal STRs are reported.

PMID: 27421760 [PubMed - as supplied by publisher]

Authors' Response.

Recent Research Articles from UNTHSC - Wed, 07/13/2016 - 06:30

Authors' Response.

J Forensic Sci. 2015 Nov;60(6):1669-1670

Authors: Moretti TR, Budowle B, Buckleton JS

PMID: 27404296 [PubMed - as supplied by publisher]

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