40 CFR 180.1179 - Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and Rhizophoria...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Plant extract derived from Opuntia...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and...

40 CFR 180.1179 - Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and Rhizophoria...

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Plant extract derived from Opuntia...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and...

40 CFR 180.1179 - Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and Rhizophoria...

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Plant extract derived from Opuntia...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and...

40 CFR 180.1179 - Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and Rhizophoria...

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Plant extract derived from Opuntia...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and...

40 CFR 180.1179 - Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and Rhizophoria...

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Plant extract derived from Opuntia...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and...

In vitro propagation of Homalomena aromatica Schott., an endangered aromatic medicinal herb of Northeast India.

PubMed

Raomai, Shiveirou; Kumaria, Suman; Tandon, Pramod

2013-04-01

A successful report on the in vitro propagation of Homalomena aromatica via rhizome axillary bud multiplication is presented. Rhizome bud explants were cultured on Murashige and Skoog medium supplemented with various concentrations of cytokinins to induce multiple shoot formation for micropropagation. The highest number of shoots was achieved in MS medium supplemented with 2.0 mg l(-1) 6-benzylaminopurine. The regenerated shoots rooted most efficiently on half-strength MS medium supplemented with 0.5 mg l(-1) α-naphthalene acetic acid. The regenerated plantlets showed no morphological differences from the parent plant. This protocol takes approximately 6 months to reach the acclimatization stage from the initiation stage and facilitates commercial and rapid propagation of H. aromatica.

Evolving R Coronae Borealis Stars with MESA

NASA Astrophysics Data System (ADS)

Clayton, Geoffrey C.; Lauer, Amber; Chatzopoulos, Emmanouil; Frank, Juhan

2018-01-01

R Coronae Borealis (RCB) stars form a small class of cool, carbon-rich supergiants that have almost no hydrogen. They undergo extreme, irregular declines in brightness of up to 8 magnitudes due to the formation of thick clouds of carbon dust. Two scenarios have been proposed for the origin of an RCB star: the merger of a CO/He white dwarf (WD) binary and a final helium-shell flash. We are using a combination of 3D hydrodynamics codes and the 1D MESA (Modules for Experiments in Stellar Astrophysics) stellar evolution code including nucleosynthesis to construct post-merger spherical models based on realistic merger progenitor models and on our hydrodynamical simulations, and then following the evolution into the region of the HR diagram where RCB stars are located. We are investigating nucleosynthesis in the dynamically accreting material of CO/He WD mergers which may provide a suitable environment for significant production of 18O and the very low 16O/18O values observed.Our MESA modeling consists of two steps: first mimicking the WD merger event using two different techniques, (a) by choosing a very high mass accretion rate with appropriate abundances and (b) by applying "stellar engineering" to an initial CO WD model to account for the newly merged material by applying an entropy adjusting procedure. Second, we follow the post-merger evolution using a large nuclear reaction network including the effects of convective and rotational instabilities to the mixing of material in order to match the observed RCB abundances. MESA follows the evolution of the merger product as it expands and cools to become an RCB star. We then examine the surface abundances and compare them to the observed RCB abundances. We also investigate how long fusion continues in the He shell near the core and how this processed material is mixed up to the surface of the star. We then model the later evolution of RCB stars to determine their likely lifetimes and endpoints when they have returned to being a WD. Solving the mystery of how the RCB stars evolve will lead to a better understanding of other important types of stellar merger events such as Type Ia SNe.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rauscher, Emily; Showman, Adam P., E-mail: rauscher@astro.princeton.edu

As a planet ages, it cools and its radius shrinks at a rate set by the efficiency with which heat is transported from the interior out to space. The bottleneck for this transport is at the boundary between the convective interior and the radiative atmosphere; the opacity there sets the global cooling rate. Models of planetary evolution are often one dimensional (1D), such that the radiative-convective boundary (RCB) is defined by a single temperature, pressure, and opacity. In reality the spatially inhomogeneous stellar heating pattern and circulation in the atmosphere could deform the RCB, allowing heat from the interior tomore » escape more efficiently through regions with lower opacity. We present an analysis of the degree to which the RCB could be deformed and the resultant change in the evolutionary cooling rate. In this initial work we calculate the upper limit for this effect by comparing an atmospheric structure in local radiative equilibrium to its 1D equivalent. We find that the cooling through an uneven RCB could be enhanced over cooling through a uniform RCB by as much as 10%-50%. We also show that the deformation of the RCB (and the enhancement of the cooling rate) increases with a greater incident stellar flux or a lower inner entropy. Our results indicate that this mechanism could significantly change a planet's thermal evolution, causing it to cool and shrink more quickly than would otherwise be expected. This may exacerbate the well-known difficulty in explaining the very large radii observed for some hot Jupiters.« less

Description of strain 3CB-1, a genomovar of Thauera aromatica, capable of degrading 3-chlorobenzoate coupled to nitrate reduction.

PubMed

Song, B; Palleroni, N J; Häggblom, M M

2000-03-01

A Gram-negative bacterium, strain 3CB-1, isolated from a 3-chlorobenzoate enrichment culture inoculated with a sediment sample is capable of degrading various aromatic compounds and halogenated derivatives with nitrate as electron acceptor. Compounds capable of serving as carbon and energy sources include 3-chlorobenzoate, 3-bromobenzoate, 2-fluorobenzoate, 4-fluorobenzoate, benzoate, 3-hydroxybenzoate, 4-hydroxybenzoate, 3-aminobenzoate, protocatechuate, m-cresol and p-cresol. Oxygen, nitrate and nitrite were used as electron acceptors for growth. Cells are Gram-negative short rods with peritrichous flagellation. The predominant fatty acids are cis-9-hexadecenoic acid (16:1 omega 7c), hexadecanoic acid (16:0), octadecanoic acid (18:0), octadecenoic acid (18:1), 3-hydroxydecanoic acid (10:0 3OH) and dodecanoic acid (12:0). The sequence of the 16S rRNA gene, as well as the fatty acid composition, indicate that the strain is a member of the genus Thauera in the beta-subclass of the Proteobacteria and very close to Thauera aromatica. DNA-DNA hybridization and nutrient screening indicate that strain 3CB-1 is a genomovar of Thauera aromatica with the proposed name Thauera aromatica genomovar chlorobenzoica.

A framework to evaluate research capacity building in health care

PubMed Central

Cooke, Jo

2005-01-01

Background Building research capacity in health services has been recognised internationally as important in order to produce a sound evidence base for decision-making in policy and practice. Activities to increase research capacity for, within, and by practice include initiatives to support individuals and teams, organisations and networks. Little has been discussed or concluded about how to measure the effectiveness of research capacity building (RCB) Discussion This article attempts to develop the debate on measuring RCB. It highlights that traditional outcomes of publications in peer reviewed journals and successful grant applications may be important outcomes to measure, but they may not address all the relevant issues to highlight progress, especially amongst novice researchers. They do not capture factors that contribute to developing an environment to support capacity development, or on measuring the usefulness or the 'social impact' of research, or on professional outcomes. The paper suggests a framework for planning change and measuring progress, based on six principles of RCB, which have been generated through the analysis of the literature, policy documents, empirical studies, and the experience of one Research and Development Support Unit in the UK. These principles are that RCB should: develop skills and confidence, support linkages and partnerships, ensure the research is 'close to practice', develop appropriate dissemination, invest in infrastructure, and build elements of sustainability and continuity. It is suggested that each principle operates at individual, team, organisation and supra-organisational levels. Some criteria for measuring progress are also given. Summary This paper highlights the need to identify ways of measuring RCB. It points out the limitations of current measurements that exist in the literature, and proposes a framework for measuring progress, which may form the basis of comparison of RCB activities. In this way it could contribute to establishing the effectiveness of these interventions, and establishing a knowledge base to inform the science of RCB. PMID:16253133

Predictive value of PET-CT for pathological response in stages II and III breast cancer patients following neoadjuvant chemotherapy with docetaxel.

PubMed

García García-Esquinas, Marta A; Arrazola García, Juan; García-Sáenz, José A; Furió-Bacete, V; Fuentes Ferrer, Manuel E; Ortega Candil, Aída; Cabrera Martín, María N; Carreras Delgado, José L

2014-01-01

To prospectively study the value of PET-CT with fluorine-18 fluorodeoxyglucose (FDG) to predict neoadjuvant chemotherapy (NAC) response of locoregional disease of stages II and III breast cancer patients. A written informed consent and approval were obtained from the Ethics Committee. PET-CT accuracy in the prediction of pathologic complete response (pCR) after NAC was studied in primary tumors and lymph node metastasis in 43 women (mean age: 50 years: range: 27-71 years) with histologically proven breast cancer between December 2009 and January 2011. PET-CT was performed at baseline and after NAC. SUV(max) percentage changes (ΔSUV(max)) were compared with pathology findings at surgery. Receiver-operator characteristic (ROC) analysis was used to discriminate between locoregional pCR and non-pCR. In patients not achieving pCR, it was investigated if ΔSUV(max) could accurately identify the residual cancer burden (RCB) classes: RCB-I (minimal residual disease (MRD)), RCB-II (moderate RD), and RCB-III (extensive RD). pCR was obtained in 11 patients (25.6%). Residual disease was found in 32 patients (74.4%): 16 (37.2%) RCB-I, 15 (35.6%) RCB-II and 2 (4.7%) RCB-III. Sensitivity, specificity, and accuracy to predict pCR were 90.9%, 90.6%, and 90.7%, respectively. Specificity was 94.1% in the identification of a subset of patients who had either pCR or MRD. Accuracy of ΔSUV(max) in the locoregional disease of stages II and III breast cancer patients after NAC is high for the identification of pCR cases. Its specificity is potentially sufficient to identify a subgroup of patients who could be managed with conservative surgery. Copyright © 2013 Elsevier España, S.L. and SEMNIM. All rights reserved.

Evolution and Operations of the Reston Virginia Commuter Bus Service

DOT National Transportation Integrated Search

1977-08-01

The report focuses on documenting and assessing the evolution and operations of the Reston Commuter Bus (RCB). RCB is a good example of a community group overcoming many legal, regulatory, and institutional constraints to develop and refine a viable ...

Implementing Responsibility Centre Budgeting

ERIC Educational Resources Information Center

Vonasek, Joseph

2011-01-01

Recently, institutes of higher education (universities) have shown a renewed interest in organisational structures and operating methodologies that generate productivity and innovation; responsibility centre budgeting (RCB) is one such process. This paper describes the underlying principles constituting RCB, its origin and structural elements, and…

Alternative energy production pathways in Taenia crassiceps cysticerci in vitro exposed to a benzimidazole derivative (RCB20).

PubMed

Fraga, Carolina Miguel; Da Costa, Tatiane Luiza; De Castro, Ana Maria; Reynoso-Ducoing, Olivia; Ambrosio, Javier; Hernández-Campos, Alicia; Castillo, Rafael; Vinaud, Marina Clare

2016-04-01

Biochemical studies of benzimidazole derivatives are important to determine their mode of action and activity against parasites. The lack of antihelminthic alternatives to treat parasitic infections and albendazole resistance cases make the search for new antiparasitary drugs of utmost importance. The 6-chloro-5-(1-naphthyloxy)-2-(trifluoromethyl)-1H-benzimidazole (RCB20) is a benzimidazole derivative with promising effect. This study evaluated the effect of different concentrations of RCB20 in the alternative energetic pathway of in vitro Taenia crassiceps cysticerci. The parasites were in vitro exposed to 6.5 and 13 µM of RCB20 and albendazole sulfoxide (ABZSO). The quantification of acetate, acetoacetate, β-hydroxybutyrate, fumarate and propionate was performed by high-performance liquid chromatography. The quantification of urea, creatinine and total proteins was performed by spectrophotometry. The increase in β-hydroxybutyrate reflects the enhancement of the fatty acid oxidation in the treated groups. Volatile fatty acids secretion, acetate and propionate, was increased in the treated groups. The secretion mechanisms of the treated parasites were impaired due to organic acids increased concentrations in the cysticerci. It is possible to conclude that the metabolic effect on alternative energetic pathways is slightly increased in the parasites treated with RCB20 than the ones treated with ABZSO.

A thematic analysis of the role of the organisation in building allied health research capacity: a senior managers' perspective.

PubMed

Golenko, Xanthe; Pager, Susan; Holden, Libby

2012-08-27

Evidence-based practice aims to achieve better health outcomes in the community. It relies on high quality research to inform policy and practice; however research in primary health care continues to lag behind that of other medical professions. The literature suggests that research capacity building (RCB) functions across four levels; individual, team, organisation and external environment. Many RCB interventions are aimed at an individual or team level, yet evidence indicates that many barriers to RCB occur at an organisational or external environment level. This study asks senior managers from a large healthcare organisation to identify the barriers and enablers to RCB. The paper then describes strategies for building allied health (AH) research capacity at an organisational level from a senior managers' perspective. This qualitative study is part of a larger collaborative RCB project. Semi-structured in-depth interviews were conducted with nine allied health senior managers. Recorded interviews were transcribed and NVivo was used to analyse findings and emergent themes were defined. The dominant themes indicate that the organisation plays an integral role in building AH research capacity and is the critical link in creating synergy across the four levels of RCB. The organisation can achieve this by incorporating research into its core business with a whole of organisation approach including its mission, vision and strategic planning. Critical success factors include: developing a co-ordinated and multidisciplinary approach to attain critical mass of research-active AH and enhance learning and development; support from senior managers demonstrated through structures, processes and systems designed to facilitate research; forming partnerships to increase collaboration and sharing of resources and knowledge; and establishing in internal framework to promote recognition for research and career path opportunities. This study identifies four key themes: whole of organisation approach; structures, processes and systems; partnerships and collaboration; and dedicated research centres, units and positions. These themes form the foundation of a model which can be applied to assist in achieving synergy across the four levels of RCB, overcome barriers and create an environment that supports and facilitates research development in AH.

Effect of drying method to antioxidants capacity of Limnophila aromatica

NASA Astrophysics Data System (ADS)

Yen, Tran Thi Ngoc; Vu, Nguyen Hoang

2017-09-01

Limnophila aromatica is widely used in South East Asian countries to make spices in food and medicine in traditional medicine. The use value of vegetables is known because some of the lesser constituents in plants are called antioxidants. These active ingredients have not been fully researched and their pharmacological effects are underestimated. In this study, the drying temperature at 40 °C was showed that the antioxidant activity decreased the most. The drying temperature of 50 °C is suitable for convection drying method and drying temperature of 60 °C suitable for vacuum drying, as it retains the most antioxidant properties. Regarding the drying method, freeze drying proved to be effective when retaining high antioxidant capacity. Using The convection drying at 50 °C and the vacuum drying at 60 °C, the antioxidant activity of Limnophila aromatica was not different. Over 6 weeks of preservation, the dried product has deterioration in antioxidant properties.

THE HOT R CORONAE BOREALIS STAR DY CENTAURI IS A BINARY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kameswara Rao, N.; Lambert, David L.; McArthur, Barbara

2012-11-20

The remarkable hot R Coronae Borealis (RCB) star DY Cen is revealed to be the first and only binary system to be found among the RCB stars and their likely relatives, including the extreme helium stars and the hydrogen-deficient carbon stars. Radial velocity determinations from 1982 to 2010 have shown that DY Cen is a single-lined spectroscopic binary in an eccentric orbit with a period of 39.67 days. It is also one of the hottest and most H-rich member of the class of RCB stars. The system may have evolved from a common envelope to its current form.

Analysis of volatile secondary metabolites from Colombian Xylopia aromatica (Lamarck) by different extraction and headspace methods and gas chromatography.

PubMed

Stashenko, Elena E; Jaramillo, Beatriz E; Martínez, Jairo René

2004-01-30

Hydrodistillation (HD), simultaneous distillation-solvent extraction (SDE), microwave-assisted hydrodistillation (MWHD), and supercritical fluid (CO2) extraction (SFE), were employed to isolate volatile secondary metabolites from Colombian Xylopia aromatica (Lamarck) fruits. Static headspace (S-HS), simultaneous purge and trap (P&T) in solvent (CH2Cl2), and headspace (HS) solid-phase microextraction (SPME) were utilised to obtain volatile fractions from fruits of X. aromatica trees, which grow wild in Central and South America, and are abundant in Colombia. Kováts indices, mass spectra or standard compounds, were used to identify more than 50 individual components in the various volatile fractions. beta-Phellandrene was the main component found in the HD and MWHD essential oils, SDE and SFE extracts (61, 65, 57, and ca. 40%, respectively), followed by beta-myrcene (9.1, 9.3, 8.2 and 5.1%), and alpha-pinene (8.1, 7.3, 8.1 and 5.9%). The main components present in the volatile fractions of the X. aromatica fruits, isolated by S-HS, P&T and HS-SPME were beta-phellandrene (53.8, 35.7 and 39%), beta-myrcene (13.3, 12.3 and 10.1%), p-mentha-1(7),8-diene (7.1, 10.6 and 10.4%), alpha-phellandrene (2.2, 5.0 and 6.4%), and p-cymene (2.2,4.7 and 4.4%), respectively.

Interim heterogeneity changes measured using entropy texture features on T2-weighted MRI at 3.0 T are associated with pathological response to neoadjuvant chemotherapy in primary breast cancer.

PubMed

Henderson, Shelley; Purdie, Colin; Michie, Caroline; Evans, Andrew; Lerski, Richard; Johnston, Marilyn; Vinnicombe, Sarah; Thompson, Alastair M

2017-11-01

To investigate whether interim changes in hetereogeneity (measured using entropy features) on MRI were associated with pathological residual cancer burden (RCB) at final surgery in patients receiving neoadjuvant chemotherapy (NAC) for primary breast cancer. This was a retrospective study of 88 consenting women (age: 30-79 years). Scanning was performed on a 3.0 T MRI scanner prior to NAC (baseline) and after 2-3 cycles of treatment (interim). Entropy was derived from the grey-level co-occurrence matrix, on slice-matched baseline/interim T2-weighted images. Response, assessed using RCB score on surgically resected specimens, was compared statistically with entropy/heterogeneity changes and ROC analysis performed. Association of pCR within each tumour immunophenotype was evaluated. Mean entropy percent differences between examinations, by response category, were: pCR: 32.8%, RCB-I: 10.5%, RCB-II: 9.7% and RCB-III: 3.0%. Association of ultimate pCR with coarse entropy changes between baseline/interim MRI across all lesions yielded 85.2% accuracy (area under ROC curve: 0.845). Excellent sensitivity/specificity was obtained for pCR prediction within each immunophenotype: ER+: 100%/100%; HER2+: 83.3%/95.7%, TNBC: 87.5%/80.0%. Lesion T2 heterogeneity changes are associated with response to NAC using RCB scores, particularly for pCR, and can be useful across all immunophenotypes with good diagnostic accuracy. • Texture analysis provides a means of measuring lesion heterogeneity on MRI images. • Heterogeneity changes between baseline/interim MRI can be linked with ultimate pathological response. • Heterogeneity changes give good diagnostic accuracy of pCR response across all immunophenotypes. • Percentage reduction in heterogeneity is associated with pCR with good accuracy and NPV.

Serum metabonomic analysis of protective effects of Curcuma aromatica oil on renal fibrosis rats.

PubMed

Zhao, Liangcai; Zhang, Haiyan; Yang, Yunjun; Zheng, Yongquan; Dong, Minjian; Wang, Yaqiang; Bai, Guanghui; Ye, Xinjian; Yan, Zhihan; Gao, Hongchang

2014-01-01

Curcuma aromatica oil is a traditional herbal medicine demonstrating protective and anti-fibrosis activities in renal fibrosis patients. However, study of its mechanism of action is challenged by its multiple components and multiple targets that its active agent acts on. Nuclear magnetic resonance (NMR)-based metabonomics combined with clinical chemistry and histopathology examination were performed to evaluate intervening effects of Curcuma aromatica oil on renal interstitial fibrosis rats induced by unilateral ureteral obstruction. The metabolite levels were compared based on integral values of serum 1H NMR spectra from rats on 3, 7, 14, and 28 days after the medicine administration. Time trajectory analysis demonstrated that metabolic profiles of the agent-treated rats were restored to control levels after 7 days of dosage. The results confirmed that the agent would be an effective anti-fibrosis medicine in a time-dependent manner, especially in early renal fibrosis stage. Targeted metabolite analysis showed that the medicine could lower levels of lipid, acetoacetate, glucose, phosphorylcholine/choline, trimethylamine oxide and raise levels of pyruvate, glycine in the serum of the rats. Serum clinical chemistry and kidney histopathology examination dovetailed well with the metabonomics data. The results substantiated that Curcuma aromatica oil administration can ameliorate renal fibrosis symptoms by inhibiting some metabolic pathways, including lipids metabolism, glycolysis and methylamine metabolism, which are dominating targets of the agent working in vivo. This study further strengthens the novel analytical approach for evaluating the effect of traditional herbal medicine and elucidating its molecular mechanism.

A Primer on Responsibility Centre Budgeting and Responsibility Centre Management. Professional File, Winter 1999, Number 17.

ERIC Educational Resources Information Center

Lang, Daniel W.

This monograph is a "how-to" manual on responsibility center budgeting (RCB) and responsibility center management (RCM) in the context of Canadian and U.S. institutions. It explains how RCB/RCM works in practice and discusses some of the problems encountered in implementing this strategy at a number of Canadian and U.S. universities. The…

76 FR 41259 - Change in Bank Control Notices; Acquisitions of Shares of a Bank or Bank Holding Company

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-13

... Family control group; to retain control of RCB Holding Company, Inc., Claremore, Oklahoma, parent of RCB... FEDERAL RESERVE SYSTEM Change in Bank Control Notices; Acquisitions of Shares of a Bank or Bank Holding Company The notificants listed below have applied under the Change in Bank Control Act (12 U.S.C...

Passive acoustic mapping of cavitation using eigenspace-based robust Capon beamformer in ultrasound therapy.

PubMed

Lu, Shukuan; Hu, Hong; Yu, Xianbo; Long, Jiangying; Jing, Bowen; Zong, Yujin; Wan, Mingxi

2018-03-01

Pulse-echo imaging technique can only play a role when high intensity focused ultrasound (HIFU) is turned off due to the interference between the primary HIFU signal and the transmission pulse. Passive acoustic mapping (PAM) has been proposed as a tool for true real-time monitoring of HIFU therapy. However, the most-used PAM algorithm based on time exposure acoustic (TEA) limits the quality of cavitation image. Recently, robust Capon beamformer (RCB) has been used in PAM to provide improved resolution and reduced artifacts over TEA-based PAM, but the presented results have not been satisfactory. In the present study, we applied an eigenspace-based RCB (EISRCB) method to further improve the PAM image quality. The optimal weighting vector of the proposed method was found by projecting the RCB weighting vector onto the desired vector subspace constructed from the eigenstructure of the covariance matrix. The performance of the proposed PAM was validated by both simulations and in vitro histotripsy experiments. The results suggested that the proposed PAM significantly outperformed the conventionally used TEA and RCB-based PAM. The comparison results between pulse-echo images of the residual bubbles and cavitation images showed the potential of our proposed PAM in accurate localization of cavitation activity during HIFU therapy. Copyright © 2017 Elsevier B.V. All rights reserved.

Chemical composition and inhibitory activities on dipeptidyl peptidase IV and pancreatic lipase of two underutilized species from the Brazilian Savannah: Oxalis cordata A.St.-Hil. and Xylopia aromatica (Lam.) Mart.

PubMed

Oliveira, Verena B; Araújo, Raquel L B; Eidenberger, Thomas; Brandão, Maria G L

2018-03-01

Brazil has the greatest vegetal biodiversity in the world, but products derived from native species are not optimally utilized. Oxalis cordata and Xylopia aromatica are two underutilized species whose leaves and fruits, respectively, have been used as food in the 19th century. In this study, we used chemical and in vitro assays to evaluate the potential of these species as functional foods. The inhibitory activity on pancreatic lipase and DPP-IV were evaluated using the crude extracts and fractions ethyl acetate, butanol and water of these two species. For polyphenols determination, samples were prepared with different solvents and these were analysed by chromatographic and spectroscopic methods. Finally, fatty acids profile was determinated by gas chromatography. The crude extract (IC 50 =0.84mg/ml), ethyl acetate extract (IC 50 =0.88mg/ml) an aqueous fraction (IC 50 =0.63mg/ml) of C. cordata were inhibitory on pancreatic lipase but inactive against dipeptidyl peptidase IV (DPP-IV). Extracts from X. aromatica were inactive against the lipase pancreatic enzyme, but a butanolic fraction inhibited DPP-IV (IC 50 =0.71±0.05mg/ml). The phenolic acids orientin/isorientin, chlorogenic acid (0.32g/100g) and the flavonoid derivatives rutin (0.27g/100g), quercetin and luteolin were observed in all products. Additionally, fatty acid quantification showed that oleic (7.5g/100g) and linoleic acid (6.5g/100g) were predominant in X. aromatica fruit. This study confirms the potential for the use of both plants as functional foods due to their nutritional value, biological activity and important phytochemical content. Copyright © 2017 Elsevier Ltd. All rights reserved.

An evaluation of the 'Designated Research Team' approach to building research capacity in primary care.

PubMed

Cooke, Jo; Nancarrow, Susan; Dyas, Jane; Williams, Martin

2008-06-27

This paper describes an evaluation of an initiative to increase the research capability of clinical groups in primary and community care settings in a region of the United Kingdom. The 'designated research team' (DRT) approach was evaluated using indicators derived from a framework of six principles for research capacity building (RCB) which include: building skills and confidence, relevance to practice, dissemination, linkages and collaborations, sustainability and infrastructure development. Information was collated on the context, activities, experiences, outputs and impacts of six clinical research teams supported by Trent Research Development Support Unit (RDSU) as DRTs. Process and outcome data from each of the teams was used to evaluate the extent to which the DRT approach was effective in building research capacity in each of the six principles (as evidenced by twenty possible indicators of research capacity development). The DRT approach was found to be well aligned to the principles of RCB and generally effective in developing research capabilities. It proved particularly effective in developing linkages, collaborations and skills. Where research capacity was slow to develop, this was reflected in poor alignment between the principles of RCB and the characteristics of the team, their activities or environment. One team was unable to develop a research project and the funding was withdrawn at an early stage. For at least one individual in each of the remaining five teams, research activity was sustained beyond the funding period through research partnerships and funding successes. An enabling infrastructure, including being freed from clinical duties to undertake research, and support from senior management were found to be important determinants of successful DRT development. Research questions of DRTs were derived from practice issues and several projects generated outputs with potential to change daily practice, including the use of research evidence in practice and in planning service changes. The DRT approach was effective at RCB in teams situated in a supportive organisation and in particular, where team members could be freed from clinical duties and management backing was strong. The developmental stage of the team and the research experience of constituent members also appeared to influence success. The six principles of RCB were shown to be useful as a framework for both developing and evaluating RCB initiatives.

Comparative analysis of procoagulant and fibrinogenolytic activity of crude protease fractions of turmeric species.

PubMed

Shivalingu, B R; Vivek, H K; Nafeesa, Zohara; Priya, B S; Swamy, S Nanjunda

2015-08-22

Turmeric rhizome is a traditional herbal medicine, which has been widely used as a remedy to stop bleeding on fresh cuts and for wound healing by the rural and tribal population of India. To validate scientific and therapeutic application of turmeric rhizomes to stop bleeding on fresh cuts and its role in wound healing process. The water extracts of thoroughly scrubbed and washed turmeric rhizomes viz., Curcuma aromatica Salisb., Curcuma longa L., Curcuma caesia Roxb., Curcuma amada Roxb. and Curcuma zedoria (Christm.) Roscoe. were subjected to salting out and dialysis. The dialyzed crude enzyme fractions (CEFs) were assessed for proteolytic activity using casein as substrate and were also confirmed by caseinolytic zymography. Its coagulant activity and fibrinogenolytic activity were assessed using human citrated plasma and fibrinogen, respectively. The type of protease(s) in CEFs was confirmed by inhibition studies using specific protease inhibitors. The CEFs of C. aromatica, C. longa and C. caesia showed 1.89, 1.21 and 1.07 folds higher proteolytic activity, respectively, compared to papain. In contrast to these, C. amada and C. zedoria exhibited moderate proteolytic activity. CEFs showed low proteolytic activities compared to trypsin. The proteolytic activities of CEFs were confirmed by caseinolytic zymography. The CEFs of C. aromatica, C. longa and C. caesia showed complete hydrolysis of Aα, Bβ and γ subunits of human fibrinogen, while C. amada and C. zedoria showed partial hydrolysis. The CEFs viz., C. aromatica, C. longa, C. caesia, C. amada and C. zedoria exhibited strong procoagulant activity by reducing the human plasma clotting time from 172s (Control) to 66s, 84s 88s, 78s and 90s, respectively. The proteolytic activity of C. aromatica, C. longa, C. caesia and C. amada was inhibited (>82%) by PMSF, suggesting the possible presence of a serine protease(s). However, C. zedoria showed significant inhibition (60%) against IAA and moderate inhibition (30%) against PMSF, indicating the presence of cysteine and serine protease(s). The CEFs of turmeric species exhibited strong procoagulant activity associated with fibrinogenolytic activity. This study provides the scientific credence to turmeric in its propensity to stop bleeding and wound healing process practiced by traditional Indian medicine. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Very Large Telescope Interferometer observations of the dust geometry around R Coronae Borealis stars

NASA Astrophysics Data System (ADS)

Bright, S. N.; Chesneau, O.; Clayton, G. C.; De Marco, O.; Leão, I. C.; Nordhaus, J.; Gallagher, J. S.

2011-06-01

We are investigating the formation and evolution of dust around the hydrogen-deficient supergiants known as R Coronae Borealis (RCB) stars. We aim to determine the connection between the probable merger past of these stars and their current dust-production activities. We carried out high angular resolution interferometric observations of three RCB stars, namely RY Sgr, V CrA and V854 Cen, with the mid-infrared interferometer (MIDI) on the Very Large Telescope Interferometer (VLTI), using two telescope pairs. The baselines ranged from 30 to 60 m, allowing us to probe the dusty environment at very small spatial scales (˜50 mas or 400R★). The observations of the RCB star dust environments were interpreted using both geometrical models and one-dimensional radiative transfer codes. From our analysis, we find that asymmetric circumstellar material is apparent in RY Sgr, may also exist in V CrA and is possible for V854 Cen. Overall, we find that our observations are consistent with dust forming in clumps ejected randomly around the RCB star so that over time they create a spherically symmetric distribution of dust. However, we conclude that the determination of whether there is a preferred plane of dust ejection must wait until a time series of observations are obtained. Based on observations made with the Very Large Telescope Interferometer at Paranal Observatory under programme 079.D-0415.

RCB stars from double degenerate white dwarf mergers

NASA Astrophysics Data System (ADS)

Staff, Jan; Wiggins, Brandon K.; Marcello, Dominic; Motl, Patrick; Clayton, Geoffrey C.

2018-01-01

We have conducted grid based and SPH based hydrodynamic simulations of white dwarf mergers, to investigate the role of dredge-up and mixing during the merger. The goal is to test if sufficiently little 16O can be brought up to the surface to explain the observed 16O to 18O ratio of order unity found in RCB stars. In all simulations, the total mass is ~< 1 M⊙. By initializing both the grid based and the SPH simulations with the same setup, we can compare the results from these different methods. In most of the simulations, more than 0.01 M⊙ of 16O is brought up to the surface. Hence a similar mass of 18O must be produced in order to explain the observed oxygen ratio. However,in SPH simulations where the accretor is a hybrid He/CO white dwarf, much less 16O is brought to the surface, making this an excellent candidate for the progenitor of RCB stars.

Bioactive annonaceous acetogenins from the bark of Xylopia aromatica.

PubMed

Colman-Saizarbitoria, T; Zambrano, J; Ferrigni, N R; Gu, Z M; Ng, J H; Smith, D L; McLaughlin, J L

1994-04-01

Bioactive Annonaceous acetogenins have been isolated from the EtOH extract of the bark of Xylopia aromatica by bioactivity-directed fractionation using lethality to brine shrimp. These acetogenins include xylopianin [1 , xylopiacin [2], and xylomaticin [3], which are three new mono-tetrahydrofuran ring type acetogenins, in addition to the known compounds, annomontacin, gigantetronenin, gigantetrocin A, and annonacin. Compounds 1 and 2 are unusual in having hydroxylation at C-8; 3 has the same functionalities as annonacin but with 37 carbons instead of 35 carbons. The structures were elucidated by spectral analysis of the parent compounds and/or simple chemical derivatives. These acetogenins showed cytotoxicities, comparable to adriamycin, against three human solid tumor cell lines.

Two new bioactive monotetrahydrofuran Annonaceous acetogenins from the bark of Xylopia aromatica.

PubMed

Colman-Saizarbitoria, T; Gu, Z M; McLaughlin, J L

1994-12-01

Xylopien [1] and xylomatenin [2], two new bioactive monotetrahydrofuran Annonaceous acetogenins, have been isolated from an EtOH extract of the bark of Xylopia aromatica, using bioactivity-directed fractionation employing lethality to brine shrimp. These new compounds each have a double bond in the hydrocarbon chain and have been identified as C-23, C-24 dehydro analogs of xylopiacin and xylomaticin. Their structures were elucidated by spectral analyses of the parent compounds and/or simple chemical derivatives. Their absolute stereochemistries have been established by 1H- and 2D nmr experiments utilizing the production of Mosher esters. These acetogenins showed cytotoxic potencies superior to adriamycin against three human solid tumor cell lines.

A potential utilization of end-of-life tyres as recycled carbon black in EPDM rubber.

PubMed

Sagar, M; Nibedita, K; Manohar, N; Kumar, K Raj; Suchismita, S; Pradnyesh, A; Reddy, A Babul; Sadiku, E Rotimi; Gupta, U N; Lachit, P; Jayaramudu, J

2018-04-01

End-of-life (EOL) tyres and their decomposition present severe environmental concern due to their resistance to moisture, oxygen, natural degradation, etc. Pyrolysis is considered to be the most effective and sustainable process for recycling, due to its eco-friendly process. The current work studied the effect of recycled carbon black (rCB), obtained from the pyrolysis of EOL tyres, on the properties of ethylene propylene diene rubber (EPDM). The rCB was characterized by scanning electron microscopy (SEM), thermogravimetric analysis (TGA) and chemical methods. rCB was incorporated solely, into a conventional EPDM formulation and also in combination with N550 carbon black. The physico-mechanical properties of the EPDM vulcanizates, before and after aging, were succinctly studied by SEM, TGA, Differential Scanning Calorimetry (DSC), tensile tests and cross-link density. The average particle size of rCB was observed to be 8 µm and the ash content was observed to be higher when compared to the conventional N550 carbon black, which was evident, by the TGA and SEM-EDX analyses. The reinforcing effect and the cross-link density of the rCB-filled vulcanizates were found to be marginally inferior in comparison to the conventional carbon black (N550). The morphology of the tensile- and tear-fractured surfaces were studied by SEM and it was observed that the breaking mechanism follows the rubber chain detachment from the surface mode. Copyright © 2018 Elsevier Ltd. All rights reserved.

Perspective: Electrospray photoelectron spectroscopy: From multiply-charged anions to ultracold anions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Lai-Sheng, E-mail: Lai-Sheng-Wang@brown.edu

2015-07-28

Electrospray ionization (ESI) has become an essential tool in chemical physics and physical chemistry for the production of novel molecular ions from solution samples for a variety of spectroscopic experiments. ESI was used to produce free multiply-charged anions (MCAs) for photoelectron spectroscopy (PES) in the late 1990 s, allowing many interesting properties of this class of exotic species to be investigated. Free MCAs are characterized by strong intramolecular Coulomb repulsions, which create a repulsive Coulomb barrier (RCB) for electron emission. The RCB endows many fascinating properties to MCAs, giving rise to meta-stable anions with negative electron binding energies. Recent developmentmore » in the PES of MCAs includes photoelectron imaging to examine the influence of the RCB on the electron emission dynamics, pump-probe experiments to examine electron tunneling through the RCB, and isomer-specific experiments by coupling PES with ion mobility for biological MCAs. The development of a cryogenically cooled Paul trap has led to much better resolved PE spectra for MCAs by creating vibrationally cold anions from the room temperature ESI source. Recent advances in coupling the cryogenic Paul trap with PE imaging have allowed high-resolution PE spectra to be obtained for singly charged anions produced by ESI. In particular, the observation of dipole-bound excited states has made it possible to conduct vibrational autodetachment spectroscopy and resonant PES, which yield much richer vibrational spectroscopic information for dipolar free radicals than traditional PES.« less

Purification and characterization of novel fibrin(ogen)olytic protease from Curcuma aromatica Salisb.: Role in hemostasis.

PubMed

Shivalingu, B R; Vivek, H K; Priya, B S; Soujanya, K N; Swamy, S Nanjunda

2016-12-01

The proteases from turmeric species have procoagulant and fibrinogenolytic activity. This provides a scientific basis for traditional use of turmeric to stop bleeding and promote wound healing processes. Our previous studies revealed that fibrinogenolytic action of crude enzyme fraction of Curcuma aromatica Salisb., was found to be more influential than those of Curcuma longa L., Curcuma caesia Roxb., Curcuma amada Roxb. and Curcuma zedoria (Christm.) Roscoe. Hence, the purpose of this study is to purify and characterize protease from C. aromatica and to explore its role in wound healing process. The protease was purified by Sephadex G-50 gel permeation chromatography. Peak with potent proteolytic activity was subjected to rechromatography and then checked for homogeneity by SDS-PAGE and native PAGE. Furthermore purity of the peak was assessed by RP-HPLC and MALDI-TOF. The biochemical properties, type of protease, kinetic studies, fibrinogenolytic, coagulant and fibrinolytic activities were carried out. The two proteolytic peaks were fractionated in gel permeation chromatography. Among these, the peak-II showed potent proteolytic activity with specific activity of 10units/mg/min and named as C. aromatica protease-II (CAP-II). This protein resolved into a single sharp band both in SDS-PAGE (reducing and non-reducing) as well as in native (acidic) PAGE. It is a monomeric protein, showing sharp peak in RP-HPLC and its relative molecular mass was found to be 12.378kDa. The caseinolytic and fibrinolytic activity of CAP-II was completely inhibited by phenylmethylsulfonylfluoride (PMSF). The CAP-II exhibited optimum temperature of 45°C and optimum pH of 7.5. The Km and Vmax of CAP-II was found to be 1.616µg and 1.62units/mg/min respectively. The CAP-II showed hydrolysis of all three subunits of fibrinogen in the order Aα>Bß>γ. The CAP-II exhibited strong procoagulant activity by reducing the human plasma clotting time. It also showed fibrinolytic activity by complete hydrolysis of α-polymer and γ-γ dimer present in fibrin. The CAP-II is a novel serine protease from C. aromatica, which has been demonstrated to stop bleeding and initiate wound healing through its procoagulant and fibrin(ogen)olytic activities. Our study demonstrates the possible role of CAP-II, as therapeutic enzyme to stop bleeding at the time of wounding. Copyright © 2016 Elsevier GmbH. All rights reserved.

DUST AROUND R CORONAE BOREALIS STARS. II. INFRARED EMISSION FEATURES IN AN H-POOR ENVIRONMENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia-Hernandez, D. A.; Rao, N. Kameswara; Lambert, D. L., E-mail: agarcia@iac.es, E-mail: nkrao@iiap.res.in, E-mail: dll@astro.as.utexas.edu

2013-08-20

Residual Spitzer/Infrared Spectrograph spectra for a sample of 31 R Coronae Borealis (RCB) stars are presented and discussed in terms of narrow emission features superimposed on the quasi-blackbody continuous infrared emission. A broad {approx}6-10 {mu}m dust emission complex is seen in the RCBs showing an extreme H-deficiency. A secondary and much weaker {approx}11.5-15 {mu}m broad emission feature is detected in a few RCBs with the strongest {approx}6-10 {mu}m dust complex. The Spitzer infrared spectra reveal for the first time the structure within the {approx}6-10 {mu}m dust complex, showing the presence of strong C-C stretching modes at {approx}6.3 and 8.1 {mu}mmore » as well as of other dust features at {approx}5.9, 6.9, and 7.3 {mu}m, which are attributable to amorphous carbonaceous solids with little or no hydrogen. The few RCBs with only moderate H-deficiencies display the classical ''unidentified infrared bands (UIRs)'' and mid-infrared features from fullerene-related molecules. In general, the characteristics of the RCB infrared emission features are not correlated with the stellar and circumstellar properties, suggesting that the RCB dust features may not be dependent on the present physical conditions around RCB stars. The only exception seems to be the central wavelength of the 6.3 {mu}m feature, which is blueshifted in those RCBs showing also the UIRs, i.e., the RCBs with the smallest H deficiency.« less

Minocycline HCl microspheres reduce red-complex bacteria in periodontal disease therapy.

PubMed

Goodson, J Max; Gunsolley, John C; Grossi, Sara G; Bland, Paul S; Otomo-Corgel, Joan; Doherty, Frances; Comiskey, Judy

2007-08-01

The objective of this trial was to measure the antimicrobial effects of a minocycline HCl microsphere (MM) local drug-delivery system when used as an adjunct to scaling and root planing (SRP). DNA probe analysis for 40 bacteria was used to evaluate the oral bacteria of 127 subjects with moderate to advanced chronic periodontitis. Subjects were randomly assigned to either SRP alone (N = 65) or MM + SRP (N = 62). The primary endpoints of this study were changes in numbers and proportions of the red-complex bacteria (RCB) and the sum of Porphyromonas gingivalis, Tannerella forsythia (formally T. forsythensis), and Treponema denticola relative to 40 oral bacteria at each test site from baseline to day 30. Numbers of RCB from the five test sites were averaged to provide a value for each subject. MM + SRP reduced the proportion of RCB by 6.49% and the numbers by 9.4 x 10(5). The reduction in RCB proportions and numbers by SRP alone (5.03% and 5.1 x 10(5), respectively) was significantly less. In addition, MM + SRP reduced probing depth by 1.38 mm (compared to 1.01 mm by SRP alone), bleeding on probing was reduced by 25.2% (compared to 13.8% by SRP alone), and a clinical attachment level gain of 1.16 mm (compared to 0.80 mm by SRP alone) was achieved. These observations support the hypothesis that RCBs are responsible for periodontal disease and that local antimicrobial therapy using MM + SRP effectively reduces numbers of RCBs and their proportions to a greater extent than SRP alone.

Multi-jagged: A scalable parallel spatial partitioning algorithm

DOE PAGES

Deveci, Mehmet; Rajamanickam, Sivasankaran; Devine, Karen D.; ...

2015-03-18

Geometric partitioning is fast and effective for load-balancing dynamic applications, particularly those requiring geometric locality of data (particle methods, crash simulations). We present, to our knowledge, the first parallel implementation of a multidimensional-jagged geometric partitioner. In contrast to the traditional recursive coordinate bisection algorithm (RCB), which recursively bisects subdomains perpendicular to their longest dimension until the desired number of parts is obtained, our algorithm does recursive multi-section with a given number of parts in each dimension. By computing multiple cut lines concurrently and intelligently deciding when to migrate data while computing the partition, we minimize data movement compared to efficientmore » implementations of recursive bisection. We demonstrate the algorithm's scalability and quality relative to the RCB implementation in Zoltan on both real and synthetic datasets. Our experiments show that the proposed algorithm performs and scales better than RCB in terms of run-time without degrading the load balance. Lastly, our implementation partitions 24 billion points into 65,536 parts within a few seconds and exhibits near perfect weak scaling up to 6K cores.« less

The Dust Properties of Hot R Coronae Borealis Stars and a Wolf-Rayet Central Star of a Planetary Nebula: In Search of the Missing Link

NASA Technical Reports Server (NTRS)

Clayton, Geoffrey C.; De Marco, O.; Whitney, B. A.; Babler, B.; Gallagher, J. S.; Nordhaus, J.; Speck, A. K.; Wolff, M. J.; Freeman, W. R.; Camp, K. A.;

The Autophagic Degradation of Chloroplasts via Rubisco-Containing Bodies Is Specifically Linked to Leaf Carbon Status But Not Nitrogen Status in Arabidopsis1[W][OA

PubMed Central

Izumi, Masanori; Wada, Shinya; Makino, Amane; Ishida, Hiroyuki

2010-01-01

Autophagy is an intracellular process facilitating the vacuolar degradation of cytoplasmic components and is important for nutrient recycling during starvation. We previously demonstrated that chloroplasts can be partially mobilized to the vacuole by autophagy via spherical bodies named Rubisco-containing bodies (RCBs). Although chloroplasts contain approximately 80% of total leaf nitrogen and represent a major carbon and nitrogen source for new growth, the relationship between leaf nutrient status and RCB production remains unclear. We examined the effects of nutrient factors on the appearance of RCBs in leaves of transgenic Arabidopsis (Arabidopsis thaliana) expressing stroma-targeted fluorescent proteins. In excised leaves, the appearance of RCBs was suppressed by the presence of metabolic sugars, which were added externally or were produced during photosynthesis in the light. The light-mediated suppression was relieved by the inhibition of photosynthesis. During a diurnal cycle, RCB production was suppressed in leaves excised at the end of the day with high starch content. Starchless mutants phosphoglucomutase and ADP-Glc pyrophosphorylase1 produced a large number of RCBs, while starch-excess mutants starch-excess1 and maltose-excess1 produced fewer RCBs. In nitrogen-limited plants, as leaf carbohydrates were accumulated, RCB production was suppressed. We propose that there exists a close relationship between the degradation of chloroplast proteins via RCBs and leaf carbon but not nitrogen status in autophagy. We also found that the appearance of non-RCB-type autophagic bodies was not suppressed in the light and somewhat responded to nitrogen in excised leaves, unlike RCBs. These results imply that the degradation of chloroplast proteins via RCBs is specifically controlled in autophagy. PMID:20807997

Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to Escherichia coli Genome

PubMed Central

Roymondal, Uttam; Das, Shibsankar; Sahoo, Satyabrata

2009-01-01

We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene. We outline a simple approach to assess the strength of RCB (RCBS) in genes as a guide to their likely expression levels and illustrate this with an analysis of Escherichia coli (E. coli) genome. Our efforts to quantitatively predict gene expression levels in E. coli met with a high level of success. Surprisingly, we observe a strong correlation between RCBS and protein length indicating natural selection in favour of the shorter genes to be expressed at higher level. The agreement of our result with high protein abundances, microarray data and radioactive data demonstrates that the genomic expression profile available in our method can be applied in a meaningful way to the study of cell physiology and also for more detailed studies of particular genes of interest. PMID:19131380

R CORONAE BOREALIS STARS IN M31 FROM THE PALOMAR TRANSIENT FACTORY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang Sumin; Bildsten, Lars; Cao Yi

2013-04-20

We report the discovery of R Coronae Borealis (RCB) stars in the Andromeda galaxy (M31) using the Palomar Transient Factory (PTF). RCB stars are rare hydrogen-deficient, carbon-rich supergiant variables, most likely the merger products of two white dwarfs. These new RCBs, including two confirmed ones and two candidates, are the first to be found beyond the Milky Way and the Magellanic Clouds. All of M31 RCBs showed >1.5 mag irregular declines over timescales of weeks to months. Due to the limiting magnitude of our data (R Almost-Equal-To 21-22 mag), these RCB stars have R Almost-Equal-To 19.5-20.5 mag at maximum light,more » corresponding to M{sub R} = -4 to -5, making them some of the most luminous RCBs known. Spectra of two objects show that they are warm RCBs, similar to the Milky Way RCBs RY Sgr and V854 Cen. We consider these results, derived from a pilot study of M31 variables, as an important proof-of-concept for the study of rare bright variables in nearby galaxies with the PTF or other synoptic surveys.« less

HPLC quantitation of kaurane diterpenes in Xylopia species.

PubMed

de Melo, A C; Cota, B B; de Oliveira, A B; Braga, F C

2001-01-01

Xylopia frutescens is a tree native to the Brazilian Amazon whose seeds are rich in kaurenoic acid, a diterpene that showed in vitro activity against Trypanosoma cruzi. Aiming to find out alternative sources for kaurenoic acid, the content of some kaurane diterpenes was evaluated in X. aromatica and X. brasiliensis, species occurring in the Cerrado area of Minas Gerais, and also in X. frutescens. A reversed phase HPLC isocratic method was developed and validated to perform the assays. Kaurenoic acid was found to be the most abundant diterpene within the analyzed species, with a 3.16+/-0.97% content in the seeds of X. frutescens, which also presented the highest amount of xylopic acid (1.09+/-0.33%). The highest concentration of 16-alpha-hydroxykauranoic acid (1.96+/-1.58%) was found in the stems of X. aromatica.

Correlative Cryo-Tem Cryo-Stxm and Cryo-Shxm Investigation of Selenium Bioreduction in a Contaminated Aquifer

NASA Astrophysics Data System (ADS)

Fakra, S.; Luef, B.; Tyliszczak, T.; Castelle, C. J.; Mullin, S. W.; Hug, L. A.; Williams, K. H.; Marcus, M.; Banfield, J. F.

2015-12-01

Accurate mapping of the composition and ultrastructure of minerals and cells is key to understanding biogeochemical process in contaminated environments. Here we developed two apparatus that allow correlation of cryogenic transmission electron microscopy (TEM), synchrotron hard X-ray microprobe (SHXM) and scanning transmission X-ray microscopy (STXM) datasets. These cryogenic methods enabled precise determination of the distribution, valence state and structure of selenium in intact biofilms sampled during a biostimulation experiment in a contaminated aquifer near Rifle, CO, USA. Results were replicated in the laboratory via anaerobic selenate-reducing enrichment cultures. 16S rRNA analyses of field-derived biofilm indicated the dominance of Betaproteobacteria from the Comamonadaceae family, and uncultivated members of the Simplicispira genus. The major product in field and culture-derived biofilms consists of ~25-300 nm red amorphous Se0 aggregates of colloidal nanoparticles. Correlative analyses of the cultures provided direct evidence for microbial dissimilatory reduction of Se(VI) to Se(IV) to Se0. X-ray diffraction and Se K-edge extended X-ray absorption fine structure spectroscopy revealed red amorphous Se0 with a first shell Se-Se interatomic distance of 2.339 ± 0.003 Å. STXM showed that these aggregates are strongly associated with a protein-rich biofilm matrix containing acidic polysaccharides. From Rifle groundwater, we isolated a strain that shares 98.9% 16S rRNA gene sequence identity with Dechloromonas aromatica RCB and grows anaerobically by oxidizing acetate and reducing selenate. We refer to this isolate as Dechloromonas selenatis strain RGW99. 3D cryo-electron tomography showed that Se0 particles do not form inside the cytoplasm but rather originate in the cell membrane. The end product of selenate reduction by D. selenatis is 240 ± 66 nm diameter red amorphous Se0 colloidal aggregates. This product was found to be stable for months. Overall, these results established a role for D. selenatis RGW99 in selenate reduction in the Rifle aquifer and provided new insights into the nature and stability of selenium bioreduction products in the subsurface.

Ant-like stone beetles on the roof of the world. Cephenniini of Nepal and Bhutan (Coleoptera, Staphylinidae, Scydmaeninae).

PubMed

Jałoszyński, Paweł

2017-11-15

The tribe Cephenniini is for the first time reported to occur in the Himalaya Mountains, and 58 species are described: Cephennomicrus arunensis sp. n., Cm. acupunctatus sp. n., Cm. taplejungensis sp. n., Hlavaciellus primitivus sp. n., Cephennodes (s. str.) cavifrons sp. n., C. (s. str.) pampinosus sp. n., C. (s. str.) bagmatianus sp. n., C. (s. str.) popeye sp. n., C. (s. str.) clavodentatus sp. n., C. (s. str.) meredaranus sp. n., C. (s. str.) yangrianus sp. n., C. (s. str.) suturalis sp. n., C. (s. str.) karnaliensis sp. n., C. (s. str.) churtanus sp. n., C. (s. str.) sermathangensis sp. n., C. (s. str.) tipulipes sp. n., C. (s. str.) yeti sp. n., C. (s. str.) inflaticornis sp. n., C. (s. str.) dolakhanus sp. n., C. (s. str.) manangensis sp. n., C. (s. str.) martensi sp. n., C. (s. str.) paramartensi sp. n., C. (s. str.) monolaminatus sp. n., C. (s. str.) thakanus sp. n., C. (s. str.) annapurnaensis sp. n., C. (s. str.) parbatensis sp. n., C. (s. str.) letheanus sp. n., C. (s. str.) myagdiensis sp. n., C. (s. str.) malla sp. n., C. (s. str.) gorkha sp. n., C. (s. str.) tharepatianus sp. n., C. (s. str.) minisulcatus sp. n., C. (s. str.) mustangensis sp. n., C. (s. str.) lalitpuranus sp. n., C. (s. str.) paralalitpuranus sp. n., C. (s. str.) bahrabisensis sp. n., C. (s. str.) bilaminatus sp. n., C. (s. str.) ghorepanianus sp. n., C. (s. str.) cordilaminatus sp. n., C. (s. str.) mangmayanus sp. n. C. (s. str.) bilobatus sp. n., C. (s. str.) gokarnaensis sp. n., C. (s. str.) pseudogokarnaensis sp. n., C. (s. str.) mahisapala sp. n., C. (s. str.) licchavi sp. n., C. (s. str.) gopala sp. n., C. (s. str.) paniporuanus sp. n., C. (s. str.) brachyclavatus sp. n., C. (s. str.) phulchokianus sp. n., C. (s. str.) pokharensis sp. n., C. (s. str.) newar sp. n., C. (s. str.) kusunda sp. n., C. (s. str.) sindhupalchowk sp. n., C. (s. str.) furcatus sp. n., C. (s. str.) penicillipes sp. n., C. (s. str.) sulcatus sp. n., C. (s. str.) kalopanianus sp. n., and C. (s. str.) poonensis sp. n. Cephennodes popeye occurs in Bhutan; all remaining species inhabit Nepal. Four new species groups are established in Cephennodes, and a checklist of all Cephennodes species placed in species groups is given. The presumably plesiomorphic morphological structures of H. primitivus are discussed, and comparative notes on the Himalayan Cephenniini fauna are presented.

Scrap tyre recycling process with molten zinc as direct heat transfer and solids separation fluid: A new reactor concept.

PubMed

Riedewald, Frank; Goode, Kieran; Sexton, Aidan; Sousa-Gallagher, Maria J

2016-01-01

Every year about 1.5 billion tyres are discarded worldwide representing a large amount of solid waste, but also a largely untapped source of raw materials. The objective of the method was to prove the concept of a novel scrap tyre recycling process which uses molten zinc as the direct heat transfer fluid and, simultaneously, uses this media to separate the solids products (i.e. steel and rCB) in a sink-float separation at an operating temperature of 450-470 °C. This methodology involved: •construction of the laboratory scale batch reactor,•separation of floating rCB from the zinc,•recovery of the steel from the bottom of the reactor following pyrolysis.

Color improvement by irradiation of Curcuma aromatica extract for industrial application

NASA Astrophysics Data System (ADS)

Kim, Jae Kyung; Jo, Cheorun; Hwang, Han Joon; Park, Hyun Jin; Kim, Young Ji; Byun, Myung Woo

2006-03-01

Curcuma species are medicinal herbs with various pharmacological activities. They have a characteristic yellow color and contain curcuminoids which are natural antioxidants. In this study, Curcuma aromatica (CA) and Curcuma longa (CL) extracts were gamma-irradiated for improving the color, and the irradiation effects on the curcuminoids contents in CA and CL extracts were determined in order to evaluate if CA can replace CL on the market, where the price of CA is 70% lower than the price of CL. The Hunter color L*-values were increased significantly in all the samples with increasing dose, while the a*-values and b*-values decreased, which implies that the color of the CA and CL extracts changed from dark yellow to brighter yellow. Curcuminoids contents of all the samples were evaluated, and CA contains more curcuminoids than CL. These results indicated that irradiation improved the properties of CA for possible industrial use in manufacturing food and cosmetic industrial products.

Floral scent compounds of Amazonian Annonaceae species pollinated by small beetles and thrips.

PubMed

Jürgens, A; Webber, A C; Gottsberger, G

2000-11-01

Chemical analysis (GC-MS) yielded a total of 58 volatile compounds in the floral scents of six species of Annonaceae distributed in four genera (Xylopia, Anaxagorea, Duguetia, and Rollinia), Xylopia aromatica is pollinated principally by Thysanoptera and secondarily by small beetles (Nitidulidae and Staphylinidae), whereas the five other species were pollinated by Nitidulidae and Staphylinidae only. Although the six Annonaceae species attract a similar array of pollinator groups, the major constituents of their floral scents are of different biochemical origin. The fragrances of flowers of Anaxagorea brevipes and Anaxagorea dolichocarpa were dominated by esters of aliphatic acids (ethyl 2-methylbutanoate, ethyl 3-methylbutanoate), which were not detected in the other species. Monoterpenes (limonene, p-cymene, alpha-pinene) were the main scent compounds of Duguetia asterotricha, and naphthalene prevailed in the scent of Rollinia insignis flowers. The odors of X. aromatica and Xylopia benthamii flowers were dominated by high amounts of benzenoids (methylbenzoate, 2-phenylethyl alcohol).

THE DUST PROPERTIES OF TWO HOT R CORONAE BOREALIS STARS AND A WOLF-RAYET CENTRAL STAR OF A PLANETARY NEBULA: IN SEARCH OF A POSSIBLE LINK

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clayton, Geoffrey C.; Gallagher, J. S.; Freeman, W. R.

2011-08-15

We present new Spitzer/IRS spectra of two hot R Coronae Borealis (RCB) stars, one in the Galaxy, V348 Sgr, and one lying in the Large Magellanic Cloud, HV 2671. These two objects may constitute a link between the RCB stars and the late Wolf-Rayet ([WCL]) class of central stars of planetary nebulae (CSPNe), such as CPD -56{sup 0} 8032, that has little or no hydrogen in their atmospheres. HV 2671 and V348 Sgr are members of a rare subclass that has significantly higher effective temperatures than most RCB stars, but shares the traits of hydrogen deficiency and dust formation thatmore » define the cooler RCB stars. The [WC] CSPN star, CPD -56{sup 0} 8032, displays evidence of dual-dust chemistry showing both polycyclic aromatic hydrocarbons (PAHs) and crystalline silicates in its mid-IR spectrum. HV 2671 shows strong PAH emission but no sign of having crystalline silicates. The spectrum of V348 Sgr is very different from that of CPD -56{sup 0} 8032 and HV 2671. The PAH emission seen strongly in the other two stars is not present. Instead, the spectrum is dominated by a broad emission centered at about 8.2 {mu}m. This feature is not identified with either PAHs or silicates. Several other cool RCB stars, novae, and post-asymptotic giant branch stars show similar features in their IR spectra. The mid-IR spectrum of CPD -56{sup 0} 8032 shows emission features that may be associated with C{sub 60}. The other two stars do not show evidence of C{sub 60}. The different nature of the dust around these stars does not help us in establishing further links that may indicate a common origin. HV 2671 has also been detected by Herschel/PACS and SPIRE. V348 Sgr and CPD -56{sup 0} 8032 have been detected by AKARI/Far-Infrared Surveyor. These data were combined with Spitzer, IRAS, Two Micron All Sky Survey, and other photometry to produce their spectral energy distributions (SEDs) from the visible to the far-IR. Monte Carlo radiative transfer modeling was used to study the circumstellar dust around these stars. HV 2671 and CPD -56{sup 0} 8032 require both a flared inner disk with warm dust and an extended diffuse envelope with cold dust to fit their SEDs. The SED of V348 Sgr can be fit with a much smaller disk and envelope. The cold dust in the extended diffuse envelopes inferred around HV 2671 and CPD -56{sup 0} 8032 may consist of interstellar medium swept up during mass-loss episodes.« less

Macrootlocus, a CAD Design Tool for Feedback Control Systems

DTIC Science & Technology

1989-12-01

var Form :DecForm; Str :DecStr; begin 125 Form.Style, :. FixedDecimal; Forrr.Digits :. 0; Num2Str(Form, 1, Str ); lntToStr :. Str ; end; { lntToStr...School Monterey, CA 93943 15. Hong-on Kim SMC2665 Naval Postgraduate School Monterey, CA 93943 16. Kang, Mung Hung SMC1375 Naval Postgraduate School

Survival disparities in patients with lymphoma according to place of residence and treatment provider: a population-based study.

PubMed

Loberiza, Fausto R; Cannon, Anthony J; Weisenburger, Dennis D; Vose, Julie M; Moehr, Matt J; Bast, Martin A; Bierman, Philip J; Bociek, R Gregory; Armitage, James O

2009-11-10

Health disparities exist according to an individual's place of residence. We evaluated the association between primary area of residence (urban v rural) according to treatment provider (university based v community based) and overall survival in patients with lymphoma and determined whether there are patient groups that could benefit from better coordination of care. Population-based, retrospective cohort study of 2,330 patients with centrally confirmed lymphoma from Nebraska and surrounding states and treated by university-based or community-based oncologists from 1982 to 2006. Among urban residents, 321 (14%) were treated by university-based providers (UUB) and 816 (35%) were treated by community-based providers (UCB). Among rural residents, 332 (14%) were treated by university-based providers (RUB), and 861 (37%) were treated by community-based providers (RCB). The relative risk (RR) of death among UUB, UCB, and RUB were not statistically different. However, RCB had a higher risk of death (RR, 1.37; 95% CI, 1.14 to 1.65; P = .01; and RR, 1.26; 95% CI, 1.06 to 1.49; P = .01) when compared with UUB and RUB, respectively. This association was true in both low- and intermediate-risk patients. Among high-risk patients, UCB, RUB, and RCB were all at higher risk of death when compared with UUB. Survival outcomes of patients with lymphoma may be associated with place of residence and treatment provider. High-risk patients from rural areas may benefit from better coordination of care.

Venezenin: a new bioactive Annonaceous acetogenin from the bark of Xylopia aromatica.

PubMed

Colman-Saizarbitoria, T; Gu, Z M; Zhao, G X; Zeng, L; Kozlowski, J F; McLaughlin, J L

1995-04-01

Asimicin and a new cytotoxic Annonaceous acetogenin, venezenin [1], were isolated from the bark of Xylopia aromatica by bioactivity-directed fractionation using lethality to brine shrimp. Compound 1 represents an unusual type of C37 Annonaceous acetogenin, lacking either tetrahydrofuran (THF) or epoxide rings and possessing a double bond located two methylenes away from a vicinal diol in the hydrocarbon chain. The structure of 1 was elucidated by 1H- and 13C-nmr, COSY, single-relayed COSY, and by HMBC techniques, and derivatization. Annomontacin 10-one [6] and 18/21-cis-annomontacin-10-one [7], two semi-synthetic mono-THF acetogenins were prepared from 1. These acetogenins showed cytotoxicity, comparable or superior to adriamycin, against three human solid tumor cell lines. Reduction of the 10-keto of 1 to the racemic OH-10 derivative enhanced the bioactivity, as did the conversion of 1 to 6 and 7. Venezenin [1], like other Annonaceous acetogenins, showed inhibition of oxygen uptake by rat liver mitochondria and demonstrated that the THF ring may not be essential to this mode of action.

Factors Affecting the Accumulation of Curcumin in Microrhizomes of Curcuma aromatica Salisb

PubMed Central

Zhang, Xiaoxia; Sun, Shulan; Wang, Xiaojing

2015-01-01

Curcuminoids, and mainly curcumin, are potential therapeutic agents for the prevention of various diseases; however, little is known about the factors that influence their accumulation in Curcuma species. In this study, the effects of factors such as sucrose concentration, different ratios of 6-benzylaminopurine (6-BA) and α-naphthalene acetic acid (NAA), and light quality on the accumulation of curcumin and other curcuminoids in Curcuma aromatica were investigated. Microrhizomes grown on media containing 3% sucrose produced more curcumin and other curcuminoids than those grown on higher concentrations. Moreover, when compared to other ratios of 6-BA and NAA, microrhizomes induced on 3% sucrose media supplemented with 3.0 mg/L 6-BA and 0.5 mg/L NAA produced more curcumin and other curcuminoids; however, the amount was less than in microrhizomes grown on 3% sucrose alone. We determined that a 5% sucrose medium supplemented with 3.0 mg/L of 6-BA and 0.5 mg/L of NAA enhanced the levels of curcumin and curcuminoids and that exposure to red light further increased production. PMID:25722985

Factors affecting the accumulation of curcumin in microrhizomes of Curcuma aromatica Salisb.

PubMed

Wu, Ke; Zhang, Xiaoxia; Sun, Shulan; Wang, Xiaojing

2015-01-01

Curcuminoids, and mainly curcumin, are potential therapeutic agents for the prevention of various diseases; however, little is known about the factors that influence their accumulation in Curcuma species. In this study, the effects of factors such as sucrose concentration, different ratios of 6-benzylaminopurine (6-BA) and α-naphthalene acetic acid (NAA), and light quality on the accumulation of curcumin and other curcuminoids in Curcuma aromatica were investigated. Microrhizomes grown on media containing 3% sucrose produced more curcumin and other curcuminoids than those grown on higher concentrations. Moreover, when compared to other ratios of 6-BA and NAA, microrhizomes induced on 3% sucrose media supplemented with 3.0 mg/L 6-BA and 0.5 mg/L NAA produced more curcumin and other curcuminoids; however, the amount was less than in microrhizomes grown on 3% sucrose alone. We determined that a 5% sucrose medium supplemented with 3.0 mg/L of 6-BA and 0.5 mg/L of NAA enhanced the levels of curcumin and curcuminoids and that exposure to red light further increased production.

Bias of health estimates obtained from chronic disease and risk factor surveillance systems using telephone population surveys in Australia: results from a representative face-to-face survey in Australia from 2010 to 2013.

PubMed

Dal Grande, Eleonora; Chittleborough, Catherine R; Campostrini, Stefano; Taylor, Anne W

2016-04-18

Emerging communication technologies have had an impact on population-based telephone surveys worldwide. Our objective was to examine the potential biases of health estimates in South Australia, a state of Australia, obtained via current landline telephone survey methodologies and to report on the impact of mobile-only household on household surveys. Data from an annual multi-stage, systematic, clustered area, face-to-face population survey, Health Omnibus Survey (approximately 3000 interviews annually), included questions about telephone ownership to assess the population that were non-contactable by current telephone sampling methods (2006 to 2013). Univariable analyses (2010 to 2013) and trend analyses were conducted for sociodemographic and health indicator variables in relation to telephone status. Relative coverage biases (RCB) of two hypothetical telephone samples was undertaken by examining the prevalence estimates of health status and health risk behaviours (2010 to 2013): directory-listed numbers, consisting mainly of landline telephone numbers and a small proportion of mobile telephone numbers; and a random digit dialling (RDD) sample of landline telephone numbers which excludes mobile-only households. Telephone (landline and mobile) coverage in South Australia is very high (97%). Mobile telephone ownership increased slightly (7.4%), rising from 89.7% in 2006 to 96.3% in 2013; mobile-only households increased by 431% over the eight year period from 5.2% in 2006 to 27.6% in 2013. Only half of the households have either a mobile or landline number listed in the telephone directory. There were small differences in the prevalence estimates for current asthma, arthritis, diabetes and obesity between the hypothetical telephone samples and the overall sample. However, prevalence estimate for diabetes was slightly underestimated (RCB value of -0.077) in 2013. Mixed RCB results were found for having a mental health condition for both telephone samples. Current smoking prevalence was lower for both hypothetical telephone samples in absolute differences and RCB values: -0.136 to -0.191 for RDD landline samples and -0.129 to -0.313 for directory-listed samples. These findings suggest landline-based sampling frames used in Australia, when appropriately weighted, produce reliable representative estimates for some health indicators but not for all. Researchers need to be aware of their limitations and potential biased estimates.

[Development of Chinese forensic Y-STR DNA database].

PubMed

Ge, Jian-Ye; Yan, Jiang-Wei; Xie, Qun; Sun, Hong-Yu; Zhou, Huai-Gu; Li, Bin

2013-06-01

Y chromosome is a male-specific paternal inherited chromosome. The STR markers on Y chromosome have been widely used in forensic practices. This article summarizes the characteristics of Y-STR and some factors are considered of selecting appropriate Y-STR markers for Chinese population. The prospects of existing and potential forensic applications of Y-STR profiles are discussed including familial excluding, familial searching, crowd source deducing, mixture sample testing, and kinship identifying. The research, development, verification of Y-STR kit, Y-STR mutation rate, and search software are explored and some suggestions are given.

Using probabilistic theory to develop interpretation guidelines for Y-STR profiles.

PubMed

Taylor, Duncan; Bright, Jo-Anne; Buckleton, John

2016-03-01

Y-STR profiling makes up a small but important proportion of forensic DNA casework. Often Y-STR profiles are used when autosomal profiling has failed to yield an informative result. Consequently Y-STR profiles are often from the most challenging samples. In addition to these points, Y-STR loci are linked, meaning that evaluation of haplotype probabilities are either based on overly simplified counting methods or computationally costly genetic models, neither of which extend well to the evaluation of mixed Y-STR data. For all of these reasons Y-STR data analysis has not seen the same advances as autosomal STR data. We present here a probabilistic model for the interpretation of Y-STR data. Due to the fact that probabilistic systems for Y-STR data are still some way from reaching active casework, we also describe how data can be analysed in a continuous way to generate interpretational thresholds and guidelines. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Current state-of-art of STR sequencing in forensic genetics.

PubMed

Alonso, Antonio; Barrio, Pedro A; Müller, Petra; Köcher, Steffi; Berger, Burkhard; Martin, Pablo; Bodner, Martin; Willuweit, Sascha; Parson, Walther; Roewer, Lutz; Budowle, Bruce

2018-05-11

The current state of validation and implementation strategies of MPS technology for the analysis of STR markers for forensic genetics use is described, covering the topics of the current catalogue of commercial MPS-STR panels, leading MPS-platforms, and MPS-STR data analysis tools. In addition, the developmental and internal validation studies carried out to date to evaluate reliability, sensitivity, mixture analysis, concordance, and the ability to analyze challenged samples are summarized. The results of various MPS-STR population studies that showed a large number of new STR sequence variants that increase the power of discrimination in several forensically-relevant loci are also presented. Finally, various initiatives developed by several international projects and standardization (or guidelines) groups to facilitate application of MPS technology for STR marker analyses are discussed in regard to promoting a standard STR sequence nomenclature, performing population studies to detect sequence variants, and developing a universal system to translate sequence variants into a simple STR nomenclature (numbers and letters) compatible with national STR databases. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Evaluation of catch basin grates : final report.

DOT National Transportation Integrated Search

1972-10-01

The Louisiana Department of Highways has adopted new designs for the Standard Plans for the RCB 22X catch basin to replace the old standard cast iron grate with either a welded bar steel grate or an alternate riveted steel reticuline grate. This revi...

Determination of entrance loss coefficients for pre-cast reinforced concrete box culverts.

DOT National Transportation Integrated Search

2012-12-01

There is an increased interest in constructing Pre-Cast (PC) Twin and Triple Reinforced Concrete Box (RCB) culverts : in Iowa due to the efficiency associated with their production in controlled environment and decrease of the construction : time at ...

Effect of high-pressure processing and milk on the anthocyanin composition and antioxidant capacity of strawberry-based beverages.

PubMed

Tadapaneni, Ravi Kiran; Banaszewski, Katarzyna; Patazca, Eduardo; Edirisinghe, Indika; Cappozzo, Jack; Jackson, Lauren; Burton-Freeman, Britt

2012-06-13

The present study investigated processing strategies and matrix effects on the antioxidant capacity (AC) and polyphenols (PP) content of fruit-based beverages: (1) strawberry powder (Str) + dairy, D-Str; (2) Str + water, ND-Str; (3) dairy + no Str, D-NStr. Beverages were subjected to high-temperature-short-time (HTST) and high-pressure processing (HPP). AC and PP were measured before and after processing and after a 5 week shelf-life study. Unprocessed D-Str had significantly lower AC compared to unprocessed ND-Str. Significant reductions in AC were apparent in HTST- compared to HPP-processed beverages (up to 600 MPa). PP content was significantly reduced in D-Str compared to ND-Str and in response to HPP and HTST in all beverages. After storage (5 weeks), AC and PP were reduced in all beverages compared to unprocessed and week 0 processed beverages. These findings indicate potentially negative effects of milk and processing on AC and PP of fruit-based beverages.

DO R CORONAE BOREALIS STARS FORM FROM DOUBLE WHITE DWARF MERGERS?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Staff, Jan. E.; Clayton, Geoffrey C.; Tohline, Joel E.

2012-09-20

A leading formation scenario for R Coronae Borealis (RCB) stars invokes the merger of degenerate He and CO white dwarfs (WDs) in a binary. The observed ratio of {sup 16}O/{sup 18}O for RCB stars is in the range of 0.3-20 much smaller than the solar value of {approx}500. In this paper, we investigate whether such a low ratio can be obtained in simulations of the merger of a CO and a He WD. We present the results of five three-dimensional hydrodynamic simulations of the merger of a double WD system where the total mass is 0.9 M{sub Sun} and themore » initial mass ratio (q) varies between 0.5 and 0.99. We identify in simulations with q {approx}< 0.7 a feature around the merged stars where the temperatures and densities are suitable for forming {sup 18}O. However, more {sup 16}O is being dredged up from the C- and O-rich accretor during the merger than the amount of {sup 18}O that is produced. Therefore, on the dynamical timescale over which our hydrodynamics simulation runs, an {sup 16}O/{sup 18}O ratio of {approx}2000 in the 'best' case is found. If the conditions found in the hydrodynamic simulations persist for 10{sup 6} s the oxygen ratio drops to 16 in one case studied, while in a hundred years it drops to {approx}4 in another case studied, consistent with the observed values in RCB stars. Therefore, the merger of two WDs remains a strong candidate for the formation of these enigmatic stars.« less

Singular Location and Signaling Profile of Adenosine A2A-Cannabinoid CB1 Receptor Heteromers in the Dorsal Striatum.

PubMed

Moreno, Estefanía; Chiarlone, Anna; Medrano, Mireia; Puigdellívol, Mar; Bibic, Lucka; Howell, Lesley A; Resel, Eva; Puente, Nagore; Casarejos, María J; Perucho, Juan; Botta, Joaquín; Suelves, Nuria; Ciruela, Francisco; Ginés, Silvia; Galve-Roperh, Ismael; Casadó, Vicent; Grandes, Pedro; Lutz, Beat; Monory, Krisztina; Canela, Enric I; Lluís, Carmen; McCormick, Peter J; Guzmán, Manuel

2018-04-01

The dorsal striatum is a key node for many neurobiological processes such as motor activity, cognitive functions, and affective processes. The proper functioning of striatal neurons relies critically on metabotropic receptors. Specifically, the main adenosine and endocannabinoid receptors present in the striatum, ie, adenosine A 2A receptor (A 2A R) and cannabinoid CB 1 receptor (CB 1 R), are of pivotal importance in the control of neuronal excitability. Facilitatory and inhibitory functional interactions between striatal A 2A R and CB 1 R have been reported, and evidence supports that this cross-talk may rely, at least in part, on the formation of A 2A R-CB 1 R heteromeric complexes. However, the specific location and properties of these heteromers have remained largely unknown. Here, by using techniques that allowed a precise visualization of the heteromers in situ in combination with sophisticated genetically modified animal models, together with biochemical and pharmacological approaches, we provide a high-resolution expression map and a detailed functional characterization of A 2A R-CB 1 R heteromers in the dorsal striatum. Specifically, our data unveil that the A 2A R-CB 1 R heteromer (i) is essentially absent from corticostriatal projections and striatonigral neurons, and, instead, is largely present in striatopallidal neurons, (ii) displays a striking G protein-coupled signaling profile, where co-stimulation of both receptors leads to strongly reduced downstream signaling, and (iii) undergoes an unprecedented dysfunction in Huntington's disease, an archetypal disease that affects striatal neurons. Altogether, our findings may open a new conceptual framework to understand the role of coordinated adenosine-endocannabinoid signaling in the indirect striatal pathway, which may be relevant in motor function and neurodegenerative diseases.

Establishment of monitoring methods for autophagy in rice reveals autophagic recycling of chloroplasts and root plastids during energy limitation.

PubMed

Izumi, Masanori; Hidema, Jun; Wada, Shinya; Kondo, Eri; Kurusu, Takamitsu; Kuchitsu, Kazuyuki; Makino, Amane; Ishida, Hiroyuki

2015-04-01

Autophagy is an intracellular process leading to vacuolar or lysosomal degradation of cytoplasmic components in eukaryotes. Establishment of proper methods to monitor autophagy was a key step in uncovering its role in organisms, such as yeast (Saccharomyces cerevisiae), mammals, and Arabidopsis (Arabidopsis thaliana), in which chloroplastic proteins were found to be recycled by autophagy. Chloroplast recycling has been predicted to function in nutrient remobilization for growing organs or grain filling in cereal crops. Here, to develop our understanding of autophagy in cereals, we established monitoring methods for chloroplast autophagy in rice (Oryza sativa). We generated transgenic rice-expressing fluorescent protein (FP) OsAuTophaGy8 (OsATG8) fusions as autophagy markers. FP-ATG8 signals were delivered into the vacuolar lumen in living cells of roots and leaves mainly as vesicles corresponding to autophagic bodies. This phenomenon was not observed upon the addition of wortmannin, an inhibitor of autophagy, or in an ATG7 knockout mutant. Markers for the chloroplast stroma, stromal FP, and FP-labeled Rubisco were delivered by a type of autophagic body called the Rubisco-containing body (RCB) in the same manner. RCB production in excised leaves was suppressed by supply of external sucrose or light. The release of free FP caused by autophagy-dependent breakdown of FP-labeled Rubisco was induced during accelerated senescence in individually darkened leaves. In roots, nongreen plastids underwent both RCB-mediated and entire organelle types of autophagy. Therefore, our newly developed methods to monitor autophagy directly showed autophagic degradation of leaf chloroplasts and root plastids in rice plants and its induction during energy limitation. © 2015 American Society of Plant Biologists. All Rights Reserved.

Tricuspid Regurgitation and Mortality in Patients with Transvenous Permanent Pacemaker Leads

PubMed Central

Delling, Francesca N.; Hassan, Zena K.; Piatkowski, Gail; Tsao, Connie W.; Rajabali, Alefiyah; Markson, Lawrence J.; Zimetbaum, Peter J.; Manning, Warren J.; Chang, James D.; Mukamal, Kenneth J.

2016-01-01

Estimates of the prevalence and importance of significant tricuspid regurgitation (STR) related to implantable device leads are based mainly on case reports, small observational studies or mixed samples that include defibrillators. We sought to assess whether patients with permanent pacemaker (PPM) leads have an increased risk of STR and to determine mortality associated with PPM-related TR in a large longitudinal single-center cohort. We examined the prevalence of STR (defined as moderate-severe or ≥ 3+) among all echocardiograms performed between 2005 and 2011 excluding those with defibrillators. We then examined mortality risk according to the prevalence of PPM and STR after adjusting for cardiac co-morbidities, left ventricular (LV) systolic/diastolic function, and pulmonary artery hypertension. We screened 93592 echocardiograms (1245 with PPM) among 58556 individual patients (634 with PPM). The prevalence of STR was higher in patients following PPM placement (mean age 79 ± 3 years; 54% males) compared to patients without a PPM (adjusted odds ratio 2.32, 95% confidence interval [CI], 1.54–3.49; p<0.0001). Among patients with a PPM lead, the presence of STR was associated with increased mortality (adjusted hazard ratios [HR] 1.40, 95% CI 1.04–2.11, p=0.027 versus no STR). Compared to having neither a PPM lead nor STR, adjusted HR for death were 2.13 (95% CI, 1.93–2.34) for STR but no PPM, 1.04 (0.89–1.22) for PPM without STR, and 1.55 (1.13–2.14) for PPM with STR. In conclusion, in a sample comprising over 58,000 individual patients, PPM leads are associated with higher risk of STR after adjustment for LV systolic/diastolic function and pulmonary artery hypertension; similarly to STR from other cardiac pathologies, PPM-related STR is associated with increased mortality. PMID:26833208

Aromatic compounds produced by Periconia atropurpurea, an endophytic fungus associated with Xylopia aromatica.

PubMed

Teles, Helder Lopes; Sordi, Renata; Silva, Geraldo Humberto; Castro-Gamboa, Ian; Bolzani, Vanderlan da Silva; Pfenning, Ludwig Heinrich; de Abreu, Lucas Magalhães; Costa-Neto, Claudio Miguel; Young, Maria Claudia Marx; Araújo, Angela Regina

2006-12-01

6,8-Dimethoxy-3-(2'-oxo-propyl)-coumarin (1) and 2,4-dihydroxy-6-[(1'E,3'E)-penta-1',3'-dienyl]-benzaldehyde (2), in addition to the known compound periconicin B (3), were isolated from the ethyl acetate extract of Periconia atropurpurea, an endophytic fungus obtained from the leaves of Xylopia aromatica, a native plant of the Brazilian Cerrado. Their chemical structures were assigned based on analyses of MS, 1D and 2D-NMR spectroscopic experiments. Biological analyses were performed using two mammalian cell lines, human cervix carcinoma (HeLa) and Chinese hamster ovary (CHO). The results showed that compound 1 had no effect when compared to the control group, which was treated with the vehicle (DMSO). Compound 2 was able to induce a slight increase in cell proliferation of HeLa (37% of increase) and CHO (38% of increase) cell lines. Analysis of compound 3 showed that it has potent cytotoxic activity against both cell lines, with an IC50 of 8.0 microM. Biological analyses using the phytopathogenic fungi Cladosporium sphaerospermum and C. cladosporioides revealed that also 2 showed potent antifungal activity compared to nystatin.

[In vitro absorption mechanism of strychnine and the transport interaction with liquiritin in Caco-2 cell monolayer model].

PubMed

Wang, Jun-jun; Liao, Xiao-huan; Ye, Min; Chen, Yong

2010-09-01

To study the effect of liquiritin (Liq) on the transport of strychnine (Str) in Caco-2 cell monolayer model, the transport parameters of Str, such as apparent permeability coefficient (P app (B-->A) and P app (A-->B)) and cumulative transport amount (TRcum), were determined and comparatively analyzed when Str was used solely and co-used with Liq. The effect of drug concentrations, conveying times, P-glycoprotein (P-gp) inhibitor verapamil and conveying liquor pH values on the transport of Str were also investigated. The results indicated that the absorption of Str in Caco-2 cell monolayer model was well and the passive transference was the main intestinal absorption mechanism of Str in the Caco-2 monolayer model, along with the excretion action mediated by P-gp. Liq enhanced the absorption of Str. Meanwhile, conveying liquor pH value had significant influence on the excretion transport of Str.

Revision of the genus Ptomaphagus Hellwig from eastern Asia (Coleoptera, Leiodidae, Cholevinae).

PubMed

Wang, Cheng-Bin; Perreau, Michel; Růžička, Jan; Nishikawa, Masaaki

2017-01-01

The species belonging to the genus Ptomaphagus Hellwig, 1795 (Coleoptera, Leiodidae, Cholevinae, Ptomaphagini) from eastern Asia are assigned to three species groups. Group yasutoshii has a single species: P. (s. str.) yasutoshii Nishikawa, 1993 from Taiwan, China. Group nepalensis with three species: P. (s. str.) nepalensis Perreau, 1988 from Nepal and P. (s. str.) masumotoi Nishikawa, 2011 from Thailand are redescribed, and P. (s. str.) piccoloi Wang, Růžička, Nishikawa, Perreau & Hayashi, 2016 is recorded for the first time from China (Zhejiang). Group sibiricus with seven species, including two newly described Chinese ones P. (s. str.) funiu sp. n. from Henan, and P. (s. str.) haba sp. n. from Yunnan, and five known species: P. (s. str.) chenggongi Wang, Nishikawa, Perreau, Růžička & Hayashi, 2016, P. (s. str.) hayashii Wang, Růžička, Perreau, Nishikawa & Park, 2016, P. (s. str.) kuntzeni Sokolowski, 1957 (distribution records from Myanmar excluded), P. (s. str.) sibiricus Jeannel, 1934 and P. (s. str.) tingtingtae Wang, Nishikawa, Perreau, Růžička & Hayashi, 2016. Specimens of other undescribed species of the group sibiricus are also recorded, revealing a high diversity of this genus in eastern Asia, especially in central and north Sichuan, China, which essentially remains to be investigated. Relevant morphological characters of the examined species are illustrated with colour plates, and their known distributions are mapped. A key to species of Ptomaphagus from eastern Asia is provided.

TREATABILITY STUDY BULLETIN: MOBILE VOLUME REDUCTION UNIT AT THE SAND CREEK SUPERFUND SITE

EPA Science Inventory

The Risk Reduction Engineering Laboratory (RREL) Releases Control Branch (RCB) has developed a pilot-scale Mobile Volume Reduction Unit (VRU) to determine the feasibility of soil washing for the remediation of contaminated soils. This mobile unit, mounted on two trailers, can pro...

Interfacial Fracture Toughness of Adhesive Resin Cement-Lithium-Disilicate/Resin-Composite Blocks.

PubMed

Mesmar, Samer; Ruse, N Dorin

2017-09-15

Resin composite blocks (RCB) are advocated as alternative to ceramic blocks (CB). Prior to use, adherence to these materials should characterized. This study aimed to test the null hypothesis (H 0 ) that material and surface treatment combinations do not influence interfacial fracture toughness (K IC ) of a self-cured adhesive resin cement [RelyX Ultimate (RXU)] to RCB or CB, under nonaged and aged conditions. Two RCB, Lava Ultimate (LU) and Enamic (EN), and one CB, IPS e.max Press (EMP) were used. Half-size [(6 × 6 × 6 × 6 mm)] specimens were prepared for EMP (n = 30), EN (n = 30), and LU (n = 60). RCB specimens were prepared by wet cutting/grinding, while CB specimens were pressed. Surfaces of EMP and EN were preconditioned with hydrofluoric acid (5%); surfaces of LU were sandblasted with either 27 μm alumina (LUS) or 30 μm silica-modified alumina Rocatec soft (LUR). All specimens were bonded with Scotchbond Universal adhesive and RXU. Additionally, twenty (4 × 4 × 4 × 8 mm) RXU specimens were prepared. All specimens were stored in water at 37°C and tested after 1 and 60 days. Interfacial K IC was determined with the notchless triangular prism specimen K IC test. Results were analyzed with two-way ANOVA and Scheffé multiple means comparisons (α = 0.05). Preconditioned and selected fractured surfaces were characterized with scanning electron microscopy. At 24 hours, LUS-RXU and LUR-RXU had significantly higher interfacial K IC than EN-RXU and EMP-RXU and were not different from K IC of RXU. Aging lead to a significant decrease in K IC of RXU and interfacial K IC of LUS-RXU, LUR-RXU, and EMP-RXU; interfacial K IC of EN-RXU was not affected. Based on the results, H 0 was rejected. Under the conditions of this study, at 24 hours, interfacial K IC of LUS-RXU and LUR-RXU was superior to EMP-RXU and EN-RXU. Aging in water at 37°C did not affect interfacial K IC of EN-RXU but adversely affected K IC of RXU and the other interfacial K IC . The results suggest that RXU and its adherence to LU and EMP deteriorates upon exposure to water at 37°C. In making clinical decisions related to material selection, practitioners should consider in vitro results. © 2017 by the American College of Prosthodontists.

INCREASES IN FUNCTIONAL CONNECTIVITY BETWEEN PREFRONTAL CORTEX AND STRIATUM DURING CATEGORY LEARNING

PubMed Central

Antzoulatos, Evan G.; Miller, Earl K.

2014-01-01

SUMMARY Functional connectivity between the prefrontal cortex (PFC) and striatum (STR) is thought critical for cognition, and has been linked to conditions like autism and schizophrenia. We recorded from multiple electrodes in PFC and STR while monkeys acquired new categories. Category learning was accompanied by an increase in beta-band synchronization of LFPs between, but not within, the PFC and STR. After learning, different pairs of PFC-STR electrodes showed stronger synchrony for one or the other category, suggesting category-specific functional circuits. This category-specific synchrony was also seen between PFC spikes and STR LFPs, but not the reverse, reflecting the direct monosynaptic connections from the PFC to STR. However, causal connectivity analyses suggested that the polysynaptic connections from STR to the PFC exerted a stronger overall influence. This supports models positing that the basal ganglia “train” the PFC. Category learning may depend on the formation of functional circuits between the PFC and STR. PMID:24930701

Single Tablet Regimen Usage and Efficacy in the Treatment of HIV Infection in Australia

PubMed Central

Armstrong, B.; Chan, D. J.; Stewart, M. J.; Fagan, D.; Smith, D.

2015-01-01

Single tablet regimens (STRs) for HIV infection improve patient satisfaction, quality of life, medication adherence, and virological suppression compared to multitablet regimens (MTRs). This is the first study assessing STR uptake and durability in Australia. This retrospective audit of all patients receiving an STR (n = 299) at a large Sydney HIV clinic (January 2012–December 2013) assessed patient demographics, treatment prior to STR, HIV RNA load and CD4 during MTR and STR dosing, and reasons for STR switch. 206 patients switched from previous antiretroviral treatment to an STR, of which 88% switched from an MTR. Reasons for switching included desire to simplify treatment (57%), reduced side effects or toxicity (18%), and cost-saving for the patient. There was no switching for virological failure. Compared to when on an MTR, patients switching to an STR had significantly lower HIV RNA counts (p < 0.001) and significantly higher CD4 counts (p < 0.001). The discontinuation rate from STR was very low and all patients who switched to an STR maintained virological suppression throughout the study duration, although the study is limited by the absence of a control group. PMID:26550490

Effects of rainfall exclusion on leaf gas exchange traits and osmotic adjustment in mature canopy trees of Dryobalanops aromatica (Dipterocarpaceae) in a Malaysian tropical rain forest.

PubMed

Inoue, Yuta; Ichie, Tomoaki; Kenzo, Tanaka; Yoneyama, Aogu; Kumagai, Tomo'omi; Nakashizuka, Tohru

2017-10-01

Climate change exposes vegetation to unusual levels of drought, risking a decline in productivity and an increase in mortality. It still remains unclear how trees and forests respond to such unusual drought, particularly Southeast Asian tropical rain forests. To understand leaf ecophysiological responses of tropical rain forest trees to soil drying, a rainfall exclusion experiment was conducted on mature canopy trees of Dryobalanops aromatica Gaertn.f. (Dipterocarpaceae) for 4 months in an aseasonal tropical rain forest in Sarawak, Malaysia. The rainfall was intercepted by using a soft vinyl chloride sheet. We compared the three control and three treatment trees with respect to leaf water use at the top of the crown, including stomatal conductance (gsmax), photosynthesis (Amax), leaf water potential (predawn: Ψpre; midday: Ψmid), leaf water potential at turgor loss point (πtlp), osmotic potential at full turgor (π100) and a bulk modulus of elasticity (ε). Measurements were taken using tree-tower and canopy-crane systems. During the experiment, the treatment trees suffered drought stress without evidence of canopy dieback in comparison with the control trees; e.g., Ψpre and Ψmid decreased with soil drying. Minimum values of Ψmid in the treatment trees decreased during the experiment, and were lower than πtlp in the control trees. However, the treatment trees also decreased their πtlp by osmotic adjustment, and the values were lower than the minimum values of their Ψmid. In addition, the treatment trees maintained gs and Amax especially in the morning, though at midday, values decreased to half those of the control trees. Decreasing leaf water potential by osmotic adjustment to maintain gs and Amax under soil drying in treatment trees was considered to represent anisohydric behavior. These results suggest that D. aromatica may have high leaf adaptability to drought by regulating leaf water consumption and maintaining turgor pressure to improve its leaf water relations. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

U.S. EPA, Pesticide Product Label, , 07/17/1984

EPA Pesticide Factsheets

2011-04-14

... ff~(;t bcgirullng \\I;hen qta!":~ reSU:',C'5 gro'wo't.h ill t.ile G!'ring (t"~~rcb-;\\} rll}. Rcpelit. at 7 to 10 day ... 1 : .I 1 L t "rll~lt l Iy l! ~ I '" I ' , • , ,t '.; r • ',.r ...

Early Surgery for Endocarditis Complicated by Preoperative Cerebral Emboli Is Not Associated With Worsened Outcomes

PubMed Central

Sorabella, Robert A.; Han, Sang Myung; Grbic, Mark; Wu, Yeu Sanz; Takyama, Hiroo; Kurlansky, Paul; Borger, Michal A.; Argenziano, Michael; Gordon, Rachel; George, Isaac

2015-01-01

Background Valve surgery for patients presenting with infective endocarditis (IE) complicated by stroke is thought to carry elevated risk of postoperative complications. Our aim is to compare outcomes of IE patients who undergo surgery early after diagnosis of septic cerebral emboli with patients without preoperative emboli. Methods All patients undergoing surgery for left-sided IE between 1996–2013 at our institution were reviewed. Patients undergoing surgery > 14 days after embolic stroke diagnosis (n=11) and those with purely hemorrhagic lesions were excluded from analysis (n=7). In total, 308 were included in the study and stratified according to the presence (STR, n=54) or absence of a preoperative septic cerebral embolus (NoSTR, n=254). Primary outcomes of interest were development of new postoperative stroke and 30-day mortality. Results Mean time to surgical intervention from stroke onset was 6.0 ± 4.1 days. S. aureus (39% STR vs. 21% NoSTR, p = 0.004) and annular abscess at surgery (52% STR vs. 27% NoSTR, p < 0.001) were more prevalent in STR patients. There was no significant difference in 30-day mortality (9.3% STR vs. 7.1% NoSTR, p = 0.57) or rate of new postoperative stroke [5 (9.4%) STR vs. 12 (4.7%) NoSTR, p = 0.19] between groups. Additionally, there was no difference in 10-year survival between groups (log rank p = 0.74). Conclusions Early surgical intervention in patients with IE complicated by preoperative septic cerebral emboli does not lead to significantly worse postoperative outcomes. Early surgery for IE following embolic stroke warrants consideration, particularly in patients with high-risk features such as S. aureus and/or annular abscess. PMID:26116483

Strychnine-sensitive modulation is selective for non-noxious somatosensory input in the spinal cord of the rat.

PubMed

Sherman, S E; Loomis, C W

1996-08-01

Touch-evoked allodynia, an important symptom of clinical neural injury pain, can be modelled acutely and reversibly in the urethane-anesthetized rat using intrathecal (i.t.) strychnine (STR). Allodynia, after i.t. STR (40 micrograms), is manifest as a significant enhancement of cardiovascular and motor responses evoked by normally innocuous brushing of the hair (hair deflection), as compared to responses evoked by either hair deflection after i.t. saline (SAL), or to i.t. STR (40 micrograms) with no tactile stimulus. The present study investigated: (1) the pharmacology of afferent neural inputs involved in STR-dependent allodynia using neonatal capsaicin and the non-NMDA receptor antagonist 2,3-dihydroxy-6-nitro-7-sulfamoyl-benzo[f]quinoxaline (NBQX); and (2) the effect of i.t. STR on responses evoked by peripheral noxious stimulation. Neonatal capsaicin (25 mg/kg, s.c., post-natal day (PND) 1, and 50 mg/kg, s.c., PND 2, 3, 4, 11, 25, 55 and 85) significantly attenuated the responses evoked by noxious mechanical, thermal or chemical stimuli, but had no effect on STR-dependent allodynia. All hair deflection-evoked, STR-dependent responses were dose-dependently inhibited by i.t. NBQX. The ED50 values and 95% confidence intervals were 10.4 micrograms (5.5-19.6) for the motor withdrawal response, 14.4 micrograms (8.6-24.0) for changes in MAP and 12.2 micrograms (6.8-21.8) for changes in HR. Cortical EEG synchrony was unchanged by i.t. NBQX confirming its spinal locus of action. Intrathecal STR neither reduced nor enhanced the responses elicited by noxious stimuli in capsaicin- or vehicle-pretreated rats. These results indicate that STR-dependent allodynia is initiated by primary afferents not normally involved in nociception (possibly A beta-fibers), and that STR-sensitive modulation in the spinal cord is selective for non-noxious sensory input. The sensitivity of STR-dependent allodynia to non-NMDA receptor antagonists, and the failure of i.t. STR to produce hyperalgesia to mechanical, thermal or chemical noxious stimuli, confirm the independence of nociceptive pathways and STR-sensitive afferent inputs in this model.

New taxonomic and faunistic data on the Himalayan Lesteva Latreille, 1797 (Coleoptera: Staphylinidae: Omaliinae).

PubMed

Shavrin, Alexey V

2016-12-05

New taxonomic and faunistc data for seven species of the genus Lesteva Latreille, 1797 of the Himalayas are presented. Two species are redescribed: L. (s.str.) kargilensis Cameron, 1934 and L. (s.str.) steeli Lohse, 1982. The aedeagus of L. (s.str.) steeli is illustrated. One synonym is proposed: L. (s.str.) brevipennis Cameron, 1941 = L. pakistana Coiffait, 1984 syn. n. A lectotype and paralectotypes for L. (s.str.) torrentum Cameron, 1924 are designated. A key to species known from the Himalayan Region is provided.

Secondary metabolite profiling of Curcuma species grown at different locations using GC/TOF and UPLC/Q-TOF MS.

PubMed

Lee, Jueun; Jung, Youngae; Shin, Jeoung-Hwa; Kim, Ho Kyoung; Moon, Byeong Cheol; Ryu, Do Hyun; Hwang, Geum-Sook

2014-07-04

Curcuma, a genus of rhizomatous herbaceous species, has been used as a spice, traditional medicine, and natural dye. In this study, the metabolite profile of Curcuma extracts was determined using gas chromatography-time of flight mass spectrometry (GC/TOF MS) and ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS) to characterize differences between Curcuma aromatica and Curcuma longa grown on the Jeju-do or Jin-do islands, South Korea. Previous studies have performed primary metabolite profiling of Curcuma species grown in different regions using NMR-based metabolomics. This study focused on profiling of secondary metabolites from the hexane extract of Curcuma species. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) plots showed significant differences between the C. aromatica and C. longa metabolite profiles, whereas geographical location had little effect. A t-test was performed to identify statistically significant metabolites, such as terpenoids. Additionally, targeted profiling using UPLC/Q-TOF MS showed that the concentration of curcuminoids differed depending on the plant origin. Based on these results, a combination of GC- and LC-MS allowed us to analyze curcuminoids and terpenoids, the typical bioactive compounds of Curcuma, which can be used to discriminate Curcuma samples according to species or geographical origin.

Intracellular Localization of Arabidopsis Sulfurtransferases1

PubMed Central

Bauer, Michael; Dietrich, Christof; Nowak, Katharina; Sierralta, Walter D.; Papenbrock, Jutta

2004-01-01

Sulfurtransferases (Str) comprise a group of enzymes widely distributed in archaea, eubacteria, and eukaryota which catalyze the transfer of a sulfur atom from suitable sulfur donors to nucleophilic sulfur acceptors. In all organisms analyzed to date, small gene families encoding Str proteins have been identified. The gene products were localized to different compartments of the cells. Our interest concerns the localization of Str proteins encoded in the nuclear genome of Arabidopsis. Computer-based prediction methods revealed localization in different compartments of the cell for six putative AtStrs. Several methods were used to determine the localization of the AtStr proteins experimentally. For AtStr1, a mitochondrial localization was demonstrated by immunodetection in the proteome of isolated mitochondria resolved by one- and two-dimensional gel electrophoresis and subsequent blotting. The respective mature AtStr1 protein was identified by mass spectrometry sequencing. The same result was obtained by transient expression of fusion constructs with the green fluorescent protein in Arabidopsis protoplasts, whereas AtStr2 was exclusively localized to the cytoplasm by this method. Three members of the single-domain AtStr were localized in the chloroplasts as demonstrated by transient expression of green fluorescent protein fusions in protoplasts and stomata, whereas the single-domain AtStr18 was shown to be cytoplasmic. The remarkable subcellular distribution of AtStr15 was additionally analyzed by transmission electron immunomicroscopy using a monospecific antibody against green fluorescent protein, indicating an attachment to the thylakoid membrane. The knowledge of the intracellular localization of the members of this multiprotein family will help elucidate their specific functions in the organism. PMID:15181206

Intracellular localization of Arabidopsis sulfurtransferases.

PubMed

Bauer, Michael; Dietrich, Christof; Nowak, Katharina; Sierralta, Walter D; Papenbrock, Jutta

2004-06-01

Sulfurtransferases (Str) comprise a group of enzymes widely distributed in archaea, eubacteria, and eukaryota which catalyze the transfer of a sulfur atom from suitable sulfur donors to nucleophilic sulfur acceptors. In all organisms analyzed to date, small gene families encoding Str proteins have been identified. The gene products were localized to different compartments of the cells. Our interest concerns the localization of Str proteins encoded in the nuclear genome of Arabidopsis. Computer-based prediction methods revealed localization in different compartments of the cell for six putative AtStrs. Several methods were used to determine the localization of the AtStr proteins experimentally. For AtStr1, a mitochondrial localization was demonstrated by immunodetection in the proteome of isolated mitochondria resolved by one- and two-dimensional gel electrophoresis and subsequent blotting. The respective mature AtStr1 protein was identified by mass spectrometry sequencing. The same result was obtained by transient expression of fusion constructs with the green fluorescent protein in Arabidopsis protoplasts, whereas AtStr2 was exclusively localized to the cytoplasm by this method. Three members of the single-domain AtStr were localized in the chloroplasts as demonstrated by transient expression of green fluorescent protein fusions in protoplasts and stomata, whereas the single-domain AtStr18 was shown to be cytoplasmic. The remarkable subcellular distribution of AtStr15 was additionally analyzed by transmission electron immunomicroscopy using a monospecific antibody against green fluorescent protein, indicating an attachment to the thylakoid membrane. The knowledge of the intracellular localization of the members of this multiprotein family will help elucidate their specific functions in the organism.

Forensic evaluation of STR typing reliability in lung cancer.

PubMed

Zhang, Peng; Zhu, Ying; Li, Yongguo; Zhu, Shisheng; Ma, Ruoxiang; Zhao, Minzhu; Li, Jianbo

2018-01-01

Short tandem repeats (STR) analysis is the gold standard method in the forensics field for personal identification and paternity testing. In cancerous tissues, STR markers are gaining attention, with some studies showing increased instability. Lung cancer, which is one of the most commonmalignancies, has become the most lethal among all cancers. In certain situations, lung cancer tissues may be the only resource available for forensic analysis. Therefore, evaluating the reliability of STR markers in lung cancer tissues is required to avoid false exclusions. In this study, 75 lung cancer tissue samples were examined to evaluate the reliability of various STR markers. Out of the 75 examined samples, 24 of the cancerous samples (32%) showed genetic alterations on at least one STR loci, totaling 55 times. The most common type of STR variation was a partial loss of heterozygosity, with the D5S818 loci having the highest variation frequency and no alterations detected on the D2S441 and Penta E loci. Moreover, STR variation frequencies were shown to increase with an increased patient age and increased clinical and pathological characteristics, thus an older patient with an advanced stage of progression exhibited a higher variation frequency. Overall, this study provides forensic scientists with further insight into STR analysis relating to lung cancer tissue. Copyright © 2017 Elsevier B.V. All rights reserved.

Prospective Impact of Responsibility Center Budgeting on Communication and Theatre Programs: View from a State Supported University.

ERIC Educational Resources Information Center

Dick, Robert C.

In response to the nationwide trend toward increased financial pressures and growing demands by state legislatures for accountability, several large universities (including Indiana University) have adopted various forms of "responsibility center budgeting" (RCB), which has fiscal implications for programs in speech communication and…

Neural Network Research: A Personal Perspective,

DTIC Science & Technology

1988-03-01

problems in computer science and technology today. Still others do both. Whatever the focus, here isafidred to adre efforts of a wide variety of gifted ...Still others do both. Whatever the focus, here is a field ready to challenge and reward the sustained efforts of a wide variety of gifted people. 14 7eN. a rcb

Molecular Mechanism Underlying the Entomotoxic Effect of Colocasia esculenta Tuber Agglutinin against Dysdercus cingulatus

PubMed Central

Roy, Amit; Das, Sampa

2015-01-01

Colocasia esculenta tuber agglutinin (CEA), a mannose binding lectin, exhibits insecticidal efficacy against different hemipteran pests. Dysdercus cingulatus, red cotton bug (RCB), has also shown significant susceptibility to CEA intoxication. However, the molecular basis behind such entomotoxicity of CEA has not been addressed adequately. The present study elucidates the mechanism of insecticidal efficacy of CEA against RCB. Confocal and scanning electron microscopic analyses documented CEA binding to insect midgut tissue, resulting in an alteration of perimicrovillar membrane (PMM) morphology. Internalization of CEA into insect haemolymph and ovary was documented by western blotting analyses. Ligand blot followed by mass spectrometric identification revealed the cognate binding partners of CEA as actin, ATPase and cytochrome P450. Deglycosylation and mannose inhibition assays indicated the interaction to probably be mannose mediated. Bioinformatic identification of putative glycosylation or mannosylation sites in the binding partners further supports the sugar mediated interaction. Correlating entomotoxicity of CEA with immune histological and binding assays to the insect gut contributes to a better understanding of the insecticidal potential of CEA and endorses its future biotechnological application.

Standardizing of Pathology in Patients Receiving Neoadjuvant Chemotherapy.

PubMed

Bossuyt, Veerle; Symmans, W Fraser

2016-10-01

The use of neoadjuvant systemic therapy for the treatment of breast cancer patients is increasing. Pathologic response in the form of pathologic complete response (pCR) and grading systems of partial response, such as the residual cancer burden (RCB) system, gives valuable prognostic information for patients and is used as a primary endpoint in clinical trials. The breast cancer and pathology communities are responding with efforts to standardize pathology in patients receiving neoadjuvant chemotherapy. In this review, we summarize the challenges that postneoadjuvant systemic therapy surgical specimens pose and how pathologists and the multidisciplinary team can work together to optimize handling of these specimens. Multidisciplinary communication is essential. A single, standardized approach to macroscopic and microscopic pathologic examination makes it possible to provide reliable response information. This approach employs a map of tissue sections to correlate clinical, gross, microscopic, and imaging findings in order to report the presence of pCR (ypT0 ypN0 and ypT0/is ypN0) versus residual disease, the ypT and ypN stage using the current AJCC/UICC staging system, and the RCB.

A Large Population Genetic Study of 15 Autosomal Short Tandem Repeat Loci for Establishment of Korean DNA Profile Database

PubMed Central

Yoo, Seong Yeon; Cho, Nam Soo; Park, Myung Jin; Seong, Ki Min; Hwang, Jung Ho; Song, Seok Bean; Han, Myun Soo; Lee, Won Tae; Chung, Ki Wha

2011-01-01

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10-17. This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications. PMID:21597912

A large population genetic study of 15 autosomal short tandem repeat loci for establishment of Korean DNA profile database.

PubMed

Yoo, Seong Yeon; Cho, Nam Soo; Park, Myung Jin; Seong, Ki Min; Hwang, Jung Ho; Song, Seok Bean; Han, Myun Soo; Lee, Won Tae; Chung, Ki Wha

2011-07-01

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10(-17). This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications.

Bacteria and bacterial DNA in atherosclerotic plaque and aneurysmal wall biopsies from patients with and without periodontitis

PubMed Central

Armingohar, Zahra; Jørgensen, Jørgen J.; Kristoffersen, Anne Karin; Abesha-Belay, Emnet; Olsen, Ingar

2014-01-01

Background Several studies have reported an association between chronic periodontitis (CP) and cardiovascular diseases. Detection of periodontopathogens, including red complex bacteria (RCB), in vascular lesions has suggested these bacteria to be involved in the pathogenesis of atherosclerosis and abdominal aortic aneurysms. Objective In this study, we investigate bacteria and their DNA in vascular biopsies from patients with vascular diseases (VD; i.e. abdominal aortic aneurysms, atherosclerotic carotid, and common femoral arteries), with and without CP. Methods DNA was extracted from vascular biopsies selected from 40 VD patients: 30 with CP and 10 without CP. The V3-V5 region of the 16S rDNA (V3-V5) was polymerase chain reaction (PCR)-amplified, and the amplicons were cloned into Escherichia coli, sequenced, and classified (GenBank and the Human Oral Microbiome database). Species-specific primers were used for the detection of Porphyromonas gingivalis. In addition, 10 randomly selected vascular biopsies from the CP group were subjected to scanning electron microscopy (SEM) for visualization of bacteria. Checkerboard DNA–DNA hybridization was performed to assess the presence of RCB in 10 randomly selected subgingival plaque samples from CP patients. Results A higher load and mean diversity of bacteria were detected in vascular biopsies from VD patients with CP compared to those without CP. Enterobacteriaceae were frequently detected in vascular biopsies together with cultivable, commensal oral, and not-yet-cultured bacterial species. While 70% of the subgingival plaque samples from CP patients showed presence of RCB, only P. gingivalis was detected in one vascular biopsy. Bacterial cells were seen in all 10 vascular biopsies examined by SEM. Conclusions A higher bacterial load and more diverse colonization were detected in VD lesions of CP patients as compared to patients without CP. This indicated that a multitude of bacterial species both from the gut and the oral cavity, rather than exclusively periodontopathogens, may be involved as additional risk factors in the pathogenesis of VD. PMID:25006361

Characterization of genetic sequence variation of 58 STR loci in four major population groups.

PubMed

Novroski, Nicole M M; King, Jonathan L; Churchill, Jennifer D; Seah, Lay Hong; Budowle, Bruce

2016-11-01

Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X-chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups. Seven hundred and forty six autosomal, 227 X-chromosome, and 324 Y-chromosome STR alleles were identified by sequence compared with 357 autosomal, 107 X-chromosome, and 189 Y-chromosome STR alleles that were identified by length. Within the observed sequence variation, 227 autosomal, 156 X-chromosome, and 112 Y-chromosome novel alleles were identified and described. One hundred and seventy six autosomal, 123 X-chromosome, and 93 Y-chromosome sequence variants resided within STR repeat regions, and 86 autosomal, 39 X-chromosome, and 20 Y-chromosome variants were located in STR flanking regions. Three markers, D18S51, DXS10135, and DYS385a-b had 1, 4, and 1 alleles, respectively, which contained both a novel repeat region variant and a flanking sequence variant in the same nucleotide sequence. There were 50 markers that demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. These population data illustrate the genetic variation that exists in the commonly used STR markers in the selected population samples and provide allele frequencies for statistical calculations related to STR profiling with MPS data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

17 to 23: A novel complementary mini Y-STR panel to extend the Y-STR databases from 17 to 23 markers for forensic purposes.

PubMed

Núñez, Carolina; Baeta, Miriam; Ibarbia, Nerea; Ortueta, Urko; Jiménez-Moreno, Susana; Blazquez-Caeiro, José Luis; Builes, Juan José; Herrera, Rene J; Martínez-Jarreta, Begoña; de Pancorbo, Marian M

2017-04-01

A Y-STR multiplex system has been developed with the purpose of complementing the widely used 17 Y-STR haplotyping (AmpFlSTR Y Filer® PCR Amplification kit) routinely employed in forensic and population genetic studies. This new multiplex system includes six additional STR loci (DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643) to reach the 23 Y-STR of the PowerPlex® Y23 System. In addition, this kit includes the DYS456 and DYS385 loci for traceability purposes. Male samples from 625 individuals from ten worldwide populations were genotyped, including three sample sets from populations previously published with the 17 Y-STR system to expand their current data. Validation studies demonstrated good performance of the panel set in terms of concordance, sensitivity, and stability in the presence of inhibitors and artificially degraded DNA. The results obtained for haplotype diversity and discrimination capacity with this multiplex system were considerably high, providing further evidences of the suitability of this novel Y-STR system for forensic purposes. Thus, the use of this multiplex for samples previously genotyped with 17 Y-STRs will be an efficient and low-cost alternative to complete the set of 23 Y-STRs and improve allele databases for population and forensic purposes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular analysis of ivy cells of the hippocampal CA1 stratum radiatum using spectral identification of immunofluorophores

PubMed Central

Somogyi, Jozsef; Szabo, Andras; Somogyi, Peter; Lamsa, Karri

2012-01-01

Neuronal nitric oxide synthase-expressing (nNOS+) GABAergic interneurons are common in hippocampal stratum (str.) radiatum. However, these cells are less well characterized than nNOS+ ivy cells in str. pyramidale or neurogliaform cells (NGC) in str. lacunosum-moleculare. Here we have studied the laminar distribution of the axons and dendrites, and the immunoreactivity of these neurons recorded in rat hippocampal slices. We have used spectral analysis of antibody- or streptavidin-conjugated fluorophores to improve recognition of genuine signals in reactions for molecules such as nNOS and neuropeptide-Y (NPY). We found that most nNOS+ cells with soma in the CA1 area str. radiatum exhibit characteristic properties of ivy cells, and were positive for NPY and negative for reelin. However, laminar distributions of their neurites differ from original characterization of ivy cells with the soma in or close to str. pyramidale. Both their dendrites and axon are mainly in str. radiatum and to a lesser extent in str. oriens, and in addition often extend to str. lacunosum-moleculare. We conclude that ivy cells in str. radiatum may predominantly be feedforward inhibitory interneurons in the CA1 area, and their axonal output delivering GABA, NPY, and NO can influence both the entorhinal cortex innervated and the CA3 innervated zones pre- and post-synaptically. Spectral analysis of fluorophores provides an objective algorithm to analyze signals in immunoreactions for neurochemical markers. PMID:22666191

Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population.

PubMed

Liu, Yao-Shun; Chen, Jian-Gang; Mei, Ting; Guo, Yu-Xin; Meng, Hao-Tian; Li, Jian-Fei; Wei, Yuan-Yuan; Jin, Xiao-Ye; Zhu, Bo-Feng; Zhang, Li-Ping

2017-08-15

We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations.

[Application of multiple polymorphism genetic markers in determination of half sibling sharing a same mother].

PubMed

Que, Ting-zhi; Zhao, Shu-min; Li, Cheng-tao

2010-08-01

Determination strategies for half sibling sharing a same mother were investigated through the detection of autosomal and X-chromosomal STR (X-STR) loci and polymorphisms on hypervariable (HV) region of mitochondrial DNA (mtDNA). Genomic DNA were extracted from blood stain samples of the 3 full siblings and one dubious half sibling sharing the same mother with them. Fifteen autosomal STR loci were genotyped by Sinofiler kit, and 19 X-STR loci were genotyped by Mentype Argus X-8 kit and 16 plex in-house system. Polymorphisms of mtDNA HV-I and HV-II were also detected with sequencing technology. Full sibling relationship between the dubious half sibling and each of the 3 full siblings were excluded based on the results of autosomal STR genotyping and calculation of full sibling index (FSI) and half sibling index (HIS). Results of sequencing for mtDNA HV-I and HV-II showed that all of the 4 samples came from a same maternal line. X-STR genotyping results determined that the dubious half sibling shared a same mother with the 3 full siblings. It is reliable to combine three different genotyping technologies including autosomal STR, X-STR and sequencing of mtDNA HV-I and HV-II for determination of half sibling sharing a same mother.

Water Treatment Residuals and Scrap Tire Rubber as Green Sorbents for Removal of Stormwater Metals.

PubMed

Deng, Yang; Morris, Ciapha; Rakshit, Sudipta; Landa, Edward; Punamiya, Pravin; Sarkar, Dibyendu

2016-06-01

Bench scale tests were performed to evaluate two recycled wastes, water treatment residuals (WTR) and scrap tire rubber (STR), for adsorption of selected metals from urban stormwater, and assess their release from used sorbents. Aluminum-WTR alone could rapidly and effectively remove Cu, Pb, and Zn, while STR alone continuously released Zn accompanied with Cu and Pb adsorption. Zn leaching from STR was significantly reduced in the presence of WTR. Very little metals released from used combined adsorbents in NaNO3 solution, and only part of them were extracted with EDTA (a strong chelating agent), suggesting that metal release is not a concern in a typical stormwater condition. A combination of WTR and STR is a new, effective method for mitigation of urban stormwater metals-WTR can inhibit the STR leaching, and STR improves the hydraulic permeability of WTR powders, a limiting factor for stormwater flow when WTR is used alone.

[Application of Multiple Genetic Markers in a Case of Determination of Half Sibling].

PubMed

Yang, Xue; Shi, Mei-sen; Yuan, Li; Lu, Di

2016-02-01

A case of half sibling was determined with multiple genetic markers, which could be potentially applied for determination of half sibling relationship from same father. Half sibling relationship was detected by 39 autosomal STR genetic markers, 23 Y-chromosomal STR genetic markers and 12 X -chromosomal STR genetic markers among ZHAO -1, ZHAO -2, ZHAO -3, ZHAO -4, and ZHAO-5. According to autosomal STR, Y-STR and X-STR genotyping results, it was determined that ZHAO-4 (alleged half sibling) was unrelated with ZHAO-1 and ZHAO-2; however, ZHAO-3 (alleged half sibling), ZHAO-5 (alleged half sibling) shared same genetic profile with ZHAO-1, and ZHAO-2 from same father. It is reliable to use multiple genetic markers and family gene reconstruction to determine half sibling relationship from same father, but it is difficult to determination by calculating half sibling index with ITO and discriminant functions.

Deviatoric Constitutive Relationship for Anisotropic Materials

DTIC Science & Technology

1987-06-01

SEFF = VMISES ICHECK (1) = 0 DEPSBP = 0. CALL XFORM (STR(I),STR(2),STR(3),STR(4),STR(5),STR(6), & SR2 ,SZ2 ,ST2 ,SZT2 ,SRT2 ,SRZ2,-TH) GO TO 310...END I F C c Yield h a s occured: D e t e r m i n e ALF, t h e f r a c t i o n of s t r a i n c t h a t is pre-y ie ld . C I F ( ICHECK ...c e l s e m u s t d e t e r m i n e e l a s t i c f r a c t i o n ( a l f ) (see V a v r i c k , J o h n s o n ) C ICHECK (1) = 1 TERM1 = 0

The scotopic threshold response of the dark-adapted electroretinogram of the mouse.

PubMed

Saszik, Shannon M; Robson, John G; Frishman, Laura J

2002-09-15

The most sensitive response in the dark-adapted electroretinogram (ERG), the scotopic threshold response (STR) which originates from the proximal retina, has been identified in several mammals including humans, but previously not in the mouse. The current study established the presence and assessed the nature of the mouse STR. ERGs were recorded from adult wild-type C57/BL6 mice anaesthetized with ketamine (70 mg kg(-1)) and xylazine (7 mg kg(-1)). Recordings were between DTL fibres placed under contact lenses on the two eyes. Monocular test stimuli were brief flashes (lambda(max) 462 nm; -6.1 to +1.8 log scotopic Troland seconds(sc td s)) under fully dark-adapted conditions and in the presence of steady adapting backgrounds (-3.2 to -1.7 log sc td). For the weakest test stimuli, ERGs consisted of a slow negative potential maximal approximately 200 ms after the flash, with a small positive potential preceding it. The negative wave resembled the STR of other species. As intensity was increased, the negative potential saturated but the positive potential (maximal approximately 110 ms) continued to grow as the b-wave. For stimuli that saturated the b-wave, the a-wave emerged. For stimulus strengths up to those at which the a-wave emerged, ERG amplitudes measured at fixed times after the flash (110 and 200 ms) were fitted with a model assuming an initially linear rise of response amplitude with intensity, followed by saturation of five components of declining sensitivity: a negative STR (nSTR), a positive STR (pSTR), a positive scotopic response (pSR), PII (the bipolar cell component) and PIII (the photoreceptor component). The nSTR and pSTR were approximately 3 times more sensitive than the pSR, which was approximately 7 times more sensitive than PII. The sensitive positive components dominated the b-wave up to > 5 % of its saturated amplitude. Pharmacological agents that suppress proximal retinal activity (e.g. GABA) minimized the pSTR, nSTR and pSR, essentially isolating PII which rose linearly with intensity before showing hyperbolic saturation. The nSTR, pSTR and pSR were desensitized by weaker backgrounds than those desensitizing PII. In conclusion, ERG components of proximal retinal origin that are more sensitive to test flashes and adapting backgrounds than PII provide the 'threshold' negative and positive (b-wave) responses of the mouse dark-adapted ERG. These results support the use of the mouse ERG in studies of proximal retinal function.

Constructing STR multiplex assays.

PubMed

Butler, John M

2005-01-01

Multiplex polymerase chain reaction (PCR) refers to the simultaneous amplification of multiple regions of deoxyribonucleic acid (DNA) using PCR. Commercial short tandem repeat (STR) assays that can coamplify as many as 16 different loci have become widely used in forensic DNA typing. This chapter will focus on some of the aspects of constructing robust STR multiplex assays, including careful design and quality control of PCR primers. Examples from the development of a cat STR 12plex and a human Y chromosome STR 20plex are used to illustrate the importance of various parts of the protocol. Primer design parameters and Internet-accessible resources are discussed, as are solutions to problems with residual dye artifacts that result from impure primers.

Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population

PubMed Central

Liu, Yao-Shun; Chen, Jian-Gang; Mei, Ting; Guo, Yu-Xin; Meng, Hao-Tian; Li, Jian-Fei; Wei, Yuan-Yuan; Jin, Xiao-Ye; Zhu, Bo-Feng; Zhang, Li-Ping

2017-01-01

We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations. PMID:28903432

A massively parallel strategy for STR marker development, capture, and genotyping.

PubMed

Kistler, Logan; Johnson, Stephen M; Irwin, Mitchell T; Louis, Edward E; Ratan, Aakrosh; Perry, George H

2017-09-06

Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without a reference genome, and an approach for highly parallel target STR recovery. We employed our approach to capture a panel of 5000 STRs from a test group of diademed sifakas (Propithecus diadema, n = 3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci-97.3-99.6% of STRs characterized with ≥10x non-redundant sequence coverage. We then tested our STR capture strategy on P. diadema fecal DNA, and report robust initial results and suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from flanking regions. Our method provides a cost-effective and scalable solution for rapid recovery of large STR and SNP datasets in any species without needing a reference genome, and can be used even with suboptimal DNA more easily acquired in conservation and ecological studies. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Redox shuttles for high voltage cathodes

DOEpatents

Zhang, Lu; Zhang, Zhengcheng; Amine, Khalil; Chen, Zonghai

2015-03-03

A compound has general Formula I, II, III, or IV: ##STR00001## where X and Y are independently a group of Formula (A): ##STR00002## and Z a group of Formula (B): ##STR00003## The compounds may be used in electrolytes and electrochemical devices.

Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons.

PubMed

Kim, Eun Hye; Lee, Hwan Young; Yang, In Seok; Jung, Sang-Eun; Yang, Woo Ick; Shin, Kyoung-Jin

2016-05-01

The next-generation sequencing (NGS) method has been utilized to analyze short tandem repeat (STR) markers, which are routinely used for human identification purposes in the forensic field. Some researchers have demonstrated the successful application of the NGS system to STR typing, suggesting that NGS technology may be an alternative or additional method to overcome limitations of capillary electrophoresis (CE)-based STR profiling. However, there has been no available multiplex PCR system that is optimized for NGS analysis of forensic STR markers. Thus, we constructed a multiplex PCR system for the NGS analysis of 18 markers (13CODIS STRs, D2S1338, D19S433, Penta D, Penta E and amelogenin) by designing amplicons in the size range of 77-210 base pairs. Then, PCR products were generated from two single-sources, mixed samples and artificially degraded DNA samples using a multiplex PCR system, and were prepared for sequencing on the MiSeq system through construction of a subsequent barcoded library. By performing NGS and analyzing the data, we confirmed that the resultant STR genotypes were consistent with those of CE-based typing. Moreover, sequence variations were detected in targeted STR regions. Through the use of small-sized amplicons, the developed multiplex PCR system enables researchers to obtain successful STR profiles even from artificially degraded DNA as well as STR loci which are analyzed with large-sized amplicons in the CE-based commercial kits. In addition, successful profiles can be obtained from mixtures up to a 1:19 ratio. Consequently, the developed multiplex PCR system, which produces small size amplicons, can be successfully applied to STR NGS analysis of forensic casework samples such as mixtures and degraded DNA samples. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Modifications of Gait as Predictors of Natural Osteoarthritis Progression in STR/Ort Mice

PubMed Central

Poulet, Blandine; de Souza, Roberto; Knights, Chancie B; Gentry, Clive; Wilson, Alan M; Bevan, Stuart; Chang, Yu-Mei; Pitsillides, Andrew A

2014-01-01

Objective Osteoarthritis (OA) is a common chronic disease for which disease-modifying therapies are not currently available. Studies to seek new targets for slowing the progress of OA rely on mouse models, but these do not allow for longitudinal monitoring of disease development. This study was undertaken to determine whether gait can be used to measure disease severity in the STR/Ort mouse model of spontaneous OA and whether gait changes are related to OA joint pain. Methods Gait was monitored using a treadmill-based video system. Correlations between OA severity and gait at 3 treadmill speeds were assessed in STR/Ort mice. Gait and pain behaviors of STR/Ort mice and control CBA mice were analyzed longitudinally, with monthly assessments. Results The best speed to identify paw area changes associated with OA severity in STR/Ort mice was found to be 17 cm · seconds−1. Paw area was modified with age in CBA and STR/Ort mice, but this began earlier in STR/Ort mice and correlated with the onset of OA at 20 weeks of age. In addition, task noncompliance appeared at 20 weeks. Surprisingly, STR/Ort mice did not show any signs of pain with OA development, even when treated with the opioid antagonist naloxone, but did exhibit normal pain behaviors in response to complete Freund's adjuvant–induced arthritis. Conclusion The present results identify an animal model in which OA severity and OA pain can be studied in isolation from one another. The findings suggest that paw area and treadmill noncompliance may be useful tools to longitudinally monitor nonpainful OA development in STR/Ort mice. This will help in providing a noninvasive means of assessing new therapies to slow the progression of OA. PMID:24623711

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

PubMed

Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

2015-05-01

Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

Filipino DNA variation at 12 X-chromosome short tandem repeat markers.

PubMed

Salvador, Jazelyn M; Apaga, Dame Loveliness T; Delfin, Frederick C; Calacal, Gayvelline C; Dennis, Sheila Estacio; De Ungria, Maria Corazon A

2018-06-08

Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results. Here, we report X-STR data from 143 unrelated Filipino male individuals who were genotyped via conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) using the 12 X-STR loci included in the Investigator ® Argus X-12 kit (Qiagen) and via massively parallel sequencing (MPS) of seven X-STR loci included in the ForenSeq ™ DNA Signature Prep kit of the MiSeq ® FGx ™ Forensic Genomics System (Illumina). Allele calls between PCR-CE and MPS systems were consistent (100% concordance) across seven overlapping X-STRs. Allele and haplotype frequencies and other parameters of forensic interest were calculated based on length (PCR-CE, 12 X-STRs) and sequence (MPS, seven X-STRs) variations observed in the population. Results of our study indicate that the 12 X-STRs in the PCR-CE system are highly informative for the Filipino population. MPS of seven X-STR loci identified 73 X-STR alleles compared with 55 X-STR alleles that were identified solely by length via PCR-CE. Of the 73 sequence-based alleles observed, six alleles have not been reported in the literature. The population data presented here may serve as a reference Philippine frequency database of X-STRs for forensic casework applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Monthly Levels and Criteria Considerations of Nutrient, pH, Alkalinity and Ionic Variables in Runoff Containment Basins in Ornamental Plant Nurseries.

USDA-ARS?s Scientific Manuscript database

Triplicate water samples were collected monthly from 9 waterways (8 recycling containment basins (RCBs) and 1 stream) on 4 commercial ornamental plant nurseries from February to July, and from 1 RCB and nursery from April to October. Four RCBs, one per nursery, were actively utilized as an irrigatio...

Entire Photodamaged Chloroplasts Are Transported to the Central Vacuole by Autophagy[OPEN

PubMed Central

2017-01-01

Turnover of dysfunctional organelles is vital to maintain homeostasis in eukaryotic cells. As photosynthetic organelles, plant chloroplasts can suffer sunlight-induced damage. However, the process for turnover of entire damaged chloroplasts remains unclear. Here, we demonstrate that autophagy is responsible for the elimination of sunlight-damaged, collapsed chloroplasts in Arabidopsis thaliana. We found that vacuolar transport of entire chloroplasts, termed chlorophagy, was induced by UV-B damage to the chloroplast apparatus. This transport did not occur in autophagy-defective atg mutants, which exhibited UV-B-sensitive phenotypes and accumulated collapsed chloroplasts. Use of a fluorescent protein marker of the autophagosomal membrane allowed us to image autophagosome-mediated transport of entire chloroplasts to the central vacuole. In contrast to sugar starvation, which preferentially induced distinct type of chloroplast-targeted autophagy that transports a part of stroma via the Rubisco-containing body (RCB) pathway, photooxidative damage induced chlorophagy without prior activation of RCB production. We further showed that chlorophagy is induced by chloroplast damage caused by either artificial visible light or natural sunlight. Thus, this report establishes that an autophagic process eliminates entire chloroplasts in response to light-induced damage. PMID:28123106

STR data for the AmpFlSTR Profiler loci from the three main ethnic population groups (Malay, Chinese and Indian) in Malaysia.

PubMed

Lim, K B; Jeevan, N H; Jaya, P; Othman, M I; Lee, Y H

2001-06-01

Allele frequencies for the nine STRs genetic loci included in the AmpFlSTR Profiler kit were obtained from samples of unrelated individuals comprising 139-156 Malays, 149-153 Chinese and 132-135 Indians, residing in Malaysia.

The Communications Toolbox for MATLAB and E0 3513 Laboratory Design

DTIC Science & Technology

1994-03-24

lengtli(quanchj)-1)) sxniejbinnuMs=bin...nums(1:6) %;.. M.asure dhe quantization noise sig-toLia.is~snr(s1 ,quansig); str --numn2str(sigjoQnois); %Plot 4...compressed quantized signal exp..comp=expmnd(quansig2,mu2,tmx(quansi2)); %use maximum signal value =nrw.ccwnp-snr(s,exp~coinp); str -num2str(sir..comp); MPot...8217) ylabelCAmplitude’) grid cig %Part 2--Observe fte differences in the spectra Program mung Laboratory 3B Key-age 3 319 %for two types of pulse-modulatWd signals

STR data for 15 autosomal STR markers from Paraná (Southern Brazil).

PubMed

Alves, Hemerson B; Leite, Fábio P N; Sotomaior, Vanessa S; Rueda, Fábio F; Silva, Rosane; Moura-Neto, Rodrigo S

2014-03-01

Allelic frequencies for 15 STR autosomal loci, using AmpFℓSTR® Identifiler™, forensic, and statistical parameters were calculated. All loci reached the Hardy-Weinberg equilibrium. The combined power of discrimination and mean power of exclusion were 0.999999999999999999 and 0.9999993, respectively. The MDS plot and NJ tree analysis, generated by FST matrix, corroborated the notion of the origins of the Paraná population as mainly European-derived. The combination of these 15 STR loci represents a powerful strategy for individual identification and parentage analyses for the Paraná population.

Analysis of 16 autosomal STRs and 17 Y-STRs in an indigenous Maya population from Guatemala.

PubMed

Cardoso, Sergio; Sevillano, Rubén; Illescas, María J; de Pancorbo, Marian Martínez

2016-03-01

The aim of this study was to contribute new data on autosomal STR and Y-STR markers of the Mayas from Guatemala in order to improve available databases of forensic interest. We analyzed 16 autosomal STR markers in a population sample of 155 indigenous Maya and 17 Y-chromosomal STR markers in the 100 males of the sample. Deviations from Hardy-Weinberg equilibrium and linkage disequilibrium between autosomal STR markers were not observed at any loci. The combined power of exclusion was estimated as 99.9991% and the combined power of discrimination was >99.999999999999%. Haplotype diversity of Y-STRs was calculated as 0.9984 ± 0.0018 and analysis of pairwise genetic distances (Rst) supported the Native American background of the population.

A case of false mother included with 46 autosomal STR markers.

PubMed

Li, Li; Lin, Yuan; Liu, Yan; Zhu, Ruxin; Zhao, Zhenmin; Que, Tingzhi

2015-01-01

For solving a maternity case, 19 autosomal short tandem repeats (STRs) were amplified using the AmpFℓSTR(®) Sinofiler(TM) kit and PowerPlex(®) 16 System. Additional 27 autosomal STR loci were analyzed using two domestic kits AGCU 21+1 and STRtyper-10G. The combined maternity index (CMI) was calculated to be 3.3 × 10(13), but the putative mother denied that she had given birth to the child. In order to reach an accurate conclusion, further testing of 20 X-chromosomal short tandem repeats (X-STRs), 40 single nucleotide polymorphism (SNP) loci, and mitochondrial DNA (mtDNA) was carried out. The putative mother and the boy shared at least one allele at all 46 tested autosomal STR loci. But, according to the profile data of 20 X-STR and 40 SNP markers, different genotypes at 13 X-STR loci and five SNP loci excluded maternity. Mitochondrial profiles also clearly excluded the mother as a parent of the son because they have multiple differences. It was finally found that the putative mother is the sister of the biological father. Different kinds of genetic markers needfully supplement the use of autosomal STR loci in case where the putative parent is suspected to be related to the true parent.

Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population.

PubMed

Hirata, Satoshi; Kojima, Kaname; Misawa, Kazuharu; Gervais, Olivier; Kawai, Yosuke; Nagasaki, Masao

2018-05-01

Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.

Identification of Skeletal Remains of Communist Armed Forces Victims During and After World War II: Combined Y-chromosome Short Tandem Repeat (STR) and MiniSTR Approach

PubMed Central

Marjanović, Damir; Durmić-Pašić, Adaleta; Kovačević, Lejla; Avdić, Jasna; Džehverović, Mirela; Haverić, Sanin; Ramić, Jasmin; Kalamujić, Belma; Bilela, Lada Lukić; Škaro, Vedrana; Projić, Petar; Bajrović, Kasim; Drobnič, Katja; Davoren, Jon; Primorac, Dragan

2009-01-01

Aim To report on the use of STR, Y-STRs, and miniSTRs typing methods in the identification of victims of revolutionary violence and crimes against humanity committed by the Communist Armed Forces during and after World War II in which bodies were exhumed from mass and individual graves in Slovenia. Methods Bone fragments and teeth were removed from human remains found in several small and closely located hidden mass graves in the Škofja Loka area (Lovrenska Grapa and Žolšče) and 2 individual graves in the Ljubljana area (Podlipoglav), Slovenia. DNA was isolated using the Qiagen DNA extraction procedure optimized for bone and teeth. Some DNA extracts required additional purification, such as N-buthanol treatment. The QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. Initially, PowerPlex 16 kit was used to simultaneously analyze 15 short tandem repeat (STR) loci. The PowerPlex S5 miniSTR kit and AmpFℓSTR® MiniFiler PCR Amplification Kit was used for additional analysis if preliminary analysis yielded weak partial or no profiles at all. In 2 cases, when the PowerPlex 16 profiles indicated possible relatedness of the remains with reference samples, but there were insufficient probabilities to call the match to possible male paternal relatives, we resorted to an additional analysis of Y-STR markers. PowerPlex® Y System was used to simultaneously amplify 12 Y-STR loci. Fragment analysis was performed on an ABI PRISM 310 genetic analyzer. Matching probabilities were estimated using the DNA-View software. Results Following the Y-STR analysis, 1 of the “weak matches” previously obtained based on autosomal loci, was confirmed while the other 1 was not. Combined standard STR and miniSTR approach applied to bone samples from 2 individual graves resulted in positive identifications. Finally, using the same approach on 11 bone samples from hidden mass grave Žološče, we were able to obtain 6 useful DNA profiles. Conclusion The results of this study, in combination with previously obtained results, demonstrate that Y-chromosome testing and miniSTR methodology can contribute to the identification of human remains of victims of revolutionary violence from World War II. PMID:19480024

Effect of supplemental sodium chloride and hydrochloric acid added to initial starter diets containing spray-dried blood plasma and lactose on resulting performance and nitrogen digestibility of 3-week-old weaned pigs.

PubMed

Mahan, D C; Wiseman, T D; Weaver, E; Russell, L

1999-11-01

Four experiments evaluated the efficacy of Na or Cl or their combination added to weanling pig diets that contained plasma protein and lactose on pig performance and N digestibility. The four experiments used a total of 563 crossbred pigs weaned at 22+/-1 d of age averaging 6.4 kg body weight. The basal diet in each experiment contained 5.8% plasma protein and 20% lactose and analyzed .20% Na and .23% Cl. In Exp. 1, NaCl was added to treatment diets at 0, .20, .40, or .60%. The trial was conducted for a 21 d period in a randomized complete block (RCB) design in seven replicates. Improved growth rates (P < .01) and gain:feed ratios (P < .01) occurred up to a dietary salt level of .40%. In Exp. 2, we evaluated the interaction of Na and Cl on pig performance. The experiment was a 2 x 2 factorial arrangement in a RCB design conducted in seven replicates. Total dietary Na was .20 or .36%, and Cl was included at .25 or .45%. Although there was a numerical increase in pig gains with added Na, the response was not significant (P > .15), but both gains (P < .01) and gain:feed ratios (P < .01) increased at the higher dietary Cl level. In Exp. 3, we evaluated the effect of five dietary levels of Cl added at .06% increments to a basal diet that analyzed .34% Na and .20% Cl on postweaning pig performance. The experiment was a RCB design conducted in eight replicates. A growth response (P < .01) to the .38% Cl level occurred during the initial 14-d postweaning period and to the .32% Cl level from 14 to 21 d. Gain:feed ratio increased each week with added Cl, but it was significant only for the period from d 0 to 7 d (P < .01). A N digestibility trial, using the diets of Exp. 3, constituted Exp. 4, and groups of three pigs per stainless steel metabolism crate were pair-fed to pigs fed the basal diet. The experiment was a RCB design conducted in three replicates over a 3-wk period. The results demonstrated a weekly decrease in fecal N (P < .01), no effect on urinary N (P < .15), improved N retention (P < .01), and an improved apparent N digestibility (P < .01) to the .38% dietary Cl concentration during the initial 2 wk postweaning. These experiments suggest that although plasma protein contributed Na and Cl to the initial diets of weaned pigs, additional Na and Cl, but particularly Cl, improved pig growth, N retention, and N digestibility. The results suggest a dietary minimum of .38% total Cl level during the initial 2 wk postweaning.

Allele frequency distribution for 21 autosomal STR loci in Bhutan.

PubMed

Kraaijenbrink, Thirsa; van Driem, George L; Tshering of Gaselô, Karma; de Knijff, Peter

2007-07-20

We studied the allele frequency distribution of 21 autosomal STR loci contained in the AmpFlSTR Identifiler (Applied Biosystems), the Powerplex 16 (Promega) and the FFFL (Promega) multiplex PCR kits among 936 individuals from the Royal Kingdom of Bhutan. As such these are the first published autosomal DNA results from this country.

Program level evaluation of ASAP diagnosis, referral and rehabilitation efforts. Volume 4, Development of the short term rehabilitation (STR) study

DOT National Transportation Integrated Search

1976-09-01

The present report discusses the development, implementation, and current status of the Short Term Rehabilitation (STR) Study initiates by the NHTSA in 1974. Experimental designs employed by each of the 11 ASAP/STR sites for the assignment of mid-ran...

The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions.

PubMed

Gutiérrez-Preciado, Ana; Vargas-Chávez, Carlos; Reyes-Prieto, Mariana; Ordoñez, Omar F; Santos-García, Diego; Rosas-Pérez, Tania; Valdivia-Anistro, Jorge; Rebollar, Eria A; Saralegui, Andrés; Moya, Andrés; Merino, Enrique; Farías, María Eugenia; Latorre, Amparo; Souza, Valeria

2017-01-01

We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. 'Chiri qhucha' in Quechua means 'cold lake', which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.

A Genomic Analysis of Anaerobic Aromatic Degradation

DTIC Science & Technology

2004-07-26

bacterium Rhodopseudomonas palustris . Nature Biotech. 22: 55-61. Harrison, F. H. and C. S. Harwood. Identification of a fatty acid ß-oxidation operon...from Rhodopseudomonas palustris that is involved in the latter stages of anaerobic benzoate degradation. Submitted. b. Papers presented at meetings. (MS...in preparation). Samanta, S. K. and C. S. Harwood. 2002. The anaerobic degradation of 3-chlorobenzoate by Rhodopseudomonas palustris strain RCB100

Evaluation of cannabinoid CB1 and CB2 receptors expression in mobile tongue squamous cell carcinoma: associations with clinicopathological parameters and patients' survival.

PubMed

Theocharis, Stamatios; Giaginis, Constantinos; Alexandrou, Paraskevi; Rodriguez, Jose; Tasoulas, Jason; Danas, Eugene; Patsouris, Efstratios; Klijanienko, Jerzy

2016-03-01

Cannabinoid receptors (CB1R and CB2R) constitute essential members of the endocannabinoid system (ECS) which participates in many different functions indispensable to homeostatic regulation in several tissues, exerting also antitumorigenic effects. The present study aimed to assess the clinical significance of CB1R and CB2R protein expression in mobile tongue squamous cell carcinoma (SCC). CB1R and CB2R expression was assessed immunohistochemically on 28 mobile tongue SCC tissue samples and was analyzed in relation with clinicopathological characteristics and overall and disease-free patients' survival. CB1R, CB2R, and concomitant CB1R/CB2R expression was significantly increased in older compared to younger mobile tongue SCC patients (p = 0.0243, p = 0.0079, and p = 0.0366, respectively). Enhanced CB2R and concomitant CB1R/CB2R expression was significantly more frequently observed in female compared to male mobile tongue SCC patients (p = 0.0025 and p = 0.0016, respectively). Elevated CB2R expression was significantly more frequently observed in mobile tongue SCC patients presenting well-defined tumor shape compared to those with diffuse (p = 0.0430). Mobile tongue SCC patients presenting enhanced CB1R, CB2R, or concomitant CB1R/CB2R expression showed significantly longer overall (log-rank test, p = 0.004, p = 0.011, p = 0.018, respectively) and disease-free (log-rank test, p = 0.003, p = 0.007, p = 0.027, respectively) survival times compared to those with low expression. In multivariate analysis, CB1R was identified as an independent prognostic factor for disease-free patients' survival (Cox-regression analysis, p = 0.032). The present study provides evidence that CB1R and CB2R may play a role in the pathophysiological aspects of the mobile tongue SCC and even each molecule may constitute a potential target for the development of novel anti-cancer drugs for this type of malignancy.

Determining Y-STR mutation rates in deep-routing genealogies: Identification of haplogroup differences.

PubMed

Claerhout, Sofie; Vandenbosch, Michiel; Nivelle, Kelly; Gruyters, Leen; Peeters, Anke; Larmuseau, Maarten H D; Decorte, Ronny

2018-05-01

Knowledge of Y-chromosomal short tandem repeat (Y-STR) mutation rates is essential to determine the most recent common ancestor (MRCA) in familial searching or genealogy research. Up to now, locus-specific mutation rates have been extensively examined especially for commercially available forensic Y-STRs, while haplogroup specific mutation rates have not yet been investigated in detail. Through 450 patrilineally related namesakes distributed over 212 deep-rooting genealogies, the individual mutation rates of 42 Y-STR loci were determined, including 27 forensic Y-STR loci from the Yfiler ® Plus kit and 15 additional Y-STR loci (DYS388, DYS426, DYS442, DYS447, DYS454, DYS455, DYS459a/b, DYS549, DYS607, DYS643, DYS724a/b and YCAIIa/b). At least 726 mutations were observed over 148,596 meiosis and individual Y-STR mutation rates varied from 2.83 × 10 -4 to 1.86 × 10 -2 . The mutation rate was significantly correlated with the average allele size, the complexity of the repeat motif sequence and the age of the father. Significant differences in average Y-STR mutations rates were observed when haplogroup 'I & J' (4.03 × 10 -3 mutations/generation) was compared to 'R1b' (5.35 × 10 -3 mutations/generation) and to the overall mutation rate (5.03 × 10 -3 mutations/generation). A difference in allele size distribution was identified as the only cause for these haplogroup specific mutation rates. The haplogroup specific mutation rates were also present within the commercially available Y-STR kits (Yfiler ® , PowerPlex ® Y23 System and Yfiler ® Plus). This observation has consequences for applications where an average Y-STR mutation rate is used, e.g. tMRCA estimations in familial searching and genealogy research. Copyright © 2018 Elsevier B.V. All rights reserved.

Association between daily antiretroviral pill burden and treatment adherence, hospitalisation risk, and other healthcare utilisation and costs in a US medicaid population with HIV

PubMed Central

Cohen, Calvin J; Meyers, Juliana L; Davis, Keith L

2013-01-01

Objectives Lower pill burden leads to improved antiretroviral therapy (ART) adherence among HIV patients. Simpler dosing regimens have not been widely explored in real-world populations. We retrospectively assessed ART adherence, all-cause hospitalisation risk and costs, and other healthcare utilisation and costs in Medicaid enrollees with HIV treated with ART as a once-daily single-tablet regimen (STR) or two or more pills per day (2+PPD). Design Patients with an HIV diagnosis from 2005 to 2009 receiving complete ART (ie, two nucleoside/nucleotide reverse transcriptase inhibitors plus a third agent) for ≥60 days as STR or 2+PPD were selected and followed until the first of (1) discontinuation of the complete ART, (2) loss of enrolment or (3) end of database. Adherence was measured using the medication possession ratio. Monthly all-cause healthcare utilisation and costs were observed from regimen initiation until follow-up end. Results Of the 7381 patients who met inclusion criteria, 1797 were treated with STR and 5584 with 2+PPD. STR patients were significantly more likely to reach 95% adherence and had fewer hospitalisations than 2+PPD patients (both p<0.01). STR patients had mean (SD) total monthly costs of $2959 ($4962); 2+PPD patients had $3544 ($5811; p<0.001). Hospital costs accounted for 53.8% and pharmacy costs accounted for 32.5% of this difference. Multivariate analyses found that STR led to a 23% reduction in hospitalisations and a 17% reduction in overall healthcare costs. ART adherence appears to be a key mechanism mediating hospitalisation risk, as patients with ≥95% adherence (regardless of regimen type) had a lower hospitalisation rate compared with <95% adherence. Conclusions While it was expected that STR patients would have lower pharmacy costs, we also found that STR patients had fewer hospitalisations and lower hospital costs than 2+PPD patients, resulting in significantly lower total healthcare costs for STR patients. PMID:23906955

Evaluation of the genetic parameters and mutation analysis of 22 STR loci in the central Chinese Han population.

PubMed

Hongdan, Wang; Bing, Kang; Ning, Su; Miao, He; Bo, Zhang; Yuxin, Guo; Bofeng, Zhu; Shixiu, Liao; Zhaoshu, Zeng

2017-01-01

At present, the Han nationality is China's main ethnic group and also the most populous nation in the world. This is a great resource to study microsatellite mutations and for the study of ethnogeny. The aim of this study is to investigate the genetic polymorphisms and mutations of 22 autosomal STR loci in 2475 individuals from Henan province, China. DNA is amplified and genotyped using PowerPlex™24 system. The gene frequencies, forensic parameters, and the mutation rate of the 22 STR loci are analyzed. A total of 295 alleles are observed in this Henan Han population, and the allelic frequencies ranged from 0.0003 to 0.5036. In order to investigate the genetic relationships between the Henan Han and the other 14 different populations, our present data were compared with previously published data for the same 15 STR loci. The results indicated that the Henan Han had closer genetic relationships the groups including Minnan Han, Maonan, Yi and Guangdong Han groups while the South morocco population, the Moroccan population, the Malay group, and the Uigur stand away from Henan Han. Except of D2S441, D13S317, PentaE, D2S1338, D5S818, TPOX and D19S433, the mutation events are found in the other 15 STR loci. A total of 40 mutation events are observed in the 15 STR loci. The mutation rates are ranged from 0 to 4.85 × 10 -3 . In this study, 39 mutations are single-step mutations, and only one at FGA comprised two steps. STR mutation is commonly existed in paternity testing, while there are no STR mutation studies of the 22 STR loci in the Henan Han population. It is of great importance in forensic individual discrimination and paternal testing.

Genetic polymorphisms of 20 autosomal STR loci in the Vietnamese population from Yunnan Province, Southwest China.

PubMed

Zhang, Xiufeng; Hu, Liping; Du, Lei; Nie, Aiting; Rao, Min; Pang, Jing Bo; Nie, Shengjie

2017-05-01

The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex® 21 kit were evaluated in 522 healthy unrelated Vietnamese from Yunnan, China. All of the loci reached the Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999999999999999999999991 26 and 0.999999975, respectively. Results suggested that the 20 STR loci are highly polymorphic, which is suitable for forensic personal identification and paternity testing.

A hypervariable STR polymorphism in the CFI gene: southern origin of East Asian-specific group H alleles.

PubMed

Yuasa, Isao; Jin, Feng; Harihara, Shinji; Matsusue, Aya; Fujihara, Junko; Takeshita, Haruo; Akane, Atsushi; Umetsu, Kazuo; Saitou, Naruya; Chattopadhyay, Prasanta K

2013-09-01

Previous studies of four populations revealed that a hypervariable short tandem repeat (iSTR) in intron 7 of the human complement factor I (CFI) gene on chromosome 4q was unique, with 17 possible East Asian-specific group H alleles observed at relatively high frequencies. To develop a deeper anthropological and forensic understanding of iSTR, 1161 additional individuals from 11 Asian populations were investigated. Group H alleles of iSTR and c.1217A allele of a SNP in exon 11 of the CFI gene were associated with each other and were almost entirely confined to East Asian populations. Han Chinese in Changsha, southern China, showed the highest frequency for East Asian-specific group H alleles (0.201) among 15 populations. Group H alleles were observed to decrease gradually from south to north in 11 East Asian populations. This expansion of group H alleles provides evidence that southern China and Southeast Asia are a hotspot of Asian diversity and a genetic reservoir of Asians after they entered East Asia. The expected heterozygosity values of iSTR ranged from 0.927 in Thais to 0.874 in Oroqens, higher than those of an STR in the fibrinogen alpha chain (FGA) gene on chromosome 4q. Thus, iSTR is a useful marker for anthropological and forensic genetics. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Fast nuclear staining of head hair roots as a screening method for successful STR analysis in forensics.

PubMed

Lepez, Trees; Vandewoestyne, Mado; Van Hoofstat, David; Deforce, Dieter

2014-11-01

The success rate of STR profiling of hairs found at a crime scene is quite low and negative results of hair analysis are frequently reported. To increase the success rate of DNA analysis of hairs in forensics, nuclei in hair roots can be counted after staining the hair root with DAPI. Two staining methods were tested: a longer method with two 1h incubations in respectively a DAPI- and a wash-solution, and a fast, direct staining of the hair root on microscope slides. The two staining methods were not significantly different. The results of the STR analysis for both procedures showed that 20 nuclei are necessary to obtain at least partial STR profiles. When more than 50 nuclei were counted, full STR profiles were always obtained. In 96% of the cases where no nuclei were detected, no STR profile could be obtained. However, 4% of the DAPI-negative hair roots resulted in at least partial STR profiles. Therefore, each forensic case has to be evaluated separately in function of the importance of the evidential value of the found hair. The fast staining method was applied in 36 forensic cases on 279 hairs in total. A fast screening method using DAPI can be used to increase the success rate of hair analysis in forensics. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Effect of Rickettsia felis Strain Variation on Infection, Transmission, and Fitness in the Cat Flea (Siphonaptera: Pulicidae).

PubMed

Healy, Sean P; Brown, Lisa D; Hagstrom, Melena R; Foil, Lane D; Macaluso, Kevin R

2017-07-01

Rickettsia felis is a human pathogen transmitted by the cat flea, Ctenocephalides felis (Bouché) (str. LSU), as well as an obligate symbiont of the parthenogenic booklouse Liposcelis bostrychophila (Badonnel) (str. LSU-Lb). The influence of genetic variability in these two strains of R. felis on host specialization and fitness and possible resulting differences on infection and transmission kinetics in C. felis is unknown. Utilizing an artificial host system, cat fleas were exposed to a R. felis str. LSU-Lb-infected bloodmeal and monitored for infection at 7-d intervals for 28 d. Quantitative real-time PCR was used to determine rickettsial load and infection density in newly exposed cat fleas, and transmission frequency between cat fleas. The effect of persistent R. felis infection on cat flea F1 progeny was also assessed. At 7 d postexposure 76.7% of the cat fleas successfully acquired R. felis str. LSU-Lb. In R. felis str. LSU-Lb-exposed cat fleas, the mean infection load (6.15 × 106), infection density (0.76), and infection prevalence (91/114) were significantly greater than R. felis str. LSU infection load (3.09 × 106), infection density (0.68), and infection prevalence (76/113). A persistent R. felis str. LSU-Lb infection was detected for 28 d in adult cat fleas but neither female:male ratio distortion nor vertical transmission was observed in F1 progeny. While infection kinetics differed, with higher intensity associated with R. felis str. LSU-Lb, no distinct phenotype was observed in the F1 progeny. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

Comprehensive annotated STR physical map of the human Y chromosome: Forensic implications.

PubMed

Hanson, Erin K; Ballantyne, Jack

2006-03-01

A plethora of Y-STR markers from diverse sources have been deposited in public databases and represent potential candidates for incorporation into the next generation of Y-STR multiplexes for forensic use. Here, based upon all of the Y-STR loci that have been deposited in the human genome database (>400), we have sequentially positioned each one along the Y chromosome using the most current human genome sequencing data (NCBI Build 35). The information derived from this work defines the number and relative position of all potentially forensically relevant Y-STR loci, their location within the physical linkage map of the Y chromosome and their relationship to structural genes. We conclude that there exists at present at least 417 separate Y-STR markers available for potential forensic use, although many of these will be found to be unsuitable for other reasons. However, from this data, we were able to identify 28 pairs of duplicated loci that were given separate DYS designations and four pairs of loci with overlapping flanking regions. Removing one locus from each set of duplicates reduced the number of potentially useful loci from 417 to 389. The derived information should be useful for workers who are designing novel Y-STR multiplexes to ensure the presence of non-synonymous loci and, if so desired, to avoid loci that lie within structural genes. It may also be useful for forensic casework practitioners (or molecular anthropologists) to aid in distinguishing between chromosomal rearrangements (such as duplications and deletions) and bona fide DNA admixtures or null alleles caused by primer binding site mutations. We illustrate the practical usefulness of the chromosomal positioning data in the design of eight multiplex systems using 94 Y-STR loci.

Evaluation of the MeltPro TB/STR assay for rapid detection of streptomycin resistance in Mycobacterium tuberculosis.

PubMed

Zhang, Ting; Hu, Siyu; Li, Guoli; Li, Hui; Liu, Xiaoli; Niu, Jianjun; Wang, Feng; Wen, Huixin; Xu, Ye; Li, Qingge

2015-03-01

Rapid and comprehensive detection of drug-resistance is essential for the control of tuberculosis, which has facilitated the development of molecular assays for the detection of drug-resistant mutations in Mycobacterium tuberculosis. We hereby assessed the analytical and clinical performance of an assay for streptomycin-resistant mutations. MeltPro TB/STR is a closed-tube, dual-color, melting curve analysis-based, real-time PCR test designed to detect 15 streptomycin-resistant mutations in rpsL 43, rpsL 88, rrs 513, rrs 514, rrs 517, and rrs 905-908 of M. tuberculosis. Analytical studies showed that the accuracy was 100%, the limit of detection was 50-500 bacilli per reaction, the reproducibility in the form of Tm variation was within 1.0 °C, and we could detect 20% STR resistance in mixed bacterial samples. The cross-platform study demonstrated that the assay could be performed on six models of real-time PCR instruments. A multicenter clinical study was conducted using 1056 clinical isolates, which were collected from three geographically different healthcare units, including 709 STR-susceptible and 347 STR-resistant isolates characterized on Löwenstein-Jensen solid medium by traditional drug susceptibility testing. The results showed that the clinical sensitivity and specificity of the MeltPro TB/STR was 88.8% and 95.8%, respectively. Sequencing analysis confirmed the accuracy of the mutation types. Among all the 8 mutation types detected, rpsL K43R (AAG → AGG), rpsL K88R (AAG → AGG) and rrs 514 A → C accounted for more than 90%. We concluded that MeltPro TB/STR represents a rapid and reliable assay for the detection of STR resistance in clinical isolates. Copyright © 2014. Published by Elsevier Ltd.

Allopolyploid Origin of Chenopodium album s. str. (Chenopodiaceae): A Molecular and Cytogenetic Insight

PubMed Central

Krak, Karol; Vít, Petr; Belyayev, Alexander; Douda, Jan; Hreusová, Lucia; Mandák, Bohumil

2016-01-01

Reticulate evolution is characterized by occasional hybridization between two species, creating a network of closely related taxa below and at the species level. In the present research, we aimed to verify the hypothesis of the allopolyploid origin of hexaploid C. album s. str., identify its putative parents and estimate the frequency of allopolyploidization events. We sampled 122 individuals of the C. album aggregate, covering most of its distribution range in Eurasia. Our samples included putative progenitors of C. album s. str. of both ploidy levels, i.e. diploids (C. ficifolium, C. suecicum) and tetraploids (C. striatiforme, C. strictum). To fulfil these objectives, we analysed sequence variation in the nrDNA ITS region and the rpl32-trnL intergenic spacer of cpDNA and performed genomic in-situ hybridization (GISH). Our study confirms the allohexaploid origin of C. album s. str. Analysis of cpDNA revealed tetraploids as the maternal species. In most accessions of hexaploid C. album s. str., ITS sequences were completely or nearly completely homogenized towards the tetraploid maternal ribotype; a tetraploid species therefore served as one genome donor. GISH revealed a strong hybridization signal on the same eighteen chromosomes of C. album s. str. with both diploid species C. ficifolium and C. suecicum. The second genome donor was therefore a diploid species. Moreover, some individuals with completely unhomogenized ITS sequences were found. Thus, hexaploid individuals of C. album s. str. with ITS sequences homogenized to different degrees may represent hybrids of different ages. This proves the existence of at least two different allopolyploid lineages, indicating a polyphyletic origin of C. album s. str. PMID:27513342

Interpretation guidelines of a standard Y-chromosome STR 17-plex PCR-CE assay for crime casework.

PubMed

Roewer, Lutz; Geppert, Maria

2012-01-01

Y-STR analysis is an invaluable tool to examine evidence in sexual assault cases and in other forensic casework. Unambiguous detection of the male component in DNA mixtures with a high female background is still the main field of application of forensic Y-STR haplotyping. In the last years, powerful technologies including a 17-locus multiplex PCR assay have been introduced in the forensic laboratories. At the same time, statistical methods have been developed and adapted for interpretation of a nonrecombining, linear marker as the Y-chromosome which shows a strongly clustered geographical distribution due to the linear inheritance and the patrilocality of ancestral groups. Large population databases, namely the Y-STR Haplotype Reference Database (YHRD), have been established to assess the evidentiary value of Y-STR matches by means of frequency estimation methods (counting and extrapolation).

Phylogenetic and morphological re-evaluation of the Botryosphaeria species causing diseases of Mangifera indica.

PubMed

Slippers, Bernard; Johnson, Greg I; Crous, Pedro W; Coutinho, Teresa A; Wingfield, Brenda D; Wingfield, Michael J

2005-01-01

Species of Botryosphaeria are among the most serious pathogens that affect mango trees and fruit. Several species occur on mangoes, and these are identified mainly on the morphology of the anamorphs. Common taxa include Dothiorella dominicana, D. mangiferae (= Natrassia mangiferae), D. aromatica and an unidentified species, Dothiorella 'long'. The genus name Dothiorella, however, is acknowledged as a synonym of Diplodia. This study aimed to characterize and name the Botryosphaeria spp. associated with disease symptoms on mangoes. To achieve this isolates representing all four Dothiorella spp. mentioned above were compared with the anamorphs of known Botryosphaeria spp., based on conidial morphology and DNA sequence data. Two genomic regions were analyzed, namely the ITS rDNA and beta-tubulin regions. The morphological and molecular results confirmed that the fungi previously identified from mango as species of Dothiorella belong to Fusicoccum. Dothiorella dominicana isolates were identical to isolates of F. parvum (teleomorph = B. parva). A new epithet, namely F. mangiferum, is proposed for isolates previously treated as D. mangiferae or N. mangiferae. Isolates of D. aromatica were identified as F. aesculi (teleomorph = B. dothidea). A fourth Fusicoccum sp. also was identified as those isolates previously known as Dothiorella 'long'. A key is provided to distinguish these species based on anamorph morphology in culture. This study provides a basis for the identification of Botryosphaeria species from mango, which is important for disease control and to uphold quarantine regulations.

Simultaneous Determination of Gallic Acid, Ellagic Acid, and Eugenol in Syzygium aromaticum and Verification of Chemical Antagonistic Effect by the Combination with Curcuma aromatica Using Regression Analysis

PubMed Central

Seo, Chang-Seob; Kim, Seong-Sil; Ha, Hyekyung

2013-01-01

This study was designed to perform simultaneous determination of three reference compounds in Syzygium aromaticum (SA), gallic acid, ellagic acid, and eugenol, and to investigate the chemical antagonistic effect when combining Curcuma aromatica (CA) with SA, based on chromatographic analysis. The values of LODs and LOQs were 0.01–0.11 μg/mL and 0.03–0.36 μg/mL, respectively. The intraday and interday precisions were <3.0 of RSD values, and the recovery was in the range of 92.19–103.24%, with RSD values <3.0%. Repeatability and stability were 0.38–0.73% and 0.49–2.24%, respectively. Compared with the content of reference and relative peaks in SA and SA combined with CA (SAC), the amounts of gallic acid and eugenol were increased, while that of ellagic acid was decreased in SAC (compared with SA), and most of peak areas in SA were reduced in SAC. Regression analysis of the relative peak areas between SA and SAC showed r 2 values >0.87, indicating a linear relationship between SA and SAC. These results demonstrate that the components contained in CA could affect the extraction of components of SA mainly in a decreasing manner. The antagonistic effect of CA on SA was verified by chemical analysis. PMID:23878761

Phytotherapy in Functional Gastrointestinal Disorders.

PubMed

Kelber, Olaf; Bauer, Rudolf; Kubelka, Wolfgang

2017-01-01

Phytotherapy is an important therapeutic option in functional gastrointestinal diseases (FGID). It has a large tradition, with different approaches in different regions of the world, some of which have made their way into modern evidence-based medicine (EBM). Taking into account the number of herbs in use, and also the cumulated scientific evidence on them, FGID are possibly the most important indication in phytotherapy. This does not only apply for European phytotherapy, but also for other regions, such as Asia. Within European phytotherapy, herbs active in FGID are usually classified according to their main active constituents and their activities. Typically, the herbs used in FGID are grouped into amara, aromatica, amara aromatica combining both properties, herbs stimulating gastric secretion, herbs containing spasmolytic and carminative essential oils or spasmolytic alkaloids, mucilaginosa soothing the mucosa, and flavonoid containing drugs with anti-inflammatory properties. In phytotherapy, different plants are frequently combined to maximize effectiveness and specificity of action. Very potent combination products can be developed when the mechanisms of action of the combination partners are complementary. This approach can be demonstrated by the example of STW 5. For this herbal combination product, therapeutic efficacy in FGID has been clinically proven according to the highest standards of EBM. This example also underlines that modern rational phytotherapy is definitely part of modern EBM. Key Messages: FGID is one of the most important indications in phytotherapy and rationally combined herbal preparations are established evidence-based therapeutic options. © 2018 The Author(s) Published by S. Karger AG, Basel.

Investigating an Application of Speech-to-Text Recognition: A Study on Visual Attention and Learning Behaviour

ERIC Educational Resources Information Center

Huang, Y-M.; Liu, C-J.; Shadiev, Rustam; Shen, M-H.; Hwang, W-Y.

2015-01-01

One major drawback of previous research on speech-to-text recognition (STR) is that most findings showing the effectiveness of STR for learning were based upon subjective evidence. Very few studies have used eye-tracking techniques to investigate visual attention of students on STR-generated text. Furthermore, not much attention was paid to…

Facilitating Comprehension of Non-Native English Speakers during Lectures in English with STR-Texts

ERIC Educational Resources Information Center

Shadiev, Rustam; Wu, Ting-Ting; Huang, Yueh-Min

2018-01-01

We provided texts generated by speech-to text-recognition (STR) technology for non-native English speaking students during lectures in English in order to test whether STR-texts were useful for enhancing students' comprehension of lectures. To this end, we carried out an experiment in which 60 participants were randomly assigned to a control group…

Profiling a multiplex short tandem repeat loci from human urine with use of low cost on-site technology for verification of sample authenticity.

PubMed

Pires, Nuno M M; Tao Dong; Berntzen, Lasse; Lonningdal, Torill

2017-07-01

This work focuses on the development of a sophisticated technique via STR typing to unequivocally verify the authenticity of urine samples before sent to laboratories. STR profiling was conducted with the CSF1PO, TPOX, TH01 Multiplex System coupled with a smartphone-based detection method. The promising capability of the method to identify distinct STR profiles from urine of different persons opens the possibility to conduct sample authenticity tests. On-site STR profiling could be realized with a self-contained autonomous device with an integrated PCR microchip shown hereby.

What is the best ST-segment recovery parameter to predict clinical outcome and myocardial infarct size? Amplitude, speed, and completeness of ST-segment recovery after primary percutaneous coronary intervention for ST-segment elevation myocardial infarction.

PubMed

Kuijt, Wichert J; Green, Cindy L; Verouden, Niels J W; Haeck, Joost D E; Tzivoni, Dan; Koch, Karel T; Stone, Gregg W; Lansky, Alexandra J; Broderick, Samuel; Tijssen, Jan G P; de Winter, Robbert J; Roe, Matthew T; Krucoff, Mitchell W

ST-segment recovery (STR) is a strong mechanistic correlate of infarct size (IS) and outcome in ST-segment elevation myocardial infarction (STEMI). Characterizing measures of speed, amplitude, and completeness of STR may extend the use of this noninvasive biomarker. Core laboratory continuous 24-h 12-lead Holter ECG monitoring, IS by single-photon emission computed tomography (SPECT), and 30-day mortality of 2 clinical trials of primary percutaneous coronary intervention in STEMI were combined. Multiple ST measures (STR at last contrast injection (LC) measured from peak value; 30, 60, 90, 120, and 240min, residual deviation; time to steady ST recovery; and the 3-h area under the time trend curve [ST-AUC] from LC) were univariably correlated with IS and predictive of mortality. After multivariable adjustment for ST-parameters and GRACE risk factors, STR at 240min remained an additive predictor of mortality. Early STR, residual deviation, and ST-AUC remained associated with IS. Multiple parameters that quantify the speed, amplitude, and completeness of STR predict mortality and correlate with IS. Copyright © 2017. Published by Elsevier Inc.

Modeling service time reliability in urban ferry system

NASA Astrophysics Data System (ADS)

Chen, Yifan; Luo, Sida; Zhang, Mengke; Shen, Hanxia; Xin, Feifei; Luo, Yujie

2017-09-01

The urban ferry system can carry a large number of travelers, which may alleviate the pressure on road traffic. As an indicator of its service quality, service time reliability (STR) plays an essential part in attracting travelers to the ferry system. A wide array of studies have been conducted to analyze the STR of land transportation. However, the STR of ferry systems has received little attention in the transportation literature. In this study, a model was established to obtain the STR in urban ferry systems. First, the probability density function (PDF) of the service time provided by ferry systems was constructed. Considering the deficiency of the queuing theory, this PDF was determined by Bayes’ theorem. Then, to validate the function, the results of the proposed model were compared with those of the Monte Carlo simulation. With the PDF, the reliability could be determined mathematically by integration. Results showed how the factors including the frequency, capacity, time schedule and ferry waiting time affected the STR under different degrees of congestion in ferry systems. Based on these results, some strategies for improving the STR were proposed. These findings are of great significance to increasing the share of ferries among various urban transport modes.

Short-read, high-throughput sequencing technology for STR genotyping

PubMed Central

Bornman, Daniel M.; Hester, Mark E.; Schuetter, Jared M.; Kasoji, Manjula D.; Minard-Smith, Angela; Barden, Curt A.; Nelson, Scott C.; Godbold, Gene D.; Baker, Christine H.; Yang, Boyu; Walther, Jacquelyn E.; Tornes, Ivan E.; Yan, Pearlly S.; Rodriguez, Benjamin; Bundschuh, Ralf; Dickens, Michael L.; Young, Brian A.; Faith, Seth A.

2013-01-01

DNA-based methods for human identification principally rely upon genotyping of short tandem repeat (STR) loci. Electrophoretic-based techniques for variable-length classification of STRs are universally utilized, but are limited in that they have relatively low throughput and do not yield nucleotide sequence information. High-throughput sequencing technology may provide a more powerful instrument for human identification, but is not currently validated for forensic casework. Here, we present a systematic method to perform high-throughput genotyping analysis of the Combined DNA Index System (CODIS) STR loci using short-read (150 bp) massively parallel sequencing technology. Open source reference alignment tools were optimized to evaluate PCR-amplified STR loci using a custom designed STR genome reference. Evaluation of this approach demonstrated that the 13 CODIS STR loci and amelogenin (AMEL) locus could be accurately called from individual and mixture samples. Sensitivity analysis showed that as few as 18,500 reads, aligned to an in silico referenced genome, were required to genotype an individual (>99% confidence) for the CODIS loci. The power of this technology was further demonstrated by identification of variant alleles containing single nucleotide polymorphisms (SNPs) and the development of quantitative measurements (reads) for resolving mixed samples. PMID:25621315

"New turns from old STaRs": enhancing the capabilities of forensic short tandem repeat analysis.

PubMed

Phillips, Christopher; Gelabert-Besada, Miguel; Fernandez-Formoso, Luis; García-Magariños, Manuel; Santos, Carla; Fondevila, Manuel; Ballard, David; Syndercombe Court, Denise; Carracedo, Angel; Lareu, Maria Victoria

2014-11-01

The field of research and development of forensic STR genotyping remains active, innovative, and focused on continuous improvements. A series of recent developments including the introduction of a sixth dye have brought expanded STR multiplex sizes while maintaining sensitivity to typical forensic DNA. New supplementary kits complimenting the core STRs have also helped improve analysis of challenging identification cases such as distant pairwise relationships in deficient pedigrees. This article gives an overview of several recent key developments in forensic STR analysis: availability of expanded core STR kits and supplementary STRs, short-amplicon mini-STRs offering practical options for highly degraded DNA, Y-STR enhancements made from the identification of rapidly mutating loci, and enhanced analysis of genetic ancestry by analyzing 32-STR profiles with a Bayesian forensic classifier originally developed for SNP population data. As well as providing scope for genotyping larger numbers of STRs optimized for forensic applications, the launch of compact next-generation sequencing systems provides considerable potential for genotyping the sizeable proportion of nucleotide variation existing in forensic STRs, which currently escapes detection with CE. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Structure of Rauvolfia serpentina Strictosidine Synthase Is a Novel Six-Bladed β-Propeller Fold in Plant Proteins[W

PubMed Central

Ma, Xueyan; Panjikar, Santosh; Koepke, Juergen; Loris, Elke; Stöckigt, Joachim

2006-01-01

The enzyme strictosidine synthase (STR1) from the Indian medicinal plant Rauvolfia serpentina is of primary importance for the biosynthetic pathway of the indole alkaloid ajmaline. Moreover, STR1 initiates all biosynthetic pathways leading to the entire monoterpenoid indole alkaloid family representing an enormous structural variety of ∼2000 compounds in higher plants. The crystal structures of STR1 in complex with its natural substrates tryptamine and secologanin provide structural understanding of the observed substrate preference and identify residues lining the active site surface that contact the substrates. STR1 catalyzes a Pictet-Spengler–type reaction and represents a novel six-bladed β-propeller fold in plant proteins. Structure-based sequence alignment revealed a common repetitive sequence motif (three hydrophobic residues are followed by a small residue and a hydrophilic residue), indicating a possible evolutionary relationship between STR1 and several sequence-unrelated six-bladed β-propeller structures. Structural analysis and site-directed mutagenesis experiments demonstrate the essential role of Glu-309 in catalysis. The data will aid in deciphering the details of the reaction mechanism of STR1 as well as other members of this enzyme family. PMID:16531499

The structure of Rauvolfia serpentina strictosidine synthase is a novel six-bladed beta-propeller fold in plant proteins.

PubMed

Ma, Xueyan; Panjikar, Santosh; Koepke, Juergen; Loris, Elke; Stöckigt, Joachim

2006-04-01

The enzyme strictosidine synthase (STR1) from the Indian medicinal plant Rauvolfia serpentina is of primary importance for the biosynthetic pathway of the indole alkaloid ajmaline. Moreover, STR1 initiates all biosynthetic pathways leading to the entire monoterpenoid indole alkaloid family representing an enormous structural variety of approximately 2000 compounds in higher plants. The crystal structures of STR1 in complex with its natural substrates tryptamine and secologanin provide structural understanding of the observed substrate preference and identify residues lining the active site surface that contact the substrates. STR1 catalyzes a Pictet-Spengler-type reaction and represents a novel six-bladed beta-propeller fold in plant proteins. Structure-based sequence alignment revealed a common repetitive sequence motif (three hydrophobic residues are followed by a small residue and a hydrophilic residue), indicating a possible evolutionary relationship between STR1 and several sequence-unrelated six-bladed beta-propeller structures. Structural analysis and site-directed mutagenesis experiments demonstrate the essential role of Glu-309 in catalysis. The data will aid in deciphering the details of the reaction mechanism of STR1 as well as other members of this enzyme family.

Mutation rate estimation for 15 autosomal STR loci in a large population from Mainland China.

PubMed

Zhao, Zhuo; Zhang, Jie; Wang, Hua; Liu, Zhi-Peng; Liu, Ming; Zhang, Yuan; Sun, Li; Zhang, Hui

2015-09-01

STR, short tandem repeats, are well known as a type of powerful genetic marker and widely used in studying human population genetics. Compared with the conventional genetic markers, the mutation rate of STR is higher. Additionally, the mutations of STR loci do not lead to genetic inconsistencies between the genotypes of parents and children; therefore, the analysis of STR mutation is more suited to assess the population mutation. In this study, we focused on 15 autosomal STR loci. DNA samples from a total of 42,416 unrelated healthy individuals (19,037 trios) from the population of Mainland China collected between Jan 2012 and May 2014 were successfully investigated. In our study, the allele frequencies, paternal mutation rates, maternal mutation rates and average mutation rates were detected. Furthermore, we also investigated the relationship between paternal ages, maternal ages, area, the time of pregnancy and average mutation rate. We found that the paternal mutation rate was higher than the maternal mutation rate and the paternal, maternal, and average mutation rates had a positive correlation with paternal age, maternal age and the time of pregnancy respectively. Additionally, the average mutation rate of coastal areas was higher than that of inland areas.

Effect of operating conditions in production of diagnostic Salmonella Enteritidis O-antigen-specific monoclonal antibody in different bioreactor systems.

PubMed

Ayyildiz-Tamis, Duygu; Nalbantsoy, Ayse; Elibol, Murat; Deliloglu-Gurhan, Saime Ismet

2014-01-01

In this study, different cultivation systems such as roller bottles (RB), 5-L stirred-tank bioreactor (STR), and disposable bioreactors were used to cultivate hybridoma for lab-scale production of Salmonella Enteritidis O-antigen-specific monoclonal antibody (MAb). Hybridoma cell line was cultivated in either serum-containing or serum-free medium (SFM) culture conditions. In STR, MAb production scaled up to 4 L, and production capabilities of the cells were also evaluated in different featured production systems. Moreover, the growth parameters of the cells in all production systems such as glucose consumption, lactate and ammonia production, and also MAb productivities were determined. Collected supernatants from the reactors were concentrated by a cross-flow filtration system. In conclusion, cells were not adapted to SFM in RB and STR. Therefore, less MAb titer in both STR and RB systems with SFM was observed compared to the cultures containing fetal bovine serum-supplemented medium. A higher MAb titer was gained in the membrane-aerated system compared to those in STR and RB. Although the highest MAb titer was obtained in the static membrane bioreactor system, the highest productivity was obtained in STR operated in semicontinuous mode with overlay aeration.

The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions

PubMed Central

Reyes-Prieto, Mariana; Ordoñez, Omar F.; Santos-García, Diego; Rosas-Pérez, Tania; Valdivia-Anistro, Jorge; Rebollar, Eria A.; Saralegui, Andrés; Moya, Andrés; Merino, Enrique; Farías, María Eugenia

2017-01-01

We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina. PMID:28439458

Identifying the most likely contributors to a Y-STR mixture using the discrete Laplace method.

PubMed

Andersen, Mikkel Meyer; Eriksen, Poul Svante; Mogensen, Helle Smidt; Morling, Niels

2015-03-01

In some crime cases, the male part of the DNA in a stain can only be analysed using Y chromosomal markers, e.g. Y-STRs. This may be the case in e.g. rape cases, where the male components can only be detected as Y-STR profiles, because the fraction of male DNA is much smaller than that of female DNA, which can mask the male results when autosomal STRs are investigated. Sometimes, mixtures of Y-STRs are observed, e.g. in rape cases with multiple offenders. In such cases, Y-STR mixture analysis is required, e.g. by mixture deconvolution, to deduce the most likely DNA profiles from the contributors. We demonstrate how the discrete Laplace method can be used to separate a two person Y-STR mixture, where the Y-STR profiles of the true contributors are not present in the reference dataset, which is often the case for Y-STR profiles in real case work. We also briefly discuss how to calculate the weight of the evidence using the likelihood ratio principle when a suspect's Y-STR profile fits into a two person mixture. We used three datasets with between 7 and 21 Y-STR loci: Denmark (n=181), Somalia (n=201) and Germany (n=3443). The Danish dataset with 21 loci was truncated to 15 and 10 loci to examine the effect of the number of loci. For each of these datasets, an out of sample simulation study was performed: A total of 550 mixtures were composed by randomly sampling two haplotypes, h1 and h2, from the dataset. We then used the discrete Laplace method on the remaining data (excluding h1 and h2) to rank the contributor pairs by the product of the contributors' estimated haplotype frequencies. Successful separation of mixtures (defined by the observation that the true contributor pair was among the 10 most likely contributor pairs) was found in 42-52% of the cases for 21 loci, 69-75% for 15 loci and 92-99% for 10 loci or less depending on the dataset and how the discrete Laplace model was chosen. Y-STR mixtures with many loci are difficult to separate, but even haplotypes with 21 Y-STR loci can be separated. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Determination of the Navier slip coefficient of microchannels exploiting the streaming potential.

PubMed

Park, Hung Mok

2012-03-01

For most microchannels made of hydrophobic materials such as polymers, velocity slip occurs at the wall, affecting volumetric flow rate of electroosmotic flow Q(eof) and streaming potential (∂ϕ(str)/∂z). Since most techniques exploit Q(eof) or (∂ϕ(str)/∂z) to determine the zeta potential, ζ, it is very difficult to measure ζ of hydrophobic walls, if the slip coefficient b is not found a priori. Until now, Q(eof) and (∂ϕ(str)/∂z) are known to depend on ζ and b in a same functional form, which makes it impossible to estimate ζ or b separately using measurements of Q(eof) and (∂ϕ(str)/∂z). However, exploiting the analytic formula for Q(eof) and (∂ϕ(str)/∂z) derived in the present work, it is found that the effect of ζ and that of b on Q(eof) and (∂ϕ(str)/∂z) can be separated from each other by varying the bulk ionic concentration. Thus, the slip coefficient as well as the zeta potential of hydrophobic microchannels can be found with reasonable accuracy by means of a nonlinear curve fitting method using measured data of Q(eof) and (∂ϕ(str)/∂z) at various bulk ionic concentrations. The present method allows an accurate estimation of slip coefficient of hydrophobic microchannels, which is quite simple and cheap compared with methods employing microparticle velocimetry. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Models of Cerebral-Body Perfusion and Cerebral Chemical Transport.

DTIC Science & Technology

1988-03-01

Pressure Waves 22 Conchusion 23 References 36 A Compartmental Brain Model for Chemical Transport and CO2 Controlled Blood Flow Abstract 37 Introduction 38...surrounding the body, e.g., atmospheric pressure , pressure al high and low altitudes, high underwater pressure , vacuum and excessive gravity acceleration...Resistance of the AreriolarNenous capillary, accounting for the pressure drop observed between them. RCB Resistance of the Blood -Brain barrier (between

Quantitative magnetic resonance imaging assessments of autosomal recessive polycystic kidney disease progression and response to therapy in an animal model.

PubMed

Erokwu, Bernadette O; Anderson, Christian E; Flask, Chris A; Dell, Katherine M

2018-05-01

BackgroundAutosomal recessive polycystic kidney disease (ARPKD) is associated with significant mortality and morbidity, and currently, there are no disease-specific treatments available for ARPKD patients. One major limitation in establishing new therapies for ARPKD is a lack of sensitive measures of kidney disease progression. Magnetic resonance imaging (MRI) can provide multiple quantitative assessments of the disease.MethodsWe applied quantitative image analysis of high-resolution (noncontrast) T2-weighted MRI techniques to study cystic kidney disease progression and response to therapy in the PCK rat model of ARPKD.ResultsSerial imaging over a 2-month period demonstrated that renal cystic burden (RCB, %)=[total cyst volume (TCV)/total kidney volume (TKV) × 100], TCV, and, to a lesser extent, TKV detected cystic kidney disease progression, as well as the therapeutic effect of octreotide, a clinically available medication shown previously to slow both kidney and liver disease progression in this model. All three MRI measures correlated significantly with histologic measures of renal cystic area, although the correlation of RCB and TCV was stronger than that of TKV.ConclusionThese preclinical MRI results provide a basis for applying these quantitative MRI techniques in clinical studies, to stage and measure progression in human ARPKD kidney disease.

Short Tandem Repeat DNA Internet Database

National Institute of Standards and Technology Data Gateway

SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

Genetic polymorphisms of 15 STR loci in two Tibetan populations from Tibet Changdu and Naqu, China.

PubMed

Kang, LongLi; Yuan, Dongya; Yang, Fengying; Liu, Kai; Za, Xi

2007-07-04

The allelic distribution of 15 short tandem repeat (STR) loci included in the AmpFl STR Identifiler kit was examined in 100 Changdu Tibetan and 118 Naqu Tibetan unrelated individuals living in the Tibet Province, PR China. The distribution of these observed genotypes was not significantly different from the expected distribution according to Hardy-Weinberg equilibrium.

Lack of functionally active sweet taste receptors in the jejunum in vivo in the rat.

PubMed

Chaudhry, Rizwan M; Garg, Alok; Abdelfatah, Mohamed M; Duenes, Judith A; Sarr, Michael G

2013-08-01

When studied in enterocyte-like cell lines (Caco-2 and RIE cells), agonists and antagonists of the sweet taste receptor (STR) augment and decrease glucose uptake, respectively. We hypothesize that exposure to STR agonists and antagonists in vivo will augment glucose absorption in the rat. About 30-cm segments of jejunum in anesthetized rats were perfused with iso-osmolar solutions containing 10, 35, and 100 mM glucose solutions (n = 6 rats, each group) with and without the STR agonist 2 mM acesulfame potassium and the STR inhibitor 10 μM U-73122 (inhibitor of the phospholipase C pathway). Carrier-mediated absorption of glucose was calculated by using stereospecific and nonstereospecific (14)C-d-glucose and (3)H-l-glucose, respectively. Addition of the STR agonist acesulfame potassium to the 10, 35, and 100 mM glucose solutions had no substantive effects on glucose absorption from 2.1 ± 0.2 to 2.0 ± 0.3, 5.8 ± 0.2 to 4.8 ± 0.2, and 15.5 ± 2.3 to 15.7 ± 2.7 μmoL/min/30-cm intestinal segment (P > 0.05), respectively. Addition of the STR inhibitor (U-73122) also had no effect on absorption in the 10, 35, and 100 mM solutions from 2.3 ± 0.1 to 2.1 ± 0.2, 7.7 ± 0.5 to 7.2 ± 0.5, and 15.7 ± 0.9 to 15.2 ± 1.1 μmoL/min/30-cm intestinal segment, respectively. Provision of glucose directly into rat jejunum does not augment glucose absorption via STR-mediated mechanisms within the jejunum in the rat. Our experiments show either no major role of STRs in mediating postprandial augmentation of glucose absorption or that proximal gastrointestinal tract stimulation of STR or other luminal factors may be required for absorption of glucose to be augmented by STR. Copyright © 2013 Elsevier Inc. All rights reserved.

Non-equilibrium simulation of CH4 production through the depressurization method from gas hydrate reservoirs

NASA Astrophysics Data System (ADS)

Qorbani, Khadijeh; Kvamme, Bjørn

2016-04-01

Natural gas hydrates (NGHs) in nature are formed from various hydrate formers (i.e. aqueous, gas, and adsorbed phases). As a result, due to Gibbs phase rule and the combined first and second laws of thermodynamics CH4-hydrate cannot reach thermodynamic equilibrium in real reservoir conditions. CH4 is the dominant component in NGH reservoirs. It is formed as a result of biogenic degradation of biological material in the upper few hundred meters of subsurface. It has been estimated that the amount of fuel-gas reserve in NGHs exceed the total amount of fossil fuel explored until today. Thus, these reservoirs have the potential to satisfy the energy requirements of the future. However, released CH4 from dissociated NGHs could find its way to the atmosphere and it is a far more aggressive greenhouse gas than CO2, even though its life-time is shorter. Lack of reliable field data makes it difficult to predict the production potential, as well as safety of CH4 production from NGHs. Computer simulations can be used as a tool to investigate CH4 production through different scenarios. Most hydrate simulators within academia and industry treat hydrate phase transitions as an equilibrium process and those which employ the kinetic approach utilize simple laboratory data in their models. Furthermore, it is typical to utilize a limited thermodynamic description where only temperature and pressure projections are considered. Another widely used simplification is to assume only a single route for the hydrate phase transitions. The non-equilibrium nature of hydrate indicates a need for proper kinetic models to describe hydrate dissociation and reformation in the reservoir with respect to thermodynamics variables, CH4 mole-fraction, pressure and temperature. The RetrasoCodeBright (RCB) hydrate simulator has previously been extended to model CH4-hydrate dissociation towards CH4 gas and water. CH4-hydrate is added to the RCB data-base as a pseudo mineral. Phase transitions are treated as non-equilibrium processes under local constraint of mass and heat fluxes. In this work, we have extended RCB by adding another route for dissociation or reformation of CH4-hydrate towards CH4 into the aqueous phase and water. CH4-hydrate formation and dissociation is resolved by looking at supersaturation and undersaturation with respect to thermodynamics variables. Hydrate instability due to undersaturation of CH4 in the contacting water phase is also considered. A complete non-equilibrium thermodynamic package, developed in-house, was combined with RCB to account for competing phase transitions by considering the minimization of Gibb's free energy. The energy differences were calculated from variations in chemical potentials of hydrate and hydrate formers. Mass transport, heat transport and non-equilibrium thermodynamic effects were implemented through classical nucleation theory to model the kinetic rate of hydrate phase transitions. To illustrate our implementations we ran simulations covering time-spans in the order of hundred years. CH4 production was modelled using the depressurization method, where we employed the Messoyakha field data. We discuss our implementations, as well as results obtained from simulations utilizing our modifications.

A large-scale dataset of single and mixed-source short tandem repeat profiles to inform human identification strategies: PROVEDIt.

PubMed

Alfonse, Lauren E; Garrett, Amanda D; Lun, Desmond S; Duffy, Ken R; Grgicak, Catherine M

2018-01-01

DNA-based human identity testing is conducted by comparison of PCR-amplified polymorphic Short Tandem Repeat (STR) motifs from a known source with the STR profiles obtained from uncertain sources. Samples such as those found at crime scenes often result in signal that is a composite of incomplete STR profiles from an unknown number of unknown contributors, making interpretation an arduous task. To facilitate advancement in STR interpretation challenges we provide over 25,000 multiplex STR profiles produced from one to five known individuals at target levels ranging from one to 160 copies of DNA. The data, generated under 144 laboratory conditions, are classified by total copy number and contributor proportions. For the 70% of samples that were synthetically compromised, we report the level of DNA damage using quantitative and end-point PCR. In addition, we characterize the complexity of the signal by exploring the number of detected alleles in each profile. Copyright © 2017 Elsevier B.V. All rights reserved.

Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches.

PubMed

Qian, Xiaoqin; Hou, Jiayi; Wang, Zheng; Ye, Yi; Lang, Min; Gao, Tianzhen; Liu, Jing; Hou, Yiping

2017-09-12

There is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term 'NGS+' for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs). The high-resolution Y-SNP haplogroup and Y-STR haplotype can be obtained with NGS+. We further developed a new data-driven decision rule, FSindex, for estimating the likelihood for each retrieved pedigree. Our approach enables positive identification of pedigree from mismatched Y-STR haplotypes. It is envisaged that NGS+ will revolutionize forensic pedigree searches, especially when the person of interest was not recorded in forensic DNA database.

Genetic analysis of 19 X chromosome STR loci for forensic purposes in four Chinese ethnic groups

PubMed Central

Yang, Xingyi; Zhang, Xiaofang; Zhu, Junyong; Chen, Linli; Liu, Changhui; Feng, Xingling; Chen, Ling; Wang, Huijun; Liu, Chao

2017-01-01

A new 19 X- short tandem repeat (STR) multiplex PCR system has recently been developed, though its applicability in forensic studies has not been thoroughly assessed. In this study, 932 unrelated individuals from four Chinese ethnic groups (Han, Tibet, Uighur and Hui) were successfully genotyped using this new multiplex PCR system. Our results showed significant linkage disequilibrium between markers DXS10103 and DXS10101 in all four ethnic groups; markers DXS10159 and DXS10162, DXS6809 and DXS6789, and HPRTB and DXS10101 in Tibetan populations; and markers DXS10074 and DXS10075 in Uighur populations. The combined powers of discrimination in males and females were calculated according to haplotype frequencies from allele distributions rather than haplotype counts in the relevant population and were high in four ethnic groups. The cumulative powers of discrimination of the tested X-STR loci were 1.000000000000000 and 0.999999999997940 in females and males, respectively. All 19 X-STR loci are highly polymorphic. The highest Reynolds genetic distances were observed for the Tibet-Uighur pairwise comparisons. This study represents an extensive report on X-STR marker variation in minor Chinese populations and a comprehensive analysis of the diversity of these 19 X STR markers in four Chinese ethnic groups. PMID:28211539

Coevolution of antibiotic production and counter-resistance in soil bacteria.

PubMed

Laskaris, Paris; Tolba, Sahar; Calvo-Bado, Leo; Wellington, Elizabeth M; Wellington, Liz

2010-03-01

We present evidence for the coexistence and coevolution of antibiotic resistance and biosynthesis genes in soil bacteria. The distribution of the streptomycin (strA) and viomycin (vph) resistance genes was examined in Streptomyces isolates. strA and vph were found either within a biosynthetic gene cluster or independently. Streptomyces griseus strains possessing the streptomycin cluster formed part of a clonal complex. All S. griseus strains possessing solely strA belonged to two clades; both were closely related to the streptomycin producers. Other more distantly related S. griseus strains did not contain strA. S. griseus strains with only vph also formed two clades, but they were more distantly related to the producers and to one another. The expression of the strA gene was constitutive in a resistance-only strain whereas streptomycin producers showed peak strA expression in late log phase that correlates with the switch on of streptomycin biosynthesis. While there is evidence that antibiotics have diverse roles in nature, our data clearly support the coevolution of resistance in the presence of antibiotic biosynthetic capability within closely related soil dwelling bacteria. This reinforces the view that, for some antibiotics at least, the primary role is one of antibiosis during competition in soil for resources.

StrAuto: automation and parallelization of STRUCTURE analysis.

PubMed

Chhatre, Vikram E; Emerson, Kevin J

2017-03-24

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation - a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .

Single-cell forensic short tandem repeat typing within microfluidic droplets.

PubMed

Geng, Tao; Novak, Richard; Mathies, Richard A

2014-01-07

A short tandem repeat (STR) typing method is developed for forensic identification of individual cells. In our strategy, monodisperse 1.5 nL agarose-in-oil droplets are produced with a high frequency using a microfluidic droplet generator. Statistically dilute single cells, along with primer-functionalized microbeads, are randomly compartmentalized in the droplets. Massively parallel single-cell droplet polymerase chain reaction (PCR) is performed to transfer replicas of desired STR targets from the single-cell genomic DNA onto the coencapsulated microbeads. These DNA-conjugated beads are subsequently harvested and reamplified under statistically dilute conditions for conventional capillary electrophoresis (CE) STR fragment size analysis. The 9-plex STR profiles of single cells from both pure and mixed populations of GM09947 and GM09948 human lymphoid cells show that all alleles are correctly called and allelic drop-in/drop-out is not observed. The cell mixture study exhibits a good linear relationship between the observed and input cell ratios in the range of 1:1 to 10:1. Additionally, the STR profile of GM09947 cells could be deduced even in the presence of a high concentration of cell-free contaminating 9948 genomic DNA. Our method will be valuable for the STR analysis of samples containing mixtures of cells/DNA from multiple contributors and for low-concentration samples.

Assessment of a subset of Slowly Mutating Y-STRs for forensic and evolutionary studies.

PubMed

Baeta, Miriam; Núñez, Carolina; Villaescusa, Patricia; Ortueta, Urko; Ibarbia, Nerea; Herrera, Rene J; Blazquez-Caeiro, José Luis; Builes, Juan José; Jiménez-Moreno, Susana; Martínez-Jarreta, Begoña; de Pancorbo, Marian M

2018-05-01

Y-specific short tandem repeat (Y-STR) loci display different mutation rates and consequently are suitable for forensic, genealogical, and evolutionary studies that require different levels of timelines and resolution. Recent efforts have focused on implementing Rapidly Mutating (RM) Y-STRs to assess male specific profiles. However, due to their high mutation rate their use in kinship testing or in phylogenetic studies may be less reliable. In the present study, a novel Slowly Mutating Y-STR (SM) panel, including DYS388, DYS426, DYS461 (Y-GATA-A7.2), DYS485, DYS525, and DYS561, has been developed and evaluated in a sample set of 628 unrelated males from different worldwide populations. This panel is reproducible, sensitive, and robust for forensic applications and may be useful in conjunction with the common multiplexes, particularly in exclusion of kinship cases where minimal discrimination is reported employing the rapidly mutating Y-STR systems. Furthermore, SM Y-STR data may be of value in evolutionary studies to optimize the resolution of phylogenetic relationships generated with current Y-STR panel sets. In this study, we provide an extensive Y-STR allele and haplotype reference dataset for future applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Determination of combined sibship indices "gray zone" using 15 STR loci for central Bosnian human population.

PubMed

Musanovic, Jasmin; Filipovska-Musanovic, Marijana; Kovacevic, Lejla; Buljugic, Dzenisa; Dzehverovic, Mirela; Avdic, Jasna; Marjanovic, Damir

2012-05-01

In our previous population studies of Bosnia and Herzegovina human population, we have used autosomal STR, Y-STR, and X-STR loci, as well as Y-chromosome NRY biallelic markers. All obtained results were included in Bosnian referent database. In order of future development of applied population molecular genetics researches of Bosnia and Herzegovina human population, we have examined the effectiveness of 15 STR loci system in determination of sibship by using 15 STR loci and calculating different cut-off points of combined sibship indices (CSI) and distribution of sharing alleles. From the perspective of its application, it is very difficult and complicated to establish strict CSI cut-off values for determination of the doubtless sibship. High statistically significant difference between the means of CSI values and in distribution of alleles sharing in siblings and non-siblings was noticed (P < 0.0001). After constructing the "gray zone", only one false positive result was found in three CSI cut-off levels with the highest percent of determined sibship/non-sibship at the CSI = 0.067, confirming its practical benefit. Concerning the distribution of sharing alleles, it is recommended as an informative estimator for its usage within Bosnia and Herzegovina human population.

Similar developmental trajectories in autism and Asperger syndrome: from early childhood to adolescence.

PubMed

Szatmari, Peter; Bryson, Susan; Duku, Eric; Vaccarella, Liezanne; Zwaigenbaum, Lonnie; Bennett, Teresa; Boyle, Michael H

2009-12-01

The objective of this study was to chart the developmental trajectories of high-functioning children with autism spectrum disorders (ASD) from early childhood to adolescence using the presence and absence of structural language impairment (StrLI) as a way of differentiating autism from Asperger syndrome (AS). Sixty-four high-functioning children with ASD were ascertained at 4-6 years of age from several different regional diagnostic and treatment centers. At 6-8 years of age, the ADI-R and the Test of Oral Language Development were used to define an autism group (those with StrLI at 6-8 years of age) and an AS group (those without StrLI). Growth curve analysis was then used to chart the developmental trajectories of these children on measures of autistic symptoms, and adaptive skills in communication, daily living and socialization. Differentiating the ASD group in terms of the presence/absence of StrLI provided a better explanation of the variation in growth curves than not differentiating high-functioning ASD children. The two groups had similar developmental trajectories but the group without StrLI (the AS group) was functioning better and had fewer autistic symptoms than the group with StrLI (the autism group) on all measures across time. The differences in outcome could not be explained by non-verbal IQ or change in early language skills. Distinguishing between autism and Asperger syndrome based on the presence or absence of StrLI appears to be a clinically useful way of classifying ASD sub-types.

Validation of a combined autosomal/Y-chromosomal STR approach for analyzing typical biological stains in sexual-assault cases.

PubMed

Purps, Josephine; Geppert, Maria; Nagy, Marion; Roewer, Lutz

2015-11-01

DNA testing is an established part of the investigation and prosecution of sexual assault. The primary purpose of DNA evidence is to identify a suspect and/or to demonstrate sexual contact. However, due to highly uneven proportions of female and male DNA in typical stains, routine autosomal analysis often fails to detect the DNA of the assailant. To evaluate the forensic efficiency of the combined application of autosomal and Y-chromosomal short tandem repeat (STR) markers, we present a large retrospective casework study of probative evidence collected in sexual-assault cases. We investigated up to 39 STR markers by testing combinations of the 16-locus NGMSElect kit with both the 23-locus PowerPlex Y23 and the 17-locus Yfiler kit. Using this dual approach we analyzed DNA extracts from 2077 biological stains collected in 287 cases over 30 months. To assess the outcome of the combined approach in comparison to stand-alone autosomal analysis we evaluated informative DNA profiles. Our investigation revealed that Y-STR analysis added up to 21% additional, highly informative (complete, single-source) profiles to the set of reportable autosomal STR profiles for typical stains collected in sexual-assault cases. Detection of multiple male contributors was approximately three times more likely with Y-chromosomal profiling than with autosomal STR profiling. In summary, 1/10 cases would have remained inconclusive (and could have been dismissed) if Y-STR analysis had been omitted from DNA profiling in sexual-assault cases. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Cluster analysis of European Y-chromosomal STR haplotypes using the discrete Laplace method.

PubMed

Andersen, Mikkel Meyer; Eriksen, Poul Svante; Morling, Niels

2014-07-01

The European Y-chromosomal short tandem repeat (STR) haplotype distribution has previously been analysed in various ways. Here, we introduce a new way of analysing population substructure using a new method based on clustering within the discrete Laplace exponential family that models the probability distribution of the Y-STR haplotypes. Creating a consistent statistical model of the haplotypes enables us to perform a wide range of analyses. Previously, haplotype frequency estimation using the discrete Laplace method has been validated. In this paper we investigate how the discrete Laplace method can be used for cluster analysis to further validate the discrete Laplace method. A very important practical fact is that the calculations can be performed on a normal computer. We identified two sub-clusters of the Eastern and Western European Y-STR haplotypes similar to results of previous studies. We also compared pairwise distances (between geographically separated samples) with those obtained using the AMOVA method and found good agreement. Further analyses that are impossible with AMOVA were made using the discrete Laplace method: analysis of the homogeneity in two different ways and calculating marginal STR distributions. We found that the Y-STR haplotypes from e.g. Finland were relatively homogeneous as opposed to the relatively heterogeneous Y-STR haplotypes from e.g. Lublin, Eastern Poland and Berlin, Germany. We demonstrated that the observed distributions of alleles at each locus were similar to the expected ones. We also compared pairwise distances between geographically separated samples from Africa with those obtained using the AMOVA method and found good agreement. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

The interaction of chronic restraint stress and voluntary alcohol intake: effects on spatial memory in male rats.

PubMed

Gomez, Juan L; Lewis, Michael J; Luine, Victoria N

2012-08-01

Alcohol consumption and exposure to stressful life events activate similar neural pathways and thus result in several comparable physiological and behavioral effects. Alcoholics in treatment claim that life stressors are the leading cause of continued drinking or relapse. However, few studies have investigated the interactive effects of stress and alcohol on cognitive behavior. The effects of restraint stress, alcohol, and stress in combination with alcohol were examined on a spatial memory test, the object placement (OP) task. In addition, intake levels were measured to determine if stress altered general consumption of alcohol. Male Sprague-Dawley rats were assigned to one of four conditions: no alcohol/no stress control (CON), stress alone (STR), alcohol alone (ALC), and STR+alcohol (STR+ALC). Following each restraint stress bout, the STR+ALC and the ALC groups were given access to 8% alcohol for 1h using the two-bottle choice limited access paradigm. As predicted, the STR+ALC group significantly increased alcohol consumption, while the ALC group had consistent drinking over the 10-day treatment. On the OP task, STR and ALC groups performed at chance levels, whereas the CON and STR+ALC groups significantly discriminated between objects in the new and old locations. These data show that stress increases alcohol intake and the intake of alcohol is associated with reduction of the stress-induced impairment of spatial memory. The data have important implications for the development of alcohol abuse and its treatment. Copyright © 2012 Elsevier Inc. All rights reserved.

European Research Program on Viscous Flows

DTIC Science & Technology

1980-11-01

hochviskoser Flassigkeiten. To be published in Acta Mechanica (1980) 8.36b K.O. Felsch Ein Beitrag zur Berechnung der Str ~ mung in einer Tesla- M...R. Schilling Berechnung der ausgebillten Str ~ mung in gekrummten Kanalen R. Simon mit rechteckigem Quersclnitt. Recent developments in theoretical an...package. co 12 REFERENCES No. Author Title, etc 1.4a S.G. Sundkvist V~rmek&llors inverkan pd str ~mning och temperatur i ventiler- ade lokaler (Numerisk

Forensic Memory Analysis for Apple OS X

DTIC Science & Technology

2012-06-14

x86. Table 5. Template interface fields. Variable Python Type Description template dict template implementing the C stuct interface MBR_NAME str ...dictionary key, variable name for a struct member template[MBR_NAME] tuple dictionary value, a struct member description MBR_TYPE str C type of the...named member OFFSET int offset in bytes for the member SIZE int size in bytes for the member type FIELD str lsof field represented by member

Strömende Flüssigkeiten und Gase

NASA Astrophysics Data System (ADS)

Heintze, Joachim

Die Bemerkung über die Probleme eines allgemeingültigen Ansatzes, die wir zu Anfang von Kap. 1 machten, gilt in noch höherem Maße für die Mechanik von strömenden Flüssigkeiten; dort erreicht man sogar ziemlich rasch die Grenze der Leistungsfähigkeit der heutigen Mathematik, d. h. wir können zwar - ausgehend von den Newtonschen Gesetzen (Bd. I/3) - eine Differentialgleichung für die Strömung von Flüssigkeiten aufstellen, die sog. Navier-Stokes-Gleichung, es sind aber keine allgemein anwendbaren Lösungsverfahren für diese Gleichung bekannt. Ein Blick in die Natur und auf die vielfältigen Strömungsphänomene zeigt, dass diese Tatsache nicht verwunderlich ist.

Evaluation of incest cases of Turkey in terms of DNA profiling difficulties.

PubMed

Emre, Ramazan; Canturk, Kemal Murat; Komur, Ilhami; Dogan, Muhammed; Demirel, Husrev; Baspınar, Bunyamin

2015-11-01

We scanned suspicious 1200 paternity cases and 650 sexual abuse victims in Council of Forensic Medicine of Turkey between 2011 and 2014 and detected 50 incest cases and evaluated the forensic and genetic data of incest cases for source of DNA evidence, gender, age, SES (Socioeconomic status) and geographic location of victim, abusive person, extent of incest, pregnancy from incest and date of gestation termination and also aimed to discuss some DNA profiling difficulties. We detected incest from DNA evidences of curettage material (34%; Chorionic Villi (12%) and fetal tissue (22%)), alive baby after pregnancy (28%), sperm in vaginal swab (10%), sperm in anal swab (2%), sperm on clothing (24%) and in one case both sperm on clothing and in vaginal swab (2%). It was found that the most common incestuous relationship was elder-brother-sister incest (34%) and the second most common relationship was father-daughter incest (28%). The rarest incest was mother-son incest with only one reported case (2%). Forty-three victims (86%) were younger than 18 years old and 7 victims (14%) were older than 18 years old. Thirty-eight cases described full sexual intercourse and 31 of them culminated in pregnancy and 14 of them gave birth at the end of pregnancy. We had paternity rejection problem 3 (10%) of 31 incest cases between tested genetically related alleged fathers. Totally 20 STR loci did not discriminate the alleged fathers in two cases and we treated this problem increasing the number of STR loci and finally got the discrimination. In one case we detected same triallelic variant pattern at the same D3S1358 STR locus in both tested parents but child had not got STR variant; had only two alleles at this loci. We then evaluated the peak height values of STR variant alleles of tested persons and concluded a tetra-allelic baby without any STR incompatibility of 15 STR loci. Finally, forensic experts should aware of some DNA profiling difficulties while analyzing paternity incest cases due to increasing intra familial allelic share. We suggested that first try increasing the number of compared STR loci and secondly use alternative genetic markers and also be careful while evaluating triallelic STR variants. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Genomic Diversification in Strains of Rickettsia felis Isolated from Different Arthropods

PubMed Central

Gillespie, Joseph J.; Driscoll, Timothy P.; Verhoeve, Victoria I.; Utsuki, Tadanobu; Husseneder, Claudia; Chouljenko, Vladimir N.; Azad, Abdu F.; Macaluso, Kevin R.

2015-01-01

Rickettsia felis (Alphaproteobacteria: Rickettsiales) is the causative agent of an emerging flea-borne rickettsiosis with worldwide occurrence. Originally described from the cat flea, Ctenocephalides felis, recent reports have identified R. felis from other flea species, as well as other insects and ticks. This diverse host range for R. felis may indicate an underlying genetic variability associated with host-specific strains. Accordingly, to determine a potential genetic basis for host specialization, we sequenced the genome of R. felis str. LSU-Lb, which is an obligate mutualist of the parthenogenic booklouse Liposcelis bostrychophila (Insecta: Psocoptera). We also sequenced the genome of R. felis str. LSU, the second genome sequence for cat flea-associated strains (cf. R. felis str. URRWXCal2), which are presumably facultative parasites of fleas. Phylogenomics analysis revealed R. felis str. LSU-Lb diverged from the flea-associated strains. Unexpectedly, R. felis str. LSU was found to be divergent from R. felis str. URRWXCal2, despite sharing similar hosts. Although all three R. felis genomes contain the pRF plasmid, R. felis str. LSU-Lb carries an additional unique plasmid, pLbaR (plasmid of L. bostrychophila associated Rickettsia), nearly half of which encodes a unique 23-gene integrative conjugative element. Remarkably, pLbaR also encodes a repeats-in-toxin-like type I secretion system and associated toxin, heretofore unknown from other Rickettsiales genomes, which likely originated from lateral gene transfer with another obligate intracellular parasite of arthropods, Cardinium (Bacteroidetes). Collectively, our study reveals unexpected genomic diversity across three R. felis strains and identifies several diversifying factors that differentiate facultative parasites of fleas from obligate mutualists of booklice. PMID:25477419

Polymorphisms in IL12A and cockroach allergy in children with asthma.

PubMed

Pistiner, Michael; Hunninghake, Gary M; Soto-Quiros, Manuel E; Avila, Lydiana; Murphy, Amy; Lasky-Su, Jessica; Schuemann, Brooke; Klanderman, Barbara J; Raby, Benjamin A; Celedón, Juan C

2008-07-31

IL12A has been implicated in T-cell development and may thus influence the development of atopy and allergic diseases. We tested for association between four linkage disequilibrium (LD)-tagging SNPs (rs2243123, rs2243151, rs668998, and rs17826053) in IL12A and asthma and allergy-related (serum total and allergen-specific IgE, and skin test reactivity [STR] to two common allergens) phenotypes in two samples: 417 Costa Rican children with asthma and their parents, and 470 families of 503 white children in the Childhood Asthma Management Program (CAMP). The analysis was conducted using the family-based association test (FBAT) statistic implemented in the PBAT program. Among Costa Rican children with asthma, homozygosity for the minor allele of each of two SNPs in IL12A (rs2243123 and rs2243151) was associated with increased risks of STR to American cockroach (P

Tissue identity testing of cancer by short tandem repeat polymorphism: pitfalls of interpretation in the presence of microsatellite instability.

PubMed

Much, Melissa; Buza, Natalia; Hui, Pei

2014-03-01

Tissue identity testing by short tandem repeat (STR) polymorphism offers discriminating power in resolving tissue mix-up or contamination. However, one caveat is the presence of microsatellite unstable tumors, in which genetic alterations may drastically change the STR wild-type polymorphism leading to unexpected allelic discordance. We examined how tissue identity testing results can be altered by the presence of microsatellite instability (MSI). Eleven cases of MSI-unstable (9 intestinal and 2 endometrial adenocarcinomas) and 10 cases of MSI-stable tumors (all colorectal adenocarcinomas) were included. All had been previously tested by polymerase chain reaction testing at 5 National Cancer Institute (NCI) recommended MSI loci and/or immunohistochemistry for DNA mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). Tissue identity testing targeting 15 STR loci was performed using AmpF/STR Identifiler Amplification. Ten of 11 MSI-unstable tumors demonstrated novel alleles at 5 to 12 STR loci per case and frequently with 3 or more allelic peaks. However, all affected loci showed identifiable germline allele(s) in MSI-high tumors. A wild-type allelic profile was seen in 7 of 10 MSI-stable tumors. In the remaining 3 cases, isolated novel alleles were present at a unique single locus in addition to germline alleles. Loss of heterozygosity was observed frequently in both MSI-stable (6/11 cases) and MSI-unstable tumors (8/10 cases). In conclusion, MSI may significantly alter the wild-type allelic polymorphism, leading to potential interpretation errors of STR genotyping. Careful examination of the STR allelic pattern, high index of suspicion, and follow-up MSI testing are crucial to avoid erroneous conclusions and subsequent clinical and legal consequences. Copyright © 2014 Elsevier Inc. All rights reserved.

Menstrual cycle phase and single tablet antiretroviral medication adherence in women with HIV.

PubMed

Hessol, Nancy A; Holman, Susan; Minkoff, Howard; Cohen, Mardge H; Golub, Elizabeth T; Kassaye, Seble; Karim, Roksana; Sosanya, Oluwakemi; Shaheen, Christopher; Merhi, Zaher

2016-01-01

Suboptimal adherence to antiretroviral (ARV) therapy among HIV-infected individuals is associated with increased risk of progression to AIDS and the development of HIV resistance to ARV medications. To examine whether the luteal phase of the menstrual cycle is independently associated with suboptimal adherence to single tablet regimen (STR) ARV medication, data were analyzed from a multicenter cohort study of HIV-infected women who reported regular menstrual cycles and were taking an STR. In a cross-sectional analysis, suboptimal adherence to an STR among women in their follicular phase was compared with suboptimal adherence among women in their luteal phase. In two-way crossover analyses, whereby the same woman was assessed for STR medication adherence in both her follicular and luteal phases, the estimated exact conditional odds of non-adherence to an STR was measured. In adjusted logistic regression analysis of the cross-sectional data (N=327), women with ≤12 years of education were more than three times more likely to have suboptimal adherence (OR=3.6, p=.04) compared to those with >12 years of education. Additionally, women with Center for Epidemiological Studies Depression Scale (CES-D) scores ≥23 were 2.5-times more likely to have suboptimal adherence (OR=2.6, p=.02) compared to those with CES-D scores <23. In conditional logistic regression analyses of the crossover data (N=184), having childcare responsibilities was associated with greater odds of ≤95% adherence. Menstrual cycle phase was not associated with STR adherence in either the cross-sectional or crossover analyses. The lack of association between phase of the menstrual cycle and adherence to an STR in HIV-infected women means attention can be given to other more important risk factors for suboptimal adherence, such as depression, level of education, and childcare responsibilities.

Adult Craniopharyngioma: Case Series, Systematic Review, and Meta-Analysis.

PubMed

Dandurand, Charlotte; Sepehry, Amir Ali; Asadi Lari, Mohammad Hossein; Akagami, Ryojo; Gooderham, Peter

2017-12-18

The optimal therapeutic approach for adult craniopharyngioma remains controversial. Some advocate for gross total resection (GTR), while others advocate for subtotal resection followed by adjuvant radiotherapy (STR + XRT). To conduct a systematic review and meta-analysis assessing the rate of recurrence in the follow-up of 3 yr in adult craniopharyngioma stratified by extent of resection and presence of adjuvant radiotherapy. MEDLINE (1946-July 1, 2016) and EMBASE (1980-June 30, 2016) were systematically reviewed. From1975 to 2013, 33 patients were treated with initial surgical resection for adult onset craniopharyngioma at our center and were reviewed for inclusion in this study. Data from 22 patients were available for inclusion as a case series in the systematic review. Eligible studies (n = 21) were identified from the literature in addition to a case series of our institutional experience. Three groups were available for analysis: GTR, STR + XRT, and STR. The rates of recurrence were 17%, 27%, and 45%, respectively. The risk of developing recurrence was significant for GTR vs STR (odds ratio [OR]: 0.24, 95% confidence interval [CI]: 0.15-0.38) and STR + XRT vs STR (OR: 0.20, 95% CI: 0.10-0.41). Risk of recurrence after GTR vs STR + XRT did not reach significance (OR: 0.63, 95% CI: 0.33-1.24, P = .18). This is the first and largest systematic review focusing on the rate of recurrence in adult craniopharyngioma. Although the rates of recurrence are favoring GTR, difference in risk of recurrence did not reach significance. This study provides guidance to clinicians and directions for future research with the need to stratify outcomes per treatment modalities. Copyright © 2017 by the Congress of Neurological Surgeons

A novel, integrated forensic microdevice on a rotation-driven platform: Buccal swab to STR product in less than 2 h.

PubMed

Cox, Jordan O; DeCarmen, Teresa Sikes; Ouyang, Yiwen; Strachan, Briony; Sloane, Hillary; Connon, Cathey; Gibson, Kemper; Jackson, Kimberly; Landers, James P; Cruz, Tracey Dawson

2016-12-01

This work describes the development of a novel microdevice for forensic DNA processing of reference swabs. This microdevice incorporates an enzyme-based assay for DNA preparation, which allows for faster processing times and reduced sample handling. Infrared-mediated PCR (IR-PCR) is used for STR amplification using a custom reaction mixture, allowing for amplification of STR loci in 45 min while circumventing the limitations of traditional block thermocyclers. Uniquely positioned valves coupled with a simple rotational platform are used to exert fluidic control, eliminating the need for bulky external equipment. All microdevices were fabricated using laser ablation and thermal bonding of PMMA layers. Using this microdevice, the enzyme-mediated DNA liberation module produced DNA yields similar to or higher than those produced using the traditional (tube-based) protocol. Initial microdevice IR-PCR experiments to test the amplification module and reaction (using Phusion Flash/SpeedSTAR) generated near-full profiles that suffered from interlocus peak imbalance and poor adenylation (significant -A). However, subsequent attempts using KAPA 2G and Pfu Ultra polymerases generated full STR profiles with improved interlocus balance and the expected adenylated product. A fully integrated run designed to test microfluidic control successfully generated CE-ready STR amplicons in less than 2 h (<1 h of hands-on time). Using this approach, high-quality STR profiles were developed that were consistent with those produced using conventional DNA purification and STR amplification methods. This method is a smaller, more elegant solution than current microdevice methods and offers a cheaper, hands-free, closed-system alternative to traditional forensic methods. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Susceptibility to antimicrobials of mastitis-causing Staphylococcus aureus, Streptococcus uberis and Str. dysgalactiae from New Zealand and the USA as assessed by the disk diffusion test.

PubMed

Petrovski, K R; Grinberg, A; Williamson, N B; Abdalla, M E; Lopez-Villalobos, N; Parkinson, T J; Tucker, I G; Rapnicki, P

2015-07-01

To compare the antimicrobial susceptibility patterns of three common mastitis pathogens (Staphylococcus aureus, Streptococcus uberis and Str. dysgalactiae) isolated from milk samples from New Zealand and the USA. A total of 182 S. aureus, 126 Str. uberis and 89 Str. dysgalactiae isolates from New Zealand (107, 106 and 41, respectively) and the USA (75, 20 and 48, respectively) were assessed using the disk diffusion test. Susceptibility varied among the bacterial species. All isolates were susceptible to the amoxicillin-clavulanic acid combination. Resistance to lincomycin was most frequent (susceptibility of 8.6%) across all species. Non-susceptible (i.e. resistant or intermediate) isolates of S. aureus were identified for the three non-isoxazolyl penicillins (amoxicillin, ampicillin and penicillin: 20.6% and 36.0%) and lincomycin (99.9% and 94.6%) for NZ and the USA, respectively. Resistance to erythromycin (5.3%) and tetracyclines (6.7%) was detected only in isolates from the USA. There were differences in susceptibility between Str. uberis and Str. dysgalactiae; all streptococcal isolates demonstrated resistance to aminoglycosides (neomycin 52.4% and streptomycin 27.9%) and enrofloxacin (28%). Resistance of Str. dysgalactiae to tetracycline was almost 100.0% and to oxytetracycline 89.9%. Most of the isolates tested were susceptible to most of the antimicrobials commonly used for treatment of bovine mastitis, with the exception of the lincosamides. Susceptibility to a selected class-representative antimicrobial and at the genus level should be interpreted with caution. Differences between NZ and the USA confirm the value of national surveys to determine the susceptibility patterns of mastitis pathogens. © 2015 Australian Veterinary Association.

Chronic stress disrupts fear extinction and enhances amygdala and hippocampal Fos expression in an animal model of post-traumatic stress disorder.

PubMed

Hoffman, Ann N; Lorson, Nickolaus G; Sanabria, Federico; Foster Olive, M; Conrad, Cheryl D

2014-07-01

Chronic stress may impose a vulnerability to develop maladaptive fear-related behaviors after a traumatic event. Whereas previous work found that chronic stress impairs the acquisition and recall of extinguished fear, it is unknown how chronic stress impacts nonassociative fear, such as in the absence of the conditioned stimulus (CS) or in a novel context. Male rats were subjected to chronic stress (STR; wire mesh restraint 6 h/d/21d) or undisturbed (CON), then tested on fear acquisition (3 tone-footshock pairings), and two extinction sessions (15 tones/session) within the same context. Then each group was tested (6 tones) in the same context (SAME) or a novel context (NOVEL), and brains were processed for functional activation using Fos immunohistochemistry. Compared to CON, STR showed facilitated fear acquisition, resistance to CS extinction on the first extinction day, and robust recovery of fear responses on the second extinction day. STR also showed robust freezing to the context alone during the first extinction day compared to CON. When tested in the same or a novel context, STR exhibited higher freezing to context than did CON, suggesting that STR-induced fear was independent of context. In support of this, STR showed increased Fos-like expression in the basolateral amygdala and CA1 region of the hippocampus in both the SAME and NOVEL contexts. Increased Fos-like expression was also observed in the central amygdala in STR-NOVEL vs. CON-NOVEL. These data demonstrate that chronic stress enhances fear learning and impairs extinction, and affects nonassociative processes as demonstrated by enhanced fear in a novel context. Copyright © 2014 Elsevier Inc. All rights reserved.

Effect of Geometry on Electrokinetic Characterization of Solid Surfaces.

PubMed

Kumar, Abhijeet; Kleinen, Jochen; Venzmer, Joachim; Gambaryan-Roisman, Tatiana

2017-08-01

An analytical approach is presented to describe pressure-driven streaming current (I str ) and streaming potential (U str ) generation in geometrically complex samples, for which the classical Helmholtz-Smoluchowski (H-S) equation is known to be inaccurate. The new approach is valid under the same prerequisite conditions that are used for the development of the H-S equation, that is, the electrical double layers (EDLs) are sufficiently thin and surface conductivity and electroviscous effects are negligible. The analytical methodology is developed using linear velocity profiles to describe liquid flow inside of EDLs and using simplifying approximations to describe macroscopic flow. At first, a general expression is obtained to describe the I str generated in different cross sections of an arbitrarily shaped sample. Thereafter, assuming that the generated U str varies only along the pressure-gradient direction, an expression describing the variation of generated U str along the sample length is obtained. These expressions describing I str and U str generation constitute the theoretical foundation of this work, which is first applied to a set of three nonuniform cross-sectional capillaries and thereafter to a square array of cylindrical fibers (model porous media) for both parallel and transverse fiber orientation cases. Although analytical solutions cannot be obtained for real porous substrates because of their random structure, the new theory provides useful insights into the effect of important factors such as fiber orientation, sample porosity, and sample dimensions. The solutions obtained for the model porous media are used to device strategies for more accurate zeta potential determination of porous fiber plugs. The new approach could be thus useful in resolving the long-standing problem of sample geometry dependence of zeta potential measurements.

Genetic Variation of 25 Y-Chromosomal and 15 Autosomal STR Loci in the Han Chinese Population of Liaoning Province, Northeast China

PubMed Central

Yao, Jun; Wang, Bao-jie

2016-01-01

In the present study, we investigated the genetic characteristics of 25 Y-chromosomal and 15 autosomal short tandem repeat (STR) loci in 305 unrelated Han Chinese male individuals from Liaoning Province using AmpFISTR® Yfiler® Plus and IdentifilerTM PCR amplification kits. Population comparison was performed between Liaoning Han population and different ethnic groups to better understand the genetic background of the Liaoning Han population. For Y-STR loci, the overall haplotype diversity was 0.9997 and the discrimination capacity was 0.9607. Gene diversity values ranged from 0.4525 (DYS391) to 0.9617 (DYS385). Rst and two multi-dimensional scaling plots showed that minor differences were observed when the Liaoning Han population was compared to the Jilin Han Chinese, Beijing Han Chinese, Liaoning Manchu, Liaoning Mongolian, Liaoning Xibe, Shandong Han Chinese, Jiangsu Han Chinese, Anhui Han Chinese, Guizhou Han Chinese and Liaoning Hui populations; by contrast, major differences were observed when the Shanxi Han Chinese, Yunnan Bai, Jiangxi Han Chinese, Guangdong Han Chinese, Liaoning Korean, Hunan Tujia, Guangxi Zhuang, Gansu Tibetan, Xishuangbanna Dai, South Korean, Japanese and Hunan Miao populations. For autosomal STR loci, DP ranged from 0.9621 (D2S1338) to 0.8177 (TPOX), with PE distributing from 0.7521 (D18S51) to 0.2988 (TH01). A population comparison was performed and no statistically significant differences were detected at any STR loci between Liaoning Han, China Dong, and Shaanxi Han populations. The results showed that the 25 Y-STR and 15 autosomal STR loci in the Liaoning Han population were valuable for forensic applications and human genetics, and Liaoning Han was an independent endogenous ethnicity with a unique subpopulation structure. PMID:27483472

Antioxidant and vascular protective activities of Cratoxylum formosum, Syzygium gratum and Limnophila aromatica.

PubMed

Kukongviriyapan, Upa; Luangaram, Saowanee; Leekhaosoong, Krissadarut; Kukongviriyapan, Veerapol; Preeprame, Srisomporn

2007-04-01

Phytochemicals contained in dietary plants provide a variety of health benefits and may reduce the risk of cardiovascular diseases. The aqueous extracts from three popular Thai dietary and herbal plants, Cratoxylum formosum, Syzygium gratum, and Limnophila aromatica, were investigated for the antioxidant and vascular protective activities in the in vitro and in vivo models. The free radical scavenging and antioxidant activities of plant extracts were evaluated in vitro by the 1,1-diphenyl-2-picrylhydrazyl assay, the ferric reducing antioxidant power assay, the intracellular antioxidant activity in rat peritoneal macrophages by dihydrofluorescein assay, and the inhibition of nitric oxide (NO) production in RAW 264.7 macrophages. In an animal model of oxidative stress and vascular dysfunction, male Sprague-Dawley rats were orally administered with aqueous plant extracts (1 g/kg/d) or N-acetylcysteine (NAC; 300 mg/kg/d) as a control for 6 d. On day four, all animals except the normal control group, were administered with phenylhydrazine (PHZ) intraperitoneally. It was demonstrated that the plant extracts possessed high free radical scavenging and antioxidant activities. PHZ induced severe hemolysis and hemodynamic disturbances and treatment with the extracts and NAC significantly improved the hemodynamic status. Vascular responsiveness to bradykinin, acetylcholine, and phenylephrine in PHZ-control rats was markedly impaired, and the plant extracts or NAC largely restored the vascular responses. Moreover, the plant extracts prevented loss of blood reduced glutathione and suppressed formation of plasma malondialdehyde, plasma NO metabolites and blood superoxide anion. It was concluded that the plant extracts possess antioxidants and have potential roles in protection of vascular dysfunction.

Synergistic anticancer effects of curcumin and resveratrol in Hepa1-6 hepatocellular carcinoma cells.

PubMed

Du, Qin; Hu, Bing; An, Hong-Mei; Shen, Ke-Ping; Xu, Ling; Deng, Shan; Wei, Meng-Meng

2013-05-01

Hepatocellular carcinoma remains one of the most prevalent malignancies worldwide. Curcuma aromatica and Polygonum cuspidatum are one of the commonly used paired-herbs for liver cancer treatment. Curcumin and resveratrol are the major anticancer constituents of Curcuma aromatica and Polygonum cuspidatum, respectively. Curcumin and resveratrol have been found to exhibit a synergistic anticancer effect in colon cancer. However, the combined effect of curcumin and resveratrol against hepatocellular carcinoma remains unknown. In the present study, we evaluated the combined effects of curcumin and resveratrol in hepatocellular carcinoma Hepa1-6 cells. The results showed that curcumin and resveratrol significantly inhibited the proliferation of Hepa1-6 cells in a dose- and time-dependent manner. The combination treatment of curcumin and resveratrol elicited a synergistic antiproliferative effect in Hepa1-6 cells. The apoptosis of Hepa1-6 cells induced by the combination treatment with curcumin and resveratrol was accompanied by caspase-3, -8 and -9 activation, which was completely abrogated by a pan caspase inhibitor, Z-VAD-FMK. Combination of curcumin and resveratrol upregulated intracellular reactive oxygen species (ROS) levels in Hepa1-6 cells. The ROS scavenger, NAC, partially attenuated the apoptosis and caspase activation induced by the combination treatment of curcumin and resveratrol. In addition, the combination of curcumin and resveratrol downregulated XIAP and survivin expression. These data suggest that the combination treatment of curcumin and resveratrol is a promising novel anticancer strategy for liver cancer. The present study also provides new insights into the effective mechanism of paired-herbs in traditional Chinese medicine.

Population data of 21 autosomal STR loci in the Hausa, Igbo and Yoruba people of Nigeria.

PubMed

Okolie, Victoria O; Cisana, Selena; Schanfield, Moses S; Adekoya, Khalid O; Oyedeji, Olufemi A; Podini, Daniele

2018-05-01

The three major ethnic groups of Nigerian population namely the Hausa, Igbo and Yoruba make up 29, 21 and 18% of the total population, respectively. To provide genetic information necessary for forensic analysis, this study was carried out to determine STR allele frequencies in 102 Hausa, 128 Igbo and 134 Yoruba individuals in Nigeria using 21 STR loci including the 20 CODIS (Combined DNA Index System) loci plus SE33.

[Genetic polymorphisms of 21 non-CODIS STR loci].

PubMed

Shao, Wei-bo; Zhang, Su-hua; Li, Li

2011-02-01

To investigate genetic polymorphisms of 21 non-CODIS STR loci in Han population from the east of China and to explore their forensic application value. Twenty-one non-CODIS STR loci, were amplified with AGCU 21+1 STR kit and DNA samples were obtained from 225 unrelated individuals of the Han population from the east of China. The PCR products were analyzed with 3130 Genetic Analyzer and genotyped with GeneMapper ID v3.2 software. The genetic data were statistically analyzed with PowerStats v12.xls and Cervus 2.0 software. The distributions of 21 non-CODIS STR loci satisfied the Hardy-Weinberg equilibration. The heterozygosity (H) distributions were 0.596-0.804, the discrimination power (DP) were 0.764-0.948, the probability of exclusion of duo-testing (PEduo) were 0.176-0.492, the probability of exclusion of trios-testing (PEtrio) were 0.334-0.663, and the polymorphic information content (PIC) were 0.522-0.807. The cumulative probability of exclusion (CPE) of duo-testing was 0.999707, the CPE of trios-testing was 0.9999994, and the cumulated discrimination power (CDP) was 0.99999999999999999994. Twenty-one non-CODIS STR loci are highly polymorphic. They can be effectively used in personal identification and paternity testing in trios cases. They can also be used as supplement in the difficult cases of diad paternity testing.

Short tandem repeat analysis in Japanese population.

PubMed

Hashiyada, M

2000-01-01

Short tandem repeats (STRs), known as microsatellites, are one of the most informative genetic markers for characterizing biological materials. Because of the relatively small size of STR alleles (generally 100-350 nucleotides), amplification by polymerase chain reaction (PCR) is relatively easy, affording a high sensitivity of detection. In addition, STR loci can be amplified simultaneously in a multiplex PCR. Thus, substantial information can be obtained in a single analysis with the benefits of using less template DNA, reducing labor, and reducing the contamination. We investigated 14 STR loci in a Japanese population living in Sendai by three multiplex PCR kits, GenePrint PowerPlex 1.1 and 2.2. Fluorescent STR System (Promega, Madison, WI, USA) and AmpF/STR Profiler (Perkin-Elmer, Norwalk, CT, USA). Genomic DNA was extracted using sodium dodecyl sulfate (SDS) proteinase K or Chelex 100 treatment followed by the phenol/chloroform extraction. PCR was performed according to the manufacturer's protocols. Electrophoresis was carried out on an ABI 377 sequencer and the alleles were determined by GeneScan 2.0.2 software (Perkin-Elmer). In 14 STRs loci, statistical parameters indicated a relatively high rate, and no significant deviation from Hardy-Weinberg equilibrium was detected. We apply this STR system to paternity testing and forensic casework, e.g., personal identification in rape cases. This system is an effective tool in the forensic sciences to obtain information on individual identification.

A cross sectional observational study of research activity of allied health teams: is there a link with self-reported success, motivators and barriers to undertaking research?

PubMed

Wenke, Rachel J; Mickan, Sharon; Bisset, Leanne

2017-02-06

Team-based approaches to research capacity building (RCB) may be an efficient means to promote allied health research participation and activity. In order to tailor such interventions, a clearer understanding of current patterns of research participation within allied health teams is needed. Different self-report measures exist which evaluate a team's research capacity and participation, as well as associated barriers and motivators. However, it remains unclear how such measures are associated with a team's actual research activity (e.g., journal publications, funding received). In response, this observational study aimed to identify the research activity, self-reported success, and motivations and barriers to undertaking research of eight allied health professional (AHP) teams and to explore whether any relationships exist between the self-reported measures and actual research activity within each team. A total of 95 AHPs from eight teams completed the research capacity and culture survey to evaluate team success, barriers and motivators to undertaking research, and an audit of research activity from January 2013 to August 2014 was undertaken within each team. Kendell's correlation coefficients were used to determine the association between research activity (i.e., number of journal publications, ethically approved projects and funding received) and the self-reported measures. Seven out of eight teams rated their teams as having average success in research and demonstrated some form of research activity including at least two ethically approved projects. Research activity varied between teams, with funding received ranging from $0 to over $100,000, and half the teams not producing any journal publications. Team motivators demonstrated a stronger association with research activity compared to barriers, with the motivator "enhancing team credibility" being significantly associated with funding received. No significant association between self-reported research success and actual research activity was identified. Preliminary findings suggest that self-report measures of research success may not always correspond to actual research activity, and a combination of both these measures may be useful when planning RCB interventions. Variation in activity between teams and organisations should also be considered when tailoring RCB interventions. Reinforcing intrinsically motivating rewards of research may also be useful in promoting research participation for some teams.

[DNA quantification of blood samples pre-treated with pyramidon].

PubMed

Zhu, Chuan-Hong; Zheng, Dao-Li; Ni, Rao-Zhi; Wang, Hai-Sheng; Ning, Ping; Fang, Hui; Liu, Yan

2014-06-01

To study DNA quantification and STR typing of samples pre-treated with pyramidon. The blood samples of ten unrelated individuals were anticoagulated in EDTA. The blood stains were made on the filter paper. The experimental groups were divided into six groups in accordance with the storage time, 30 min, 1 h, 3 h, 6 h, 12 h and 24h after pre-treated with pyramidon. DNA was extracted by three methods: magnetic bead-based extraction, QIAcube DNA purification method and Chelex-100 method. The quantification of DNA was made by fluorescent quantitative PCR. STR typing was detected by PCR-STR fluorescent technology. In the same DNA extraction method, the sample DNA decreased gradually with times after pre-treatment with pyramidon. In the same storage time, the DNA quantification in different extraction methods had significant differences. Sixteen loci DNA typing were detected in 90.56% of samples. Pyramidon pre-treatment could cause DNA degradation, but effective STR typing can be achieved within 24 h. The magnetic bead-based extraction is the best method for STR profiling and DNA extraction.

StrBioLib: a Java library for development of custom computationalstructural biology applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandonia, John-Marc

2007-05-14

Summary: StrBioLib is a library of Java classes useful fordeveloping software for computational structural biology research.StrBioLib contains classes to represent and manipulate proteinstructures, biopolymer sequences, sets of biopolymer sequences, andalignments between biopolymers based on either sequence or structure.Interfaces are provided to interact with commonly used bioinformaticsapplications, including (PSI)-BLAST, MODELLER, MUSCLE, and Primer3, andtools are provided to read and write many file formats used to representbioinformatic data. The library includes a general-purpose neural networkobject with multiple training algorithms, the Hooke and Jeeves nonlinearoptimization algorithm, and tools for efficient C-style string parsingand formatting. StrBioLib is the basis for the Pred2ary secondarystructure predictionmore » program, is used to build the ASTRAL compendium forsequence and structure analysis, and has been extensively tested throughuse in many smaller projects. Examples and documentation are available atthe site below.Availability: StrBioLib may be obtained under the terms ofthe GNU LGPL license from http://strbio.sourceforge.net/Contact:JMChandonia@lbl.gov« less

StrBioLib: a Java library for development of custom computational structural biology applications.

PubMed

Chandonia, John-Marc

2007-08-01

StrBioLib is a library of Java classes useful for developing software for computational structural biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence or structure. Interfaces are provided to interact with commonly used bioinformatics applications, including (psi)-blast, modeller, muscle and Primer3, and tools are provided to read and write many file formats used to represent bioinformatic data. The library includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves non-linear optimization algorithm, and tools for efficient C-style string parsing and formatting. StrBioLib is the basis for the Pred2ary secondary structure prediction program, is used to build the astral compendium for sequence and structure analysis, and has been extensively tested through use in many smaller projects. Examples and documentation are available at the site below. StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/

Forensic molecular genetic diversity analysis of Chinese Hui ethnic group based on a novel STR panel.

PubMed

Fang, Yating; Guo, Yuxin; Xie, Tong; Jin, Xiaoye; Lan, Qiong; Zhou, Yongsong; Zhu, Bofeng

2018-03-26

In present study, the genetic polymorphisms of 22 autosomal short tandem repeat (STR) loci were analyzed in 496 unrelated Chinese Xinjiang Hui individuals. These autosomal STR loci were multiplex amplified and genotyped based on a novel STR panel. There were 246 observed alleles with the allele frequencies ranging from 0.0010 to 0.3609. All polymorphic information content values were higher than 0.7. The combined power of discrimination and the combined probability of exclusion were 0.999999999999999999999999999426766 and 0.999999999860491, respectively. Based on analysis of molecular variance method, genetic differentiation analysis between the Xinjiang Hui and other reported groups were conducted at these 22 loci. The results indicated that there were no significant differences in statistics between Hui group and Northern Han group (including Han groups from Hebei, Henan, Shaanxi provinces), and significant deviations with Southern Han group (including those from Guangdong, Guangxi provinces) at 7 loci, and Uygur group at 10 loci. To sum up, these 22 autosomal STR loci were high genetic polymorphic in Xinjiang Hui group.

Dual Probe Digital Sampling (DPDS) Technique for Rotor Flows--Review of the Development and an Assessment Based on Early Results.

DTIC Science & Technology

1982-04-01

in stark fluktuierender Str ~ mung , insbesondere in Turbo- maschinen." DLR-FB 74-34, 1974. 35. Weyer, H. B., and Schodl, R., "Unsteady Flow Measurements...Untersuchungen Uber den Einfluss der KonizitAt auf die Str ~ mung durch Turbinengitter im transsonischen Geschwindigkeitsbereich (2. Arbeits- fortschrittsbericht...Konizitit auf die Str ~5mung durch Turbinengitter im transsonischen Geschwindigkeitsbereich," DFVLR-Report lB 222 82 A 01 (1982). 91. -. ~~ ~ ;l, ;;J10

Example Level 1 Ada/SQL (Structured Query Language) System Software

DTIC Science & Technology

1987-09-01

PUTLINE ("EMPNAME JOB SALARY COMMISSION"); loop FETCH ( CURSOR ); INTO ( VEMP NAME , STR LAST ); T LEN INTEGER (STR LAST - V EMP NAME’FIRST + 1); for I in 1...begin PUT_LINE ("EMPNAME JOB SALARY DEPT"); loop FETCH (CURSOR); INTO ( VEMP NAME , STRLAST ); T_LEN := INTEGER (STRLAST - V_EMPNAME’FIRST + 1); for I in...NUMBERS OPEN ( CURSOR ); begin PUT_LINE ("EMP_NAME SALARY JOB"); loop FETCH ( CURSOR ); INTO ( VEMP NAME , STRLAST ); T_LEN := INTEGER (STR_LAST

A new species of the genus Bryodemella (s. str.) Yin, 1982 from China (Orthoptera: Acridoidea: Oedipodidae).

PubMed

Zhang, Yu-Long; Zhi, Yong-Chao; Zhang, Dao-Chuan

2018-04-23

A new species (i.e. Bryodemella (s. str.) rufifemura sp. nov. from China is described in this paper. It is similar to Bryodemella (s. str.) diamesum (Bei-Bienko, 1930), but differs from the latter by red inner side of hind femur, median keel of pronotum indistinct in metazoan, and vertical diameter of eye shorter than subocular groove in female.  The type specimens are deposited in the Museum of Hebei University (MHU), China.

[Developing forensic reference database by 18 autosomal STR for DNA identification in Republic of Belarus].

PubMed

Tsybovskii, I S; Veremeichik, V M; Kotova, S A; Kritskaya, S V; Evmenenko, S A; Udina, I G

2017-02-01

For the Republic of Belarus, development of a forensic reference database on the basis of 18 autosomal microsatellites (STR) using a population dataset (N = 1040), “familial” genotypic dataset (N = 2550) obtained from expertise performance of paternity testing, and a dataset of genotypes from a criminal registration database (N = 8756) is described. Population samples studied consist of 80% ethnic Belarusians and 20% individuals of other nationality or of mixed origin (by questionnaire data). Genotypes of 12346 inhabitants of the Republic of Belarus from 118 regional samples studied by 18 autosomal microsatellites are included in the sample: 16 tetranucleotide STR (D2S1338, TPOX, D3S1358, CSF1PO, D5S818, D8S1179, D7S820, THO1, vWA, D13S317, D16S539, D18S51, D19S433, D21S11, F13B, and FGA) and two pentanucleotide STR (Penta D and Penta E). The samples studied are in Hardy–Weinberg equilibrium according to distribution of genotypes by 18 STR. Significant differences were not detected between discrete populations or between samples from various historical ethnographic regions of the Republic of Belarus (Western and Eastern Polesie, Podneprovye, Ponemanye, Poozerye, and Center), which indicates the absence of prominent genetic differentiation. Statistically significant differences between the studied genotypic datasets also were not detected, which made it possible to combine the datasets and consider the total sample as a unified forensic reference database for 18 “criminalistic” STR loci. Differences between reference database of the Republic of Belarus and Russians and Ukrainians by the distribution of the range of autosomal STR also were not detected, corresponding to a close genetic relationship of the three Eastern Slavic nations mediated by common origin and intense mutual migrations. Significant differences by separate STR loci between the reference database of Republic of Belarus and populations of Southern and Western Slavs were observed. The necessity of using original reference database for support of forensic expertise practice in the Republic of Belarus was demonstrated.

Thresholds of Disturbance: Land Management Effects on Vegetation and Nitrogen Dynamics

DTIC Science & Technology

2005-03-31

Legume 3 18 0.0435 Rhus aromatica Shrub 2 35 0.0002 Aesculus pavia Tree 0 10 0.0198 Celtis sp. Tree 1 30 0.0002 Crataegus sp. Tree 13 62 0.0001...Shrub 37 63 0.0001 Aesculus pavia Tree 0 12 0.0043 Cercis canadensis Tree 0 13 0.0021 Crataegus sp. Tree 22 49 0.0222 Fraxinus americana Tree 0 11... Aesculus pavia Tree 0 15 0.0126 Ilex opaca Tree 0 27 0.0003 Liquidambar styraciflua Tree 18 75 0.0001 Quercus falcata Tree 9 79 0.0001 Quercus

Massively parallel sequencing of 32 forensic markers using the Precision ID GlobalFiler™ NGS STR Panel and the Ion PGM™ System.

PubMed

Wang, Zheng; Zhou, Di; Wang, Hui; Jia, Zhenjun; Liu, Jing; Qian, Xiaoqin; Li, Chengtao; Hou, Yiping

2017-11-01

Massively parallel sequencing (MPS) technologies have proved capable of sequencing the majority of the key forensic STR markers. By MPS, not only the repeat-length size but also sequence variations could be detected. Recently, Thermo Fisher Scientific has designed an advanced MPS 32-plex panel, named the Precision ID GlobalFiler™ NGS STR Panel, where the primer set has been designed specifically for the purpose of MPS technologies and the data analysis are supported by a new version HID STR Genotyper Plugin (V4.0). In this study, a series of experiments that evaluated concordance, reliability, sensitivity of detection, mixture analysis, and the ability to analyze case-type and challenged samples were conducted. In addition, 106 unrelated Han individuals were sequenced to perform genetic analyses of allelic diversity. As expected, MPS detected broader allele variations and gained higher power of discrimination and exclusion rate. MPS results were found to be concordant with current capillary electrophoresis methods, and single source complete profiles could be obtained stably using as little as 100pg of input DNA. Moreover, this MPS panel could be adapted to case-type samples and partial STR genotypes of the minor contributor could be detected up to 19:1 mixture. Aforementioned results indicate that the Precision ID GlobalFiler™ NGS STR Panel is reliable, robust and reproducible and have the potential to be used as a tool for human forensics. Copyright © 2017 Elsevier B.V. All rights reserved.

Polymorphism analysis and evaluation of nine non-CODIS STR loci in the Han population of Southern China.

PubMed

Tong, Da Yue; Wu, Xin Yao; Sun, Hong Yu; Zhao, Hu; Lu, Hui Ling

2010-11-01

Knowledge of allele and genotype frequencies is an essential prerequisite to the use of any human polymorphism in forensic work. To study the genetic polymorphism and evaluate the application value of nine STR loci. Genotyping of nine STR loci, including D11S2368, D12S391, D13S325, D18S1364, D22-GATA198B05, D6S1043, D2S1772, D7S3048 and D8S1132, of 1050 unrelated individuals was performed with the STR_Typer_10_v1 kit and Genetic Analyzer 3100 and analyzed with PowerState V12.xls and Arlequin ver 3.11 analyzing software. Allele frequency distribution was statistically analyzed and Hardy-Weinberg equilibrium determined. Several common parameters used in forensic sciences were found: the heterozygosity (H) ranged from 0.827 to 0.892; the matching probability (MP) ranged from 0.029 to 0.074; the power of discrimination (PD) ranged from 0.926 to 0.971; the power of exclusion (PE) ranged from 0.649 to 0.779; the polymorphic information content (PIC) ranged from 0.77 to 0.86; and the typical paternity index (TPI) ranged from 2.88 to 4.62. The results indicate that nine STR loci are high polymorphic among the Han population in Southern China. This set of polymorphic STR loci is a useful tool in forensic paternity testing and anthropological study.

Disambiguating ventral striatum fMRI-related bold signal during reward prediction in schizophrenia

PubMed Central

Morris, R W; Vercammen, A; Lenroot, R; Moore, L; Langton, J M; Short, B; Kulkarni, J; Curtis, J; O'Donnell, M; Weickert, C S; Weickert, T W

2012-01-01

Reward detection, surprise detection and prediction-error signaling have all been proposed as roles for the ventral striatum (vStr). Previous neuroimaging studies of striatal function in schizophrenia have found attenuated neural responses to reward-related prediction errors; however, as prediction errors represent a discrepancy in mesolimbic neural activity between expected and actual events, it is critical to examine responses to both expected and unexpected rewards (URs) in conjunction with expected and UR omissions in order to clarify the nature of ventral striatal dysfunction in schizophrenia. In the present study, healthy adults and people with schizophrenia were tested with a reward-related prediction-error task during functional magnetic resonance imaging to determine whether schizophrenia is associated with altered neural responses in the vStr to rewards, surprise prediction errors or all three factors. In healthy adults, we found neural responses in the vStr were correlated more specifically with prediction errors than to surprising events or reward stimuli alone. People with schizophrenia did not display the normal differential activation between expected and URs, which was partially due to exaggerated ventral striatal responses to expected rewards (right vStr) but also included blunted responses to unexpected outcomes (left vStr). This finding shows that neural responses, which typically are elicited by surprise, can also occur to well-predicted events in schizophrenia and identifies aberrant activity in the vStr as a key node of dysfunction in the neural circuitry used to differentiate expected and unexpected feedback in schizophrenia. PMID:21709684

Allele frequencies for 13 STRs loci in a Western Anatolia population and their forensic evaluation.

PubMed

Baransel Isir, Aysun; Ozkorkmaz, Abdulmuttalip; Pehlivan, Sacide

2015-01-01

Numerous studies demonstrated that STRs have become powerful tools in forensic case work. To profile DNA samples from 104 Turkish males for 13 autosomal, STR markers intended for human identification purposes and to estimate the allele frequency distribution in forensic cases in a Turkish population. Thirteen autosomal STR loci, namely D3S1358, D2S1338, D16S539, D8S1179, D21S11, D18S51, TH01, D13S317, D7S820, CSF1PO, TPOX, D5S818 and FGA, were analysed in a sample of 104 healthy and unrelated Turkish individuals who have been living in the city of İzmir. All loci were amplified by using AmpFlSTR Identifier Kit. Genetic analysis was carried out on an ABI PRISM 310 Genetic Analyser. For each locus, 6-15 alleles were found with frequencies ranging from 0.005-0.514 and heterozygosities ranging from 0.686-0.868. The PIC value was highly significant (0.999). The 13 STR loci in the AmpFlSTR Identifier Kit are suitable for forensic identification and paternity tests due to high heterozygosity. The observed PD value is sufficiently high for human identification purposes. In conclusion, the 13 STR loci seem to be useful markers for personal identification and forensic case work in the Turkish population. The results also demonstrate the importance of region-specific studies.

Evaluation of a 13-loci STR multiplex system for Cannabis sativa genetic identification.

PubMed

Houston, Rachel; Birck, Matthew; Hughes-Stamm, Sheree; Gangitano, David

2016-05-01

Marijuana (Cannabis sativa) is the most commonly used illicit substance in the USA. The development of a validated method using Cannabis short tandem repeats (STRs) could aid in the individualization of samples as well as serve as an intelligence tool to link multiple cases. For this purpose, a modified 13-loci STR multiplex method was optimized and evaluated according to ISFG and SWGDAM guidelines. A real-time PCR quantification method for C. sativa was developed and validated, and a sequenced allelic ladder was also designed to accurately genotype 199 C. sativa samples from 11 U.S. Customs and Border Protection seizures. Distinguishable DNA profiles were generated from 127 samples that yielded full STR profiles. Four duplicate genotypes within seizures were found. The combined power of discrimination of this multilocus system is 1 in 70 million. The sensitivity of the multiplex STR system is 0.25 ng of template DNA. None of the 13 STR markers cross-reacted with any of the studied species, except for Humulus lupulus (hops) which generated unspecific peaks. Phylogenetic analysis and case-to-case pairwise comparison of 11 cases using F st as genetic distance revealed the genetic association of four groups of cases. Moreover, due to their genetic similarity, a subset of samples (N = 97) was found to form a homogeneous population in Hardy-Weinberg and linkage equilibrium. The results of this research demonstrate the applicability of this 13-loci STR system in associating Cannabis cases for intelligence purposes.

[Forensic Application of HuaxiaTM Platinum Kit].

PubMed

Wang, Y L; Sheng, X; Li, M; Chen, Y L; Lin, Y; Chen, L Q

2017-04-01

To investigate the genetic polymorphism of 23 autosomal STR loci of Huaxia™ Platinum kit in Chinese Han population, and to evaluate the forensic efficiency of Huaxia™ Platinum kit. A total of 500 unrelated healthy individuals from Han population were genotyped with Huaxia™ Platinum kit. The frequency distribution and the parameter of population genetics of STR loci were analysed statistically. Huaxia™ Platinum kit was compared with other 7 commercial STR kits commonly seen at home and abroad in the number of STR loci, interior label, fluorescent mark, total number of alleles in Ladder and system effectiveness. All the 23 autosomal STR loci were consistent with Hardy-Weinberg equilibrium （ P >0.05）. The discrimination power was 0.791 5-0.986 2. The polymorphism information content （PIC） was 0.559 0-0.914 0. The combined discrimination power （CDP） was 1-4.1×10⁻²⁸, while combined probability of paternity exclusion in trio （CPET） and in duo （CPED） were 1-4.1×10⁻¹⁰ and 1-8.4×10⁻⁷, respectively. Compared with other 7 kits, Huaxia™ Platinum kit contained the most number of alleles within the Ladder. All the 23 autosomal STR loci of Huaxia™ Platinum kit with highly polymorphic in Han population can be used for paternity testing and individual identification. Compared with other 7 kits, it appears that Huaxia™ Platinum kit can provide more genetic information. Copyright© by the Editorial Department of Journal of Forensic Medicine

The Interaction of Streptococcal Enolase with Canine Plasminogen: The Role of Surfaces in Complex Formation

PubMed Central

Balhara, Vinod; Deshmukh, Sasmit S.; Kálmán, László; Kornblatt, Jack A.

2014-01-01

The enolase from Streptococcus pyogenes (Str enolase F137L/E363G) is a homo-octamer shaped like a donut. Plasminogen (Pgn) is a monomeric protein composed of seven discrete separated domains organized into a lock washer. The enolase is known to bind Pgn. In past work we searched for conditions in which the two proteins would bind to one another. The two native proteins in solution would not bind under any of the tried conditions. We found that if the structures were perturbed binding would occur. We stated that only the non-native Str enolase or Pgn would interact such that we could detect binding. We report here the results of a series of dual polarization interferometry (DPI) experiments coupled with atomic force microscopy (AFM), isothermal titration calorimetry (ITC), dynamic light scattering (DLS), and fluorescence. We show that the critical condition for forming stable complexes of the two native proteins involves Str enolase binding to a surface. Surfaces that attract Str enolase are a sufficient condition for binding Pgn. Under certain conditions, Pgn adsorbed to a surface will bind Str enolase. PMID:24520380

[Analysis of free foetal DNA in maternal plasma using STR loci].

PubMed

Vodicka, R; Vrtel, R; Procházka, M; Santavá, A; Dusek, L; Vrbická, D; Singh, R; Krejciríková, E; Schneiderová, E; Santavý, J

2006-01-01

Problems of maternal and foetal genotype differentiation of maternal plasma in pregnant women are solved generally by real-time systems. In this case the specific probes are used to distinguish particular genotype. Mostly gonosomal sequences are utilised to recognise the male foetus. This work describes possibilities in free foetal DNA detection and quantification by STR. Artificial genotype mixtures ranging from 0,2 % to 100 % to simulate maternal and paternal genotypes and 27 DNA samples from pregnant women in different stage of pregnancy were used for DNA quantification and detection. Foetal genotype was confirmed by biological father genotyping. The detection was performed in STR from 21st chromosome Down syndrome (DS) responsible region by innovated (I) QF PCR which allows to reveal and quantify even very rare DNA mosaics. The STR quantification was assessed in artificial mixtures of genotypes and discriminability of particular genotypes was on the level of few percent. Foetal DNA was detected in 74 % of tested samples. The IQF PCR application in quantification and differentiation between maternal and foetal genotypes by STR loci could have importance in non-invasive prenatal diagnostics as another possible marker for DS risk assessment.

"The devil's in the detail": Release of an expanded, enhanced and dynamically revised forensic STR Sequence Guide.

PubMed

Phillips, C; Gettings, K Butler; King, J L; Ballard, D; Bodner, M; Borsuk, L; Parson, W

2018-05-01

The STR sequence template file published in 2016 as part of the considerations from the DNA Commission of the International Society for Forensic Genetics on minimal STR sequence nomenclature requirements, has been comprehensively revised and audited using the latest GRCh38 genome assembly. The list of forensic STRs characterized was expanded by including supplementary autosomal, X- and Y-chromosome microsatellites in less common use for routine DNA profiling, but some likely to be adopted in future massively parallel sequencing (MPS) STR panels. We outline several aspects of sequence alignment and annotation that required care and attention to detail when comparing sequences to GRCh37 and GRCh38 assemblies, as well as the necessary matching of MPS-based allele descriptions to previously established repeat region structures described in initial sequencing studies of the less well known forensic STRs. The revised sequence guide is now available in a dynamically updated FTP format from the STRidER website with a date-stamped change log to allow users to explore their own MPS data with the most up-to-date forensic STR sequence information compiled in a simple guide. Copyright © 2018 Elsevier B.V. All rights reserved.

Genetic polymorphisms, forensic efficiency and phylogenetic analysis of 15 autosomal STR loci in the Kazak population of Ili Kazak Autonomous Prefecture, northwestern China.

PubMed

Feng, Chunmei; Wang, Xin; Wang, Xiaolong; Yu, Hao; Zhang, Guohua

2018-03-01

We investigated the frequencies of 15 autosomal STR loci in the Kazak population of the Ili Kazak Autonomous Prefecture with the aim of expanding the available population information in human genetic databases and for forensic DNA analysis. Genetic polymorphisms of 15 autosomal short tandem repeat (STR) loci were analysed in 456 individuals of the Kazak population from Ili Kazakh Autonomous Prefecture, northwestern China. A total of 173 alleles at 15 autosomal STR loci were found; the allele frequencies ranged from 0.5022-0.0011. The combined power of discrimination and exclusion statistics for the 15 STR loci were 0.999 999 999 85 and 0.999 998 800 65, respectively. In addition, phylogenetic analysis involving the Ili Uygur population and other relevant populations was carried out. A neighbour-joining tree and multidimensional scaling plot were generated based on Nei's standard genetic distance. Results of the population comparison indicated that the Ili Uygur population was most closely related genetically to the Uygur populations from other regions in China. These findings are consistent with the historical and geographic backgrounds of these populations.

Interim analysis of STR effectiveness

DOT National Transportation Integrated Search

1978-01-01

The present report describes the status of the NHTSA Short Term Rehabilitation Study (STR) as of December, 1977, and summarizes the progress of data collection efforts by the eleven participating ASAP projects. Outcome measures considered as indicati...

Direct Calculation of Short Circuit Reactance, Winding Strength, and Inherent Forms of Output Transformers (Direkte Berechung der Kurzschlussreaktanzen, Wicklungskraefte und Eigenformen von Leistungstransformatoren)

DTIC Science & Technology

2001-01-01

die elektrische Leitfiihigkeit a,. und die relative Permeabilitat Yrn auf. In die Leiter sind harmonisch von der Zeit abhdngige Str ~me eingeprligt, die...Zusammengefasst werden die Beziehungen (5.15) dann durch Mit den Maschen- und Knotengleichungen sind die Abhdngigkeiten der Str ~ime und Span- nungen...besteht aus t Spalten und kennzeichnet die Tore, an denen Str ~me eingeprdgt sind. Daher ist sie gemdl3 [TnT] J,,,5, wenn in Tor bein Strom eingepriigt ist

Social stress contagion in rats: Behavioural, autonomic and neuroendocrine correlates.

PubMed

Carnevali, Luca; Montano, Nicola; Statello, Rosario; Coudé, Gino; Vacondio, Federica; Rivara, Silvia; Ferrari, Pier Francesco; Sgoifo, Andrea

2017-08-01

The negative emotional consequences associated with life stress exposure in an individual can affect the emotional state of social partners. In this study, we describe an experimental rat model of social stress contagion and its effects on social behaviour and cardiac autonomic and neuroendocrine functions. Adult male Wistar rats were pair-housed and one animal (designated as "demonstrator" (DEM)) was submitted to either social defeat stress (STR) by an aggressive male Wild-type rat in a separate room or just exposed to an unfamiliar empty cage (control condition, CTR), once a day for 4 consecutive days. We evaluated the influence of cohabitation with a STR DEM on behavioural, cardiac autonomic and neuroendocrine outcomes in the cagemate (defined "observer" (OBS)). After repeated social stress, STR DEM rats showed clear signs of social avoidance when tested in a new social context compared to CTR DEM rats. Interestingly, also their cagemate STR OBSs showed higher levels of social avoidance compared to CTR OBSs. Moreover, STR OBS rats exhibited a higher heart rate and a larger shift of cardiac autonomic balance toward sympathetic prevalence (as indexed by heart rate variability analysis) immediately after the first reunification with their STR DEMs, compared to the control condition. This heightened cardiac autonomic responsiveness habituated over time. Finally, STR OBSs showed elevated plasma corticosterone levels at the end of the experimental protocol compared to CTR OBSs. These findings demonstrate that cohabitation with a DEM rat, which has experienced repeated social defeat stress, substantially disrupts social behaviour and induces short-lasting cardiac autonomic activation and hypothalamic-pituitary-adrenal axis hyperactivity in the OBS rat, thus suggesting emotional state-matching between the OBS and the DEM rats. We conclude that this rodent model may be further exploited for investigating the neurobiological bases of negative affective sharing between social partners under chronic social stress conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

An Ultra-High Discrimination Y Chromosome Short Tandem Repeat Multiplex DNA Typing System

PubMed Central

Hanson, Erin K.; Ballantyne, Jack

2007-01-01

In forensic casework, Y chromosome short tandem repeat markers (Y-STRs) are often used to identify a male donor DNA profile in the presence of excess quantities of female DNA, such as is found in many sexual assault investigations. Commercially available Y-STR multiplexes incorporating 12–17 loci are currently used in forensic casework (Promega's PowerPlex® Y and Applied Biosystems' AmpFlSTR® Yfiler®). Despite the robustness of these commercial multiplex Y-STR systems and the ability to discriminate two male individuals in most cases, the coincidence match probabilities between unrelated males are modest compared with the standard set of autosomal STR markers. Hence there is still a need to develop new multiplex systems to supplement these for those cases where additional discriminatory power is desired or where there is a coincidental Y-STR match between potential male participants. Over 400 Y-STR loci have been identified on the Y chromosome. While these have the potential to increase the discrimination potential afforded by the commercially available kits, many have not been well characterized. In the present work, 91 loci were tested for their relative ability to increase the discrimination potential of the commonly used ‘core’ Y-STR loci. The result of this extensive evaluation was the development of an ultra high discrimination (UHD) multiplex DNA typing system that allows for the robust co-amplification of 14 non-core Y-STR loci. Population studies with a mixed African American and American Caucasian sample set (n = 572) indicated that the overall discriminatory potential of the UHD multiplex was superior to all commercial kits tested. The combined use of the UHD multiplex and the Applied Biosystems' AmpFlSTR® Yfiler® kit resulted in 100% discrimination of all individuals within the sample set, which presages its potential to maximally augment currently available forensic casework markers. It could also find applications in human evolutionary genetics and genetic genealogy. PMID:17668066

Skewing of the genetic architecture at the ZMYM3 human-specific 5' UTR short tandem repeat in schizophrenia.

PubMed

Alizadeh, F; Bozorgmehr, A; Tavakkoly-Bazzaz, J; Ohadi, M

2018-06-01

Differential expansion of a number of human short tandem repeats (STRs) at the critical core promoter and 5' untranslated region (UTR) support the hypothesis that at least some of these STRs may provide a selective advantage in human evolution. Following a genome-wide screen of all human protein-coding gene 5' UTRs based on the Ensembl database ( http://www.ensembl.org ), we previously reported that the longest STR in this interval is a (GA) 32 , which belongs to the X-linked zinc finger MYM-type containing 3 (ZMYM3) gene. In the present study, we analyzed the evolutionary implication of this region across evolution and examined the allele and genotype distribution of the "exceptionally long" STR by direct sequencing of 486 Iranian unrelated male subjects consisting of 196 cases of schizophrenia (SCZ) and 290 controls. We found that the ZMYM3 transcript containing the STR is human-specific (ENST00000373998.5). A significant allele variance difference was observed between the cases and controls (Levene's test for equality of variances F = 4.00, p < 0.03). In addition, six alleles were observed in the SCZ patients that were not detected in the control group ("disease-only" alleles) (mid p exact < 0.0003). Those alleles were at the extreme short and long ends of the allele distribution curve and composed 4% of the genotypes in the SCZ group. In conclusion, we found skewing of the genetic architecture at the ZMYM3 STR in SCZ. Further, we found a bell-shaped distribution of alleles and selection against alleles at the extreme ends of this STR. The ZMYM3 STR sets a prototype, the evolutionary course of which determines the range of alleles in a particular species. Extreme "disease-only" alleles and genotypes may change our perspective of adaptive evolution and complex disorders. The ZMYM3 gene "exceptionally long" STR should be sequenced in SCZ and other human-specific phenotypes/characteristics.

Genetic analysis of 15 autosomal and 12 Y-STR loci in the Espirito Santo State population, Brazil.

PubMed

Wolfgramm, Eldamária de Vargas; Silva, Beatriz Candida; Aguiar, Vitor Resende da Costa; Malta, Frederico Scott Varela; de Castro, Amanda Mafia; Ferreira, Alessandro Clayton de Souza; Prezoti, Alessandra Nunes Loureiro; de Paula, Flavia; Louro, Iúri Drumond

2011-06-01

This study provides population genetic data for individuals of Vitoria, Espirito Santo, Brazil, a location not yet characterized for STR frequencies used for genetic identification studies. Allelic frequencies and other population data analysis are reported for the 15 autosomal-STR loci included in the PowerPlex(®)16 kit (CSF1PO, D13S317, D16S539, D18S51, D21S11, D3S1358, D5S818, D7S820, D8S1179, FGA, Penta D, Penta E, TPOX, TH01 and vWA). Allele and haplotype frequencies, gene diversity and discrimination capacity were also estimated for the PowerPlex(®) Y System (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439). Blood samples were obtained from 226 unrelated volunteers (135 males and 91 females) residents in the city of Vitoria, representing a typical sample of the mixed ethnicity present in the Espirito Santo State, Brazil. Within the tested population, the total number of individuals typed for specific markers is: 226 for D13S317, D21S11, D3S1358, D7S820, D8S1179 and FGA; 225 for D16S539 and D5S818; 224 for D18S51; 223 for CSF1PO; 222 for Penta D and vWA; 220 for Penta E; 207 for TPOX and 142 for TH01. Y-STR haplotypes were analyzed for 102 unrelated males, being 71 of them present in the 135 autosomal-STR sample, and 31 new males tested only for Y-STR markers. All autosomal markers were in Hardy-Weinberg Equilibrium. Y-STR analysis identified 101 haplotypes, being 100 of them unique. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Microbial Iron Cycling in Acidic Geothermal Springs of Yellowstone National Park: Integrating Molecular Surveys, Geochemical Processes, and Isolation of Novel Fe-Active Microorganisms

PubMed Central

Kozubal, Mark A.; Macur, Richard E.; Jay, Zackary J.; Beam, Jacob P.; Malfatti, Stephanie A.; Tringe, Susannah G.; Kocar, Benjamin D.; Borch, Thomas; Inskeep, William P.

2012-01-01

Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats in Yellowstone National Park. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 88°C and pH 2.4 to 3.6. All iron oxide mats exhibited high diversity of crenarchaeal sequences from the Sulfolobales, Thermoproteales, and Desulfurococcales. The predominant Sulfolobales sequences were highly similar to Metallosphaera yellowstonensis str. MK1, previously isolated from one of these sites. Other groups of archaea were consistently associated with different types of iron oxide mats, including undescribed members of the phyla Thaumarchaeota and Euryarchaeota. Bacterial sequences were dominated by relatives of Hydrogenobaculum spp. above 65–70°C, but increased in diversity below 60°C. Cultivation of relevant iron-oxidizing and iron-reducing microbial isolates included Sulfolobus str. MK3, Sulfobacillus str. MK2, Acidicaldus str. MK6, and a new candidate genus in the Sulfolobales referred to as Sulfolobales str. MK5. Strains MK3 and MK5 are capable of oxidizing ferrous iron autotrophically, while strain MK2 oxidizes iron mixotrophically. Similar rates of iron oxidation were measured for M. yellowstonensis str. MK1 and Sulfolobales str. MK5. Biomineralized phases of ferric iron varied among cultures and field sites, and included ferric oxyhydroxides, K-jarosite, goethite, hematite, and scorodite depending on geochemical conditions. Strains MK5 and MK6 are capable of reducing ferric iron under anaerobic conditions with complex carbon sources. The combination of geochemical and molecular data as well as physiological observations of isolates suggests that the community structure of acidic Fe mats is linked with Fe cycling across temperatures ranging from 53 to 88°C. PMID:22470372

Haplotype analysis of the polymorphic 40 Y-STR markers in Chinese populations.

PubMed

Ou, Xueling; Wang, Ying; Liu, Chao; Yang, Donggui; Zhang, Chuchu; Deng, Shujiao; Sun, Hongyu

2015-11-01

Forty Y-STR loci were analyzed in 1128 males from the following six Chinese ethnic populations: Han (n=300), Hui (n=244), Korean (n=100), Mongolian (n=100), Uighur (n=284) and Tibetan (n=100), utilizing two new generation multiplex Y-STR systems, AGCU Y24 STR and GFS Y24 STR genotyping kits, which allow for the genotyping of 24 loci from a single amplification reaction in each system. The lowest estimates of genetic diversity (below 0.5) correspond to markers DYS391 (0.441658) and DYS437 (0.496977), and the greatest diversity corresponds to markers DYS385a/b (0.969919) and DYS527a/b (0.94676). A considerable number of duplicate and off-ladder alleles were also revealed. Additionally, there were 1111 different haplotypes identified from the total 1128 samples, of which 1095 were unique. Notably, no shared haplotypes between populations were observed. The estimated overall haplotype diversity (HD) was 0.999085, and its discrimination capacity (DC) was 0.970745. An MDS plot based on the genetic distances between populations showed the genetic similarity of the southern Han population to the Northern populations of Hui, Korean, Mongolian and Uighur and a clear genetic departure of the Tibetan population from other populations. For the Y STR markers, population substructure correction was considered when calculating the rarity of the Y STR profile. However, because the haplotype based Fst values are extremely small within the present data (0.000153 with 40 Y-STRs), no substructure correction is required to estimate the rarity of a haplotype comprising 40 markers. In summary, the results of our study indicate that the 40 Y-STRs have a high level of polymorphism in Chinese ethnic groups and could therefore be a powerful tool for forensic applications and population genetic studies. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Multiple Stars in the Field

DTIC Science & Technology

2008-01-01

Southern Observatory Karl - Schwarzschild -Str. 2 85748 Garching Germany :--. ,") 1 ’< ’ I () ___ I Andrei Tokovinin Inter-American Observatory...Chile Monika Petr-Gotzens European Southern Observatory Karl -Schwarschild-Str. 2 85748 Garching Germany Series Editor Bruno Leibundgut European

Electromagnetic analysis of the slotted-tube resonator with a circular cross section for MRI applications.

PubMed

Benabdallah, Nadia; Benahmed, Nasreddine; Benyoucef, Boumediene; Bouhmidi, Rachid; Khelif, M'Hamed

2007-08-21

In this paper we present electromagnetic (EM) analysis of the unloaded slotted-tube resonator (STR) with a circular cross section, using the finite element method (FEM) and method of moments (MoM) in two dimensions. This analysis allows the determination of the primary parameters: [L] and [C] matrices, optimization of the field homogeneity, and simulates the frequency response of S(11) at the RF port of the designed STR. The optimum configuration is presented, taking into account the effect of the thickness of the STR and the effect of the RF shield. As an application, we present the design results of a MRI probe using the STR and operating at 500 MHz (proton imaging at 11.74 T). The resonator has -69.37 dB minimum reflection and an unloaded quality factor (Q(o)) > 500 at 500 MHz.

Genetic analysis of 20 autosomal STR loci in the Miao ethnic group from Yunnan Province, Southwest China.

PubMed

Zhang, Xiufeng; Hu, Liping; Du, Lei; Nie, Aiting; Rao, Min; Pang, Jing Bo; Xiran, Zeng; Nie, Shengjie

2017-05-01

The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex ® 21 kit were evaluated from 748 unrelated healthy individuals of the Miao ethnic minority living in the Yunnan province in southwestern China. All of the loci reached Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The genetic relationship between the Miao population and other Chinese populations were also estimated. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999 999 999 999 999 999 999 991 26 and 0.999 999 975, respectively. The results suggested that the 20 STR loci were highly polymorphic, which makes them suitable for forensic personal identification and paternity testing. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of a rapid 21-plex autosomal STR typing system for forensic applications.

PubMed

Yang, Meng; Yin, Caiyong; Lv, Yuexin; Yang, Yaran; Chen, Jing; Yu, Zailiang; Liu, Xu; Xu, Meibo; Chen, Feng; Wu, Huijuan; Yan, Jiangwei

2016-10-01

DNA-STR genotyping technology has been widely used in forensic investigations. Even with such success, there is a great need to reduce the analysis time. In this study, we established a new rapid 21-plex STR typing system, including 13 CODIS loci, Penta D, Penta E, D12S391, D2S1338, D6S1043, D19S433, D2S441 and Amelogenin loci. This system could shorten the amplification time to a minimum of 90 min and does not require DNA extraction from the samples. Validation of the typing system complied with the Scientific Working Group on DNA Analysis Methods (SWGDAM) and the Chinese National Standard (GA/T815-2009) guidelines. The results demonstrated that this 21-plex STR typing system was a valuable tool for rapid criminal investigation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Analysis on genetic polymorphism of 5 STR loci selected from X chromosome].

PubMed

Liu, Qi-ji; Gong, Yao-qin; Zhang, Xi-yu; Gao, Gui-min; Li, Jiang-xia; Guo, Yi-shou

2005-02-01

To select short tandem repeats(STR) from X chromosome. STR is a universal genetic marker that has changeable polymorphism and stable heredity in human genome. It is a specific DNA segment composed of 2-6 base pairs as its core sequence. It is an ideal DNA marker used in linkage analysis and gene mapping. In this study, 8 short tandem repeats were selected from two genomic clones on X chromosome by using BCM Search Launcher. Primers amplifying the STR loci were designed by using Primer 3.0 according to the unique sequence flanking the STRs. Polymorphisms of the short tandem repeats in Chinese population were evaluated by PCR amplification and PAGE. Five of these STRs were polymorphic. Chi-square test indicated that the distribution of genotypes agreed with Hardy-Weinberg equilibrium (P>0.05). Five polymorphic short tandem repeats have been identified on chromosome X and will be useful for linkage analysis and gene mapping.

STR-validator: an open source platform for validation and process control.

PubMed

Hansson, Oskar; Gill, Peter; Egeland, Thore

2014-11-01

This paper addresses two problems faced when short tandem repeat (STR) systems are validated for forensic purposes: (1) validation is extremely time consuming and expensive, and (2) there is strong consensus about what to validate but not how. The first problem is solved by powerful data processing functions to automate calculations. Utilising an easy-to-use graphical user interface, strvalidator (hereafter referred to as STR-validator) can greatly increase the speed of validation. The second problem is exemplified by a series of analyses, and subsequent comparison with published material, highlighting the need for a common validation platform. If adopted by the forensic community STR-validator has the potential to standardise the analysis of validation data. This would not only facilitate information exchange but also increase the pace at which laboratories are able to switch to new technology. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER).

PubMed

Bodner, Martin; Bastisch, Ingo; Butler, John M; Fimmers, Rolf; Gill, Peter; Gusmão, Leonor; Morling, Niels; Phillips, Christopher; Prinz, Mechthild; Schneider, Peter M; Parson, Walther

2016-09-01

The statistical evaluation of autosomal Short Tandem Repeat (STR) genotypes is based on allele frequencies. These are empirically determined from sets of randomly selected human samples, compiled into STR databases that have been established in the course of population genetic studies. There is currently no agreed procedure of performing quality control of STR allele frequency databases, and the reliability and accuracy of the data are largely based on the responsibility of the individual contributing research groups. It has been demonstrated with databases of haploid markers (EMPOP for mitochondrial mtDNA, and YHRD for Y-chromosomal loci) that centralized quality control and data curation is essential to minimize error. The concepts employed for quality control involve software-aided likelihood-of-genotype, phylogenetic, and population genetic checks that allow the researchers to compare novel data to established datasets and, thus, maintain the high quality required in forensic genetics. Here, we present STRidER (http://strider.online), a publicly available, centrally curated online allele frequency database and quality control platform for autosomal STRs. STRidER expands on the previously established ENFSI DNA WG STRbASE and applies standard concepts established for haploid and autosomal markers as well as novel tools to reduce error and increase the quality of autosomal STR data. The platform constitutes a significant improvement and innovation for the scientific community, offering autosomal STR data quality control and reliable STR genotype estimates. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates

PubMed Central

Willems, Thomas; Gymrek, Melissa; Poznik, G. David; Tyler-Smith, Chris; Erlich, Yaniv

2016-01-01

Short tandem repeats (STRs) are mutation-prone loci that span nearly 1% of the human genome. Previous studies have estimated the mutation rates of highly polymorphic STRs by using capillary electrophoresis and pedigree-based designs. Although this work has provided insights into the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown. Here, we harnessed whole-genome sequencing data to estimate the mutation rates of Y chromosome STRs (Y-STRs) with 2–6 bp repeat units that are accessible to Illumina sequencing. We genotyped 4,500 Y-STRs by using data from the 1000 Genomes Project and the Simons Genome Diversity Project. Next, we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data by using a high-resolution SNP-based phylogeny. After extensive intrinsic and extrinsic validations, we harnessed MUTEA to derive mutation-rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulting in the largest collection of Y-STR mutation rates to date. Using our estimates, we identified determinants of STR mutation rates and built a model to predict rates for STRs across the genome. These predictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, rivaling the load of all other known variant types. Finally, we identified Y-STRs with potential applications in forensics and genetic genealogy, assessed the ability to differentiate between the Y chromosomes of father-son pairs, and imputed Y-STR genotypes. PMID:27126583

Contingency Operations during Failure of Inertial Attitude Acquisition Due to Star Tracker Blinding for Three-Axes-Stabilized Interplanetary Spacecraft

NASA Technical Reports Server (NTRS)

Keil, Joachim; Herfort, Ulrich

2007-01-01

The three interplanetary ESA missions Mars-Express, Rosetta and Venus-Express (launched 2003, 2004 and 2005 resp.) are three-axes stabilized spacecraft (s/c) that estimate their inertial attitude (i.e. the attitude of the s/c w.r.t. the inertial frame) using measurements from a redundant set of star trackers (STR). Each s/c is equipped with four reaction wheels, a reaction control system based on thrusters and a redundant set of ring laser gyroscopes (gyros). The STR h/w layout of the three s/c is identical whereas there is a difference in the star pattern recognition algorithm of Rosetta which uses five neighbouring stars around a central star instead of star triads. The Rosetta algorithm has been implemented to cope with the presence of false stars which are expected to be seen during operations around the comet. The attitude acquisition capability from lost in space is different also in terms of AOCMS: The survival mode of Rosetta which is entered upon STR failure is presented. The AOCMS of Mars- and Venus-Express manages temporary STR outages during sky occultation by the planet not even by using redundancy. Though, a blinding of both STR during cruise lasting for the order of days confronts the ground operators with the limits of the AOCMS design. The operations and analyses that have been planned and partially been performed to compensate for the outage of the STR are demonstrated for Mars-Express. The caution measures taken before Venus orbit insertion of Venus-Express are detailed.

Stochastic sampling effects in STR typing: Implications for analysis and interpretation.

PubMed

Timken, Mark D; Klein, Sonja B; Buoncristiani, Martin R

2014-07-01

The analysis and interpretation of forensic STR typing results can become more complicated when reduced template amounts are used for PCR amplification due to increased stochastic effects. These effects are typically observed as reduced heterozygous peak-height balance and increased frequency of undetected alleles (allelic "dropout"). To investigate the origins of these effects, a study was performed using the AmpFlSTR(®) Identifiler Plus(®) and MiniFiler(®) kits to amplify replicates from a dilution series of NIST Human DNA Quantitation Standard (SRM(®) 2372A). The resulting amplicons were resolved and detected on two different genetic analyzer platforms, the Applied Biosystems 3130xL and 3500 analyzers. Results from our study show that the four different STR/genetic analyzer combinations exhibited very similar peak-height ratio statistics when normalized for the amount of template DNA in the PCR. Peak-height ratio statistics were successfully modeled using the Poisson distribution to simulate pre-PCR stochastic sampling of the alleles, confirming earlier explanations that sampling is the primary source for peak-height imbalance in reduced template dilutions. In addition, template-based pre-PCR sampling simulations also successfully predicted allelic dropout frequencies, as modeled by logistic regression methods, for the low-template DNA dilutions. We discuss the possibility that an accurately quantified DNA template might be used to characterize the linear signal response for data collected using different STR kits or genetic analyzer platforms, so as to provide a standardized approach for comparing results obtained from different STR/CE combinations and to aid in validation studies. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Optimization and validation of a fast amplification protocol for AmpFlSTR® Profiler Plus® for rapid forensic human identification.

PubMed

Laurin, Nancy; Frégeau, Chantal

2012-01-01

The goal of this work was to optimize and validate a fast amplification protocol for the multiplex amplification of the STR loci included in AmpFlSTR(®) Profiler Plus(®) to expedite human DNA identification. By modifying the cycling conditions and by combining the use of a DNA polymerase optimized for high speed PCR (SpeedSTAR™ HS) and a more efficient thermal cycler instrument (Bio-RAD C1000™), we were able to reduce the amplification process from 4h to 26 min. No modification to the commercial AmpFlSTR(®) Profiler Plus(®) primer mix was required. When compared to the current Royal Canadian Mounted Police (RCMP) amplification protocol, no differences with regards to specificity, sensitivity, heterozygote peak height ratios and overall profile balance were noted. Moreover, complete concordance was obtained with profiles previously generated with the standard amplification protocol and minor alleles in mixture samples were reliably typed. An increase in n-4 stutter ratios (2.2% on average for all loci) was observed for profiles amplified with the fast protocol compared to the current procedure. Our results document the robustness of this rapid amplification protocol for STR profiling using the AmpFlSTR(®) Profiler Plus(®) primer set and demonstrate that comparable data can be obtained in substantially less time. This new approach could provide an alternative option to current multiplex STR typing amplification protocols in order to increase throughput or expedite time-sensitive cases. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Community structure, diversity and total biomass of tree species at Kapur dominated forests in Peninsular Malaysia

NASA Astrophysics Data System (ADS)

Norafida, N. A. Nik; Nizam, M. S.; Juliana, W. A. Wan

2013-11-01

A study was conducted to determine the species composition, diversity and biomass of Kapur (Dryobalanops aromatica Gaertn.f.) dominated forests in Peninsular Malaysia. Three forests were selected in different geographical zones, namely Bukit Bauk Virgin Jungle Reserve (BBVJR), Terengganu, Lesong Forest Reserve (LFR), Pahang and Gunung Belumut Recreational Forest (GBRF), Johor. Thirty plots of 0.1 ha (50 m × 20 m) were established with a total sampling area of 1.0 ha at each forest site. All trees with ≥5 cm diameter at breast height (dbh) were tagged, measured and voucher specimens were collected. Floristic composition in the study plot at BBVJR recorded 55 families, 147 genera and 336 species. In LFR, there were 52 families, 138 genera and 288 species, whereas in GBRF there were 52 families, 132 genera and 271 species. D. aromatica was the most important species in all study plots with the Importance Value Index (IVi) of 17.81%, 23.01% and 16.25% in BBVJR, LFR and GBRF, respectively. Similar trend at family level showed the Dipterocarpaceae was the most important family in each of the areas with the family Importance Value Index (FIVi) of 27.95% (BBVJR), 26.09% (LFR) and 27.16% (GBRF). Shannon diversity index (H'f) and Shannon evenness index (J'f) of trees at BBVJR was 5.02 and 0.86; LFR was 4.63 and 0.82; and GBRF was 4.82 and 0.86, respectively. Sorensen's community similarity coefficient (CCs) showed that tree communities between BBVJR, LFR and GBRF had low similarities with values of 0.3 to 0.4. The highest total biomass estimated was in LFR with a value of 739.44 t/ha, followed by BBVJR at 701.34 t/ha and GBRF at 606.29 t/ha.

Combining Different NLP Methods for HUMINT Report Analysis

DTIC Science & Technology

2009-10-01

JENGE, Silverius KAWALETZ, Ulrich SCHADE Fraunhofer-Institut für Kommunikation, Informationsverarbeitung und Ergonomie (FKIE) Neuenahrer Str. 20 53343...ES) Fraunhofer-Institut für Kommunikation, Informationsverarbeitung und Ergonomie (FKIE) Neuenahrer Str. 20 53343 Wachtberg-Werthhoven Germany 8

Improving empirical evidence on differentiating closely related men with RM Y-STRs: A comprehensive pedigree study from Pakistan.

PubMed

Adnan, Atif; Ralf, Arwin; Rakha, Allah; Kousouri, Nefeli; Kayser, Manfred

2016-11-01

Y-chromosomal short tandem repeat (Y-STR) markers are commonly used in forensic genetics. Male-specific haplotypes provided by commercial Y-STR kits allow discriminating between many - but not all - unrelated men, while they mostly fail to separate related ones. Aiming to improve male relative and paternal lineage differentiation, a set of 13 rapidly-mutating (RM) Y-STRs was previously identified and introduced to forensic Y-chromosome analysis. Recently, their value was highlighted by separating 99% of over 12,200 unrelated men from 111 global populations, as well as 29% of over 2500 male relative pairs, the vast majority were father-sons. Here, we provide improved empirical evidence on differentiating closely related men with RM Y-STRs, most notably beyond father-sons, where previous data were limited. After careful quality control including genetic relationship testing, we used 572 Pakistani men belonging to 99 2-4 generation pedigrees covering 1568 pairs of men related by 1-6 meioses. Of those, 45% were differentiated by one or more of the 13 RM Y-STR markers. In contrast, only 14.7% of a subset of 1484 pairs from 94 pedigrees were separated by the commercial AmpFlSTR Y-filer kit. Combining previously published and new data, an overall differentiation rate of 35.3% was revealed for the RM Y-STR set based on 4096 pairs of men related by 1-20 meioses, compared to 9.6% with Y-filer based on 3645 pairs. Using father-son pair data from the present and previous studies, we provide updated RM Y-STR mutation rates. Locus-specific mutation rates ranged from 2.0×10 -3 (7.0×10 -4 -4.3×10 -3 ) to 6.9×10 -2 (6.1×10 -2 -7.9×10 -2 ) based on 2741-3143 meioses, with an average rate across all 13 RM Y-STR markers of 1.8×10 -2 (1.7×10 -2 -1.9×10 -2 ) based on 800 mutations from 44,922 meioses. The high haplotype diversity (h=0.9996) we observed among the unrelated men (N=105) underlines the value of this RM Y-STR set to differentiate paternal lineages even from endogamous populations such as from Pakistan. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Large variability in synaptic N-methyl-D-aspartate receptor density on interneurons and a comparison with pyramidal-cell spines in the rat hippocampus.

PubMed

Nyíri, G; Stephenson, F A; Freund, T F; Somogyi, P

2003-01-01

Pyramidal cells receive input from several types of GABA-releasing interneurons and innervate them reciprocally. Glutamatergic activation of interneurons involves both alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and N-methyl-D-aspartate (NMDA) type glutamate receptors expressed in type I synapses, mostly on their dendritic shafts. On average, the synaptic AMPA receptor content is several times higher on interneurons than in the spines of pyramidal cells. To compare the NMDA receptor content of synapses, we used a quantitative postembedding immunogold technique on serial electron microscopic sections, and analysed the synapses on interneuron dendrites and pyramidal cell spines in the CA1 area. Because all NMDA receptors contain the obligatory NR1 subunit, receptor localisation was carried out using antibodies recognising all splice variants of the NR1 subunit. Four populations of synapse were examined: i). on spines of pyramidal cells in stratum (str.) radiatum and str. oriens; ii). on parvalbumin-positive interneuronal dendritic shafts in str. radiatum; iii). on randomly found dendritic shafts in str. oriens and iv). on somatostatin-positive interneuronal dendritic shafts and somata in str. oriens. On average, the size of the synapses on spines was about half of those on interneurons. The four populations of synapse significantly differed in labelling for the NR1 subunit. The median density of NR1 subunit labelling was highest on pyramidal cell spines. It was lowest in the synapses on parvalbumin-positive dendrites in str. radiatum, where more than half of these synapses were immunonegative. In str. oriens, synapses on interneurons had a high variability of receptor content; some dendrites were similar to those in str. radiatum, including the proximal synapses of somatostatin-positive cells, whereas others had immunoreactivity for the NR1 subunit similar to or higher than synapses on pyramidal cell spines. These results show that synaptic NMDA receptor density differs between pyramidal cells and interneurons. Some interneurons may have a high NMDA receptor content, whereas others, like some parvalbumin-expressing cells, a particularly low synaptic NMDA receptor content. Consequently, fast glutamatergic activation of interneurons is expected to show cell type-specific time course and state-dependent dynamics.

Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements.

PubMed

Parson, Walther; Ballard, David; Budowle, Bruce; Butler, John M; Gettings, Katherine B; Gill, Peter; Gusmão, Leonor; Hares, Douglas R; Irwin, Jodi A; King, Jonathan L; Knijff, Peter de; Morling, Niels; Prinz, Mechthild; Schneider, Peter M; Neste, Christophe Van; Willuweit, Sascha; Phillips, Christopher

2016-05-01

The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that provide a precise description of the repeat allele structure of a STR marker and variants that may reside in the flanking areas of the repeat region. When a STR contains a complex arrangement of repeat motifs, the level of genetic polymorphism revealed by the sequence data can increase substantially. As repeat structures can be complex and include substitutions, insertions, deletions, variable tandem repeat arrangements of multiple nucleotide motifs, and flanking region SNPs, established capillary electrophoresis (CE) allele descriptions must be supplemented by a new system of STR allele nomenclature, which retains backward compatibility with the CE data that currently populate national DNA databases and that will continue to be produced for the coming years. Thus, there is a pressing need to produce a standardized framework for describing complex sequences that enable comparison with currently used repeat allele nomenclature derived from conventional CE systems. It is important to discern three levels of information in hierarchical order (i) the sequence, (ii) the alignment, and (iii) the nomenclature of STR sequence data. We propose a sequence (text) string format the minimal requirement of data storage that laboratories should follow when adopting MPS of STRs. We further discuss the variant annotation and sequence comparison framework necessary to maintain compatibility among established and future data. This system must be easy to use and interpret by the DNA specialist, based on a universally accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established nomenclature for CE-based STR analysis will remain unchanged in the future, the nomenclature of sequence-based STR genotypes will need to follow updated rules and be generated by expert systems that translate MPS sequences to match CE conventions in order to guarantee compatibility between the different generations of STR data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A global monthly sea surface temperature climatology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shea, D.J.; Trenberth, K.E.; Reynolds, R.W.

1992-09-01

The paper presents a new global 2 deg x 2 deg monthly sea surface temperature (SST) climatology, referred here to as the Shea-Trenberth-Reynolds (STR) climatology, which was derived by modifying a 1950-1979-based SST climatology from the Climate Analysis Center (CAC), by using data from the Comprehensive Ocean-Atmosphere Data Set to improve the SST estimates in the regions of the Kuroshio and the Gulf Stream. A comparison of the STR climatology with the Alexander and Mobley SST climatology showed that the STR climatology is warmer in the Northern Hemisphere, and colder poleward of 45 deg S. 22 refs.

[Genetic improvement of technological characteristics of starters for fermented milk products].

PubMed

Oganesian, G G; Barsegian, A A; Grigorian, N G; Toptsian, A V

2010-01-01

Possibility for improvement of technological characteristics of lactobacilli using mutations of resistance to rifampicin (rif(r)) and streptomycin (str(r)) was studied. Using starter model of Narine Lactobacillus acidophilus INMIA-9602 Armenian diet milk product, it was showed that a possibility for selecting strains with increased rate of milk fermentation and acid production is higher in Rif(r) and Str(r) mutants induced by nitrosoguanidine than in cultures sensitive to antibiotics. The milk products obtained using Rif(r) and Str(r) strains had high viscosity, improved texture, increased amount of alive cells and good organoleptic features.

[Analysis of mitochondrial SNPs in addition to conventional STR-typing in a case of aggravated theft].

PubMed

Röper, Andrea; Reichert, Walter; Mattern, Rainer

2007-01-01

In the field of forensic DNA typing, the analysis of Short Tandem Repeats (STRs) can fail in cases of degraded DNA. The typing of coding region Single Nucleotide Polymorphisms (SNPs) of the mitochondrial genome provides an approach to acquire additional information. In the examined case of aggravated theft, both suspects could be excluded of having left the analyzed hair on the crime scene by SNP typing. This conclusion was not possible subsequent to STR typing. SNP typing of the trace on the torch light left on the crime scene increased the likelihood for suspect no. 2 to be the origin of this trace. This finding was already indicated by STR analysis. Suspect no. 1 was excluded for being the origin of this trace by SNP typing which was also indicated by STR analysis. A limiting factor for the analysis of SNPs is the maternal inheritance of mitochondrial DNA. Individualisation is not possible. In conclusion, it can be said that in the case of traces which cause problems with conventional STR typing the supplementary analysis of coding region SNPs from the mitochondrial genome is very reasonable and greatly contributes to the refinement of analysis methods in the field of forensic genetics.

Use of Sequenom Sample ID Plus® SNP Genotyping in Identification of FFPE Tumor Samples

PubMed Central

Miller, Jessica K.; Buchner, Nicholas; Timms, Lee; Tam, Shirley; Luo, Xuemei; Brown, Andrew M. K.; Pasternack, Danielle; Bristow, Robert G.; Fraser, Michael; Boutros, Paul C.; McPherson, John D.

2014-01-01

Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76–139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS). The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework. PMID:24551080

Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.

PubMed

Miller, Jessica K; Buchner, Nicholas; Timms, Lee; Tam, Shirley; Luo, Xuemei; Brown, Andrew M K; Pasternack, Danielle; Bristow, Robert G; Fraser, Michael; Boutros, Paul C; McPherson, John D

2014-01-01

Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS). The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.

Enhanced DNA Profiling of the Semen Donor in Late Reported Sexual Assaults: Use of Y-Chromosome-Targeted Pre-amplification and Next Generation Y-STR Amplification Systems.

PubMed

Hanson, Erin K; Ballantyne, Jack

2016-01-01

In some cases of sexual assault the victim may not report the assault for several days after the incident due to various factors. The ability to obtain an autosomal STR profile of the semen donor from a living victim rapidly diminishes as the post-coital interval is extended due to the presence of only a small amount of male DNA amidst an overwhelming amount of female DNA. Previously, we have utilized various technological tools to overcome the limitations of male DNA profiling in extended interval post-coital samples including the use of Y-chromosome STR profiling, cervical sample, and post-PCR purification permitting the recovery of Y-STR profiles of the male DNA from samples collected 5-6 days after intercourse. Despite this success, the reproductive biology literature reports the presence of spermatozoa in the human cervix up to 7-10 days post-coitus. Therefore, novel and improved methods for recovery of male profiles in extended interval post-coital samples were required. Here, we describe enhanced strategies, including Y-chromosome-targeted pre-amplification and next generation Y-STR amplification kits, that have resulted in the ability to obtain probative male profiles from samples collected 6-9 days after intercourse.

Genetic polymorphisms of short tandem repeat loci D13S305, D13S631 and D13S634 in the Han population of Tianjin, China.

PubMed

Shi, Yunfang; Li, Xiaozhou; Ju, Duan; Li, Yan; Zhang, Xiuling; Zhang, Ying

2015-08-01

Short tandem repeat (STR) markers, also known as microsatellites, are extensively used in mapping studies, forensics and disease diagnosis due to their small dimension and low mutation and high polymorphism rates. In recent years quantitative fluorescence polymerase chain reaction (QF-PCR) has been successfully used to amplify STR markers in the prenatal diagnosis of common chromosomal abnormalities. This method provides a diagnosis of common aneuploidies 24-48 h after sampling with low error rates and cost; however, the size of different alleles, frequency, heterozygosity and distribution of STR markers vary among different populations. In the present study three STR markers, D13S305, D13S631 and D13S634, on chromosome 13 were analyzed in 350 unrelated individuals (200 males and 150 females) from the Han population of Tianjin, China using QF-PCR. Eleven, seven and 11 alleles of each marker were observed, respectively. The frequencies of the genotypes were in good agreement with Hardy-Weinberg equilibrium (P>0.05). The results showed that these three STR markers were highly polymorphic in the Han population of Tianjin, China. The study has provided basic data for use in the prenatal diagnosis of Patau syndrome.

Genetic polymorphisms of short tandem repeat loci D13S305, D13S631 and D13S634 in the Han population of Tianjin, China

PubMed Central

SHI, YUNFANG; LI, XIAOZHOU; JU, DUAN; LI, YAN; ZHANG, XIULING; ZHANG, YING

2015-01-01

Short tandem repeat (STR) markers, also known as microsatellites, are extensively used in mapping studies, forensics and disease diagnosis due to their small dimension and low mutation and high polymorphism rates. In recent years quantitative fluorescence polymerase chain reaction (QF-PCR) has been successfully used to amplify STR markers in the prenatal diagnosis of common chromosomal abnormalities. This method provides a diagnosis of common aneuploidies 24–48 h after sampling with low error rates and cost; however, the size of different alleles, frequency, heterozygosity and distribution of STR markers vary among different populations. In the present study three STR markers, D13S305, D13S631 and D13S634, on chromosome 13 were analyzed in 350 unrelated individuals (200 males and 150 females) from the Han population of Tianjin, China using QF-PCR. Eleven, seven and 11 alleles of each marker were observed, respectively. The frequencies of the genotypes were in good agreement with Hardy-Weinberg equilibrium (P>0.05). The results showed that these three STR markers were highly polymorphic in the Han population of Tianjin, China. The study has provided basic data for use in the prenatal diagnosis of Patau syndrome. PMID:26622392

Genetic mapping of 15 human X chromosomal forensic short tandem repeat (STR) loci by means of multi-core parallelization.

PubMed

Diegoli, Toni Marie; Rohde, Heinrich; Borowski, Stefan; Krawczak, Michael; Coble, Michael D; Nothnagel, Michael

2016-11-01

Typing of X chromosomal short tandem repeat (X STR) markers has become a standard element of human forensic genetic analysis. Joint consideration of many X STR markers at a time increases their discriminatory power but, owing to physical linkage, requires inter-marker recombination rates to be accurately known. We estimated the recombination rates between 15 well established X STR markers using genotype data from 158 families (1041 individuals) and following a previously proposed likelihood-based approach that allows for single-step mutations. To meet the computational requirements of this family-based type of analysis, we modified a previous implementation so as to allow multi-core parallelization on a high-performance computing system. While we obtained recombination rate estimates larger than zero for all but one pair of adjacent markers within the four previously proposed linkage groups, none of the three X STR pairs defining the junctions of these groups yielded a recombination rate estimate of 0.50. Corroborating previous studies, our results therefore argue against a simple model of independent X chromosomal linkage groups. Moreover, the refined recombination fraction estimates obtained in our study will facilitate the appropriate joint consideration of all 15 investigated markers in forensic analysis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Novel biomixtures based on local Mediterranean lignocellulosic materials: evaluation for use in biobed systems.

PubMed

Karanasios, Evangelos; Tsiropoulos, Nikolaos G; Karpouzas, Dimitrios G; Menkissoglu-Spiroudi, Urania

2010-08-01

The composition of biomixtures strongly affect the efficacy of biobeds. Typically, biomixture consists of peat (or compost), straw (STR) and topsoil (1:2:1 by volume). Straw guarantees a continuous supply of nutrients and high microbial activity. However, in south Europe other lignocellulosic materials including sunflower crop residues (SFR), olive leaves, grape stalks (GS), orange peels, corn cobs (CC) and spent mushroom substrate (SMS) are also readily available at no cost. Their potential utilization in biomixtures instead of STR was tested in pesticide degradation and adsorption studies. The microbial activity in these biomixtures was also assessed. The GS-biomixture was the most efficient in pesticide degradation, while CC- and SFR-biomixtures showed comparable degrading efficacy with the STR-biomixture. The SMS-biomixture was also highly efficient in degrading the pesticide mixture with degradation rates being correlated with the proportion of SMS in the biomixture. Microbial respiration was positively correlated with the degradation rates of metalaxyl, azoxystrobin and chlorpyrifos, compared to phenoloxidase which showed no correlation. Biomixtures containing alternative lignocellulosic materials showed a higher adsorption affinity for terbuthylazine and metribuzin compared to the STR-biomixture. We provide first evidence that STR can be substituted in biomixtures by other lignocellulosic materials which are readily available in south Europe. (c) 2010 Elsevier Ltd. All rights reserved.

Genetic analysis of 7 medieval skeletons from Aragonese Pyrenees

PubMed Central

Núńez, Carolina; Sosa, Cecilia; Baeta, Miriam; Geppert, Maria; Turnbough, Meredith; Phillips, Nicole; Casalod, Yolanda; Bolea, Miguel; Roby, Rhonda; Budowle, Bruce; Martínez-Jarreta, Begońa

2011-01-01

Aim To perform a genetic characterization of 7 skeletons from medieval age found in a burial site in the Aragonese Pyrenees. Methods Allele frequencies of autosomal short tandem repeats (STR) loci were determined by 3 different STR systems. Mitochondrial DNA (mtDNA) and Y-chromosome haplogroups were determined by sequencing of the hypervariable segment 1 of mtDNA and typing of phylogenetic Y chromosome single nucleotide polymorphisms (Y-SNP) markers, respectively. Possible familial relationships were also investigated. Results Complete or partial STR profiles were obtained in 3 of the 7 samples. Mitochondrial DNA haplogroup was determined in 6 samples, with 5 of them corresponding to the haplogroup H and 1 to the haplogroup U5a. Y-chromosome haplogroup was determined in 2 samples, corresponding to the haplogroup R. In one of them, the sub-branch R1b1b2 was determined. mtDNA sequences indicated that some of the individuals could be maternally related, while STR profiles indicated no direct family relationships. Conclusions Despite the antiquity of the samples and great difficulty that genetic analyses entail, the combined use of autosomal STR markers, Y-chromosome informative SNPs, and mtDNA sequences allowed us to genotype a group of skeletons from the medieval age. PMID:21674829

Evaluation of power density on the bioethanol production using mesoscale oscillatory baffled reactor and stirred tank reactor

NASA Astrophysics Data System (ADS)

Yussof, H. W.; Bahri, S. S.; Mazlan, N. A.

2018-03-01

A recent development in oscillatory baffled reactor technology is down-scaling the reactor, so that it can be used for production of small-scale bioproduct. In the present study, a mesoscale oscillatory baffled reactor (MOBR) with central baffle system was developed. The reactor performance of the MOBR was compared with conventional stirred tank reactor (STR) to evaluate the performance of bioethanol fermentation using Saccharomyces cerevisiae. Evaluation was made at similar power density of 24.21, 57.38, 112.35 and 193.67 Wm-3 by varying frequency (f), amplitude (xo) and agitation speed (rpm). It was found that the MOBR improved the mixing intensity resulted in lower glucose concentration (0.988 gL-1) and higher bioethanol concentration (38.98 gL-1) after 12 hours fermentation at power density of 193.67 Wm-3. Based on the results, the bioethanol yield obtained using MOBR was 39% higher than the maximum achieved in STR. Bioethanol production using MOBR proved to be feasible as it is not only able to compete with conventional STR but also offers advantages of straight-forward scale-up, whereas it is complicated and difficult in STR. Overall, MOBR offers great prospective over the conventional STR.

Optically thin core accretion: how planets get their gas in nearly gas-free discs

NASA Astrophysics Data System (ADS)

Lee, Eve J.; Chiang, Eugene; Ferguson, Jason W.

2018-05-01

Models of core accretion assume that in the radiative zones of accreting gas envelopes, radiation diffuses. But super-Earths/sub-Neptunes (1-4 R⊕, 2-20 M⊕) point to formation conditions that are optically thin: their modest gas masses are accreted from short-lived and gas-poor nebulae reminiscent of the transparent cavities of transitional discs. Planetary atmospheres born in such environments can be optically thin to both incident starlight and internally generated thermal radiation. We construct time-dependent models of such atmospheres, showing that super-Earths/sub-Neptunes can accrete their ˜1 per cent-by-mass gas envelopes, and super-puffs/sub-Saturns their ˜20 per cent-by-mass envelopes, over a wide range of nebular depletion histories requiring no fine tuning. Although nascent atmospheres can exhibit stratospheric temperature inversions affected by atomic Fe and various oxides that absorb strongly at visible wavelengths, the rate of gas accretion remains controlled by the radiative-convective boundary (rcb) at much greater pressures. For dusty envelopes, the temperature at the rcb Trcb ≃ 2500 K is still set by H2 dissociation; for dust-depleted envelopes, Trcb tracks the temperature of the visible or thermal photosphere, whichever is deeper, out to at least ˜5 au. The rate of envelope growth remains largely unchanged between the old radiative diffusion models and the new optically thin models, reinforcing how robustly super-Earths form as part of the endgame chapter in disc evolution.

Paroxysmal nocturnal hemoglobinuria first described in 1882 by Paul Strübing: an example of cooperation between clinical and basic research.

PubMed

Wilmanns, J C

1982-12-01

The 100th anniversary of the first description of paroxysmal nocturnal hemoglobinuria by Paul Strübing presents an opportunity to analyze the premises valid for the description of this disease in addition to an attempt at an extensive pathophysiological analysis. Strübing's two papers of 1882 were way ahead of his time, when pathophysiology was just at its beginning, particularly considering the fact that neither Marchiafava, who is still commonly credited wit the first description of this disease (1911) and its recognition as a clinical entity (1928), nor his student Micheli analyzed the PNH syndrome in pathophysiological terms as carefully as Strübing. Both of the former names were given to the disease, which is generally referred to as the Marchiafava-Micheli Anemia. William Crosby, who in 1951 in a historical review of PHN first pointed out the pioneering achievement of Strübing, suggested that it was mainly due to the lack of the right "intellectual climate" at the time that so little attention was paid to his work. Still another important aspect of the early history of PNH will be described in the present paper. The analysis of Strübing's publications leads to the conclusion that he was only able to make his important contribution to medical science because he not only had the appropriate clinical setting but also the scientific backup of the famous physiologist Leonhard Landois and his institute at the University of Greifswald, which is an excellent example of scientific progress through cooperation between a clinician and a research scientist.

Direct Y-STR amplification of body fluids deposited on commonly found crime scene substrates.

PubMed

Dargay, Amanda; Roy, Reena

2016-04-01

Body fluids detected on commonly found crime scene substrates require extraction, purification and quantitation of DNA prior to amplification and generation of short tandem repeat (STR) DNA profiles. In this research Y-STR profiles were generated via direct amplification of blood and saliva deposited on 12 different substrates. These included cigarette butts, straws, grass, leaves, woodchips and seven different types of fabric. After depositing either 0.1 μL of blood or 0.5 μL of saliva, each substrate containing the dry body fluid stain was punched using a Harris 1.2 mm micro-punch. Each of these punched substrates, a total of 720 samples, containing minute amount of blood or saliva was either amplified directly without any pre-treatment, or was treated with one of the four washing reagents or buffer. In each of these five experimental groups the substrates containing the body fluid remained in the amplification reagent during the thermal cycling process. Each sample was amplified with the three direct Y-STR amplification kits; AmpFℓSTR(®) Yfiler(®) Direct, Yfiler(®) Plus Amplification Kits and the PowerPlex(®) Y23 System. Complete and concordant Y-STR profiles were successfully obtained from most of these 12 challenging crime scene objects when the stains were analyzed by at least one of the five experimental groups. The reagents and buffer were interchangeable among the three amplification kits, however, pre-treatment with these solutions did not appear to enhance the quality or the number of the full profiles generated with direct amplification. This study demonstrates that blood and saliva deposited on these simulated crime scene objects can be amplified directly. Copyright © 2016 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions.

PubMed

Tomazetto, Geizecler; Hahnke, Sarah; Wibberg, Daniel; Pühler, Alfred; Klocke, Michael; Schlüter, Andreas

2018-06-01

Proteiniphilum saccharofermentans str. M3/6 T is a recently described species within the family Porphyromonadaceae (phylum Bacteroidetes ), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways. The P. saccharofermentans str. M3/6 T genome consists of a 4,414,963 bp chromosome featuring an average GC-content of 43.63%. Genome analyses revealed that the strain possesses 3396 protein-coding sequences. Among them are 158 genes assigned to the carbohydrate-active-enzyme families as defined by the CAZy database, including 116 genes encoding glycosyl hydrolases (GHs) involved in pectin, arabinogalactan, hemicellulose (arabinan, xylan, mannan, β-glucans), starch, fructan and chitin degradation. The strain also features several transporter genes, some of which are located in polysaccharide utilization loci (PUL). PUL gene products are involved in glycan binding, transport and utilization at the cell surface. In the genome of strain M3/6 T , 64 PUL are present and most of them in association with genes encoding carbohydrate-active enzymes. Accordingly, the strain was predicted to metabolize several sugars yielding carbon dioxide, hydrogen, acetate, formate, propionate and isovalerate as end-products of the fermentation process. Moreover, P. saccharofermentans str. M3/6 T encodes extracellular and intracellular proteases and transporters predicted to be involved in protein and oligopeptide degradation. Comparative analyses between P. saccharofermentans str. M3/6 T and its closest described relative P. acetatigenes str. DSM 18083 T indicate that both strains share a similar metabolism regarding decomposition of complex carbohydrates and fermentation of sugars.

Cell surface antigens in renal tumour cells: detection by immunoluminescence and enzymatic analysis

PubMed Central

Laube, F; Göhring, B; Sann, H; Willhardt, I

2001-01-01

Two renal cell carcinoma cell lines (49RC 43STR and 75RC 2STR) were characterized by detection of the cell surface proteins: CD44(var), intercellular adhesion molecule-1 (ICAM-1), urokinase-type plasminogen activator (uPA) and its receptor and aminopeptidase N (APN). To detect their localization the immunoluminescent technique was used. In addition, the enzyme activity of uPA and APN was investigated in cell suspensions as well as in monolayers. The latter procedure was more advantageous since the additional use of HPLC permits a single registration of the fluorescent hydrolysis-product AMC (7-amino-4-methylcoumarin) without interference by cellular autofluorescence or non-reacted fluorescent substrate. Unlike 75RC 2STR, the cell line 49RC 43STR expressed high levels of uPA and APN. Contrary to that the cell line 75RC 2STR expressed high levels of ICAM-1 and CD44(v6), whereas 49RC 43STR showed a low level of ICAM-1 and no distinct light signal with anti-CD44(v6). The uPA activity was measured directly as well as indirectly (via plasmin) with the substrate Z-Gly-Gly-Arg-AMC. Both activator and plasmin activity were inhibited by D-Val-Phe-Lys-CMK and phenylmethylsulfonyl fluoride. The anti-catalytic antibody to uPA and that to uPA receptor were found to be inhibiting the uPA activity in a concentration-dependent manner. APN activity was assayed using alanine-p-nitroanilide. Peptidase activity was effectively inhibited by 1,10-phenanthroline and partly inhibited by ethylenediamine-tetraacetic acid. © 2001 Cancer Research Campaignhttp://www.bjcancer.com PMID:11556847

Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification.

PubMed

Nims, Raymond W; Sykes, Greg; Cottrill, Karin; Ikonomi, Pranvera; Elmore, Eugene

2010-12-01

The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line's species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification.

Developmental and internal validation of a novel 13 loci STR multiplex method for Cannabis sativa DNA profiling.

PubMed

Houston, Rachel; Birck, Matthew; Hughes-Stamm, Sheree; Gangitano, David

2017-05-01

Marijuana (Cannabis sativa L.) is a plant cultivated and trafficked worldwide as a source of fiber (hemp), medicine, and intoxicant. The development of a validated method using molecular techniques such as short tandem repeats (STRs) could serve as an intelligence tool to link multiple cases by means of genetic individualization or association of cannabis samples. For this purpose, a 13 loci STR multiplex method was developed, optimized, and validated according to relevant ISFG and SWGDAM guidelines. The STR multiplex consists of 13 previously described C. sativa STR loci: ANUCS501, 9269, 4910, 5159, ANUCS305, 9043, B05, 1528, 3735, CS1, D02, C11, and H06. A sequenced allelic ladder consisting of 56 alleles was designed to accurately genotype 101 C. sativa samples from three seizures provided by a U.S. Customs and Border Protection crime lab. Using an optimal range of DNA (0.5-1.0ng), validation studies revealed well-balanced electropherograms (inter-locus balance range: 0.500-1.296), relatively balanced heterozygous peaks (mean peak height ratio of 0.83 across all loci) with minimal artifacts and stutter ratio (mean stutter of 0.021 across all loci). This multi-locus system is relatively sensitive (0.13ng of template DNA) with a combined power of discrimination of 1 in 55 million. The 13 STR panel was found to be species specific for C. sativa; however, non-specific peaks were produced with Humulus lupulus. The results of this research demonstrate the robustness and applicability of this 13 loci STR system for forensic DNA profiling of marijuana samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Investigation of extended Y chromosome STR haplotypes in Sardinia.

PubMed

Lacerenza, D; Aneli, S; Di Gaetano, C; Critelli, R; Piazza, A; Matullo, G; Culigioni, C; Robledo, R; Robino, C; Calò, C

2017-03-01

Y-chromosomal variation of selected single nucleotide polymorphisms (SNPs) and 32 short tandem repeat (STR) loci was evaluated in Sardinia in three open population groups (Northern Sardinia, n=40; Central Sardinia, n=56; Southern Sardinia, n=91) and three isolates (Desulo, n=34; Benetutti, n=45, Carloforte, n=42). The tested Y-STRs consisted of Yfiler ® Plus markers and the seven rapidly mutating (RM) loci not included in the YFiler ® Plus kit (DYF399S1, DYF403S1ab, DYF404S1, DYS526ab, DYS547, DYS612, and DYS626). As expected, inclusion of additional Y-STR loci increased haplotype diversity (h), though complete differentiation of male lineages was impossible even by means of RM Y-STRs (h=0.99997). Analysis of molecular variance indicated that the three open populations were fairly homogeneous, whereas signs of genetic heterogeneity could be detected when the three isolates were also included in the analysis. Multidimensional scaling analysis showed that, even for extended haplotypes including RM Y-STR markers, Sardinians were clearly differentiated from populations of the Italian peninsula and Sicily. The only exception was represented by the Carloforte sample that, in accordance with its peculiar population history, clustered with Northern/Central Italian populations. The introduction of extended forensic Y-STR panels, including highly variable RM Y-STR markers, is expected to reduce the impact of population structure on haplotype frequency estimations. However, our results show that the availability of geographically detailed reference databases is still important for the assessment of the evidential value of a Y-haplotype match. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Identification of sperm subpopulations with defined motility characteristics in ejaculates from Ile de France rams.

PubMed

Bravo, J A; Montanero, J; Calero, R; Roy, T J

2011-11-01

The aims of this study were to identify different motile sperm subpopulations in fresh ejaculates from six Ile de France rams, by using a computer-assisted sperm motility analysis (CASA) system, and to evaluate the effects of individual ram and season on population distribution. Overall sperm motility and individual kinematic parameters of motile spermatozoa were evaluated for 125,312 spermatozoa, defined by curvilinear velocity (VCL), linear velocity (VSL), average path velocity (VAP), linearity coefficient (LIN), straightness coefficient (STR), wobble coefficient (WOB), mean amplitude of lateral head displacement (ALH) and frequency of head displacement (BCF). A multivariate cluster analysis was carried out to classify these spermatozoa into a reduced number of subpopulations according to their movement patterns. The statistical analysis clustered the whole motile sperm population into five separate groups: subpopulation 1, constituted by rapid, progressive and non sinuous spermatozoa (VCL=126.41 μm/s, STR=92.87% and LIN=86.47%); subpopulation 2, characterized by progressive spermatozoa with moderate velocity (VCL=74.74 μm/s and STR=84.03%); subpopulation 3, represented by rapid, progressive and sinuous spermatozoa (VCL=130.45 μm/s, STR=76.02% and LIN=47.68%); subpopulation 4 represents rapid nonprogressive spermatozoa (VCL=128.69 μm/s and STR=44.09%); subpopulation 5 includes poorly motile, nonprogressive spermatozoa with a very irregular trajectory (VCL=36.81 μm/s and STR=47.04%). Our results show the existence of five subpopulations of motile spermatozoa in ram ejaculates. The frequency distribution of spermatozoa within subpopulations was quite similar for the six rams, and the five subpopulations turned out to be very stable along seasons. Copyright © 2011 Elsevier B.V. All rights reserved.

Results of NanTroSEIZE Expeditions Stages 1 & 2: Deep-sea Coring Operations on-board the Deep-sea Drilling Vessel Chikyu and Development of Coring Equipment for Stage 3

NASA Astrophysics Data System (ADS)

Shinmoto, Y.; Wada, K.; Miyazaki, E.; Sanada, Y.; Sawada, I.; Yamao, M.

2010-12-01

The Nankai-Trough Seismogenic Zone Experiment (NanTroSEIZE) has carried out several drilling expeditions in the Kumano Basin off the Kii-Peninsula of Japan with the deep-sea scientific drilling vessel Chikyu. Core sampling runs were carried out during the expeditions using an advanced multiple wireline coring system which can continuously core into sections of undersea formations. The core recovery rate with the Rotary Core Barrel (RCB) system was rather low as compared with other methods such as the Hydraulic Piston Coring System (HPCS) and Extended Shoe Coring System (ESCS). Drilling conditions such as hole collapse and sea conditions such as high ship-heave motions need to be analyzed along with differences in lithology, formation hardness, water depth and coring depth in order to develop coring tools, such as the core barrel or core bit, that will yield the highest core recovery and quality. The core bit is especially important in good recovery of high quality cores, however, the PDC cutters were severely damaged during the NanTroSEIZE Stages 1 & 2 expeditions due to severe drilling conditions. In the Stage 1 (riserless coring) the average core recovery was rather low at 38 % with the RCB and many difficulties such as borehole collapse, stick-slip and stuck pipe occurred, causing the damage of several of the PDC cutters. In Stage 2, a new design for the core bit was deployed and core recovery was improved at 67 % for the riserless system and 85 % with the riser. However, due to harsh drilling conditions, the PDC core bit and all of the PDC cutters were completely worn down. Another original core bit was also deployed, however, core recovery performance was low even for plate boundary core samples. This study aims to identify the influence of the RCB system specifically on the recovery rates at each of the holes drilled in the NanTroSEIZE coring expeditions. The drilling parameters such as weight-on-bit, torque, rotary speed and flow rate, etc., were analyzed and conditions such as formation, tools, and sea conditions which directly affect core recovery have been categorized. Also discussed will be the further development of such coring equipment as the core bit and core barrel for the NanTroSEIZE Stage 3 expeditions, which aim to reach a depth of 7000 m-below the sea floor into harder formations under extreme drilling conditions.

MiniX-STR multiplex system population study in Japan and application to degraded DNA analysis.

PubMed

Asamura, H; Sakai, H; Kobayashi, K; Ota, M; Fukushima, H

2006-05-01

We sought to evaluate a more effective system for analyzing X-chromosomal short tandem repeats (X-STRs) in highly degraded DNA. To generate smaller amplicon lengths, we designed new polymerase chain reaction (PCR) primers for DXS7423, DXS6789, DXS101, GATA31E08, DXS8378, DXS7133, DXS7424, and GATA165B12 at X-linked short tandem repeat (STR) loci, devising two miniX-multiplex PCR systems. Among 333 Japanese individuals, these X-linked loci were detected in amplification products ranging in length from 76 to 169 bp, and statistical analyses of the eight loci indicated a high usefulness for the Japanese forensic practice. Results of tests on highly degraded DNA indicated the miniX-STR multiplex strategies to be an effective system for analyzing degraded DNA. We conclude that analysis by the current miniX-STR multiplex systems offers high effectiveness for personal identification from degraded DNA samples.

Sleep and errors in a group of Australian hospital nurses at work and during the commute.

PubMed

Dorrian, Jillian; Tolley, Carolyn; Lamond, Nicole; van den Heuvel, Cameron; Pincombe, Jan; Rogers, Ann E; Drew, Dawson

2008-09-01

There is a paucity of information regarding Australian nurses' sleep and fatigue levels, and whether they result in impairment. Forty-one Australian hospital nurses completed daily logbooks for one month recording work hours, sleep, sleepiness, stress, errors, near errors and observed errors (made by others). Nurses reported exhaustion, stress and struggling to remain (STR) awake at work during one in three shifts. Sleep was significantly reduced on workdays in general, and workdays when an error was reported relative to days off. The primary predictor of error was STR, followed by stress. The primary predictor of extreme drowsiness during the commute was also STR awake, followed by exhaustion, and consecutive shifts. In turn, STR awake was predicted by exhaustion, prior sleep and shift length. Findings highlight the need for further attention to these issues to optimise the safety of nurses and patients in our hospitals, and the community at large on our roads.

Evaluation of a Freezer Mill for Bone Pulverization prior to DNA Extraction: An Improved Workflow for STR Analysis.

PubMed

Morales Colón, Emely; Hernández, Mireya; Candelario, Mariel; Meléndez, María; Dawson Cruz, Tracey

2018-03-01

Traditional methods for bone pulverization typically generate heat, risking stability of DNA sample. SPEX™ has developed cryogenic grinders which introduce liquid nitrogen to cool the sample and aid in the grinding process. In this study, the Freezer Mill 6970 EFM was used with two DNA extraction methods and routine downstream STR analysis procedures. DNA from as little as 0.1 g of bone powder was used to develop full STR profiles after freezer mill pulverization, and the method was reproducible. Further, no contamination was detected upon cleaning/reuse of the sample vials. There were no significant differences in DNA yield, STR alleles detected, or peak heights using the freezer mill as compared to traditional grinding, and successful DNA profiles were achieved from as low as 0.1 g of bone powder with this method. Overall, this work indicates that this cryogenic mill method may be used as a viable alternative to traditional tissue grinders. © 2017 American Academy of Forensic Sciences.

The Potential of Cosmetic Applicators as a Source of DNA for Forensic Analysis.

PubMed

Adamowicz, Michael S; Labonte, Renáe D; Schienman, John E

2015-07-01

Personal products, such as toothbrushes, have been used as both known reference and evidentiary samples for forensic DNA analysis. This study examined the viability of a broad selection of cosmetic applicators for use as targets for human DNA extraction and short tandem repeat (STR) analysis using standard polymerase chain reaction (PCR) conditions. Applicator types included eyeliner smudgers, pencils and crayons, eye shadow sponges, mascara wands, concealer wands, face makeup sponges, pads and brushes, lipsticks and balms, and lip gloss wands. The quantity and quality of DNA extracted from each type of applicator were examined by assessing the number of loci successfully amplified and the peak balance of the heterozygous alleles in each full STR profile. While degraded DNA, stochastic amplification, and PCR inhibition were observed for some items, full STR profiles were developed for 14 of 76 applicators. The face makeup sponge applicators yielded the highest proportional number of full STR profiles (4/7). © 2015 American Academy of Forensic Sciences.

STRBase: a short tandem repeat DNA database for the human identity testing community

PubMed Central

Ruitberg, Christian M.; Reeder, Dennis J.; Butler, John M.

2001-01-01

The National Institute of Standards and Technology (NIST) has compiled and maintained a Short Tandem Repeat DNA Internet Database (http://www.cstl.nist.gov/biotech/strbase/) since 1997 commonly referred to as STRBase. This database is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes. PMID:11125125

New or little-known species of Chaetocladius s. str. Kieffer, 1911 (Diptera: Chironomidae: Orthocladiinae) from the Amur River basin (Russian Far East).

PubMed

Makarchenko, Eugenyi A; Makarchenko, Marina A; Semenchenko, Alexander A

2017-03-27

Chironomids of the subgenus Chaetocladius s. str. from the Amur River basin are revised using both morphological characters and molecular data. Three new species, C. egorych sp. nov., C. lopatinskiy sp. nov. and C. yavorskayae sp. nov., are described and figured. The pupa of C. fedotkin is described for the first time. Adult males of C. ligni and C. piger, little-known in the Far East, are redescribed and annotated, and key to males of the Chaetocladius s. str. from the Amur River basin is provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. Comparisons with corresponding regions of COI between 5 species in the subgenus produced K2P genetic distances of 8.3-12.6%, values well associated with interspecific variation. Molecular data were also used for the reconstruction of the phylogenetic relationships within the subgenus Chaetocladius s. str.

Generation of 2-Furfurylthiol by Carbon-Sulfur Lyase from the Baijiu Yeast Saccharomyces cerevisiae G20.

PubMed

Zha, Musu; Sun, Baoguo; Yin, Sheng; Mehmood, Arshad; Cheng, Lei; Wang, Chengtao

2018-03-07

2-Furfurylthiol is the representative aroma compound of Chinese sesame-flavored baijiu. Previous studies demonstrated that baijiu yeasts could generate 2-furfurylthiol using furfural and l-cysteine as precursors and that the Saccharomyces cerevisiae genes STR3 and CYS3 are closely related to 2-furfurylthiol biosynthesis. To confirm the mechanism of the STR3- and CYS3-gene products on 2-furfurylthiol biosynthesis, their encoded proteins were purified, and we confirmed their activities as carbon-sulfur lyases. Str3p and Cys3p were able to cleave the cysteine-furfural conjugate to release 2-furfurylthiol. Moreover, the characterization of the enzymatic properties of the purified proteins shows good thermal stabilities and wide pH tolerances, which enable their strong potential for various applications. These data provide direct evidence that yeast Str3p and Cys3p release 2-furfurylthiol in vitro, which can be applied to improve baijiu flavor.

A Y-chromosome STR marker should be added to commercial multiplex STR kits.

PubMed

Oz, Carla; Zaken, Neomi; Amiel, Merav; Zamir, Ashira

2008-07-01

Autosomal short tandem repeat (STR) analysis has become highly relevant in the identification of victims from mass disasters and terrorist attacks. In such events, gender misidentification can be of grave consequences, yet the list reporting amelogenin amplification failure using STR multiplex kits continues to grow. Presented here are three such examples. In the first case, we present two male suspects who demonstrated amelogenin Y-deficient results using two commercial kit procedures. The presence of their Y chromosomes was proven by obtaining a Y-haplotype. The second case demonstrated a profile from a third male suspect where only the Y homolog of the XY pair was amplified. In events such as mass disasters or terrorist attacks, timely and reliable high throughput DNA typing results are essential. As the number of reported cases of amplification failure at the amelogenin gene continues to grow, we suggest that the incorporation of a better gender identification tool in commercial kits is crucial.

[Multilocus genotyping of polymorphous STR-loci of chromosomal DNA in individual cells: technical difficulties].

PubMed

Ivanov, P L; Leonov, S N; Zemskova, E Iu; Kobylianskiĭ, A G; Dziubenko, E V

2013-01-01

This study was designed to estimate the effectiveness of special technical procedures for the enhancement of sensitivity of multiplex analysis of DNA, such as the use of low-plexity PCR systems and the whole genome preamplification technology, and the possibility of their application for the purpose of forensic medical genotyping of polymorphous STR-loci of chromosomal DNA in individual cells. The authors refused to use the imitation model (equivalent DNA dilutions) for the sake of obtaining the maximally informative data and chose to work with real preparations of solitary buccal epithelial cells isolated by the laser microdissection technique. It was shown that neither the use of the low-plexity multilocus PCR systems nor the whole genome pre-amplification technology makes possible reliable genotyping of STR-loci of chromosomal DNA in individual cells. The proposed techniques allow for DNA genotyping in preparations consisting of 10 diploid cells whereas the methods for reliable genotyping of STR-loci of chromosomal DNA in individual cells remains to be developed.

Analysis of genetic admixture in Uyghur using the 26 Y-STR loci system

PubMed Central

Bian, Yingnan; Zhang, Suhua; Zhou, Wei; Zhao, Qi; Siqintuya; Zhu, Ruxin; Wang, Zheng; Gao, Yuzhen; Hong, Jie; Lu, Daru; Li, Chengtao

2016-01-01

The Uyghur population has experienced extensive interaction with European and Eastern Asian populations historically. A set of high-resolution genetic markers could be useful to infer the genetic relationships between the Uyghur population and European and Asian populations. In this study we typed 100 unrelated Uyghur males living in southern Xinjiang at 26 Y-STR loci. Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogenetic relationship between the Uyghur population and 23 reference European or Asian populations. We found that the Uyghur population exhibited a genetic admixture of Eastern Asian and European populations, and had a slightly closer relationship with the selected European populations than the Eastern Asian populations. We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic sciences because it has a large power of discrimination and rarely exhibits common haplotypes. However, ancestry inference of Uyghur samples could be challenging due to the admixed nature of the population. PMID:26842947

Y chromosome STR typing in crime casework.

PubMed

Roewer, Lutz

2009-01-01

Since the beginning of the nineties the field of forensic Y chromosome analysis has been successfully developed to become commonplace in laboratories working in crime casework all over the world. The ability to identify male-specific DNA renders highly variable Y-chromosomal polymorphisms, the STR sequences, an invaluable addition to the standard panel of autosomal loci used in forensic genetics. The male-specificity makes the Y chromosome especially useful in cases of male/female cell admixture, namely in sexual assault cases. On the other hand, the haploidy and patrilineal inheritance complicates the interpretation of a Y-STR match, because male relatives share for several generations an identical Y-STR profile. Since paternal relatives tend to live in the geographic and cultural territory of their ancestors, the Y chromosome analysis has a potential to make inferences on the population of origin of a given DNA profile. This review addresses the fields of application of Y chromosome haplotyping, the interpretation of results, databasing efforts and population genetics aspects.

Analysis of genetic admixture in Uyghur using the 26 Y-STR loci system.

PubMed

Bian, Yingnan; Zhang, Suhua; Zhou, Wei; Zhao, Qi; Siqintuya; Zhu, Ruxin; Wang, Zheng; Gao, Yuzhen; Hong, Jie; Lu, Daru; Li, Chengtao

2016-02-04

The Uyghur population has experienced extensive interaction with European and Eastern Asian populations historically. A set of high-resolution genetic markers could be useful to infer the genetic relationships between the Uyghur population and European and Asian populations. In this study we typed 100 unrelated Uyghur males living in southern Xinjiang at 26 Y-STR loci. Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogenetic relationship between the Uyghur population and 23 reference European or Asian populations. We found that the Uyghur population exhibited a genetic admixture of Eastern Asian and European populations, and had a slightly closer relationship with the selected European populations than the Eastern Asian populations. We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic sciences because it has a large power of discrimination and rarely exhibits common haplotypes. However, ancestry inference of Uyghur samples could be challenging due to the admixed nature of the population.

Cessation of cyclic stretch induces atrophy of C2C12 myotubes.

PubMed

Soltow, Quinlyn A; Zeanah, Elizabeth H; Lira, Vitor A; Criswell, David S

2013-05-03

Cyclic stretch of differentiated myotubes mimics the loading pattern of mature skeletal muscle. We tested a cell culture model of disuse atrophy by the cessation of repetitive bouts of cyclic stretch in differentiated C2C12 myotubes. Myotubes were subjected to cyclic strain (12%, 0.7 Hz, 1 h/d) on collagen-I-coated Bioflex plates using a computer-controlled vacuum stretch apparatus (Flexcell Int.) for 2 (2dSTR) or 5 (5dSTR) consecutive days. Control cultures were maintained in the Bioflex plates without cyclic stretch for 2d or 5d. Additionally, some cultures were stretched for 2 d followed by cessation of stretch for 3d (2dSTR3dCES). Cyclic stretching (5dSTR) increased myotube diameter and overall myotube area by ~2-fold (P<0.05) compared to non-stretched controls, while cessation of stretch (2dSTR3dCES) resulted in ~80% smaller myotubes than 5dSTR cells, and 40-50% smaller than non-stretched controls (P<0.05). Further, the calpain-dependent cleavage products of αII-spectrin (150 kDa) and talin increased (3.5-fold and 2.2-fold, respectively; P<0.05) in 2dSTR3dCES myotubes, compared to non-stretched controls. The 1h cyclic stretching protocol acutely increased the phosphorylation of Akt (+4.5-fold; P<0.05) and its downstream targets, FOXO3a (+4.2-fold; P<0.05) and GSK-3β (+1.8-fold; P<0.05), which returned to baseline by 48 h after cessation of stretch. Additionally, nitric oxide production increased during stretch and co-treatment with the NOS inhibitor, l-NAME, inhibited the effects of stretch and cessation of stretch. We conclude that cessation of cyclic stretching causes myotube atrophy by activating calpains and decreasing activation of Akt. Stretch-induced myotube growth, as well as activation of atrophy signaling with cessation of stretch, are dependent on NOS activity. Copyright © 2013 Elsevier Inc. All rights reserved.

Efficacy of Rifampin Plus Clofazimine in a Murine Model of Mycobacterium ulcerans Disease

PubMed Central

Converse, Paul J.; Tyagi, Sandeep; Xing, Yalan; Li, Si-Yang; Kishi, Yoshito; Adamson, John; Nuermberger, Eric L.; Grosset, Jacques H.

2015-01-01

Treatment of Buruli ulcer, or Mycobacterium ulcerans disease, has shifted from surgical excision and skin grafting to antibiotic therapy usually with 8 weeks of daily rifampin (RIF) and streptomycin (STR). Although the results have been highly favorable, administration of STR requires intramuscular injection and carries the risk of side effects, such as hearing loss. Therefore, an all-oral, potentially less toxic, treatment regimen has been sought and encouraged by the World Health Organization. A combination of RIF plus clarithromycin (CLR) has been successful in patients first administered RIF+STR for 2 or 4 weeks. Based on evidence of efficacy of clofazimine (CFZ) in humans and mice with tuberculosis, we hypothesized that the combination of RIF+CFZ would be effective against M. ulcerans in the mouse footpad model of M. ulcerans disease because CFZ has similar MIC against M. tuberculosis and M. ulcerans. For comparison, mice were also treated with the gold standard of RIF+STR, the proposed RIF+CLR alternative regimen, or CFZ alone. Treatment was initiated after development of footpad swelling, when the bacterial burden was 4.64±0.14log10 CFU. At week 2 of treatment, the CFU counts had increased in untreated mice, remained essentially unchanged in mice treated with CFZ alone, decreased modestly with either RIF+CLR or RIF+CFZ, and decreased substantially with RIF+STR. At week 4, on the basis of footpad CFU counts, the combination regimens were ranked as follows: RIF+STR>RIF+CLR>RIF+CFZ. At weeks 6 and 8, none of the mice treated with these regimens had detectable CFU. Footpad swelling declined comparably with all of the combination regimens, as did the levels of detectable mycolactone A/B. In mice treated for only 6 weeks and followed up for 24 weeks, there were no relapses in RIF+STR treated mice, one (5%) relapse in RIF+CFZ-treated mice, but >50% in RIF+CLR treated mice. On the basis of these results, RIF+CFZ has potential as a continuation phase regimen for treatment of M. ulcerans disease. PMID:26042792

Uniqueness of the Isotropic Frame and Usefulness of the Lorentz Transformation

NASA Astrophysics Data System (ADS)

Choi, Yang-Ho

2018-05-01

According to the postulates of the special theory of relativity (STR), physical quantities such as proper times and Doppler shifts can be obtained from any inertial frame by regarding it as isotropic. Nonetheless many inconsistencies arise from the postulates, as shown in this paper. However, there are numerous experimental results that agree with the predictions of STR. It is explained why they are accurate despite the inconsistencies. The Lorentz transformation (LT), unless subject to the postulates of STR, may be a useful method to approach physics problems. As an example to show the usefulness of LT, the problem of the generalized Sagnac effect is solved by utilizing it.

Analytical and Design Study for a High-Pressure, High-Enthalpy Constricted Arc Heater

DTIC Science & Technology

1975-07-01

Stabilized Constricted Arc," NASA Technical Memorandum X-2700, February 1973. Nikuradse, J., "Gesetzm~ssigkeit der turbulenten Str ~ mung in glatten...REFERENCES FOR APPENDIX C Nikuradse, J., "Gesetzm~ssigkeit der turbulenten Str ~ mung in glatten Rohren, °’ Forschungsheft 356 (1932). Watson, V. R. and...qlI) NiT|U/pus| H& STR ~Uol] •G#S ~el~ • *SRbO0(-O• -hOR?RX~*ll -.R IO||•E*O • *) , •?•?l [*SO |.bRS8A[-aS -?~Oq~T•F~aa |5••A~?F*It - ] .~O~t [ -R2

SEADYN87 User’s Manual.

DTIC Science & Technology

1987-07-01

table or "a" (F) 10 STR (1, I) First strain in table or "b" 11 TTD (I) Damping parameter CA1 (FT) (see Note 4) 12 TMX (I) Damping parameter EA1 (F) (see...Note 4) 13 TT (2, I) Second tension in table (F) 14 STR (2, I) Second strain in table 15 TT (20,1) (repeat pairs for all table points) 16 STR (20,1...34, , "DONEŕ t (L Se Notes) 2 MUNG Node or element number 3 NDRT If VTYPE = "NODE" gives the global component direction 1 x 2-Y 4 SFSTAT Static load factor

Two new species of nocturnal bees of the genus Megalopta (Hymenoptera: Halictidae) with keys to species.

PubMed

Gonzalez, Victor H; Griswold, Terry; Ayala, Ricardo

2010-03-01

Megalopta Smith, 1853, is a Neotropical genus of nocturnal or crepuscular bees. Two subgenera are recognized with most of its nearly 30 species placed in the nominate subgenus. Species of Megalopta s. str. are more commonly collected than species of Noctoraptor Engel et al. 1997, all presumably parasites of Megalopta s. str. Two new species of Megalopta are described here: M. (Megalopta) tetewana, n. sp., from Mexico and M. (Noctoraptor) huaoranii, n. sp., from Ecuador. Identification keys to the Central American species of Megalopta s. str. and the species of the parasitic subgenus Noctoraptor are presented.

VR Lab ISS Graphics Models Data Package

NASA Technical Reports Server (NTRS)

Paddock, Eddie; Homan, Dave; Bell, Brad; Miralles, Evely; Hoblit, Jeff

2016-01-01

All the ISS models are saved in AC3D model format which is a text based format that can be loaded into blender and exported to other formats from there including FBX. The models are saved in two different levels of detail, one being labeled "LOWRES" and the other labeled "HIRES". There are two ".str" files (HIRES _ scene _ load.str and LOWRES _ scene _ load.str) that give the hierarchical relationship of the different nodes and the models associated with each node for both the "HIRES" and "LOWRES" model sets. All the images used for texturing are stored in Windows ".bmp" format for easy importing.

Prediction of autosomal STR typing success in ancient and Second World War bone samples.

PubMed

Zupanič Pajnič, Irena; Zupanc, Tomaž; Balažic, Jože; Geršak, Živa Miriam; Stojković, Oliver; Skadrić, Ivan; Črešnar, Matija

2017-03-01

Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded. Therefore the new commercial qPCR kits able to assess the degree of degradation are potentially able to predict the success of downstream short tandem repeat (STR) typing. The goal of this study was to verify the quantification step using the PowerQuant kit with regard to its suitability as a screening method for autosomal STR typing success on ancient and Second World War (WWII) skeletal remains. We analysed 60 skeletons excavated from five archaeological sites and four WWII mass graves from Slovenia. The bones were cleaned, surface contamination was removed and the bones ground to a powder. Genomic DNA was obtained from 0.5g of bone powder after total demineralization. The DNA was purified using a Biorobot EZ1 device. Following PowerQuant quantification, DNA samples were subjected to autosomal STR amplification using the NGM kit. Up to 2.51ng DNA/g of powder were extracted. No inhibition was detected in any of bones analysed. 82% of the WWII bones gave full profiles while 73% of the ancient bones gave profiles not suitable for interpretation. Four bone extracts yielded no detectable amplification or zero quantification results and no profiles were obtained from any of them. Full or useful partial profiles were produced only from bone extracts where short autosomal (Auto) and long degradation (Deg) PowerQuant targets were detected. It is concluded that STR typing of old bones after quantification with the PowerQuant should be performed only when both Auto and Deg targets are detected simultaneously with no respect to [Auto]/[Deg] ratio. Prediction of STR typing success could be made according to successful amplification of Deg fragment. The PowerQuant kit is capable of identifying bone DNA samples that will not yield useful STR profiles using the NGM kit, and it can be used as a predictor of autosomal STR typing success of bone extracts obtained from ancient and WWII skeletal remains. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Evaluation of reliability on STR typing at leukemic patients used for forensic purposes.

PubMed

Filoglu, G; Bulbul, O; Rayimoglu, G; Yediay, F E; Zorlu, T; Ongoren, S; Altuncul, H

2014-06-01

Over the past decades, main advances in the field of molecular biology, coupled with benefits in genomic technologies, have led to detailed molecular investigations in the genetic diversity generated by researchers. Short tandem repeat (STR) loci are polymorphic loci found throughout all eukaryotic genome. DNA profiling identification, parental testing and kinship analysis by analysis of STR loci have been widely used in forensic sciences since 1993. Malignant tissues may sometimes be the source of biological material for forensic analysis, including identification of individuals or paternity testing. There are a number of studies on microsatellite instability in different types of tumors by comparing the STR profiles of malignant and healthy tissues on the same individuals. Defects in DNA repair pathways (non-repair or mis-repair) and metabolism lead to an accumulation of microsatellite alterations in genomic DNA of various cancer types that result genomic instabilities on forensic analyses. Common forms of genomic instability are loss of heterozygosity (LOH) and microsatellite instability (MSI). In this study, the applicability of autosomal STR markers, which are routinely used in forensic analysis, were investigated in order to detect genotypes in blood samples collected from leukemic patients to estimate the reliability of the results when malignant tissues are used as a source of forensic individual identification. Specimens were collected from 90 acute and 10 chronic leukemia volunteers with oral swabs as well as their paired peripheral blood samples from the Oncology Centre of the Department of Hematology at Istanbul University, during the years 2010-2011. Specimens were tested and compared with 16 somatic STR loci (CSFIPO, THO1, TPOX, vWA, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11 and FGA) widely used in forensic identification and kinship. Only two STR instabilities were encountered among 100 specimens. An MSI in the FGA loci and a LOH in the D2S1338 loci were determined in two individuals separately. Our results demonstrate that the use of the biological samples from leukemia patients in forensic identification and kinship testing is questionable, especially if known microsatellite instability is available. Genetic instabilities may alter the STR polymorphism, leading to potential errors on forensic identification of individuals. Therefore, typing of autosomal STRs from leukemia patients should be performed with both healthy and malignant tissue samples of individual as references.

FaSTR DNA: a new expert system for forensic DNA analysis.

PubMed

Power, Timothy; McCabe, Brendan; Harbison, Sally Ann

2008-06-01

The automation of DNA profile analysis of reference and crime samples continues to gain pace driven in part by a realisation by the criminal justice system of the positive impact DNA technology can have in aiding in the solution of crime and the apprehension of suspects. Expert systems to automate the profile analysis component of the process are beginning to be developed. In this paper, we report the validation of a new expert system FaSTR DNA, an expert system suitable for the analysis of DNA profiles from single source reference samples and from crime samples. We compare the performance of FaSTR DNA with that of other equivalent systems, GeneMapper ID v3.2 (Applied Biosystems, Foster City, CA) and FSS-i(3) v4 (The Forensic Science Service((R)) DNA expert System Suite FSS-i(3), Forensic Science Service, Birmingham, UK) with GeneScan Analysis v3.7/Genotyper v3.7 software (Applied Biosystems, Foster City, CA, USA) with manual review. We have shown that FaSTR DNA provides an alternative solution to automating DNA profile analysis and is appropriate for implementation into forensic laboratories. The FaSTR DNA system was demonstrated to be comparable in performance to that of GeneMapper ID v3.2 and superior to that of FSS-i(3) v4 for the analysis of DNA profiles from crime samples.

High-level production of violacein by the newly isolated Duganella violaceinigra str. NI28 and its impact on Staphylococcus aureus

PubMed Central

Choi, Seong Yeol; Kim, Sooyeon; Lyuck, Sungsoo; Kim, Seung Bum; Mitchell, Robert J.

2015-01-01

A violacein-producing bacterial strain was isolated and identified as a relative of Duganella violaceinigra YIM 31327 based upon phylogenetic analyses using the 16S rRNA, gyrB and vioA gene sequences and a fatty acid methyl ester (FAME) analysis. This new strain was designated D. violaceinigra str. NI28. Although these two strains appear related based upon these analyses, the new isolate was phenotypically different from the type strain as it grew 25% faster on nutrient media and produced 45-fold more violacein. When compared with several other violacein producing strains, including Janthinobacterium lividum, D. violaceinigra str. NI28 was the best violacein producer. For instance, the crude violacein yield with D. violaceinigra str. NI28 was 6.0 mg/OD at 24 hours, a value that was more than two-fold higher than all the other strains. Finally, the antibacterial activity of D. violaceinigra str. NI28 crude violacein was assayed using several multidrug resistant Staphylococcus aureus. Addition of 30 μM crude violacein led to a 96% loss in the initial S. aureus population while the minimum inhibitory concentration was 1.8 μM. Consequently, this novel isolate represents a phenotypic variant of D. violaceinigra capable of producing much greater quantities of crude violacein, an antibiotic effective against multidrug resistant S. aureus. PMID:26489441

High-level production of violacein by the newly isolated Duganella violaceinigra str. NI28 and its impact on Staphylococcus aureus.

PubMed

Choi, Seong Yeol; Kim, Sooyeon; Lyuck, Sungsoo; Kim, Seung Bum; Mitchell, Robert J

2015-10-22

A violacein-producing bacterial strain was isolated and identified as a relative of Duganella violaceinigra YIM 31327 based upon phylogenetic analyses using the 16S rRNA, gyrB and vioA gene sequences and a fatty acid methyl ester (FAME) analysis. This new strain was designated D. violaceinigra str. NI28. Although these two strains appear related based upon these analyses, the new isolate was phenotypically different from the type strain as it grew 25% faster on nutrient media and produced 45-fold more violacein. When compared with several other violacein producing strains, including Janthinobacterium lividum, D. violaceinigra str. NI28 was the best violacein producer. For instance, the crude violacein yield with D. violaceinigra str. NI28 was 6.0 mg/OD at 24 hours, a value that was more than two-fold higher than all the other strains. Finally, the antibacterial activity of D. violaceinigra str. NI28 crude violacein was assayed using several multidrug resistant Staphylococcus aureus. Addition of 30 μM crude violacein led to a 96% loss in the initial S. aureus population while the minimum inhibitory concentration was 1.8 μM. Consequently, this novel isolate represents a phenotypic variant of D. violaceinigra capable of producing much greater quantities of crude violacein, an antibiotic effective against multidrug resistant S. aureus.

Co-overexpression of geraniol-10-hydroxylase and strictosidine synthase improves anti-cancer drug camptothecin accumulation in Ophiorrhiza pumila

PubMed Central

Cui, Lijie; Ni, Xiaoling; Ji, Qian; Teng, Xiaojuan; Yang, Yanru; Wu, Chao; Zekria, David; Zhang, Dasheng; Kai, Guoyin

2015-01-01

Camptothecin (CPT) belongs to a group of monoterpenoidindole alkaloids (TIAs) and its derivatives such as irinothecan and topothecan have been widely used worldwide for the treatment of cancer, giving rise to rapidly increasing market demands. Genes from Catharanthus roseus encoding strictosidine synthase (STR) and geraniol 10-hydroxylase (G10H), were separately and simultaneously introduced into Ophiorrhiza pumila hairy roots. Overexpression of individual G10H (G lines) significantly improved CPT production with respect to non-transgenic hairy root cultures (NC line) and single STR overexpressing lines (S lines), indicating that G10H plays a more important role in stimulating CPT accumulation than STR in O. pumila. Furthermore, co-overexpression of G10H and STR genes (SG Lines) caused a 56% increase on the yields of CPT compared to NC line and single gene transgenic lines, showed that simultaneous introduction of G10H and STR can produce a synergistic effect on CPT biosynthesis in O. pumila. The MTT assay results indicated that CPT extracted from different lines showed similar anti-tumor activity, suggesting that transgenic O. pumila hairy root lines could be an alternative approach to obtain CPT. To our knowledge, this is the first report on the enhancement of CPT production in O. pumila employing a metabolic engineering strategy. PMID:25648209

Exploring the applicability of analysing X chromosome STRs in Brazilian admixed population.

PubMed

Auler-Bittencourt, Eloisa; Iwamura, Edna Sadayo Miazato; Lima, Maria Jenny Mitraud; da Silva, Ismael Dale Cotrim Guerreiro; dos Santos, Sidney Emannuel Batista

2015-09-01

Kinship and parentage analyses always involve one sample being compared to another sample or a few samples with a specific relationship question in mind. In most cases, the analysis of autosomal STR markers is sufficient to determine the genetic kinship. However, when genetic profiles are reconstructed from supposed relatives, for whom the family configuration available for analysis is deficient, the examination may be inconclusive. This study reports practical examples of actual cases analysing the efficiency of the chromosome X STR (STR-ChrX) markers. Three cases with different degrees of efficiency and impact were selected as follows: the identification of two charred bodies in a traffic accident, in which the family setting available was not complete, and one filiation analysis resulting from rape. This is the first paper reporting the use of the multiplex STR 12 ChrX in actual cases using the software Familias 1.8 and Brazilian regional frequency data. Our study clarifies the complex analysis using this powerful tool for professionals in the forensic science community, for both civil and criminal justice. We also discuss state-of-the-art ChrX STR markers and its implications and applications for legal procedures. The data presented here should be used in other studies of complex cases to improve the progress of the current justice system. Copyright © 2015 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

Effects of Streptomycin Administration on Increases in Skeletal Muscle Fiber Permeability and Size Following Eccentric Muscle Contractions.

PubMed

Hayao, Keishi; Tamaki, Hiroyuki; Nakagawa, Kouki; Tamakoshi, Keigo; Takahashi, Hideaki; Yotani, Kengo; Ogita, Futoshi; Yamamoto, Noriaki; Onishi, Hideaki

2018-06-01

The purpose of this study was to investigate the preventive effect of streptomycin (Str) administration on changes in membrane permeability and the histomorphological characteristics of damaged muscle fibers following eccentric contraction (ECC ). Eighteen 7-week-old male Fischer 344 rats were randomly assigned to three groups: control (Cont), ECC, and ECC with Str (ECC + Str). The tibialis anterior (TA) muscles in both ECC groups were stimulated electrically and exhibited ECC. Evans blue dye (EBD), a marker of muscle fiber damage associated with increased membrane permeability, was injected 24 hr before TA muscle sampling. The number of EBD-positive fibers, muscle fiber cross-sectional area (CSA), and roundness were determined via histomorphological analysis. The ECC intervention resulted in an increased fraction of EBD-positive fibers, a larger CSA, and decreased roundness. The fraction of EBD-positive fibers was 79% lower in the ECC + Str group than in the ECC group. However, there was no difference in the CSA and roundness of the EBD-positive fibers between the two ECC groups. These results suggest that Str administration can reduce the number of myofibers that increase membrane permeability following ECC, but does not ameliorate the extent of fiber swelling in extant EBD-positive fibers. Anat Rec, 301:1096-1102, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

CCD Strömvil Photometry of M 37

NASA Astrophysics Data System (ADS)

Boyle, R. P.; Janusz, R.; Kazlauskas, A.; Philip, A. G. Davis

2001-12-01

We have been working on a program of setting up standards in the Strömvil photometric system and have been doing CCD photometry of globular and open clusters. A previous paper (Boyle et al. BAAS, AAS Meeting #193, #68.08) described the results of observations made in the open cluster M 67, which we are setting up as one of the prime standard fields for Strömvil photometry. Now we discuss our observations of M 37, made on the Vatican Advanced Technology Telescope on Mt. Graham, Arizona. One of us (R.J.) has automated the data processing by a novel method. The Strömvil group is multinational. By use of this innovative automated, yet interactive processing method, one systematically applies the same processing steps to run in IRAF by capturing them as presented in html files and submitting them to the IRAF command language. Use of the mouse avoids errors and accelerates the processing from raw data frames to calibrated photometry. From several G2 V stars in M 67 we have calculated their mean color indices and compare them to stars in M 37 to identify candidate G2 V stars there. Identifying such stars relates to the search for terrestrial exoplanets. Ultimately we will use the calibrated Strömvil indices to make photometric determinations of log g and Teff.

A Photometric Observing Program at the VATT: Setting Up a Calibration Field

NASA Astrophysics Data System (ADS)

Davis Philip, A. G.; Boyle, R. P.; Janusz, R.

2009-05-01

Philip and Boyle have been making Strömgren and then Strömvil photometric observations of open and globular clusters at the Vatican Advanced Technology Telescope located on Mt. Graham in Arizona. Our aim is to obtain CCD photometric indices good to 0.01 magnitude. Indices of this quality can later be analyzed to yield estimates of temperature, luminosity and metallicity. But we have found that the CCD chip does not yield photometry of this quality without further corrections. Our most observed cluster is the open cluster, M 67. This cluster is also very well observed in the literature. We took the best published values and created a set of "standard" stars for our field. Taking our CCD results we could calculate deltas, as a function of position on the chip, which we then applied to all the CCD frames that we obtained. With this procedure we were able to obtain the precision of 0.01 magnitudes in all the fields that we observed. When we started we were able to use the "A" two-inch square Strömgren four-color set from KPNO. Later the Vatican Observatory bought a set of 3.48 inch square Strömgren filters, The Vatican Observatory had a set of circular Vilnius filters There was also an X filter. These eight filters made our Strömvil set.

[The mutation analysis of PAH gene and prenatal diagnosis in classical phenylketonuria family].

PubMed

Yan, Yousheng; Hao, Shengju; Yao, Fengxia; Sun, Qingmei; Zheng, Lei; Zhang, Qinghua; Zhang, Chuan; Yang, Tao; Huang, Shangzhi

2014-12-01

To characterize the mutation spectrum of phenylalanine hydroxylase (PAH) gene and perform prenatal diagnosis for families with classical phenylketonuria. By stratified sequencing, mutations were detected in the exons and flaking introns of PAH gene of 44 families with classical phenylketonuria. 47 fetuses were diagnosed by combined sequencing with linkage analysis of three common short tandem repeats (STR) (PAH-STR, PAH-26 and PAH-32) in the PAH gene. Thirty-one types of mutations were identified. A total of 84 mutations were identified in 88 alleles (95.45%), in which the most common mutation have been R243Q (21.59%), EX6-96A>G (6.82%), IVS4-1G>A (5.86%) and IVS7+2T>A (5.86%). Most mutations were found in exons 3, 5, 6, 7, 11 and 12. The polymorphism information content (PIC) of these three STR markers was 0.71 (PAH-STR), 0.48 (PAH-26) and 0.40 (PAH-32), respectively. Prenatal diagnosis was performed successfully with the combined method in 47 fetuses of 44 classical phenylketonuria families. Among them, 11 (23.4%) were diagnosed as affected, 24 (51.1%) as carriers, and 12 (25.5%) as unaffected. Prenatal diagnosis can be achieved efficiently and accurately by stratified sequencing of PAH gene and linkage analysis of STR for classical phenylketonuria families.

A rapid nuclear staining test using cationic dyes contributes to efficient STR analysis of telogen hair roots.

PubMed

Lee, So-Yeon; Ha, Eun-Ju; Woo, Seung-Kyun; Lee, So-Min; Lim, Kyung-Hee; Eom, Yong-Bin

2017-07-01

Telogen hairs presented in the crime scene are commonly encountered as trace evidence. However, short tandem repeat (STR) profiling of the hairs currently have low and limited use due to poor success rate. To increase the success rate of STR profiling of telogen hairs, we developed a rapid and cost-effective method to estimate the number of nuclei in the hair roots. Five cationic dyes, Methyl green (MG), Harris hematoxylin (HH), Methylene blue (MB), Toluidine blue (TB), and Safranin O (SO) were evaluated in this study. We conducted a screening test based on microscopy and the percentage of loss with nuclear DNA, in order to select the best dye. MG was selected based on its specific nuclei staining and low adverse effect on the hair-associated nuclear DNA. We examined 330 scalp and 100 pubic telogen hairs with MG. Stained hairs were classified into five groups and analyzed by STR. The fast staining method revealed 70% (head hair) and 33.4% (pubic hair) of full (30 alleles) and high partial (18-29 alleles) STR profiling proportion from the lowest nuclei count group (one to ten nuclei). The results of this study demonstrated a rapid, specific, nondestructive, and high yield DNA profiling method applicable for screening telogen hairs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Symposium on Molecular Spectroscopy (38th) Held at Ohio State University, Columbus, Ohio on June 13-17 1983.

DTIC Science & Technology

1983-01-01

L .--TP11(E 14), GILLIBS, C-TG3, T44 BROWN, P . B . -- 316 BH1(r 15) GINGERICH, K . A. -- 18M BROWN, L . R.--TE1I, HIS DOANY, P . S ...POLAVARAPU, P . L .--RCB, RC9 SAMS, R. L . -ME1 NAGARATRNA, H. M.--RH4 Presiding over Sessions SANDHOLM, S . T.--TE3 NAKAGAWA, K .--TE4 TH end THI SASS, CRAIG...INTENSITIES IN THE A-X AND B -X CANCELLED TRANSITIONS ................................................................. 10 min. K . S .

[Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (Oncorhynchus nerka) from Eastern and Western Kamchatka].

PubMed

Khrustaleva, A M; Volkov, A A; Stoklitskaia, D S; Miuge, N S; Zelenina, D A

2010-11-01

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.

Forensic parameters of the X-STR Decaplex system in Mexican populations.

PubMed

Mariscal Ramos, C; Martínez-Cortes, G; Ramos-González, B; Rangel-Villalobos, H

2018-03-01

We studied the X-STR decaplex system in 529 DNA female samples of Mexican populations from five geographic regions. Allele frequencies and forensic parameters were estimated in each region and in the pooled Mexican population. Genotype distribution by locus was in agreement with Hardy-Weinberg expectations in each Mexican population sample. Similarly, linkage equilibrium was demonstrated between pair of loci. Pairwise comparisons and genetic distances between Mexican, Iberoamerican and one African populations were estimated and graphically represented. Interestingly, a non-significant interpopulation differentiation was detected (Fst = 0.0021; p = .74389), which allows using a global Mexican database for forensic interpretation of X-STR genotypes. Copyright © 2017 Elsevier B.V. All rights reserved.

Solar thermal propulsion for planetary spacecraft

NASA Technical Reports Server (NTRS)

Sercel, J. C.

1985-01-01

Previous studies have shown that many desirable planetary exploration missions require large injection delta-V. Solar Thermal Rocket (STR) propulsion, under study for orbit-raising applications may enhance or enable such high-energy missions. The required technology of thermal control for liquid hydrogen propellant is available for the required storage duration. Self-deploying, inflatable solar concentrators are under study. The mass penalty for passive cryogenic thermal control, liquid hydrogen tanks and solar concentrators does not compromise the specific impulse advantage afforded by the STR as compared to chemical propulsion systems. An STR injection module is characterized and performance is evaluated by comparison to electric propulsion options for the Saturn Orbiter Titan Probe (SOTP) and Uranus Flyby Uranus Probe (UFUP) missions.

Non-aqueous electrolytes for electrochemical cells

DOEpatents

Dong, Jian; Zhang, Zhengcheng; Amine, Khalil

2016-07-12

A electrolyte for a lithium battery includes a silane/siloxane compound represented by SiR.sub.4-x-yR'.sub.xR''.sub.y, by Formula II, or Formula III: ##STR00001## where each R is individually an alkenyl, alkynyl, alk(poly)enyl, alk(poly)ynyl, aryl; each R' is represented by; ##STR00002## each R'' is represented by Formula I-B; ##STR00003## R.sup.1 is an organic spacer; R.sup.2 is a bond or an organic spacer; R.sup.3 is alkyl or aryl; k is 1-15; m is 1-15; n is 1 or 2; p is 1-3; x' is 1-2; and y' is 0-2.

Functionalized polyfluorenes for use in optoelectronic devices

DOEpatents

Chichak, Kelly Scott [Clifton Park, NY; Lewis, Larry Neil [Scotia, NY; Cella, James Anthony [Clifton Park, NY; Shiang, Joseph John [Niskayuna, NY

2011-11-01

The present invention relates to process comprising reacting a polyfluorenes comprising at least one structural group of formula I ##STR00001## with an iridium (III) compound of formula II ##STR00002## The invention also relates to the polyfluorenes, which are products of the reaction, and the use of the polyfluorenes in optoelectronic devices.

Performance testing of a semi-automatic card punch system, using direct STR profiling of DNA from blood samples on FTA™ cards.

PubMed

Ogden, Samantha J; Horton, Jeffrey K; Stubbs, Simon L; Tatnell, Peter J

2015-01-01

The 1.2 mm Electric Coring Tool (e-Core™) was developed to increase the throughput of FTA(™) sample collection cards used during forensic workflows and is similar to a 1.2 mm Harris manual micro-punch for sampling dried blood spots. Direct short tandem repeat (STR) DNA profiling was used to compare samples taken by the e-Core tool with those taken by the manual micro-punch. The performance of the e-Core device was evaluated using a commercially available PowerPlex™ 18D STR System. In addition, an analysis was performed that investigated the potential carryover of DNA via the e-Core punch from one FTA disc to another. This contamination study was carried out using Applied Biosystems AmpflSTR™ Identifiler™ Direct PCR Amplification kits. The e-Core instrument does not contaminate FTA discs when a cleaning punch is used following excision of discs containing samples and generates STR profiles that are comparable to those generated by the manual micro-punch. © 2014 American Academy of Forensic Sciences.

[Analysis of genetic polymorphisms and mutations of 20 frequently used STR loci among ethnic Hans from Henan].

PubMed

Wang, Hongdan; Kang, Bing; Gao, Yue; Huo, Xiaodong; Li, Tao; Guo, Qiannan; Zhu, Bofeng; Liao, Shixiu

2017-04-10

To study the genetic polymorphisms and mutations of 20 frequently used autosomal microsatellites among ethnic Hans from Henan. Peripheral blood samples of 2604 individuals were collected. DNA was amplified and genotyped using a PowerPlex(TM) 21 system. The frequencies, forensic parameters and mutation rates of the 20 short tandem repeat (STR) loci were analyzed. A total of 323 alleles were found in this population and the allelic frequencies have ranged from 0.0003 to 0.5144. Except for D3S1358, TH01 and TPOX, mutations have been found in all of the remaining 17 STR loci, which totaled 47, with mutation rates ranging from 0 to 3.46 × 10 -3 . The 20 STR loci selected by the PowerPlex(TM) 21 system are highly polymorphic among ethnic Hans from Henan, and may be of great value in forensic and human population studies. As no similar study has been carried out previously, above results may be of great value for individual discrimination and paternal testing.

Diverse Host-Seeking Behaviors of Skin-Penetrating Nematodes

PubMed Central

Castelletto, Michelle L.; Gang, Spencer S.; Okubo, Ryo P.; Tselikova, Anastassia A.; Nolan, Thomas J.; Platzer, Edward G.; Lok, James B.; Hallem, Elissa A.

2014-01-01

Skin-penetrating parasitic nematodes infect approximately one billion people worldwide and are responsible for some of the most common neglected tropical diseases. The infective larvae of skin-penetrating nematodes are thought to search for hosts using sensory cues, yet their host-seeking behavior is poorly understood. We conducted an in-depth analysis of host seeking in the skin-penetrating human parasite Strongyloides stercoralis, and compared its behavior to that of other parasitic nematodes. We found that Str. stercoralis is highly mobile relative to other parasitic nematodes and uses a cruising strategy for finding hosts. Str. stercoralis shows robust attraction to a diverse array of human skin and sweat odorants, most of which are known mosquito attractants. Olfactory preferences of Str. stercoralis vary across life stages, suggesting a mechanism by which host seeking is limited to infective larvae. A comparison of odor-driven behavior in Str. stercoralis and six other nematode species revealed that parasite olfactory preferences reflect host specificity rather than phylogeny, suggesting an important role for olfaction in host selection. Our results may enable the development of new strategies for combating harmful nematode infections. PMID:25121736

Post-Mortem Identification of a Fire Carbonized Body by STR Genotyping.

PubMed

Dumache, Raluca; Muresan, Camelia; Ciocan, Veronica; Rogobete, Alexandru F; Enache, Alexandra

2016-10-01

Identification of bodies of unknown identity that are victims of exposure to very high temperatures, resulting from fires, plane crashes, and terrorist attacks, represents one of the most difficult sides of forensic genetics, because of the advanced state of decomposition. The aim of this study was the identification of the carbonized cadaver of a fire victim through STR genotyping. We used blood samples obtained from the iliac artery during the autopsy examination as biological samples from the unidentified victim. After DNA isolation and quantification, we proceeded to its amplification using the multiplex PCR kit AmpFlSTR Identifiler. The DNA products were separated using an ABI 3500 genetic analyzer. Further analysis of the data was done using Gene Mapper ID-X version 1.4 software. In this case, it was possible to obtain a complete DNA profile from the biological samples. Due to the fact that the amelogenin gene presented two alleles, X and Y, we concluded that the victim was a man. We conclude that STR profiling of unidentified bodies (carbonized, decomposed) represents a powerful method of human identification in forensic medicine.

Identification of genomic islands in six plant pathogens.

PubMed

Chen, Ling-Ling

2006-06-07

Genomic islands (GIs) play important roles in microbial evolution, which are acquired by horizontal gene transfer. In this paper, the GIs of six completely sequenced plant pathogens are identified using a windowless method based on Z curve representation of DNA sequences. Consequently, four, eight, four, one, two and four GIs are recognized with the length greater than 20-Kb in plant pathogens Agrobacterium tumefaciens str. C58, Rolstonia solanacearum GMI1000, Xanthomonas axonopodis pv. citri str. 306 (Xac), Xanthomonas campestris pv. campestris str. ATCC33913 (Xcc), Xylella fastidiosa 9a5c and Pseudomonas syringae pv. tomato str. DC3000, respectively. Most of these regions share a set of conserved features of GIs, including an abrupt change in GC content compared with that of the rest of the genome, the existence of integrase genes at the junction, the use of tRNA as the integration sites, the presence of genetic mobility genes, the difference of codon usage, codon preference and amino acid usage, etc. The identification of these GIs will benefit the research for the six important phytopathogens.

Concordance study between the ParaDNA® Intelligence Test, a rapid DNA profiling assay, and a conventional STR typing kit (AmpFlSTR® SGM Plus®).

PubMed

Ball, G; Dawnay, N; Stafford-Allen, B; Panasiuk, M; Rendell, P; Blackman, S; Duxbury, N; Wells, S

2015-05-01

The ParaDNA® Intelligence Test enables STR profiling directly from human biological samples and evidence items collected from crime scene in 75min. Designed for non-expert use this system allows DNA information to be available to investigators before it would typically be available from a laboratory. The ParaDNA Intelligence Test system amplifies D3S1358, D8S119, D16S539, D18S1358 and TH01 STR loci and the gender typing locus amelogenin and detects the alleles present with HyBeacon® probes. Individual DNA samples from 381 UK Caucasian individuals were analysed using AmpFlSTR® SGM Plus® and the ParaDNA Intelligence Test with the derived STR profiles compared. Here we describe the high level of concordance demonstrated between the two systems and discuss this with reference to allele frequencies and the discriminatory power offered by the ParaDNA Intelligence Test. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Low-template methods yield limited extra information for PowerPlex® Fusion 6C profiling.

PubMed

Duijs, Francisca; van de Merwe, Linda; Sijen, Titia; Benschop, Corina C G

2018-06-01

Advances in autosomal DNA profiling systems enable analyzing increased numbers of short tandem repeat (STR) loci in one reaction. Increasing the number of STR loci increases the amount of information that may be obtained from a (crime scene) sample. In this study, we examined whether even more allelic information can be obtained by applying low-template methods. To this aim, the performance of the PowerPlex® Fusion 6C STR typing system was assessed when increasing the number of PCR cycles or enhancing the capillary electrophoresis (CE) injection settings. Results show that applying these low-template methods yields limited extra information and comes at cost of more background noise. In addition, the gain in detection of alleles was much smaller when compared to the gain when applying low-template methods to the 15-loci AmpFLSTR® NGM™ system. Consequently, the PowerPlex® Fusion 6C STR typing system was implemented using standard settings only; low-template methods were not implemented for our routine forensic casework. Copyright © 2018 Elsevier B.V. All rights reserved.

An Accelerated Analytical Process for the Development of STR Profiles for Casework Samples.

PubMed

Laurin, Nancy; Frégeau, Chantal J

2015-07-01

Significant efforts are being devoted to the development of methods enabling rapid generation of short tandem repeat (STR) profiles in order to reduce turnaround times for the delivery of human identification results from biological evidence. Some of the proposed solutions are still costly and low throughput. This study describes the optimization of an analytical process enabling the generation of complete STR profiles (single-source or mixed profiles) for human identification in approximately 5 h. This accelerated process uses currently available reagents and standard laboratory equipment. It includes a 30-min lysis step, a 27-min DNA extraction using the Promega Maxwell(®) 16 System, DNA quantification in <1 h using the Qiagen Investigator(®) Quantiplex HYres kit, fast amplification (<26 min) of the loci included in AmpFℓSTR(®) Identifiler(®), and analysis of the profiles on the 3500-series Genetic Analyzer. This combination of fast individual steps produces high-quality profiling results and offers a cost-effective alternative approach to rapid DNA analysis. © 2015 American Academy of Forensic Sciences.

The Readiness to Change for Bariatric Surgery Assessment Tool: Validity, Factor Structure, and Reliability.

PubMed

Carlson, Susan M S

2017-11-01

Currently, there is no guideline or standard of practice for performing the psychiatric/psychological evaluation that is a requirement for approval for bariatric surgery. The Readiness to Change for Bariatric Surgery Assessment Tool (RCB-SAT) establishes a means for psychiatric evaluators to objectively assess the patient's cognition, beliefs, and motivation around the bariatric diet and lifestyle changes. Development of a clinical decision-making tool for assessing readiness to change in bariatric patients will be useful regarding The Strategic Plan for NIH Obesity Research. The strategic plan outlines 6 overarching themes, with the last 3 centering around creation of such a clinical decision-making tool to assess a bariatric patient's readiness to change: evaluate promising strategies for obesity prevention and treatment in realworld settings and diverse populations, harness technology and tools to advance obesity research and improve health care delivery, and facilitate integration of research results into community programs and medical practice (National Institutes of Health, 2011). The pilot tool was administered to 153 potential bariatric patients, with 61 patients completing the survey a second time. Face and content validity of the items were established through an expert review process. Principle axis factoring by means of varimax rotation with Kaiser normalization identified 15 items loading on 3 factors associated with Prochaska and DiClemente's transtheoretical model of health behavior change: precontemplation, contemplation, and action (DiClemente & Prochaska, 1998). Test-retest reliability was also established for the tool. The proposed RCB-SAT demonstrates potential for assessing a patient's readiness to change regarding the bariatric diet and lifestyle.

The effect of external coaptation on plate deformation in an ex vivo model of canine pancarpal arthrodesis.

PubMed

Woods, S; Wallace, R J; Mosley, J R

2012-01-01

Since external coaptation is applied clinically to prevent plate failure during healing in canine pancarpal arthrodesis (PCA), we tested the hypothesis that external coaptation does not significantly reduce plate strain in an experimental ex vivo model of canine PCA. Ten thoracic limbs from healthy Greyhounds euthanatized for reasons un- related to the study were harvested and the carpus was stabilised with a dorsally applied 2.7/3.5 mm hybrid PCA plate. The strain in the plate adjacent to the most distal radial screw hole (R4) and the radial carpal bone (RCB) screw hole was measured as the limbs were loaded axially to a load that approximated that of controlled walking. Each limb was tested with and without external coaptation in place. Mean strain amplitude at the RCB was -177.2 με (± 20.78) without external coaptation. Following cast application, strain reduced significantly to -34.7 με (± 9.84) (p <0.002). Mean strain at R4 was -89.4 με (± 22.10) without external support and -66.9 με (± 10.74) following application of a cast. This reduction in recorded strain was not statistically significant. The application of a cast to the distal portion of the limb significantly reduced strain in the 2.7/3.5 mm hybrid PCA plate, but the magnitude of the measured strain was low, suggesting that fatigue damage is unlikely to accumulate as a result of this type of loading and that external coaptation may not be necessary to prevent fatigue failure of the plate.

Influence of ventral tegmental area input on cortico-subcortical networks underlying action control and decision making.

PubMed

Richter, Anja; Gruber, Oliver

2018-02-01

It is argued that the mesolimbic system has a more general function in processing all salient events, including and extending beyond rewards. Saliency was defined as an event that is unexpected due to its frequency of occurrence and elicits an attentional-behavioral switch. Using functional magnetic resonance imaging (fMRI), signals were measured in response to the modulation of salience of rewarding and nonrewarding events during a reward-based decision making task, the so called desire-reason dilemma paradigm (DRD). Replicating previous findings, both frequent and infrequent, and therefore salient, reward stimuli elicited reliable activation of the ventral tegmental area (VTA) and ventral striatum (vStr). When immediate reward desiring contradicted the superordinate task-goal, we found an increased activation of the VTA and vStr when the salient reward stimuli were presented compared to the nonsalient reward stimuli, indicating a boosting of activation in these brain regions. Furthermore, we found a significantly increased functional connectivity between the VTA and vStr, confirming the boosting of vStr activation via VTA input. Moreover, saliency per se without a reward association led to an increased activation of brain regions in the mesolimbic reward system as well as the orbitofrontal cortex (OFC), inferior frontal gyrus (IFG), and anterior cingulate cortex (ACC). Finally, findings uncovered multiple increased functional interactions between cortical saliency-processing brain areas and the VTA and vStr underlying detection and processing of salient events and adaptive decision making. © 2017 Wiley Periodicals, Inc.

FvSTR1, a striatin orthologue in Fusarium virguliforme, is required for asexual development and virulence.

PubMed

Islam, Kazi T; Bond, Jason P; Fakhoury, Ahmad M

2017-08-01

The soil-borne fungus Fusarium virguliforme causes sudden death syndrome (SDS), one of the most devastating diseases of soybean in North and South America. Despite the importance of SDS, a clear understanding of the fungal pathogenicity factors that affect the development of this disease is still lacking. We have identified FvSTR1, a F. virguliforme gene, which encodes a protein similar to a family of striatin proteins previously reported to regulate signalling pathways, cell differentiation, conidiation, sexual development, and virulence in filamentous fungi. Striatins are multi-domain proteins that serve as scaffolding units in the striatin-interacting phosphatase and kinase (STRIPAK) complex in fungi and animals. To address the function of a striatin homologue in F. virguliforme, FvSTR1 was disrupted and functionally characterized using a gene knock out strategy. The resulting Fvstr1 mutants were largely impaired in conidiation and pigmentation, and displayed defective conidia and conidiophore morphology compared to the wild-type and ectopic transformants. Greenhouse virulence assays revealed that the disruption of FvSTR1 resulted in complete loss of virulence in F. virguliforme. Microtome studies using fluorescence microscopy showed that the Fvstr1 mutants were defective in their ability to colonize the vascular system. The Fvstr1 mutants also showed a reduced transcript level of genes involved in asexual reproduction and in the production of secondary metabolites. These results suggest that FvSTR1 has a critical role in asexual development and virulence in F. virguliforme.

Rapid single nucleotide polymorphism based method for hematopoietic chimerism analysis and monitoring using high-speed droplet allele-specific PCR and allele-specific quantitative PCR.

PubMed

Taira, Chiaki; Matsuda, Kazuyuki; Yamaguchi, Akemi; Uehara, Masayuki; Sugano, Mitsutoshi; Okumura, Nobuo; Honda, Takayuki

2015-05-20

Chimerism analysis is important for the evaluation of engraftment and predicting relapse following hematopoietic stem cell transplantation (HSCT). We developed a chimerism analysis for single nucleotide polymorphisms (SNPs), including rapid screening of the discriminable donor/recipient alleles using droplet allele-specific PCR (droplet-AS-PCR) pre-HSCT and quantitation of recipient DNA using AS-quantitative PCR (AS-qPCR) following HSCT. SNP genotyping of 20 donor/recipient pairs via droplet-AS-PCR and the evaluation of the informativity of 5 SNP markers for chimerism analysis were performed. Samples from six follow-up patients were analyzed to assess the chimerism via AS-qPCR. These results were compared with that determined by short tandem repeat PCR (STR-PCR). Droplet-AS-PCR could determine genotypes within 8min. The total informativity using all 5 loci was 95% (19/20). AS-qPCR provided the percentage of recipient DNA in all 6 follow-up patients without influence of the stutter peak or the amplification efficacy, which affected the STR-PCR results. The droplet-AS-PCR had an advantage over STR-PCR in terms of rapidity and simplicity for screening before HSCT. Furthermore, AS-qPCR had better accuracy than STR-PCR for quantification of recipient DNA following HSCT. The present chimerism assay compensates for the disadvantages of STR-PCR and is readily performable in clinical laboratories. Copyright © 2015 Elsevier B.V. All rights reserved.

Characterization of mutations in streptomycin-resistant Mycobacterium tuberculosis isolates in Sichuan, China and the association between Beijing-lineage and dual-mutation in gidB.

PubMed

Sun, Honghu; Zhang, Congcong; Xiang, Ling; Pi, Rui; Guo, Zhen; Zheng, Chao; Li, Song; Zhao, Yuding; Tang, Ke; Luo, Mei; Rastogi, Nalin; Li, Yuqing; Sun, Qun

2016-01-01

Mutations in rpsL, rrs, and gidB are well linked to streptomycin (STR) resistance, some of which are suggested to be potentially associated with Mycobacterium tuberculosis genotypic lineages in certain geographic regions. In this study, we aimed to investigate the mutation characteristics of streptomycin resistance and the relationship between the polymorphism of drug-resistant genes and the lineage of M. tuberculosis isolates in Sichuan, China. A total of 227 M. tuberculosis clinical isolates, including 180 STR-resistant and 47 pan-susceptible isolates, were analyzed for presence of mutations in the rpsL, rrs and gidB loci. Mutation K43R in rpsL was strongly associated with high-level streptomycin resistance (P < 0.01), while mutations in rrs and gidB potentially contributed to low-level resistance (P < 0.05). No general association was exhibited between STR resistance and Beijing genotype, however, in STR-resistant strains, Beijing genotype was significantly correlated with high-level STR resistance, as well as the rpsL mutation K43R (P < 0.01), indicating that Beijing genotype has an evolutionary advantage under streptomycin pressure. Notably, in all isolates of Beijing genotype, a dual mutation E92D (a276c) and A205A (a615g) in gidB was detected, suggesting a highly significant association between this dual mutation and Beijing genotype. Copyright © 2015 Elsevier Ltd. All rights reserved.

Does aggressive surgical resection improve survival in advanced stage 3 and 4 neuroblastoma? A systematic review and meta-analysis.

PubMed

Mullassery, Dhanya; Farrelly, Paul; Losty, Paul D

2014-11-01

The role of surgery in the management of advanced staged neuroblastoma (NBL) is controversial. A systematic review and meta-analysis is reported to address robust evidence for curative "gross total tumor resection" (GTR) in Stage 3 and Stage 4 neuroblastoma. Studies were identified using Medline, Embase, and Cochrane databases using pre-specified search terms. Primary outcomes were 5-year overall (OS) and disease-free survival (DFS) after GTR and subtotal resection (STR) in Stage 3 or 4 NBL. Data were analyzed using Review Manager. The Mantel-Haenszel method and a random effects model was utilized to calculate odds ratios (95% CI). Fifteen studies (five Stage 3 and 13 Stage 4) met full inclusion criteria. The pooled odds ratio for 5 year OS in Stage 3 following GTR compared to STR was 2.4 (95% CI 1.19-4.85). In Stage 4 disease, the pooled odds ratio for 5 year overall survival (OS) following GTR compared to STR was 1.65 (95% CI 0.96-1.91); a pooled odds ratio for 5 year DFS following GTR compared to STR was 1.55 (95% CI 1.12-2.14). A clear survival benefit is shown for GTR over STR in Stage 3 NBL only. Though some advantage can be demonstrated for GTR as defined by DFS in Stage 4 NBL GTR did not significantly improve OS in Stage 4 disease.

[Full Sibling Identification by IBS Scoring Method and Establishment of the Query Table of Its Critical Value].

PubMed

Li, R; Li, C T; Zhao, S M; Li, H X; Li, L; Wu, R G; Zhang, C C; Sun, H Y

2017-04-01

To establish a query table of IBS critical value and identification power for the detection systems with different numbers of STR loci under different false judgment standards. Samples of 267 pairs of full siblings and 360 pairs of unrelated individuals were collected and 19 autosomal STR loci were genotyped by Golden e ye™ 20A system. The full siblings were determined using IBS scoring method according to the 'Regulation for biological full sibling testing'. The critical values and identification power for the detection systems with different numbers of STR loci under different false judgment standards were calculated by theoretical methods. According to the formal IBS scoring criteria, the identification power of full siblings and unrelated individuals was 0.764 0 and the rate of false judgment was 0. The results of theoretical calculation were consistent with that of sample observation. The query table of IBS critical value for identification of full sibling detection systems with different numbers of STR loci was successfully established. The IBS scoring method defined by the regulation has high detection efficiency and low false judgment rate, which provides a relatively conservative result. The query table of IBS critical value for identification of full sibling detection systems with different numbers of STR loci provides an important reference data for the result judgment of full sibling testing and owns a considerable practical value. Copyright© by the Editorial Department of Journal of Forensic Medicine

Characterization of Streptomycin Resistance in Isolates of Erwinia amylovora in California.

PubMed

Förster, Helga; McGhee, Gayle C; Sundin, George W; Adaskaveg, James E

2015-10-01

In surveys from 2006 to 2014, streptomycin resistance in Erwinia amylovora from pear-growing areas in California declined from very high incidence in 2006 and 2007 to very low incidence in 2013 and 2014. The majority of resistant strains were designated as moderately resistant-low (MR-L), and were almost exclusively found in Sacramento County, whereas highly resistant (HR) strains were only recovered in Sutter-Yuba and San Joaquin counties. Resistance of HR strains was associated with a mutation in codon 43 of the chromosomal rpsL gene that results in a change from lysine to arginine, the same mutation that was originally reported for resistant strains from California in the mid-1970s. MR-L strains were found to harbor the strA-strB streptomycin resistance genes on transposon Tn5393a. This transposon lacks insertion sequence IS1133 that provides a promoter for efficient expression of strA-strB, resulting in lower minimum inhibitory concentrations of MR-L strains compared with those from other locations that harbor strA-strB on Tn5393::IS1133. In contrast to previously described plasmid-mediated resistance where Tn5393 is inserted in pEa34, or pEA29, Tn5393a in MR-L strains was located on plasmid pEU30. This plasmid was first described in E. amylovora from the western United States but was not associated with streptomycin resistance determinants previously. We hypothesize that Tn5393a was introduced into an E. amylovora strain carrying pEU30 and transposed into that plasmid. This hypothesis was supported by clustered regularly interspaced short palindromic repeat (CRISPR) sequence analysis that showed that two MR-L strains share the same CRISPR1 pattern as a streptomycin-sensitive strain. With current low resistance levels in California growing regions, streptomycin could be successfully used again, but applications per season should be limited and the antibiotic should be mixed and rotated with different modes of action.

Isoflurane and ketamine:xylazine differentially affect intraocular pressure-associated scotopic threshold responses in Sprague-Dawley rats.

PubMed

Choh, Vivian; Gurdita, Akshay; Tan, Bingyao; Feng, Yunwei; Bizheva, Kostadinka; McCulloch, Daphne L; Joos, Karen M

2017-10-01

Amplitudes of electroretinograms (ERG) are enhanced during acute, moderate elevation of intraocular pressure (IOP) in rats anaesthetised with isoflurane. As anaesthetics alone are known to affect ERG amplitudes, the present study compares the effects of inhalant isoflurane and injected ketamine:xylazine on the scotopic threshold response (STR) in rats with moderate IOP elevation. Isoflurane-anaesthetised (n = 9) and ketamine:xylazine-anaesthetised (n = 6) rats underwent acute unilateral IOP elevation using a vascular loop anterior to the equator of the right eye. STRs to a luminance series (subthreshold to -3.04 log scotopic cd s/m 2 ) were recorded from each eye of Sprague-Dawley rats before, during, and after IOP elevation. Positive STR (pSTR) amplitudes for all conditions were significantly smaller (p = 0.0001) for isoflurane- than for ketamine:xylazine-anaesthetised rats. In addition, ketamine:xylazine was associated with a progressive increase in pSTR amplitudes over time (p = 0.0028). IOP elevation was associated with an increase in pSTR amplitude (both anaesthetics p < 0.0001). The absolute interocular differences in IOP-associated enhancement of pSTR amplitudes for ketamine:xylazine and isoflurane were similar (66.3 ± 35.5 vs. 54.2 ± 24.1 µV, respectively). However, the fold increase in amplitude during IOP elevation was significantly higher in the isoflurane- than in the ketamine:xylazine-anaesthetised rats (16.8 ± 29.7x vs. 2.1 ± 2.7x, respectively, p = 0.0004). The anaesthetics differentially affect the STRs in the rat model with markedly reduced amplitudes with isoflurane compared to ketamine:xylazine. However, the IOP-associated enhancement is of similar absolute magnitude for the two anaesthetics, suggesting that IOP stress and anaesthetic effects operate on separate retinal mechanisms.

Recovery after chronic stress within spatial reference and working memory domains: correspondence with hippocampal morphology.

PubMed

Hoffman, A N; Krigbaum, A; Ortiz, J B; Mika, A; Hutchinson, K M; Bimonte-Nelson, H A; Conrad, C D

2011-09-01

Chronic stress results in reversible spatial learning impairments in the Morris water maze that correspond with hippocampal CA3 dendritic retraction in male rats. Whether chronic stress impacts different types of memory domains, and whether these can similarly recover, is unknown. This study assessed the effects of chronic stress with and without a post-stress delay to evaluate learning and memory deficits within two memory domains, reference and working memory, in the radial arm water maze (RAWM). Three groups of 5-month-old male Sprague-Dawley rats were either not stressed [control (CON)], or restrained (6 h/day for 21 days) and then tested on the RAWM either on the next day [stress immediate (STR-IMM)] or following a 21-day delay [stress delay (STR-DEL)]. Although the groups learned the RAWM task similarly, groups differed in their 24-h retention trial assessment. Specifically, the STR-IMM group made more errors within both the spatial reference and working memory domains, and these deficits corresponded with a reduction in apical branch points and length of hippocampal CA3 dendrites. In contrast, the STR-DEL group showed significantly fewer errors in both the reference and working memory domains than the STR-IMM group. Moreover, the STR-DEL group showed better RAWM performance in the reference memory domain than did the CON group, and this corresponded with restored CA3 dendritic complexity, revealing long-term enhancing actions of chronic stress. These results indicate that chronic stress-induced spatial working and reference memory impairments, and CA3 dendritic retraction, are reversible, with chronic stress having lasting effects that can benefit spatial reference memory, but with these lasting beneficial effects being independent of CA3 dendritic complexity. © 2011 The Authors. European Journal of Neuroscience © 2011 Federation of European Neuroscience Societies and Blackwell Publishing Ltd.

Forensic and population genetic analyses of eighteen non-CODIS miniSTR loci in the Korean population.

PubMed

Jin, Han Jun; Kim, Ki Cheol; Yoon, Cha Eun; Kim, Wook

2013-11-01

We analyzed the variation of eighteen miniSTR loci in 411 randomly chosen individuals from Korea to increase the probability that a degraded sample can be typed, as well as to provide an expanded and reliable population database. Six multiplex PCR systems were developed (multiplex I: D1S1677, D2S441 and D4S2364; multiplex II: D10S1248, D14S1434 and D22S1045; multiplex III: D12S391, D16S3253 and D20S161; multiplex IV: D3S4529, D8S1115 and D18S853; multiplex V: D6S1017, D11S4463 and D17S1301; multiplex VI: D5S2500, D9S1122 and D21S1437). Allele frequencies and forensic parameters were calculated to evaluate the suitability and robustness of these non-CODIS miniSTR systems. No significant deviation from Hardy-Weinberg equilibrium expectations were observed, except for D4S2364, D5S2500 and D20S161 loci. A multidimensional scaling plot based on allele frequencies of the six miniSTR loci (D1S1677, D2S441, D4S2364, D10S1248, D14S1434 and D22S1045) showed that Koreans appeared to have most genetic affinity with Chinese and Japanese than to other Eurasian populations compared here. The combined probability of match calculated from the 18 miniSTR loci was 2.902 × 10(-17), indicating a high degree of polymorphism. Thus, the 18 miniSTR loci can be suitable for recovering useful information for analyzing degraded forensic casework samples and for adding supplementary genetic information for a variety of analyses involving closely related individuals where there is a need for additional genetic information. Copyright © 2013 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results.

PubMed

Just, Rebecca S; Irwin, Jodi A

2018-05-01

Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input. Yet to leverage the benefits of NGS for enhanced genotyping and mixture deconvolution, the sequence variation among same-length products must be utilized in some form. Here, we propose use of the longest uninterrupted stretch (LUS) in allele designations as a simple method to represent sequence variation within the STR repeat regions and facilitate - in the nearterm - probabilistic interpretation of NGS-based typing results. An examination of published population data indicated that a reference LUS region is straightforward to define for most autosomal STR loci, and that using repeat unit plus LUS length as the allele designator can represent greater than 80% of the alleles detected by sequencing. A proof of concept study performed using a freely available probabilistic software demonstrated that the LUS length can be used in allele designations when a program does not require alleles to be integers, and that utilizing sequence information improves interpretation of both single-source and mixed contributor STR typing results as compared to using repeat unit information alone. The LUS concept for allele designation maintains the repeat-based allele nomenclature that will permit backward compatibility to extant STR databases, and the LUS lengths themselves will be concordant regardless of the NGS assay or analysis tools employed. Further, these biologically based, easy-to-derive designations uphold clear relationships between parent alleles and their stutter products, enabling analysis in fully continuous probabilistic programs that model stutter while avoiding the algorithmic complexities that come with string based searches. Though using repeat unit plus LUS length as the allele designator does not capture variation that occurs outside of the core repeat regions, this straightforward approach would permit the large majority of known STR sequence variation to be used for mixture deconvolution and, in turn, result in more informative mixture statistics in the near term. Ultimately, the method could bridge the gap from current length-based probabilistic systems to facilitate broader adoption of NGS by forensic DNA testing laboratories. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Larvicidal activity of some Cerrado plant extracts against Aedes aegypti.

PubMed

Rodrigues, A M S; De Paula, J E; Degallier, N; Molez, J E; Espindola, L S

2006-06-01

One hundred ninety hexanic and ethanolic extract from 27 plant species from the Cerrado biome of Brazil were tested for larvicidal activity against 3rd-stage Aedes aegypti larvae at 500 microg/ml. Fourteen extracts from 7 species showed activity (>65% mortality) against the larvae. Of these Dugeutia furfuracea, Piptocarpha rotundifolia, Casearia sylvestris var. lingua, Serjania lethalis, and Xylopia aromatica were active at 56.6, 162.31, 232.4, 285.76, and 384.37 microg/ml, respectively. Annona crassiflora and Cybistax antisyphilitica showed activity at 23.06 and 27.61 microg/ml. The larvicidal properties of these species are described for the first time, and may prove to be promising in active chemical compound isolation.

Technical and investigative support for high density digital satellite recording systems

NASA Technical Reports Server (NTRS)

Schultz, R. A.

1982-01-01

Dropout and defect classification are discussed with emphasis on how surface defects responsible for electronic dropouts were identified, what affect various defects could have on the application of tapes to satellite tape recorders (STR), and what type of defects might be field correctable after production of the tape but prior to installation in the STR.

Parthenogenesis in a Brazilian rainbow boa (Epicrates cenchria cenchria).

PubMed

Kinney, Matthew E; Wack, Raymund F; Grahn, Robert A; Lyons, Leslie

2013-03-01

A 22-year-old captive Brazilian rainbow boa (Epicrates cenchria cenchria) gave birth to four offspring after being housed with a vasectomized male. Sexual reproduction as a result of failed prior vasectomy, recanalization of the vas deferens, or prolonged sperm storage was ruled out using the clinical history, histopathology, and gross necropsy. Short tandem repeat (STR) DNA markers were genotyped in the male, female, and four offspring. None of the offspring possessed a diagnostic STR allele present in the potential sire. In addition, all offspring were homozygous at each STR locus evaluated, supporting parthenogenetic reproduction. This is the first report of parthenogenesis in a Brazilian rainbow boa and has implications for the conservation of reptiles maintained in captive breeding programs. © 2012 Wiley Periodicals, Inc.

The STR/ort mouse model of spontaneous osteoarthritis - an update.

PubMed

Staines, K A; Poulet, B; Wentworth, D N; Pitsillides, A A

2017-06-01

Osteoarthritis is a degenerative joint disease and a world-wide healthcare burden. Characterized by cartilage degradation, subchondral bone thickening and osteophyte formation, osteoarthritis inflicts much pain and suffering, for which there are currently no disease-modifying treatments available. Mouse models of osteoarthritis are proving critical in advancing our understanding of the underpinning molecular mechanisms. The STR/ort mouse is a well-recognized model which develops a natural form of osteoarthritis very similar to the human disease. In this Review we discuss the use of the STR/ort mouse in understanding this multifactorial disease with an emphasis on recent advances in its genetics and its bone, endochondral and immune phenotypes. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Stress of Kindergarten teachers: How we tried to detect and to reduce it by using a small and wearable ECG and acceleration measuring device?

PubMed

Shirouzu, Shigenori; Seno, Yumeka; Tobioka, Ken; Masaki, Takeo; Yasumatsu, Kiyotaka; Mishima, Norio; Sugano, Hisanobu

2015-01-01

In 2014 school year, four female teachers of Nazareth Kindergarten decided to resign (DRT) due to workplace stress caused by human relationships between themselves. Our preliminary interview investigation revealed there was a stressor (STR), a certain elder female teacher and her less polite words and attitude. Using small and wearable ECG and acceleration measuring device, we measured 24 hour's autonomic nervous system's activity (ASNA) and sleep behavior of the STR and surrounding teachers, and tried to evaluate their stress objectively and to understand the reason of STR's less polite behaviors. For comparison, we also measured female Mind-Body Medicine (MBM) patients suffering adjustment disorder and clinical depression.

Population data of 24 STRs in Mexican-Mestizo population from Monterrey, Nuevo Leon (Northeast, Mexico) based on Powerplex(®) Fusion and GlobalFiler(®) kits.

PubMed

Ramos-González, Benito; Aguilar-Velázquez, José Alonso; Chávez-Briones, María de Lourdes; Delgado-Chavarría, Juan Ramón; Alfaro-Lopez, Elizabeth; Rangel-Villalobos, Héctor

2016-03-01

The STR loci included into new commercial human identification kits compels geneticists estimating forensic parameters for interpretation purposes in forensic casework. Therefore, we studied for the first time in Mexico the GlobalFiler(®) and Powerplex(®) Fusion systems in 326 and 682 unrelated individuals, respectively. These individuals are resident of the Monterrey City of the Nuevo Leon state (Northeast, Mexico). Population data from 23 autosomal STRs and the Y-STR locus DYS391 are reported and compared against available STR data from American ethnic groups and the unique Mexican population studied with Powerplex(®) Fusion. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Minimizing inhibition of PCR-STR typing using digital agarose droplet microfluidics.

PubMed

Geng, Tao; Mathies, Richard A

2015-01-01

The presence of PCR inhibitors in forensic and other biological samples reduces the amplification efficiency, sometimes resulting in complete PCR failure. Here we demonstrate a high-performance digital agarose droplet microfluidics technique for single-cell and single-molecule forensic short tandem repeat (STR) typing of samples contaminated with high concentrations of PCR inhibitors. In our multifaceted strategy, the mitigation of inhibitory effects is achieved by the efficient removal of inhibitors from the porous agarose microgel droplets carrying the DNA template through washing and by the significant dilution of targets and remaining inhibitors to the stochastic limit within the ultralow nL volume droplet reactors. Compared to conventional tube-based bulk PCR, our technique shows enhanced (20 ×, 10 ×, and 16 ×) tolerance of urea, tannic acid, and humic acid, respectively, in STR typing of GM09948 human lymphoid cells. STR profiling of single cells is not affected by small soluble molecules like urea and tannic acid because of their effective elimination from the agarose droplets; however, higher molecular weight humic acid still partially inhibits single-cell PCR when the concentration is higher than 200 ng/μL. Nevertheless, the full STR profile of 9948 male genomic DNA contaminated with 500 ng/μL humic acid was generated by pooling and amplifying beads carrying single-molecule 9948 DNA PCR products in a single secondary reaction. This superior performance suggests that our digital agarose droplet microfluidics technology is a promising approach for analyzing low-abundance DNA targets in the presence of inhibitors. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Effect of type of cognitive task and walking speed on cognitive-motor interference during dual-task walking.

PubMed

Patel, P; Lamar, M; Bhatt, T

2014-02-28

We aimed to determine the effect of distinctly different cognitive tasks and walking speed on cognitive-motor interference of dual-task walking. Fifteen healthy adults performed four cognitive tasks: visuomotor reaction time (VMRT) task, word list generation (WLG) task, serial subtraction (SS) task, and the Stroop (STR) task while sitting and during walking at preferred-speed (dual-task normal walking) and slow-speed (dual-task slow-speed walking). Gait speed was recorded to determine effect on walking. Motor and cognitive costs were measured. Dual-task walking had a significant effect on motor and cognitive parameters. At preferred-speed, the motor cost was lowest for the VMRT task and highest for the STR task. In contrast, the cognitive cost was highest for the VMRT task and lowest for the STR task. Dual-task slow walking resulted in increased motor cost and decreased cognitive cost only for the STR task. Results show that the motor and cognitive cost of dual-task walking depends heavily on the type and perceived complexity of the cognitive task being performed. Cognitive cost for the STR task was low irrespective of walking speed, suggesting that at preferred-speed individuals prioritize complex cognitive tasks requiring higher attentional and processing resources over walking. While performing VMRT task, individuals preferred to prioritize more complex walking task over VMRT task resulting in lesser motor cost and increased cognitive cost for VMRT task. Furthermore, slow walking can assist in diverting greater attention towards complex cognitive tasks, improving its performance while walking. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

A microsatellite study for determination of allelic variation of Kurdish population-Kurdistan region-Iraq

NASA Astrophysics Data System (ADS)

Murad, Media J.; Amin, Bushra K.

2017-09-01

The purpose of this study was detecting genetic variations for the Kurdish population in Kurdistan region-Iraq, using fifteen autosomal STR loci. Buccal swabs were collected and depositing on Nucleic Card (Copan, Italia Spa) from 302 healthy unrelated Iraqi Kurds in five provinces of Kurdistan region-Iraq. Fifteen autosomal STR loci are D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA and Amelogenin included in the AmpFlSTR Identifiler® Direct PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA). No significant departure from Hardy Weinberg Equilibrium (HWE) expectations were observed in 10 from 15 STR loci analyzed (a 5% significance level was taken). The exceptions were the CSF1PO, D3S1358, D13S317, D16S539 and D2S1338 loci. Statistical parameters of forensic efficiencies were estimated for the loci, based on allelic frequencies. The mean of observed heterozygosity, expected heterozygosity and PIC values across the 15 loci were 0.762, 0.797 and 0.768 respectively, indicating high gene diversity. The combined probability of exclusion, power of discrimination, probability of matching value for all the 15 STR loci were 0.9999968; 0.9999999 and 4.966×10-17, respectively. These parameters indicated the importance of the loci for forensic genetic purposes and paternity testing.

Comparison of adherence to generic multi-tablet regimens vs. brand multi-tablet and brand single-tablet regimens likely to incorporate generic antiretroviral drugs by breaking or not fixed-dose combinations in HIV-infected patients.

PubMed

Rwagitinywa, Joseph; Lapeyre-Mestre, Maryse; Bourrel, Robert; Montastruc, Jean-Louis; Sommet, Agnès

2018-03-05

Adherence to antiretroviral (ARV) is crucial to achieve viral load suppression in HIV-infected patients. This study aimed to compare adherence to generic multi-tablet regimens (MTR) vs. brand MTR likely to incorporate ARV drugs without breaking fixed-dose combinations (FDC) and brand single-tablet regimens (STR) likely to incorporate generics by breaking the FDC. Patients aged of 18 years or over exposed to one of the generic or the brand of lamivudine (3TC), zidovudine/lamivudine (AZT/TC), nevirapine (NVP), or efavirenz (EFV), or the brand STR of efavirenz/emtricitabine/tenofovir (EFV/FTC/TDF). Adherence was measured by medication possession ratio (MPR) using both defined daily dose (DDD) and daily number of tablet recommended for adults (DNT). Adherence to generic MTR vs. brand MTR and brand STR was compared using Kruskal-Wallis. The overall median adherence was 0.97 (IQR 0.13) by DNT method and 0.97 (0.14) by DDD method. Adherence in patients exposed to generic MTR (n = 165) vs. brand MTR (n = 481) and brand STR (n = 470) was comparable by DNT and DDD methods. In conclusion, adherence to generic MTR was high and comparable with adherence to brand MTR and to STR. Utilization of DDD instead DNT to measure the MPR led to small but nonsignificant difference that has no clinical impact. © 2018 Société Française de Pharmacologie et de Thérapeutique.

Forensic genetic analysis of bone remain samples.

PubMed

Siriboonpiputtana, T; Rinthachai, T; Shotivaranon, J; Peonim, V; Rerkamnuaychoke, B

2018-03-01

DNA typing from degraded human remains is still challenging forensic DNA scientists not only in the prospective of DNA purification but also in the interpretation of established DNA profiles and data manipulation, especially in mass fatalities. In this report, we presented DNA typing protocol to investigate many skeletal remains in different degrees of decomposing. In addition, we established the grading system aiming for prior determination of the association between levels of decomposing and overall STR amplification efficacy. A total of 80 bone samples were subjected to DNA isolation using the modified DNA IQ™ System (Promega, USA) for bone extraction following with STR analysis using the AmpFLSTR Identifiler ® (Thermo Fisher Scientific, USA). In low destruction group, complete STR profiles were observed as 84.4% whereas partial profiles and non-amplified were found as 9.4% and 6.2%, respectively. Moreover, in medium destruction group, both complete and partial STR profiles were observed as 31.2% while 37.5% of this group was unable to amplify. Nevertheless, we could not purify DNA and were unable to generate STR profile in any sample from the high destroyed bone samples. Compact bones such as femur and humerus have high successful amplification rate superior than loose/spongy bones. Furthermore, costal cartilage could be a designate specimen for DNA isolation in a case of the body that was discovered approximately to 3 days after death which enabled to isolate high quality and quantity of DNA, reduce time and cost, and do not require special tools such as freezer mill. Copyright © 2018 Elsevier B.V. All rights reserved.

Beta-glucan production by Botryosphaeria rhodina in different bench-top bioreactors.

PubMed

Selbmann, L; Crognale, S; Petruccioli, M

2004-01-01

Evaluation of the technical feasibility of transferring beta-glucan production by Botryosphaeria rhodina DABAC-P82 from shaken flasks to bench-top bioreactors. Three different bioreactors were used: 3 l stirred tank reactor (STR-1) equipped with two different six-blade turbines; STR as above but equipped with a three-blade marine propeller plus draft-tube (STR-2); 2 l air-lift column reactor (ALR) equipped with an external loop. STR-1, tested at three different stirrer speeds (300, 500 and 700 rev min(-1)) appeared to be less suitable for beta-glucan production by the fungus, being maximum production (19.4 g l(-1)), productivity (0.42 g l(-1) h(-1)) and yield (0.48 g g(-1) of glucose consumed) markedly lower than those obtained in shaken culture (29.7 g l(-1), 1.23 g l(-1) h(-1) and 0.61 g g(-1), respectively). Better performances were obtained with both STR-2 and ALR. With the latter, in particular, the increase of production was accompanied by reduced fermentation time (25.7 g l(-1) after only 22 h); productivity and yield were highest (1.17 g l(-1) h(-1) and 0.62 g g(-1) of glucose consumed, respectively). Using an air-lift reactor with external loop, the scaling up from shaken flasks to bench-top bioreactor of the beta-glucan production by B. rhodina DABAC-P82 is technically feasible. Although culture conditions are still to be optimized, the results obtained using the ARL are highly promising.

Comparison of the risk factors effects between two populations: two alternative approaches illustrated by the analysis of first and second kidney transplant recipients

PubMed Central

2013-01-01

Background Whereas the prognosis of second kidney transplant recipients (STR) compared to the first ones has been frequently analyzed, no study has addressed the issue of comparing the risk factor effects on graft failure between both groups. Methods Here, we propose two alternative strategies to study the heterogeneity of risk factors between two groups of patients: (i) a multiplicative-regression model for relative survival (MRS) and (ii) a stratified Cox model (SCM) specifying the graft rank as strata and assuming subvectors of the explicatives variables. These developments were motivated by the analysis of factors associated with time to graft failure (return-to-dialysis or patient death) in second kidney transplant recipients (STR) compared to the first ones. Estimation of the parameters was based on partial likelihood maximization. Monte-Carlo simulations associated with bootstrap re-sampling was performed to calculate the standard deviations for the MRS. Results We demonstrate, for the first time in renal transplantation, that: (i) male donor gender is a specific risk factor for STR, (ii) the adverse effect of recipient age is enhanced for STR and (iii) the graft failure risk related to donor age is attenuated for STR. Conclusion While the traditional Cox model did not provide original results based on the renal transplantation literature, the proposed relative and stratified models revealed new findings that are useful for clinicians. These methodologies may be of interest in other medical fields when the principal objective is the comparison of risk factors between two populations. PMID:23915191

Risk factors for allergic rhinitis in Costa Rican children with asthma.

PubMed

Bunyavanich, S; Soto-Quiros, M E; Avila, L; Laskey, D; Senter, J M; Celedón, J C

2010-02-01

Risk factors for allergic rhinitis (AR) in asthmatics are likely distinct from those for AR or asthma alone. We sought to identify clinical and environmental risk factors for AR in children with asthma. We performed a cross-sectional study of 616 Costa Rican children aged 6-14 years with asthma. Candidate risk factors were drawn from questionnaire data, spirometry, methacholine challenge testing, skin testing, and serology. Two outcome measures, skin test reaction (STR)-positive AR and physician-diagnosed AR, were examined by logistic regression. STR-positive AR had high prevalence (80%) in Costa Rican children with asthma, and its independent risk factors were nasal symptoms after exposure to dust or mold, parental history of AR, older age at asthma onset, oral steroid use in the past year, eosinophilia, and positive IgEs to dust mite and cockroach. Physician-diagnosed AR had lower prevalence (27%), and its independent risk factors were nasal symptoms after pollen exposure, STR to tree pollens, a parental history of AR, inhaled steroid and short-acting beta2 agonist use in the past year, household mold/mildew, and fewer older siblings. A physician's diagnosis was only 29.5% sensitive for STR-positive AR. Risk factors for AR in children with asthma depend on the definition of AR. Indoor allergens drive risk for STR-positive AR. Outdoor allergens and home environmental conditions are risk factors for physician-diagnosed AR. We propose that children with asthma in Costa Rica and other Latin American nations undergo limited skin testing or specific IgE measurements to reduce the current under-diagnosis of AR.

Sequence analysis of Chinese and Japanese Curcuma drugs on the 18S rRNA gene and trnK gene and the application of amplification-refractory mutation system analysis for their authentication.

PubMed

Sasaki, Yohei; Fushimi, Hirotoshi; Cao, Hui; Cai, Shao-Qing; Komatsu, Katsuko

2002-12-01

The botanical origins of Chinese and Japanese Curcuma drugs were determined to be Curcuma longa, C. phaeocaulis, the Japanese population of C. zedoaria, C. kwangsiensis, C. wenyujin, and C. aromatica based on a comparison of their 18S rRNA gene and trnK gene sequences with those of six Curcuma species reported previously. Moreover, to develop a more convenient identification method, amplification-refractory mutation system (ARMS) analysis of both gene regions was performed on plants. The ARMS method for the 18S rRNA gene was established using two types of forward primers designed based on the nucleotide difference at position 234. When DNAs of four Curcuma species were used as templates, PCR amplification with either of the two primers only generated a fragment of 912 base pairs (bp). However, when DNAs of the purple-cloud type of C. kwangsiensis and C. wenyujin were used, PCR amplifications with both primers unexpectedly generated the fragment, suggesting that these two were heterozygotes. The ARMS method for the trnK gene was also established using a mixture of four types of specific reverse primers designed on the basis of base substitutions and indels among six species, and common reverse and forward primers. C. phaeocaulis or the Chinese population of C. zedoaria, the Japanese population of C. zedoaria or the purple-cloud type of C. kwangsiensis, the pubescent type of C. kwangsiensis or C. wenyujin, and C. aromatica were found to show specific fragments of 730, 185, 527 or 528, and 641 or 642 bp, respectively. All species including C. longa also showed a common fragment of 897-904 bp. Using both ARMS methods, together with information on producing areas, the identification of Curcuma plants was achieved. Moreover, the ARMS method for the trnK gene was also useful for authentication of Curcuma drugs.

Review of Speech-to-Text Recognition Technology for Enhancing Learning

ERIC Educational Resources Information Center

Shadiev, Rustam; Hwang, Wu-Yuin; Chen, Nian-Shing; Huang, Yueh-Min

2014-01-01

This paper reviewed literature from 1999 to 2014 inclusively on how Speech-to-Text Recognition (STR) technology has been applied to enhance learning. The first aim of this review is to understand how STR technology has been used to support learning over the past fifteen years, and the second is to analyze all research evidence to understand how…

Two-electron high potential and high capacity redox active molecules for energy storage applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Jinhua; Zhang, Lu; Burrell, Anthony K.

A non-aqueous redox flow battery includes a catholyte including a compound of formula (I), a compound of formula (II), or a compound of formula (III): ##STR00001## wherein two R groups have the formula X, wherein X is X, wherein X is a group of formula IV-A or IV-B; ##STR00002##

Sensitivity to reward: implications for overeating and overweight.

PubMed

Davis, Caroline; Strachan, Shaelyn; Berkson, Marni

2004-04-01

Sensitivity to reward (STR)-a personality trait firmly rooted in the neurobiology of the mesolimbic dopamine system-has been strongly implicated in the risk for addiction. This construct describes the ability to derive pleasure or reward from natural reinforcers like food, and from pharmacologic rewards like addictive drugs. Recently experts in the field of addiction research have acknowledged that psychomotor stimulant drugs are no longer at the heart of all addictions, and that brain circuits can also be deranged with natural rewards like food. The present study tested a model in which STR was expected to relate positively to overeating, which in turn would be associated with higher body weight in woman aged 25-45 years. As predicted, STR was correlated positively with measures of emotional overeating. Also, overweight woman were significantly more sensitive to reward than those of normal weight. Interestingly, however, the obese woman (Body Mass Index>30) were more anhedonic than the overweight woman (Body Mass Index>25<30). These findings are discussed in the context of neuroadaptations to overactivity of brain reward circuits. Results also indicate that STR may serve as a risk factor for overeating and overweight, especially in cultures such as ours where palatable, calorically-dense food is plentiful.

Science & Technology Review October/November 2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogt, R. L.; Meissner, C. N.; Kotta, P. R.

At Lawrence Livermore National Laboratory, we focus on science and technology research to ensure our nation’s security. We also apply that expertise to solve other important national problems in energy, bioscience, and the environment. Science & Technology Review is published eight times a year to communicate, to a broad audience, the Laboratory’s scientific and technological accomplishments in fulfilling its primary missions. The publication’s goal is to help readers understand these accomplishments and appreciate their value to the individual citizen, the nation, and the world. The Laboratory is operated by Lawrence Livermore National Security, LLC (LLNS), for the Department of Energy’smore » National Nuclear Security Administration. LLNS is a partnership involving Bechtel National, University of California, Babcock & Wilcox, Washington Division of URS Corporation, and Battelle in affiliation with Texas A&M University. More information about LLNS is available online at www.llnsllc.com. Please address any correspondence (including name and address changes) to S&TR, Mail Stop L-664, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, California 94551, or telephone (925) 423-3893. Our e-mail address is str-mail@llnl.gov. S&TR is available on the Web at str.llnl.gov.« less

Glucocorticoid Stress Responses of Reintroduced Tigers in Relation to Anthropogenic Disturbance in Sariska Tiger Reserve in India

PubMed Central

Bhattacharjee, Subhadeep; Kumar, Vinod; Chandrasekhar, Mithileshwari; Malviya, Manjari; Ganswindt, Andre; Ramesh, Krishnamurthy; Sankar, Kalyanasundaram; Umapathy, Govindhaswamy

2015-01-01

Tiger (Panthera tigris), an endangered species, is under severe threat from poaching, habitat loss, prey depletion and habitat disturbance. Such factors have been reported causing local extermination of tiger populations including in one of the most important reserves in India, namely Sariska Tiger Reserve (STR) in northwestern India. Consequently, tigers were reintroduced in STR between 2008 and 2010, but inadequate breeding success was observed over the years, thus invoking an investigation to ascertain physiological correlates. In the present study, we report glucocorticoid stress responses of the reintroduced tigers in relation to anthropogenic disturbance in the STR from 2011 to 2013. We found anthropogenic disturbance such as encounter rates of livestock and humans, distance to roads and efforts to kill domestic livestock associated with an elevation in fecal glucocorticoid metabolite (fGCM) concentrations in the monitored tigers. In this regard, female tigers seem more sensitive to such disturbance than males. It was possible to discern that tiger’s fGCM levels were significantly positively related to the time spent in disturbed areas. Resulting management recommendations include relocation of villages from core areas and restriction of all anthropogenic activities in the entire STR. PMID:26061171

Inner and inter population structure construction of Chinese Jiangsu Han population based on Y23 STR system

PubMed Central

Yang, Chun; Zhang, Jianqiu

2017-01-01

In this study, we analyzed the genetic polymorphisms of 23 Y-STR loci from PowerPlex® Y23 system in 916 unrelated healthy male individuals from Chinese Jiangsu Han, and observed 912 different haplotypes including 908 unique haplotypes and 4 duplicate haplotypes. The haplotype diversity reached 0.99999 and the discrimination capacity and match probability were 0.9956 and 0.0011, respectively. The gene diversity values ranged from 0.3942 at DYS438 to 0.9607 at DYS385a/b. Population differentiation within 10 Jiangsu Han subpopulations were evaluated by RST values and visualized in Neighbor-Joining trees and Multi-Dimensional Scaling plots as well as population relationships between the Jiangsu Han population and other 18 Eastern Asian populations. Such results indicated that the 23 Y-STR loci were highly polymorphic in Jiangsu Han population and played crucial roles in forensic application as well as population genetics. For the first time, we reported the genetic diversity of male lineages in Jiangsu Han population at a high-resolution level of 23 Y-STR set and consequently contributed to familial searching, offender tracking, and anthropology analysis of Jiangsu Han population. PMID:28704439

Variant Alleles, Triallelic Patterns, and Point Mutations Observed in Nuclear Short Tandem Repeat Typing of Populations in Bosnia and Serbia

PubMed Central

Huel, René L. M.; Bašić, Lara; Madacki-Todorović, Kamelija; Smajlović, Lejla; Eminović, Izet; Berbić, Irfan; Miloš, Ana; Parsons, Thomas J.

2007-01-01

Aim To present a compendium of off-ladder alleles and other genotyping irregularities relating to rare/unexpected population genetic variation, observed in a large short tandem repeat (STR) database from Bosnia and Serbia. Methods DNA was extracted from blood stain cards relating to reference samples from a population of 32 800 individuals from Bosnia and Serbia, and typed using Promega’s PowerPlex®16 STR kit. Results There were 31 distinct off-ladder alleles were observed in 10 of the 15 STR loci amplified from the PowerPlex®16 STR kit. Of these 31 alleles, 3 have not been previously reported. Furthermore, 16 instances of triallelic patterns were observed in 9 of the 15 loci. Primer binding site mismatches that affected amplification were observed in two loci, D5S818 and D8S1179. Conclusion Instances of deviations from manufacturer’s allelic ladders should be expected and caution taken to properly designate the correct alleles in large DNA databases. Particular care should be taken in kinship matching or paternity cases as incorrect designation of any of these deviations from allelic ladders could lead to false exclusions. PMID:17696304

Identification and characterization of the highly polymorphic locus D14S739 in the Han Chinese population

PubMed Central

Shao, Chengchen; Zhang, Yaqi; Zhou, Yueqin; Zhu, Wei; Xu, Hongmei; Liu, Zhiping; Tang, Qiqun; Shen, Yiwen; Xie, Jianhui

2015-01-01

Aim To systemically select and evaluate short tandem repeats (STRs) on the chromosome 14 and obtain new STR loci as expanded genotyping markers for forensic application. Methods STRs on the chromosome 14 were filtered from Tandem Repeats Database and further selected based on their positions on the chromosome, repeat patterns of the core sequences, sequence homology of the flanking regions, and suitability of flanking regions in primer design. The STR locus with the highest heterozygosity and polymorphism information content (PIC) was selected for further analysis of genetic polymorphism, forensic parameters, and the core sequence. Results Among 26 STR loci selected as candidates, D14S739 had the highest heterozygosity (0.8691) and PIC (0.8432), and showed no deviation from the Hardy-Weinberg equilibrium. 14 alleles were observed, ranging in size from 21 to 34 tetranucleotide units in the core region of (GATA)9-18 (GACA)7-12 GACG (GACA)2 GATA. Paternity testing showed no mutations. Conclusion D14S739 is a highly informative STR locus and could be a suitable genetic marker for forensic applications in the Han Chinese population. PMID:26526885

[Genetic Polymorphisms of 26 Y-STR Loci in Fujian She Nationality and Its Forensic Application].

PubMed

Bian, Ying-nan; Siyit, Tele T; Zhu, Ru-xin; Zhao, Qi; Zhang Su-hua

2015-08-01

To study the forensic application of Goldeneye DNA ID 26Y Kit in the She nationality. Through capillary electrophoresis, the genotype of 26 Y-STR loci were analyzed in 53 unrelated male individuals from Fujian She nationality. The population genetics parameters such as allele frequency and haplotype diversity were calculated. The comparisons among the She nationality and the other nationalities were analyzed. A total of 126 alleles were observed on the 26 Y-STR loci of 53 unrelated male individuals. The allele frequencies and GD value ranged from 0.010 1 to 0.886 8 and 0.211 2 to 0.846 2, respectively. The GD value was greater than 0.5 in the 19 loci. A total of 47 haplotypes were observed. Based on R(ST), multidimensional scaling plot indicated that the genetic relationship among Fujian She nationality and Minnan Han nationality was closest, followed by Southern China Han nationality and Northern China nationality. Goldeneye™ DNA ID 26Y Kit including 26 Y-STR loci has good polymorphism in the She nationality. As an additional system, it has forensic application value in some special cases.

Genetic polymorphism analyses of a novel panel of 19 X-STR loci in the Chinese Uygur ethnic minority* #

PubMed Central

Guo, Yu-xin; Chen, Jian-gang; Wang, Yan; Yan, Jiang-wei; Chen, Jing; Yao, Tian-hua; Zhang, Li-ping; Yang, Guang; Meng, Hao-tian; Zhang, Yu-dang; Mei, Ting; Liu, Yao-shun; Dong, Qian; Zhu, Bo-feng

2016-01-01

The population genetic data and forensic parameters of 19 X-chromosome short tandem repeat (X-STR) loci in Chinese Uygur ethnic minority are presented. These loci were detected in a sample of 233 (94 males and 139 females) unrelated healthy individuals. We observed 238 alleles at the 19 X-STR loci, with the corresponding gene frequencies spanning the range from 0.0021 to 0.5644. After Bonferroni correction (P>0.0026), there were no significant deviations from Hardy-Weinberg equilibrium. The cumulative power of discrimination in females and males, and the probability of exclusion of the 19 X-STR loci were 0.999 999 999 999 999 999 998 091, 0.999 999 999 999 966, and 0.999 999 986 35, respectively. The cumulative mean exclusion chance was 0.999 999 992 849 in deficiency cases, 0.999 999 999 999 628 in normal trios, and 0.999 999 998 722 in duo cases. The high value of the forensic parameters mentioned above revealed that the novel panel of 19 loci had important values for forensic applications in the Uygur group. PMID:27143264

Isolation, characterization, virulence and immunogenicity testing of field isolates of Pasteurella multocida, Staphylococcus aureus, and Streptococcus agalactiae in laboratory settings.

PubMed

Qudratullah; Muhammad, G; Saqib, M; Bilal, M Qamar

2017-08-01

The present study was designed to investigate isolation, characterization, virulence and immunogenicity testing of field isolates of Pasteurella multocida, Staphylococcus aureus, and Streptococcus agalactiae in rabbits and mice. Isolates of P. multocida, S. aureus and Str. agalactiae recovered from field cases of Hemorragic septicemia and mastitis were scrutinized for virulence/pathogenicity and immunogenicity. Mouse LD 50 of P. multocida showed that P. multocida isolate No.1 was more virulent than isolates No. 2 and 3. Virulence of isolate No.1S. aureus and Str. agalactiae revealed that 100, 80% rabbits died within 18h of inoculation. Seven-digit numerical profiles of these 4 isolates with API ® Staph test strips isolates, No.1 (6736153) showed good identification (S. aureus id=90.3%). Indirect ELISA-based serum antibody titers to P. multocida isolate No.1, S. aureus No.1, Str. agalactiae, isolate No.1 elicited high antibody titers 1.9, 1.23, 1.12 respectively. All the pathogens of Isolate No. 1 (P. multocida, S. aureus Str. agalactiae), were high antibody than others isolates. Copyright © 2017 Elsevier B.V. All rights reserved.

[Identification of Y-chromosomal Genetic Types for the Soldier's Remains from Huaihai Campaign].

PubMed

Wang, C Z; Wen, S Q; Shi, M S; Yu, X E; Wang, X J; Pan, Y L; Zhang, Y F; Li, H; Tan, J Z

2017-08-01

To identify the Y-chromosomal genetic types for the soldier's remains from Huaihai Campaign, and to offer a clue for search of their paternal relatives. DNA of the remains were extracted by the ancient DNA extraction method. Yfiler kit was used for the multiplex amplification of 17 Y-STR loci. The haplogroups of the samples were speculated. Detailed genotyping of the selected Y-SNP was performed based on the latest Y-chromosome phylogenetic tree. Haplotype-sharing analysis was done based on the data of Y-SNP and Y-STR, the closest modern individual information to the genetic relationship of remains was gained. A total of 8 Y-STR haplotypes were observed on 17 Y-STR loci of 8 male individuals. Furthermore, 6 Y-SNP haplogroups were identified, which were O2a1-M95+, O1a1-P203+, O3*-M122+/M234-, D1-M15+, C3*-ST and R1a1-M17+. Identification of Y-chromosomal genetic types for the soldier's remains from Huaihai Campaign shows a reference value on inferring the geographical origins of old materials. Copyright© by the Editorial Department of Journal of Forensic Medicine

Glucocorticoid Stress Responses of Reintroduced Tigers in Relation to Anthropogenic Disturbance in Sariska Tiger Reserve in India.

PubMed

Bhattacharjee, Subhadeep; Kumar, Vinod; Chandrasekhar, Mithileshwari; Malviya, Manjari; Ganswindt, Andre; Ramesh, Krishnamurthy; Sankar, Kalyanasundaram; Umapathy, Govindhaswamy

2015-01-01

Tiger (Panthera tigris), an endangered species, is under severe threat from poaching, habitat loss, prey depletion and habitat disturbance. Such factors have been reported causing local extermination of tiger populations including in one of the most important reserves in India, namely Sariska Tiger Reserve (STR) in northwestern India. Consequently, tigers were reintroduced in STR between 2008 and 2010, but inadequate breeding success was observed over the years, thus invoking an investigation to ascertain physiological correlates. In the present study, we report glucocorticoid stress responses of the reintroduced tigers in relation to anthropogenic disturbance in the STR from 2011 to 2013. We found anthropogenic disturbance such as encounter rates of livestock and humans, distance to roads and efforts to kill domestic livestock associated with an elevation in fecal glucocorticoid metabolite (fGCM) concentrations in the monitored tigers. In this regard, female tigers seem more sensitive to such disturbance than males. It was possible to discern that tiger's fGCM levels were significantly positively related to the time spent in disturbed areas. Resulting management recommendations include relocation of villages from core areas and restriction of all anthropogenic activities in the entire STR.

Norfolk Lake Highway Bridges, Baxter County, Arkansas, White River and Tributaries, North Fork River, Arkansas Foundation Report.

DTIC Science & Technology

1983-06-01

50 19 F20 mi mune d o f Cry-o Hadboto swi ve I I OL~~ Hzr Har Str 5 -45 H0 Back on !4rpn -USANDY DOLQ-1rrE - Vod ’og - 2 R r Ard - ard ---5 2 r...t OFOPALC70 * C",.. 0E- ** 36.78 1466.581 R~ktt I lrAtI- SAND Str 33 19 Is.. /2 mn CEIMnq GROUT - - 1 1M *-..dd Rou. 156:22 Stem Ke 465.4 /-yecg...FCAO O . . - L o ’ str Woeror e E.-IS 533.4’ I0 Rate cont L C , Dolomite - Grey - Hard 21 nd 17rpm 57. - Silic Kelly & DH Ass: 532.9’ 50 10.2 -S, -a’i

[Individual Identification of Cartilage by Direct Amplification in Mass Disasters].

PubMed

Wang, C H; Xu, C; Li, X Q; Wu, Y; Du, Z

2017-06-01

To explore the effectiveness of direct amplification for the STR analysis of cartilage, and to accelerate the effectiveness of disaster victim identification. Eighty-eight cartilage samples were directly amplified by PowerPle® 21 kit, and the results of genotyping were compared with that obtained by the magnetic beads method. In 88 cartilage samples, the STR genotypes were successfully detected from 84 samples by direct amplification and magnetic beads method, and both the results of genotyping by two method were consistent. Direct amplification with PowerPlex® 21 kit can be used for STR genotyping of cartilages. This method is operated easily and promptly, which has a potential application in the individual identification of mass disasters. Copyright© by the Editorial Department of Journal of Forensic Medicine

Allele frequency distribution for 21 autosomal STR loci in Nepal.

PubMed

Kraaijenbrink, T; van Driem, G L; Opgenort, J R M L; Tuladhar, N M; de Knijff, P

2007-05-24

The allele frequency distributions of 21 autosomal loci contained in the AmpFlSTR Identifiler, the Powerplex 16 and the FFFL multiplex PCR kits, was studied in 953 unrelated individuals from Nepal. Several new alleles (i.e. not yet reported in the NIST Short Tandem Repeat DNA Internet DataBase [http://www.cstl.nist.gov/biotech/strbase/]) have been detected in the process.

Population genetic data of the NGM SElect STR loci in Chinese Han population from Zhejiang region, China.

PubMed

Zhou, Anju; Wu, Weiwei; Liu, Qiuling; Wu, Yeda; Lu, Dejian

2013-03-01

Genetic variations of the 17 NGM SElect STR loci in Chinese Han samples from the Zhejiang region were analyzed. The results show that the NGM SElect is a highly genetic informative system in Zhejiang Han, and this population shows quite different genetic data from other major populations in the world with the exception of the Fujian Han.

Age Estimation with DNA: From Forensic DNA Fingerprinting to Forensic (Epi)Genomics: A Mini-Review.

PubMed

Parson, Walther

2018-01-01

Forensic genetics developed from protein-based techniques a quarter of a century ago and became famous as "DNA fingerprinting," this being based on restriction fragment length polymorphisms (RFLPs) of high-molecular-weight DNA. The amplification of much smaller short tandem repeat (STR) sequences using the polymerase chain reaction soon replaced RFLP analysis and advanced to become the gold standard in genetic identification. Meanwhile, STR multiplexes have been developed and made commercially available which simultaneously amplify up to 30 STR loci from as little as 15 cells or fewer. The enormous information content that comes with the large variety of observed STR genotypes allows for genetic individualisation (with the exception of identical twins). Carefully selected core STR loci form the basis of intelligence-led DNA databases that provide investigative leads by linking unsolved crime scenes and criminals through their matched STR profiles. Nevertheless, the success of modern DNA fingerprinting depends on the availability of reference material from suspects. In order to provide new investigative leads in cases where such reference samples are absent, forensic scientists started to explore the prediction of phenotypic traits from the DNA of the evidentiary sample. This paradigm change now uses DNA and epigenetic markers to forecast characteristics that are useful to triage further investigative work. So far, the best investigated externally visible characteristics are eye, hair and skin colour, as well as geographic ancestry and age. Information on the chronological age of a stain donor (or any sample donor) is elemental for forensic investigations in a number of aspects and has, therefore, been explored by researchers in some detail. Among different methodological approaches tested to date, the methylation-sensitive analysis of carefully selected DNA markers (CpG sites) has brought the most promising results by providing prediction accuracies of ±3-4 years, which can be comparable to, or even surpass those from, eyewitness reports. This mini-review puts recent developments in age estimation via (epi)genetic methods in the context of the requirements and goals of forensic genetics and highlights paths to follow in the future of forensic genomics. © 2018 S. Karger AG, Basel.

Peri-procedural ST segment resolution during Primary Percutaneous Coronary Intervention (PPCI) for acute myocardial infarction: predictors and clinical consequences.

PubMed

Karamasis, Grigoris V; Russhard, Paul; Al Janabi, Firas; Parker, Michael; Davies, John R; Keeble, Thomas R; Clesham, Gerald J

ECG ST segment resolution (STR) has been used to assess myocardial perfusion in STEMI patients undergoing PPCI. However, in most of the studies ECGs recorded at different time points after the actual procedure have been used, limiting the options of therapeutic interventions while the patient is still in the catheterisation laboratory. The aim of this study was to investigate the presence and clinical consequences of intra-procedural STR during PPCI. We analysed 12 lead ECGs recorded at the onset and the end of the PPCI procedure, measuring STR in the lead with maximum ST elevation on the initial recording. STR was defined as good when > 50% compared to baseline. Pre and immediately post PPCI ECGs were recorded in 467 STEMI cases whilst the patient was on the catheter lab table. Mean patient age was 63 (+/- 12) years old and 75% were men. Mean duration of symptoms to admission was 3.8 (+/- 3.4) hours and 51% of infarcts were anterior. Good ST resolution at the end of the procedure was seen in 46.5% of patients and was observed more commonly in inferior compared to anterior infarcts (60.1% vs. 32.6%, p<0.001), and in current smokers (53.2% vs. 42.4%, p=0.031). In patients presenting with symptoms for < 4 hours, good STR was more common (74% vs. 66%, p=0.019). Thrombus aspiration was used more frequently in patients who had good STR (88.5% vs 79.8% p=0.011). Patients with good ST resolution had a shorter mean hospital length of stay (3.8 vs. 4.5 days, p=0.009) and a higher left ventricular ejection fraction (49.9% vs. 44.2%, p<0.001) measured by transthoracic echocardiography prior to discharge. Good peri-procedural ST resolution was seen in less than half of STEMI patients undergoing PPCI. There were important clinical consequences of good ST resolution. Identification of suboptimal peri-procedural ST resolution could help identify patients who may benefit from new treatments aimed at protecting the microcirculation, whilst the patients are still in the angiography laboratory. Copyright © 2017 Elsevier Inc. All rights reserved.

The development of miniplex primer sets for the analysis of degraded DNA

NASA Astrophysics Data System (ADS)

McCord, Bruce; Opel, Kerry; Chung, Denise; Drabek, Jiri; Tatarek, Nancy; Meadows Jantz, Lee; Butler, John

2005-05-01

In this project, a new set of multiplexed PCR reactions has been developed for the analysis of degraded DNA. These DNA markers, known as Miniplexes, utilize primers that have shorter amplicons for use in short tandem repeat (STR) analysis of degraded DNA. In our work we have defined six of these new STR multiplexes, each of which consists of 3 to 4 reduced size STR loci, and each labeled with a different fluorescent dye. When compared to commercially available STR systems, reductions in size of up to 300 basepairs are possible. In addition, these newly designed amplicons consist of loci that are fully compatible with the the national computer DNA database known as CODIS. To demonstrate compatibility with commercial STR kits, a concordance study of 532 DNA samples of Caucasian, African American, and Hispanic origin was undertaken There was 99.77% concordance between allele calls with the two methods. Of these 532 samples, only 15 samples showed discrepancies at one of 12 loci. These occurred predominantly at 2 loci, vWA and D13S317. DNA sequencing revealed that these locations had deletions between the two primer binding sites. Uncommon deletions like these can be expected in certain samples and will not affect the utility of the Miniplexes as tools for degraded DNA analysis. The Miniplexes were also applied to enzymatically digested DNA to assess their potential in degraded DNA analysis. The results demonstrated a greatly improved efficiency in the analysis of degraded DNA when compared to commercial STR genotyping kits. A series of human skeletal remains that had been exposed to a variety of environmental conditions were also examined. Sixty-four percent of the samples generated full profiles when amplified with the Miniplexes, while only sixteen percent of the samples tested generated full profiles with a commercial kit. In addition, complete profiles were obtained for eleven of the twelve Miniplex loci which had amplicon size ranges less than 200 base pairs. These data clearly demonstrate that smaller PCR amplicons provide an attractive alternative to mitochondrial DNA for forensic analysis of degraded DNA.

Analysis of fingerprint samples, testing various conditions, for forensic DNA identification.

PubMed

Ostojic, Lana; Wurmbach, Elisa

2017-01-01

Fingerprints can be of tremendous value for forensic biology, since they can be collected from a wide variety of evident types, such as handles of weapons, tools collected in criminal cases, and objects with no apparent staining. DNA obtained from fingerprints varies greatly in quality and quantity, which ultimately affects the quality of the resulting STR profiles. Additional difficulties can arise when fingerprint samples show mixed STR profiles due to the handling of multiple persons. After applying a tested protocol for sample collection (swabbing with 5% Triton X-100), DNA extraction (using an enzyme that works at elevated temperatures), and PCR amplification (AmpFlSTR® Identifiler® using 31cycles) extensive analysis was performed to better understand the challenges inherent to fingerprint samples, with the ultimate goal of developing valuable profiles (≥50% complete). The impact of time on deposited fingerprints was investigated, revealing that while the quality of profiles deteriorated, full STR profiles could still be obtained from samples after 40days of storage at room temperature. By comparing the STR profiles from fingerprints of the dominant versus the non-dominant hand, we found a slightly better quality from the non-dominant hand, which was not always significant. Substrates seem to have greater effects on fingerprints. Tests on glass, plastic, paper and metal (US Quarter dollar, made of Cu and Ni), common substrates in offices and homes, showed best results for glass, followed by plastic and paper, while almost no profiles were obtained from a Quarter dollar. Important for forensic casework, we also assessed three-person mixtures of touched fingerprint samples. Unlike routinely used approaches for sampling evidence, the surface of an object (bottle) was sectioned into six equal parts and separate samples were taken from each section. The samples were processed separately for DNA extraction and STR amplification. The results included a few single source profiles and distinguishable two person mixtures. On average, this approach led to two profiles ≥50% complete per touched object. Some STR profiles were obtained more than once thereby increasing the confidence. Copyright © 2016 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

DUST AROUND R CORONAE BOREALIS STARS. I. SPITZER/INFRARED SPECTROGRAPH OBSERVATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anibal Garcia-Hernandez, D.; Kameswara Rao, N.; Lambert, David L., E-mail: agarcia@iac.es, E-mail: nkrao@iiap.res.in, E-mail: dll@astro.as.utexas.edu

2011-09-20

Spitzer/infrared spectrograph (IRS) spectra from 5 to 37 {mu}m for a complete sample of 31 R Coronae Borealis stars (RCBs) are presented. These spectra are combined with optical and near-infrared photometry of each RCB at maximum light to compile a spectral energy distribution (SED). The SEDs are fitted with blackbody flux distributions and estimates are made of the ratio of the infrared flux from circumstellar dust to the flux emitted by the star. Comparisons for 29 of the 31 stars are made with the Infrared Astronomical Satellite (IRAS) fluxes from three decades earlier: Spitzer and IRAS fluxes at 12 {mu}mmore » and 25 {mu}m are essentially equal for all but a minority of the sample. For this minority, the IRAS to Spitzer flux ratio exceeds a factor of three. The outliers are suggested to be stars where formation of a dust cloud or dust puff is a rare event. A single puff ejected prior to the IRAS observations may have been reobserved by Spitzer as a cooler puff at a greater distance from the RCB. RCBs which experience more frequent optical declines have, in general, a circumstellar environment containing puffs subtending a larger solid angle at the star and a quasi-constant infrared flux. Yet, the estimated subtended solid angles and the blackbody temperatures of the dust show a systematic evolution to lower solid angles and cooler temperatures in the interval between IRAS and Spitzer. Dust emission by these RCBs and those in the LMC is similar in terms of total 24 {mu}m luminosity and [8.0]-[24.0] color index.« less

SUBARU/HDS STUDY OF HE 1015-2050: SPECTRAL EVIDENCE OF R CORONAE BOREALIS LIGHT DECLINE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goswami, Aruna; Aoki, Wako, E-mail: aruna@iiap.res.in

2013-02-01

Hydrogen deficiency and a sudden optical light decline of about 6-8 mag are two principal characteristics of R Coronae Borealis (RCB) stars. The high latitude carbon star HE 1015-2050 was identified as a hydrogen-deficient carbon star from low-resolution spectroscopy. Photometric data of the Catalina Real-Time Transient Survey gathered between 2006 February and 2012 May indicate that the object exhibits no variability. However, a high-resolution (R {approx} 50, 000) optical spectrum of this object obtained with the 8.2 m Subaru telescope using High Dispersion Spectrograph on the 2012 January 13 offers sufficient spectral evidence that the object is a cool HdCmore » star of RCB type undergoing light decline. In contrast to the Na I D broad absorption features seen in the low-resolution spectra on several occasions, the high-resolution spectrum exhibits Na I D{sub 2} and D{sub 1} features in emission. A few emission lines due to Mg I, Sc II, Ti I, Ti II, Fe II, and Ba I are also observed in the spectrum of this object for the first time. Such emission features combined with neutral and singly ionized lines of Ca, Ti, Fe, etc., in absorption are reportedly seen in RCBs spectra in the early stage of decline or during the recovery to maximum. Further, the light decline of RCBs is ascribed to the formation of a cloud of soot that obscures the visible photosphere. The presence of such circumstellar material is evident from the polarimetric observations with an estimated V-band percentage polarization of {approx}1.7% for this object.« less

First report of Lecanodiaspis dendrobii Douglas, 1892 (Hemiptera: Lecanodiaspididae) and the associated parasitoid Cephaleta sp. (Hymenoptera: Pteromalidae) in Brazil.

PubMed

Marsaro Júnior, A L; Peronti, A L B G; Costa, V A; Morais, E G F; Pereira, P R V S

2016-02-01

Lecanodiaspis dendrobii Douglas, 1892 (Hemiptera: Coccoidea: Lecanodiaspididae) and the associated parasitoid Cephaleta sp. (Hymenoptera: Pteromalidae) are reported for the first time in Brazil. Specimens of this scale insect were collected on branches and stems of Acacia mangium Willd., Leucaena leucocephala (Lam.) de Wit (Fabaceae), Morus nigra L. (Moraceae), Citrus reticulata Blanco (Rutaceae), Tectona grandis L. f. (Verbenaceae), Anacardium occidentale (Anacardiaceae), Annona squamosa L. and Xylopia aromatica (Lam.) Mart. (Annonaceae), in three municipalities of the Roraima state. All plants here mentioned are recorded for the first time as a host for L. dendrobii. Morphological characters of L. dendrobii and symptoms presented by the host plants infested by this pest are included in this work.

Risk Factors for Allergic Rhinitis in Costa Rican Children with Asthma

PubMed Central

Bunyavanich, Supinda; Soto-Quiros, Manuel E.; Avila, Lydiana; Laskey, Daniel; Senter, Jody M.; Celedón, Juan C.

2009-01-01

Background Risk factors for allergic rhinitis (AR) in asthmatics are likely distinct from those for AR or asthma alone. We sought to identify clinical and environmental risk factors for AR in children with asthma. Methods We performed a cross-sectional study of 616 Costa Rican children aged 6–14 years with asthma. Candidate risk factors were drawn from questionnaire data, spirometry, methacholine challenge testing, skin testing, and serology. Two outcome measures, skin test reaction (STR)-positive AR and physician-diagnosed AR, were examined by logistic regression. Results STR-positive AR had high prevalence (80%) in Costa Rican children with asthma, and its independent risk factors were nasal symptoms after exposure to dust or mold, parental history of AR, older age at asthma onset, oral steroid use in the past year, eosinophilia, and positive IgEs to dust mite and cockroach. Physician-diagnosed AR had lower prevalence (27%), and its independent risk factors were nasal symptoms after pollen exposure, STR to tree pollens, a parental history of AR, inhaled steroid and short-acting β2 agonist use in the past year, household mold/mildew, and fewer older siblings. A physician’s diagnosis was only 29.5% sensitive for STR-positive AR. Conclusions Risk factors for AR in children with asthma depend on the definition of AR. Indoor allergens drive risk for STR-positive AR. Outdoor allergens and home environmental conditions are risk factors for physician-diagnosed AR. We propose that children with asthma in Costa Rica and other Latin American nations undergo limited skin testing or specific IgE measurements to reduce the current under-diagnosis of AR. PMID:19796208

Glycinergic inhibition of BAT sympathetic premotor neurons in rostral raphe pallidus.

PubMed

Conceição, Ellen Paula Santos da; Madden, Christopher J; Morrison, Shaun F

2017-06-01

The rostral raphe pallidus (rRPa) contains sympathetic premotor neurons controlling thermogenesis in brown adipose tissue (BAT). We sought to determine whether a tonic activation of glycine A receptors (Gly A R) in the rRPa contributes to the inhibitory regulation of BAT sympathetic nerve activity (SNA) and of cardiovascular parameters in anesthetized rats. Nanoinjection of the Gly A R antagonist, strychnine (STR), into the rRPa of intact rats increased BAT SNA (peak: +495%), BAT temperature (T BAT , +1.1°C), expired CO 2 , (+0.4%), core body temperature (T CORE , +0.2°C), mean arterial pressure (MAP, +4 mmHg), and heart rate (HR, +57 beats/min). STR into rRPa in rats with a postdorsomedial hypothalamus transection produced similar increases in BAT thermogenic and cardiovascular parameters. Glycine nanoinjection into the rRPa evoked a potent inhibition of the cooling-evoked increases in BAT SNA (nadir: -74%), T BAT (-0.2°C), T CORE (-0.2°C), expired CO 2 (-0.2%), MAP (-8 mmHg), and HR (-22 beats/min) but had no effect on the increases in these variables evoked by STR nanoinjection into rRPa. Nanoinjection of GABA into the rRPa inhibited the STR-evoked BAT SNA (nadir: -86%) and reduced the expired CO 2 (-0.4%). Blockade of glutamate receptors in rRPa reduced the STR-evoked increases in BAT SNA (nadir: -61%), T BAT (-0.5°C), expired CO 2 (-0.3%), MAP (-9 mmHg), and HR (-33 beats/min). We conclude that a tonically active glycinergic input to the rRPa contributes to the inhibitory regulation of the discharge of BAT sympathetic premotor neurons and of BAT thermogenesis and energy expenditure. Copyright © 2017 the American Physiological Society.

Dopamine D3 receptor antagonism contributes to blonanserin-induced cortical dopamine and acetylcholine efflux and cognitive improvement.

PubMed

Huang, Mei; Kwon, Sunoh; Oyamada, Yoshihiro; Rajagopal, Lakshmi; Miyauchi, Masanori; Meltzer, Herbert Y

2015-11-01

Blonanserin is a novel atypical antipsychotic drug (APD), which, unlike most atypical APDs, has a slightly higher affinity for dopamine (DA) D2 than serotonin (5-HT)2A receptors, and is an antagonist at both, as well as at D3 receptors. The effects of atypical APDs to enhance rodent cortical, hippocampal, limbic, and dorsal striatal (dSTR) DA and acetylcholine (ACh) release, contribute to their ability to improve novel object recognition (NOR) in rodents treated with sub-chronic (sc) phencyclidine (PCP) and cognitive impairment associated with schizophrenia (CIAS). Here we determined the ability of blonanserin, the D3 antagonist NGB 2904, and the typical APD, haloperidol, a D2 antagonist, to enhance neurotransmitter efflux in the medial prefrontal cortex (mPFC) and dSTR of mice, and to ameliorate the scPCP-induced deficit in NOR in rats. Blonanserin, 10mg/kg, i.p., increased DA, norepinephrine (NE), and ACh efflux in mPFC and dSTR. NGB 2904, 3mg/kg, increased DA and ACh, but not NE, efflux in mPFC, and DA, but not ACh, efflux in dSTR. Haloperidol increased DA and NE efflux in dSTR only. The selective D3 agonist PD 128907 partially blocked the blonanserin-induced cortical ACh, DA, NE and striatal DA efflux. NGB 2904, 3mg/kg, like blonanserin, 1mg/kg, and the combination of sub-effective doses of NGB 2904 and blonanserin (both 0.3mg/kg), ameliorated the scPCP-induced NOR deficit in rats. These results suggest that D3 receptor blockade may contribute to the ability of blonanserin to increase cortical DA and ACh efflux, as well as to restore NOR and improve CIAS. Copyright © 2015 Elsevier Inc. All rights reserved.

Impact of timing of radiotherapy in patients with newly diagnosed glioblastoma.

PubMed

Randolph, David M; McTyre, Emory R; Paulsson, Anna K; Holmes, Jordan A; Hinson, William H; Lesser, Glenn J; Strowd, Roy; Lo, Hui-Wen; Laxton, Adrian W; Tatter, Stephen B; Debinski, Waldemar; Chan, Michael D

2016-12-01

To further evaluate if a delay in the start of radiation therapy (RT) affects patient outcomes for glioblastoma (GBM). From May 1999 to May 2010, a total of 161 patients underwent surgery followed by RT for GBM. We assessed overall survival (OS) and progression free survival (PFS), stratified by extent of surgical resection. Included in the analysis were genomic predictors of progression. Median time from surgery to start of RT was 20days for biopsy alone, 28days for subtotal resection (STR) and 28days for gross total resection (GTR). For all patients, a delay >28days did not result in a difference in PFS when compared to no delay (6.7 vs. 6.9 months, p=0.07). PFS was improved in biopsy or STR patients with a >28day delay to start of RT (4.2 vs. 6.7 months, p=0.006). OS was also improved in patients receiving biopsy or STR with a >28day delay to start of RT (12.3 vs. 7.8 months, p=0.005). Multivariable analysis (MVA) demonstrated an improvement in OS and PFS with time to RT >28days for biopsy or STR patients (HR 0.52 p=0.008 and HR 0.48 p=0.02, respectively). In this retrospective review of GBM patients treated at a single institution, OS and PFS were not different between time to RT >28days compared to <28 days. There was a modest improvement in both PFS and OS in patients who received biopsy or STR with time to RT >28 days. Copyright © 2016 Elsevier B.V. All rights reserved.

A Mechanism of Unidirectional Transformation, Leading to Antibiotic Resistance, Occurs within Nasopharyngeal Pneumococcal Biofilm Consortia

PubMed Central

2018-01-01

ABSTRACT Streptococcus pneumoniae acquires genes for resistance to antibiotics such as streptomycin (Str) or trimethoprim (Tmp) by recombination via transformation of DNA released by other pneumococci and closely related species. Using naturally transformable pneumococci, including strain D39 serotype 2 (S2) and TIGR4 (S4), we studied whether pneumococcal nasopharyngeal transformation was symmetrical, asymmetrical, or unidirectional. Incubation of S2Tet and S4Str in a bioreactor simulating the human nasopharynx led to the generation of SpnTet/Str recombinants. Double-resistant pneumococci emerged soon after 4 h postinoculation at a recombination frequency (rF) of 2.5 × 10−4 while peaking after 8 h at a rF of 1.1 × 10−3. Acquisition of antibiotic resistance genes by transformation was confirmed by treatment with DNase I. A high-throughput serotyping method demonstrated that all double-resistant pneumococci belonged to one serotype lineage (S2Tet/Str) and therefore that unidirectional transformation had occurred. Neither heterolysis nor availability of DNA for transformation was a factor for unidirectional transformation given that the density of each strain and extracellular DNA (eDNA) released from both strains were similar. Unidirectional transformation occurred regardless of the antibiotic-resistant gene carried by donors or acquired by recipients and regardless of whether competence-stimulating peptide-receptor cross talk was allowed. Moreover, unidirectional transformation occurred when two donor strains (e.g., S4Str and S19FTmp) were incubated together, leading to S19FStr/Tmp but at a rF 3 orders of magnitude lower (4.9 × 10−6). We finally demonstrated that the mechanism leading to unidirectional transformation was due to inhibition of transformation of the donor by the recipient. PMID:29764945

STR Profiling for Discrimination between Wild and Domestic Swine Specimens and between Main Breeds of Domestic Pigs Reared in Belarus.

PubMed

Rębała, Krzysztof; Rabtsava, Alina A; Kotova, Svetlana A; Kipen, Viachaslau N; Zhurina, Natalja V; Gandzha, Alla I; Tsybovsky, Iosif S

2016-01-01

A panel comprising 16 short tandem repeats (STRs) and a gender-specific amelogenin marker was worked out and tested for robustness in discrimination between wild and domestic swine subspecies encountered in Europe, between regional populations of wild boars and between main breeds of domestic pigs reared in Belarus. The STR dataset comprised 310 wild boars, inhabiting all administrative regions of Belarus, and 313 domestic pigs, representing three local and three cosmopolitan lines. Additionally, a total of 835 wild boars were genotyped for the presence of melanocortin 1 receptor (MC1R) alleles specific for domestic pigs. Correctness of assignment of STR profiles to appropriate populations was measured by log-likelihood ratios (log-LRs). All samples were correctly identified as wild boars or domestic pigs with average log-LR of 42.4 (LR = 2.6×1018). On the other hand, as many as 50 out of 835 (6.0%) genotyped wild boars from Belarus possessed MC1R alleles specific to domestic pigs, demonstrating supremacy of our STR profiling system over traditional differentiation between wild boars and domestic pigs, based on single binary markers. Mean log-LRs for allocation of wild boars to their regions of origin and of domestic pigs to appropriate breeds were 2.3 (LR = 9.7) and 13.4 (LR = 6.6×105), respectively. Our results demonstrate the developed STR profiling system to be a highly efficient tool for differentiation between wild and domestic swine subspecies and between diverse breeds of domestic pigs as well as for verification of genetic identity of porcine specimens for the purpose of forensic investigations of wildlife crimes, assurance of veterinary public health, parentage control in animal husbandry, food safety management and traceability of livestock products.

STR Profiling for Discrimination between Wild and Domestic Swine Specimens and between Main Breeds of Domestic Pigs Reared in Belarus

PubMed Central

Rębała, Krzysztof; Rabtsava, Alina A.; Kotova, Svetlana A.; Kipen, Viachaslau N.; Zhurina, Natalja V.; Gandzha, Alla I.; Tsybovsky, Iosif S.

2016-01-01

A panel comprising 16 short tandem repeats (STRs) and a gender-specific amelogenin marker was worked out and tested for robustness in discrimination between wild and domestic swine subspecies encountered in Europe, between regional populations of wild boars and between main breeds of domestic pigs reared in Belarus. The STR dataset comprised 310 wild boars, inhabiting all administrative regions of Belarus, and 313 domestic pigs, representing three local and three cosmopolitan lines. Additionally, a total of 835 wild boars were genotyped for the presence of melanocortin 1 receptor (MC1R) alleles specific for domestic pigs. Correctness of assignment of STR profiles to appropriate populations was measured by log-likelihood ratios (log-LRs). All samples were correctly identified as wild boars or domestic pigs with average log-LR of 42.4 (LR = 2.6×1018). On the other hand, as many as 50 out of 835 (6.0%) genotyped wild boars from Belarus possessed MC1R alleles specific to domestic pigs, demonstrating supremacy of our STR profiling system over traditional differentiation between wild boars and domestic pigs, based on single binary markers. Mean log-LRs for allocation of wild boars to their regions of origin and of domestic pigs to appropriate breeds were 2.3 (LR = 9.7) and 13.4 (LR = 6.6×105), respectively. Our results demonstrate the developed STR profiling system to be a highly efficient tool for differentiation between wild and domestic swine subspecies and between diverse breeds of domestic pigs as well as for verification of genetic identity of porcine specimens for the purpose of forensic investigations of wildlife crimes, assurance of veterinary public health, parentage control in animal husbandry, food safety management and traceability of livestock products. PMID:27851802

Improved human observer performance in digital reconstructed radiograph verification in head and neck cancer radiotherapy.

PubMed

Sturgeon, Jared D; Cox, John A; Mayo, Lauren L; Gunn, G Brandon; Zhang, Lifei; Balter, Peter A; Dong, Lei; Awan, Musaddiq; Kocak-Uzel, Esengul; Mohamed, Abdallah Sherif Radwan; Rosenthal, David I; Fuller, Clifton David

2015-10-01

Digitally reconstructed radiographs (DRRs) are routinely used as an a priori reference for setup correction in radiotherapy. The spatial resolution of DRRs may be improved to reduce setup error in fractionated radiotherapy treatment protocols. The influence of finer CT slice thickness reconstruction (STR) and resultant increased resolution DRRs on physician setup accuracy was prospectively evaluated. Four head and neck patient CT-simulation images were acquired and used to create DRR cohorts by varying STRs at 0.5, 1, 2, 2.5, and 3 mm. DRRs were displaced relative to a fixed isocenter using 0-5 mm random shifts in the three cardinal axes. Physician observers reviewed DRRs of varying STRs and displacements and then aligned reference and test DRRs replicating daily KV imaging workflow. A total of 1,064 images were reviewed by four blinded physicians. Observer errors were analyzed using nonparametric statistics (Friedman's test) to determine whether STR cohorts had detectably different displacement profiles. Post hoc bootstrap resampling was applied to evaluate potential generalizability. The observer-based trial revealed a statistically significant difference between cohort means for observer displacement vector error ([Formula: see text]) and for [Formula: see text]-axis [Formula: see text]. Bootstrap analysis suggests a 15% gain in isocenter translational setup error with reduction of STR from 3 mm to [Formula: see text]2 mm, though interobserver variance was a larger feature than STR-associated measurement variance. Higher resolution DRRs generated using finer CT scan STR resulted in improved observer performance at shift detection and could decrease operator-dependent geometric error. Ideally, CT STRs [Formula: see text]2 mm should be utilized for DRR generation in the head and neck.

Technical note: developmental validation of a novel 6-dye typing system with 36 Y-STR loci.

PubMed

Du, Weian; Feng, Peipei; Huang, Hongyan; Wu, Weibin; Zhang, Lei; Guo, Yulin; Liu, Changhui; Liu, Hong; Liu, Chao; Chen, Ling

2018-05-30

Y-chromosomal short tandem repeats (Y-STRs) have proven to be very useful in investigating sexual assault cases and in paternity lineage differentiation. However, currently available commercial Y-STR multiplex amplification systems bear the limitations in the identification of related males from the same paternal lineage due to there being an insufficient number of loci in any single amplification kit. The aim of this study was to establish and validate a novel 6-dye, 36-plex Y-STR multiplex amplification system that incorporated all of the loci present in the Yfiler™ Plus kit (DYS19, DYS385a/b, DYF387S1, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, Y_GATA_H4) as well as a further nine highly polymorphic Y-STR loci (DYS388, DYS444, DYS447, DYS522, DYS527a/b, DYS549, DYS596, DYS643). The novel system was optimized and validated by a series of studies that tested the effect of different PCR-based conditions as well as the species specificity, sensitivity, stability, stutter precision, suitability for use on DNA mixtures, reproducibility, and parallel testing of the system, as well as its performance on casework samples and population analysis, according to the SWGDAM developmental validation guidelines. A total of 246 haplotypes were found for the 36 Y-STRs among 247 Guangdong Han unrelated males. Collectively, the results demonstrate that the developed 36-plex Y-STR system is sensitive, robust, reliable, and highly informative for use in forensic genetics.

The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit.

PubMed

Hussing, C; Bytyci, R; Huber, C; Morling, N; Børsting, C

2018-05-24

Some STR loci have internal sequence variations, which are not revealed by the standard STR typing methods used in forensic genetics (PCR and fragment length analysis by capillary electrophoresis (CE)). Typing of STRs with next-generation sequencing (NGS) uncovers the sequence variation in the repeat region and in the flanking regions. In this study, 363 Danish individuals were typed for 56 STRs (26 autosomal STRs, 24 Y-STRs, and 6 X-STRs) using the ForenSeq™ DNA Signature Prep Kit to establish a Danish STR sequence database. Increased allelic diversity was observed in 34 STRs by the PCR-NGS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were around four times larger than the numbers of alleles determined by repeat length alone. Thirteen SNPs and one InDel were identified in the flanking regions of 12 STRs. Furthermore, 36 single positions and five longer stretches in the STR flanking regions were found to have dubious genotyping quality. The combined match probability of the 26 autosomal STRs was 10,000 times larger using the PCR-NGS assay than by using PCR-CE. The typical paternity indices for trios and duos were 500 and 100 times larger, respectively, than those obtained with PCR-CE. The assay also amplified 94 SNPs selected for human identification. Eleven of these loci were not in Hardy-Weinberg equilibrium in the Danish population, most likely because the minimum threshold for allele calling (30 reads) in the ForenSeq™ Universal Analysis Software was too low and frequent allele dropouts were not detected.

Comparative sensitivity and inhibitor tolerance of GlobalFiler® PCR Amplification and Investigator® 24plex QS kits for challenging samples.

PubMed

Elwick, Kyleen; Mayes, Carrie; Hughes-Stamm, Sheree

2018-05-01

In cases such as mass disasters or missing persons, human remains are challenging to identify as they may be fragmented, burnt, been buried, decomposed, and/or contain inhibitory substances. This study compares the performance of a relatively new STR kit in the US market (Investigator® 24plex QS kit; Qiagen) with the GlobalFiler® PCR Amplification kit (Thermo Fisher Scientific) when genotyping highly inhibited and low level DNA samples. In this study, DNA samples ranging from 1 ng to 7.8 pg were amplified to define the sensitivity of two systems. In addition, DNA (1 ng and 0.1 ng input amounts) was spiked with various concentrations of five inhibitors common to human remains (humic acid, melanin, hematin, collagen, calcium). Furthermore, bone (N = 5) and tissue samples from decomposed human remains (N = 6) were used as mock casework samples for comparative analysis with both STR kits. The data suggest that the GlobalFiler® kit may be slightly more sensitive than the Investigator® kit. On average STR profiles appeared to be more balanced and average peak heights were higher when using the GlobalFiler® kit. However, the data also show that the Investigator® kit may be more tolerant to common PCR inhibitors. While both STR kits showed a decrease in alleles as the inhibitor concentration increased, more complete profiles were obtained when the Investigator® kit was used. Of the 11 bone and decomposed tissue samples tested, 8 resulted in more complete and balanced STR profiles when amplified with the GlobalFiler® kit. Copyright © 2018 Elsevier B.V. All rights reserved.

[Mutation Analysis of 19 STR Loci in 20 723 Cases of Paternity Testing].

PubMed

Bi, J; Chang, J J; Li, M X; Yu, C Y

2017-06-01

To observe and analyze the confirmed cases of paternity testing, and to explore the mutation rules of STR loci. The mutant STR loci were screened from 20 723 confirmed cases of paternity testing by Goldeneye 20A system．The mutation rates, and the sources, fragment length, steps and increased or decreased repeat sequences of mutant alleles were counted for the analysis of the characteristics of mutation-related factors. A total of 548 mutations were found on 19 STR loci, and 557 mutation events were observed. The loci mutation rate was 0.07‰-2.23‰. The ratio of paternal to maternal mutant events was 3.06:1. One step mutation was the main mutation, and the number of the increased repeat sequences was almost the same as the decreased repeat sequences. The repeat sequences were more likely to decrease in two steps mutation and above. Mutation mainly occurred in the medium allele, and the number of the increased repeat sequences was almost the same as the decreased repeat sequences. In long allele mutations, the decreased repeat sequences were significantly more than the increased repeat sequences. The number of the increased repeat sequences was almost the same as the decreased repeat sequences in paternal mutation, while the decreased repeat sequences were more than the increased in maternal mutation. There are significant differences in the mutation rate of each locus. When one or two loci do not conform to the genetic law, other detection system should be added, and PI value should be calculated combined with the information of the mutate STR loci in order to further clarify the identification opinions. Copyright© by the Editorial Department of Journal of Forensic Medicine

Muscle oxygenation and glycolysis in females with trapezius myalgia during stress and repetitive work using microdialysis and NIRS.

PubMed

Sjøgaard, Gisela; Rosendal, Lars; Kristiansen, Jesper; Blangsted, Anne K; Skotte, Jørgen; Larsson, Britt; Gerdle, Björn; Saltin, Bengt; Søgaard, Karen

2010-03-01

The aim of this investigation was to study female workers active in the labour market for differences between those with trapezius myalgia (MYA) and without (CON) during repetitive pegboard (PEG) and stress (STR) tasks regarding (1) relative muscle load, (2) trapezius muscle blood flow, (3) metabolite accumulation, (4) oxygenation, and (5) pain development. Among 812 female employees (age 30-60 years) at 7 companies with high prevalence of neck/shoulder complaints, clinical examination identified 43 MYA and 19 CON. At rest, during PEG, and STR the trapezius muscle was measured using (1) EMG and MMG, (2) microdialysis, and (3) NIRS. Further, subjective pain ratings were scored (VAS). EMGrms in %MVE (Maximal Voluntary EMG-activity), was significantly higher among MYA than CON during PEG (11.74 +/- 9.09 vs. 7.42 +/- 5.56%MVE) and STR (5.47 +/- 5.00 vs. 3.28 +/- 1.94%MVE). MANOVA showed a group and time effect regarding data from the microdialysis: for MYA versus CON group differences demonstrated lower muscle blood flow and higher lactate and pyruvate concentrations. Potassium and glucose only showed time effects. NIRS showed similar initial decreases in oxygenation with PEG in both groups, but only in CON a significant increase back to baseline during PEG. VAS score at rest was highest among MYA and increased during PEG, but not for CON. The results showed significant differences between CON and MYA regarding muscle metabolism at rest and with PEG and STR. Higher relative muscle load during PEG and STR, insufficient muscle blood flow and oxygenation may account for the higher lactate, pyruvate and pain responses among MYA versus CON.

Northern Slavs from Serbia do not show a founder effect at autosomal and Y-chromosomal STRs and retain their paternal genetic heritage.

PubMed

Rębała, Krzysztof; Veselinović, Igor; Siváková, Daniela; Patskun, Erika; Kravchenko, Sergey; Szczerkowska, Zofia

2014-01-01

Studies on Y-chromosomal markers revealed significant genetic differentiation between Southern and Northern (Western and Eastern) Slavic populations. The northern Serbian region of Vojvodina is inhabited by Southern Slavic Serbian majority and, inter alia, Western Slavic (Slovak) and Eastern Slavic (Ruthenian) minorities. In the study, 15 autosomal STR markers were analysed in unrelated Slovaks, Ruthenians and Serbs from northern Serbia and western Slovakia. Additionally, Slovak males from Serbia were genotyped for 17 Y-chromosomal STR loci. The results were compared to data available for other Slavic populations. Genetic distances for autosomal markers revealed homogeneity between Serbs from northern Serbia and Slovaks from western Slovakia and distinctiveness of Serbian Slovaks and Ruthenians. Y-STR variation showed a clear genetic departure of the Slovaks and Ruthenians inhabiting Vojvodina from their Serbian neighbours and genetic similarity to the Northern Slavic populations of Slovakia and Ukraine. Admixture estimates revealed negligible Serbian paternal ancestry in both Northern Slavic minorities of Vojvodina, providing evidence for their genetic isolation from the Serbian majority population. No reduction of genetic diversity at autosomal and Y-chromosomal markers was found, excluding genetic drift as a reason for differences observed at autosomal STRs. Analysis of molecular variance detected significant population stratification of autosomal and Y-chromosomal microsatellites in the three Slavic populations of northern Serbia, indicating necessity for separate databases used for estimations of frequencies of autosomal and Y-chromosomal STR profiles in forensic casework. Our results demonstrate that regarding Y-STR haplotypes, Serbian Slovaks and Ruthenians fit in the Eastern European metapopulation defined in the Y chromosome haplotype reference database. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Draft genome sequence of Lactococcus garvieae str. PAQ102015-99, an outbreak strain isolated from a commercial trout farm in the Northwestern United States.

USDA-ARS?s Scientific Manuscript database

We announce the draft genome assembly of Lactococcus garvieae str. PAQ102015-99, a recently isolated strain from an outbreak of lactococcosis at a commercial trout farm in the Northwestern US. The draft genome comprises 14 contigs totaling 2,068,357 bp with an N50 of 496,618 bp and average G+C conte...

Performance of Identifiler Direct and PowerPlex 16 HS on the Applied Biosystems 3730 DNA Analyzer for processing biological samples archived on FTA cards.

PubMed

Laurin, Nancy; DeMoors, Anick; Frégeau, Chantal

2012-09-01

Direct amplification of STR loci from biological samples collected on FTA cards without prior DNA purification was evaluated using Identifiler Direct and PowerPlex 16 HS in conjunction with the use of a high throughput Applied Biosystems 3730 DNA Analyzer. In order to reduce the overall sample processing cost, reduced PCR volumes combined with various FTA disk sizes were tested. Optimized STR profiles were obtained using a 0.53 mm disk size in 10 μL PCR volume for both STR systems. These protocols proved effective in generating high quality profiles on the 3730 DNA Analyzer from both blood and buccal FTA samples. Reproducibility, concordance, robustness, sample stability and profile quality were assessed using a collection of blood and buccal samples on FTA cards from volunteer donors as well as from convicted offenders. The new developed protocols offer enhanced throughput capability and cost effectiveness without compromising the robustness and quality of the STR profiles obtained. These results support the use of these protocols for processing convicted offender samples submitted to the National DNA Data Bank of Canada. Similar protocols could be applied to the processing of casework reference samples or in paternity or family relationship testing. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Microwave-assisted Synthesis of Benzimidazole Derivatives from Citronellal in Kaffir Lime (Citrus hystrix DC.) Oil

NASA Astrophysics Data System (ADS)

Sapri Ramadhan, Dwi; Warsito; Dhiaul Iftitah, Elvina

2018-01-01

Benzimidazoles are an important group of heterocyclic aromatic organic compound in the field of medicinal chemistry. It plays a very important role in pharmacological activity such as, analgesic, antiinflammatory, antibacterial, anti ungal, anti iral, antithelmenthic, anti convulsant, antihypertensive, and antiulcer. The synthesis of benzimidazole derivative under microwave irradiation of citronellal as raw material which is extracted from Citrus hystrix DC. (kaffir lime) leaves. The reaction using methanol and dichloromethane as solvent with variation of reaction time at 30, 40, 50, 60, and 70 minutes and mole ratio of citronellal to 1,2-phenylenediamine, 1:1, 1:1.5, and 1:2, respectively. Synthesis products was characterized by FT-IR and GC-MS. The optimum reaction time was obtained at 60 minutes in the present of dichloromethane and 1:2 mole ratio of citronellal to 1,2-phenylenediamine. The yield of the product is 42.19%. Structure of the synthesized compound were assigned on spectrum bands for C=N str at 1661 cm-1, C-N str at 1271 cm-1, C=C str of benzene ring at 1622 and 1456 cm-1 and C=C str of alkene at 1379 cm-1. GC-MS analysis showed single peak with retention time of 15.339 minute and m/z 242.

Direct qPCR quantification using the Quantifiler(®) Trio DNA quantification kit.

PubMed

Liu, Jason Yingjie

2014-11-01

The effectiveness of a direct quantification assay is essential to the adoption of the combined direct quantification/direct STR workflow. In this paper, the feasibility of using the Quantifiler(®) Trio DNA quantification kit for the direct quantification of forensic casework samples was investigated. Both low-level touch DNA samples and blood samples were collected on PE swabs and quantified directly. The increased sensitivity of the Quantifiler(®) Trio kit enabled the detection of less than 10pg of DNA in unprocessed touch samples and also minimizes the stochastic effect experienced by different targets in the same sample. The DNA quantity information obtained from a direct quantification assay using the Quantifiler(®) Trio kit can also be used to accurately estimate the optimal input DNA quantity for a direct STR amplification reaction. The correlation between the direct quantification results (Quantifiler(®) Trio kit) and the direct STR results (GlobalFiler™ PCR amplification kit(*)) for low-level touch DNA samples indicates that direct quantification using the Quantifiler(®) Trio DNA quantification kit is more reliable than the Quantifiler(®) Duo DNA quantification kit for predicting the STR results of unprocessed touch DNA samples containing less than 10pg of DNA. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis.

PubMed

Tamura, Tomonori; Osawa, Motoki; Ochiai, Eriko; Suzuki, Takanori; Nakamura, Takashi

2015-09-01

The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Comparing survival outcomes of gross total resection and subtotal resection with radiotherapy for craniopharyngioma: a meta-analysis.

PubMed

Wang, Guoqing; Zhang, Xiaoyang; Feng, Mengzhao; Guo, Fuyou

2018-06-01

Recent studies suggest that subtotal resection (STR) followed by radiation therapy (RT) is an appealing alternative to gross total resection (GTR) for craniopharyngioma, but it remains controversial. We conducted a meta-analysis to determine whether GTR is superior to STR with RT for craniopharyngioma. A systematic search was performed for articles published until October 2017 in the PubMed, Embase, and Cochrane Central databases. The endpoints of interest are overall survival and progression-free survival. Pooled hazard ratios (HRs) and corresponding 95% confidence intervals (CIs) were calculated using a fixed or random-effects model. The data were analyzed using Review Manager 5.3 software. A total of 744 patients (seven cohort studies) were enrolled for analyses. There were no significant differences between the GTR and STR with RT groups when the authors compared the pooled HRs at the end of the follow-up period. Overall survival (pooled HR = 0.76, 95% CI: 0.46-1.25, P = 0.28) and progression-free survival (pooled HR = 1.52, 95% CI: 0.42-5.44, P = 0.52) were similar between the two groups. The current meta-analysis suggests that GTR and STR with RT have the similar survival outcomes for craniopharyngioma. Copyright © 2018 Elsevier Inc. All rights reserved.

Usefulness of autosomal STR polymorphisms beyond forensic purposes: data on Arabic- and Berber-speaking populations from central Morocco.

PubMed

Gaibar, Maria; Esteban, María Esther; Via, Marc; Harich, Nourdin; Kandil, Mostafa; Fernández-Santander, Ana

2012-07-01

This work describes, for the first time, the profile of Middle Atlas Berbers and Arabic-speaking central Moroccans for 15 autosomal STR loci widely used in forensic sciences. The main objectives were to determine the degree of heterogeneity among different Moroccan samples to identify geographic or linguistic patterns and to evaluate the usefulness of forensic STRs in anthropological studies. Blood samples were collected from 71 Arabic-speakers and 75 Berbers from the regions of Doukkala (central-west coast) and Khenifra (Middle Atlas), respectively. The AmpFlSTR Identifier kit was used to genotype 15 autosomal STR in both samples. Middle Atlas Berbers showed slightly higher genetic variation values compared to Arabic-speakers, both in the number of alleles and heterozygosity. In order to assess population relationships, data from Morocco, Algeria, Tunisia, Libya, Egypt, Kuwait, Qatar, Palestine, Syria, South-Spain and Turkey were included in the analysis. Within Morocco, genetic distances followed a clear geographic pattern. In the Arabic-speaking sample the genetic proportion of 'Arabian' admixture was estimated in 13%. The low value of admixture suggests that the Arabization of Morocco had a reduced demographic impact, which should be taken with caution because it is based on autosomal STRs with low inter-population variation levels.

A Catharanthus roseus BPF-1 homologue interacts with an elicitor-responsive region of the secondary metabolite biosynthetic gene Str and is induced by elicitor via a JA-independent signal transduction pathway.

PubMed

van der Fits, L; Zhang, H; Menke, F L; Deneka, M; Memelink, J

2000-11-01

Plants respond to pathogen attack by induction of various defence responses, including the biosynthesis of protective secondary metabolites. In Catharanthus roseus, the elicitor-induced expression of the terpenoid indole alkaloid biosynthetic gene Strictosidine synthase (Str) is mediated via the plant stress hormonejasmonate. In the promoters of several defence-related genes, cis-acting elements have been identified that are important for transcriptional regulation upon stress signals. Here we show that an upstream region in the Str promoter confers responsiveness to partially purified yeast elicitor and jasmonate. Yeast one-hybrid screening with this element as a bait identified a MYB-like protein, which shows high homology to parsley box P-binding factor-1 (PcBPF-1). In vitro analyses showed that the Str promoter fragment contained a novel binding site for BPF-1-like proteins with higher binding affinity than the previously described box P. CrBPF-1 mRNA accumulated rapidly in elicitor-treated C. roseus suspension cells, whereas no induction was observed with jasmonate. Inhibitor studies indicated that CrBPF-1 plays a role in an elicitor-responsive but jasmonate-independent signal transduction pathway, acting downstream of protein phosphorylation and calcium influx.

Virulent Bacteriophages Can Target O104:H4 Enteroaggregative Escherichia coli in the Mouse Intestine

PubMed Central

Maura, Damien; Galtier, Matthieu; Le Bouguénec, Chantal

2012-01-01

In vivo bacteriophage targeting of enteroaggregative Escherichia coli (EAEC) was assessed using a mouse intestinal model of colonization with the O104:H4 55989Str strain and a cocktail of three virulent bacteriophages. The colonization model was shown to mimic asymptomatic intestinal carriage found in humans. The addition of the cocktail to drinking water for 24 h strongly decreased ileal and weakly decreased fecal 55989Str concentrations in a dose-dependent manner. These decreases in ileal and fecal bacterial concentrations were only transient, since 55989Str concentrations returned to their original levels 3 days later. These transient decreases were independent of the mouse microbiota, as similar results were obtained with axenic mice. We studied the infectivity of each bacteriophage in the ileal and fecal environments and found that 55989Str bacteria in the mouse ileum were permissive to all three bacteriophages, whereas those in the feces were permissive to only one bacteriophage. Our results provide the first demonstration that bacterial permissivity to infection with virulent bacteriophages is not uniform throughout the gut; this highlights the need for a detailed characterization of the interactions between bacteria and bacteriophages in vivo for the further development of phage therapy targeting intestinal pathogens found in the gut of asymptomatic human carriers. PMID:23006754

Haplotype data for 23 Y-chromosome markers in a reference sample from Bosnia and Herzegovina.

PubMed

Kovačević, Lejla; Fatur-Cerić, Vera; Hadzic, Negra; Čakar, Jasmina; Primorac, Dragan; Marjanović, Damir

2013-06-01

To detect polymorphisms of 23 Y-chromosomal short tandem repeat (STR) loci, including 6 new loci, in a reference database of male population of Bosnia and Herzegovina, as well as to assess the importance of increasing the number of Y-STR loci utilized in forensic DNA analysis. The reference sample consisted of 100 healthy, unrelated men originating from Bosnia and Herzegovina. Sample collection using buccal swabs was performed in all geographical regions of Bosnia and Herzegovina in the period from 2010 to 2011. DNA samples were typed for 23 Y STR loci, including 6 new loci: DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643, which are included in the new PowerPlex® Y 23 amplification kit. The absolute frequency of generated haplotypes was calculated and results showed that 98 samples had unique Y 23 haplotypes, and that only two samples shared the same haplotype. The most polymorphic locus was DYS418, with 14 detected alleles and the least polymorphic loci were DYS389I, DYS391, DYS437, and DYS393. This study showed that by increasing the number of highly polymorphic Y STR markers, to include those tested in our analysis, leads to a reduction of repeating haplotypes, which is very important in the application of forensic DNA analysis.

Time reversal for localization of sources of infrasound signals in a windy stratified atmosphere.

PubMed

Lonzaga, Joel B

2016-06-01

Time reversal is used for localizing sources of recorded infrasound signals propagating in a windy, stratified atmosphere. Due to the convective effect of the background flow, the back-azimuths of the recorded signals can be substantially different from the source back-azimuth, posing a significant difficulty in source localization. The back-propagated signals are characterized by negative group velocities from which the source back-azimuth and source-to-receiver (STR) distance can be estimated using the apparent back-azimuths and trace velocities of the signals. The method is applied to several distinct infrasound arrivals recorded by two arrays in the Netherlands. The infrasound signals were generated by the Buncefield oil depot explosion in the U.K. in December 2005. Analyses show that the method can be used to substantially enhance estimates of the source back-azimuth and the STR distance. In one of the arrays, for instance, the deviations between the measured back-azimuths of the signals and the known source back-azimuth are quite large (-1° to -7°), whereas the deviations between the predicted and known source back-azimuths are small with an absolute mean value of <1°. Furthermore, the predicted STR distance is off only by <5% of the known STR distance.

Technology Insertion-Engineering Services Process Characterization Task Order No. 1. Book 2 of 3. Database Documentation Book. OO-ALC MANPGP (Wheels - WCD’S)

DTIC Science & Technology

1989-12-15

RElOVE MASKINE TAPE .00!91 .002 000 Al RCB-OH-W2 1.00 REMY WHL HLF F/PAINT CONVYOR .00833 .010 0040 E RWr- BBP -0 1.00 BALPOCE WEEL HALF .0773 .093 0050 5...16S601-819 16W6-35-3-2 15 ART SHE 160 PULTIPLE LA-10 L"L R/H AIM 9 1441--1-M -36A 7 472-M 1L--11. z.I-- PARK AN)E 161814, LEf-N sE. r& ffA t- 1450-00-. b

An Undergraduate Laboratory Experiment for Upper-Level Forensic Science, Biochemistry, or Molecular Biology Courses: Human DNA Amplification Using STR Single Locus Primers by Real-Time PCR with SYBR Green Detection

ERIC Educational Resources Information Center

Elkins, Kelly M.; Kadunc, Raelynn E.

2012-01-01

In this laboratory experiment, real-time polymerase chain reaction (real-time PCR) was conducted using published human TPOX single-locus DNA primers for validation and various student-designed short tandem repeat (STR) primers for Combined DNA Index System (CODIS) loci. SYBR Green was used to detect the amplification of the expected amplicons. The…

A functional difference in information processing between orbitofrontal cortex and ventral striatum during decision-making behaviour.

PubMed

Stott, Jeffrey J; Redish, A David

2014-11-05

Both orbitofrontal cortex (OFC) and ventral striatum (vStr) have been identified as key structures that represent information about value in decision-making tasks. However, the dynamics of how this information is processed are not yet understood. We recorded ensembles of cells from OFC and vStr in rats engaged in the spatial adjusting delay-discounting task, a decision-making task that involves a trade-off between delay to and magnitude of reward. Ventral striatal neural activity signalled information about reward before the rat's decision, whereas such reward-related signals were absent in OFC until after the animal had committed to its decision. These data support models in which vStr is directly involved in action selection, but OFC processes decision-related information afterwards that can be used to compare the predicted and actual consequences of behaviour. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Interpreting short tandem repeat variations in humans using mutational constraint

PubMed Central

Gymrek, Melissa; Willems, Thomas; Reich, David; Erlich, Yaniv

2017-01-01

Identifying regions of the genome that are depleted of mutations can reveal potentially deleterious variants. Short tandem repeats (STRs), also known as microsatellites, are among the largest contributors of de novo mutations in humans. However, per-locus studies of STR mutations have been limited to highly ascertained panels of several dozen loci. Here, we harnessed bioinformatics tools and a novel analytical framework to estimate mutation parameters for each STR in the human genome by correlating STR genotypes with local sequence heterozygosity. We applied our method to obtain robust estimates of the impact of local sequence features on mutation parameters and used this to create a framework for measuring constraint at STRs by comparing observed vs. expected mutation rates. Constraint scores identified known pathogenic variants with early onset effects. Our metric will provide a valuable tool for prioritizing pathogenic STRs in medical genetics studies. PMID:28892063

Rare Sequence Variation in the Genome Flanking a Short Tandem Repeat Locus Can Lead to a Question of “Nonmaternity”

PubMed Central

Deucher, Anne; Chiang, Tsoyu; Schrijver, Iris

2010-01-01

Typing of STR (short tandem repeat) alleles is used in a variety of applications in clinical molecular pathology, including evaluations for maternal cell contamination. Using a commercially available STR typing assay for maternal cell contamination performed in conjunction with prenatal diagnostic testing, we were posed with apparent nonmaternity when the two fetal samples did not demonstrate the expected maternal allele at one locus. By designing primers external to the region amplified by the primers from the commercial assay and by performing direct sequencing of the resulting amplicon, we were able to determine that a guanine to adenine sequence variation led to primer mismatch and allele dropout. This explained the apparent null allele shared between the maternal and fetal samples. Therefore, although rare, allele dropout must be considered whenever unexplained homozygosity at an STR locus is observed. PMID:20203001

The role of semantic memory in short-term recall: effect of strategic retrieval ability in an elderly population.

PubMed

Larigauderie, Pascale; Michaud, Aurelie; Vicente, Siobhan

2011-03-01

The present paper examines the relationship between two classic phenomena: semantic effects in short-term recall (STR) tasks, which are interpreted as indicating the involvement of long-term memory (LTM) in the functioning of short-term memory, on the one hand, and the existence of individual differences amongst elderly people in strategic retrieval ability (i.e., the ability to activate representations in LTM in a controlled way) on the other hand. Forty elderly participants completed a STR task under four different conditions which were thought to differentially involve LTM representations. Several executive functions, among which the strategic retrieval ability, were evaluated. The results showed that the participants who obtained the best performances in terms of strategic retrieval ability, and only in this executive ability, also exhibited better performances in the STR task, in particular when this task was performed under conditions which favored the use of LTM.

Isolating cells from female/male blood mixtures using florescence in situ hybridization combined with low volume PCR and its application in forensic science.

PubMed

Feng, Lei; Li, Cai-Xia; Han, Jun-Ping; Xu, Cheng; Hu, Lan

2015-11-01

To obtain single-source short tandem repeat (STR) profiles in trace female/male blood mixture samples, we combined florescence in situ hybridization (FISH), laser microdissection, and low volume PCR (LV-PCR) to isolate male/female cells and improve sensitivity. The results showed that isolation of as few as 10 leukocytes was sufficient to yield full STR profiles in fresh female or male blood samples for 32 independent tests with a low additional alleles rate (3.91%) and drop-out alleles rate (5.01%). Moreover, this procedure was tested in two fresh blood mixture series at three ratios (1:5, 1:10, and 1:20), two mock female/male blood mixture casework samples, and one practical casework sample. Male and female STR profiles were successfully detected in all of these samples, showing that this procedure could be used in forensic casework in the future.

Capillary sample introduction of polymerase chain reaction (PCR) products separated in ultrathin slab gels.

PubMed

Bullard, K M; Hietpas, P B; Ewing, A G

1998-01-01

Polymerase chain reaction (PCR) amplified short tandem repeat (STR) samples from the HUMVWF locus have been analyzed using a unique sample introduction and separation technique. A single capillary is used to transfer samples onto an ultrathin slab gel (57 microm thin). This ultrathin nondenaturing polyacrylamide gel is used to separate the amplified fragments, and laser-induced fluorescence with ethidium bromide is used for detection. The feasibility of performing STR analysis using this system has been investigated by examining the reproducibility for repeated samples. Reproducibility is examined by comparing the migration of the 14 and 17 HUMVWF alleles on three consecutive separations on the ultrathin slab gel. Using one locus, separations match in migration time with the two alleles 42 s apart for each of the three consecutive separations. This technique shows potential to increase sample throughput in STR analysis techniques although separation resolution still needs to be improved.

Population genetic data of the AmpFℓSTR® Identifiler® Plus and PowerPlex® 16 HS STR loci in four Canadian populations.

PubMed

Laurin, Nancy; Milot, Emmanuel

2014-03-01

Allele frequencies and forensically relevant population statistics were estimated for the short tandem repeat (STR) loci of the AmpFℓSTR® Identifiler® Plus and PowerPlex® 16 HS amplification kits, including D2S1338, D19S433, Penta D, and Penta E, for three First Nations Aboriginal populations and for Caucasians in Canada. The cumulative power of discrimination was ≥ 0.999999999999984 and the cumulative power of exclusion was ≥ 0.999929363 for both amplification systems in all populations. No significant departure from Hardy-Weinberg equilibrium was detected for D2S1338, D19S433, Penta D, and Penta E or the 13 Combined DNA Index System core STR loci after correction for multiple testing. Significant genetic diversity was observed between these four populations. Comparison with published frequency data for other populations is also presented.

Cost analysis of initial highly active antiretroviral therapy regimens for managing human immunodeficiency virus-infected patients according to clinical practice in a hospital setting.

PubMed

Colombo, Giorgio L; Castagna, Antonella; Di Matteo, Sergio; Galli, Laura; Bruno, Giacomo; Poli, Andrea; Salpietro, Stefania; Carbone, Alessia; Lazzarin, Adriano

2014-01-01

In the study reported here, single-tablet regimen (STR) versus (vs) multi-tablet regimen (MTR) strategies were evaluated through a cost analysis in a large cohort of patients starting their first highly active antiretroviral therapy (HAART). Adult human immunodeficiency virus (HIV) 1-naïve patients, followed at the San Raffaele Hospital, Milan, Italy, starting their first-line regimen from June 2008 to April 2012 were included in the analysis. The most frequently used first-line HAART regimens (>10%) were grouped into two classes: 1) STR of tenofovir disoproxil fumarate (TDF) + emtricitabine (FTC) + efavirenz (EFV) and 2) MTR including TDF + FTC + EFV, TDF + FTC + atazanavir/ritonavir (ATV/r), TDF + FTC + darunavir/ritonavir (DRV/r), and TDF + FTC + lopinavir/ritoavir (LPV/r). Data were analyzed from the point of view of the Lombardy Regional Health Service. HAART, hospitalizations, visits, medical examinations, and other concomitant non-HAART drug costs were evaluated and price variations included. Descriptive statistics were calculated for baseline demographic, clinical, and laboratory characteristics; associations between categorical variables and type of antiretroviral strategy (STR vs MTR) were examined using chi-square or Fisher's exact tests. At multivariate analysis, the generalized linear model was used to identify the predictive factors of the overall costs of the first-line HAART regimens. A total of 474 naïve patients (90% male, mean age 42.2 years, mean baseline HIV-RNA 4.50 log 10 copies/mL, and cluster of differentiation 4 [CD4+] count of 310 cells/μL, with a mean follow-up of 28 months) were included. Patients starting an STR treatment were less frequently antibody-hepatitis C virus positive (4% vs 11%, P=0.040), and had higher mean CD4+ values (351 vs 297 cells/μL, P=0.004) than MTR patients. The mean annual cost per patient in the STR group was €9,213.00 (range: €6,574.71-€33,570.00) and €14,277.00 (range: €5,908.89-€82,310.30) among MTR patients. At multivariate analysis, after adjustment for age, sex, antibody-hepatitis C virus status, HIV risk factors, baseline CD4+, and HIV-RNA, the cost analysis was significantly lower among patients starting an STR treatment than those starting an MTR (adjusted mean: €12,096.00 vs €16,106.00, P=0.0001). STR was associated with a lower annual cost per patient than MTR, thus can be considered a cost-saving strategy in the treatment of HIV patients. This analysis is an important tool for policy makers and health care professionals to make short- and long-term cost projections and thus assess the impact of these on available budgets.

Effect of oral meloxicam on health and performance of beef steers relative to bulls castrated on arrival at the feedlot.

PubMed

Coetzee, J F; Edwards, L N; Mosher, R A; Bello, N M; O'Connor, A M; Wang, B; Kukanich, B; Blasi, D A

2012-03-01

Castration in weaned calves is stressful and affects profitability by reducing ADG and increasing susceptibility to disease. This study evaluated the effect of meloxicam, a nonsteroidal anti-inflammatory drug (NSAID), on performance and health of calves received as steers compared with bull calves surgically castrated on arrival at the feedlot. British × Continental bulls (n = 145) and steers (n = 113; BW = 193 to 285 kg) were transported for 12 h in 3 truckloads (d 0), weighed, and randomly assigned to receive either lactose placebo (CONT; 1 mg/kg) or meloxicam (MEL; 1 mg/kg) suspended in water and administered per os, 24 h before castration. On d 1, bulls were surgically castrated (CAST) and steers were processed without castration (STR). Combinations of CONT/MEL and CAST/STR were allocated to 24 pens (6 pens per treatment) of 8 to 14 calves each. Pen was the experimental unit. Plasma meloxicam concentrations at the time of castration (d 1) were determined by HPLC-mass spectroscopy. Pen-level ADG, DMI, and G:F were estimated using BW obtained on d 0, 14, and 28 and weigh-back of feed. Individual animals were classified as sick based on a depression score of ≥2 on a 5-point scale and a rectal temperature of ≥39.8°C. On d 0, 1, and 14, calf chute temperament was evaluated using a 4-point scale. Data were analyzed using generalized linear mixed models and survival curve analyses. Castration reduced pen ADG (P < 0.001) and G:F (P < 0.001) from d 1 to 14, yet no effects (P > 0.45) were apparent by d 28. For all treatment groups, DMI increased with days on feed (P < 0.0001) but was less in CAST compared with STR calves (P < 0.016) throughout the study. From d 15 to 28, ADG increased (P = 0.0011) in CAST but not STR calves, and G:F decreased (P = 0.0004) in STR but not CAST calves. In CAST calves only, MEL treatment reduced the pen-level first pull rate (P = 0.04) and reduced bovine respiratory disease morbidity rate (P = 0.03). The frequency of chute escape behavior was greater on arrival and at castration in CAST vs. STR calves (P < 0.01) but not significantly different at d 14 (P = 0.22). Mean MEL concentrations at castration were no different between treated STR and CAST calves (P = 0.70). Meloxicam administration before castration in postweaning calves reduced the incidence of respiratory disease at the feedlot. These findings have implications for developing NSAID protocols for use in calves at castration with respect to addressing animal health and welfare concerns.

In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB

PubMed Central

2013-01-01

Background Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiation hybrid of buffalo and these reported STR can be used further in final gap plugging and “finishing” expected in de novo genome assembly. QTL and gene mapping needs mining of putative STR from buffalo genome at equal interval on each and every chromosome. Such markers have potential role in improvement of desirable characteristics, such as high milk yields, resistance to diseases, high growth rate. The STR mining from whole genome and development of user friendly database is yet to be done to reap the benefit of whole genome sequence. Description By in silico microsatellite mining of whole genome, we have developed first STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database (http://cabindb.iasri.res.in/buffsatdb/) which is a web based relational database of 910529 microsatellite markers, developed using PHP and MySQL database. Microsatellite markers have been generated using MIcroSAtellite tool. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes, motif type (mono-hexa), repeat motif and repeat kind (simple and composite). The search may be customised by limiting location of STR on chromosome as well as number of markers in that range. This is a novel approach and not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of the selected markers enabling researcher to select markers of choice at desired interval over the chromosome. The unique add-on of degenerate bases further helps in resolving presence of degenerate bases in current buffalo assembly. Conclusion Being first buffalo STR database in the world , this would not only pave the way in resolving current assembly problem but shall be of immense use for global community in QTL/gene mapping critically required to increase knowledge in the endeavour to increase buffalo productivity, especially for third world country where rural economy is significantly dependent on buffalo productivity. PMID:23336431

Prognostic value of tumor-infiltrating lymphocytes on residual disease after primary chemotherapy for triple-negative breast cancer: a retrospective multicenter study

PubMed Central

Dieci, M. V.; Criscitiello, C.; Goubar, A.; Viale, G.; Conte, P.; Guarneri, V.; Ficarra, G.; Mathieu, M. C.; Delaloge, S.; Curigliano, G.; Andre, F.

2014-01-01

Background There is a need to develop surrogates for treatment efficacy in the neoadjuvant setting to speed-up drug development and stratify patients according to outcome. Preclinical studies showed that chemotherapy induces an antitumor immune response. In order to develop new surrogates for drug efficacy, we assessed the prognostic value of tumor-infiltrating lymphocytes (TIL) on residual disease after neoadjuvant chemotherapy (NACT) in patients with triple-negative breast cancer (TNBC). Patients and methods Three hundred four TNBC patients with residual disease after NACT were retrospectively identified in three different hospitals. Hematoxylin and eosin-stained slides from surgical postchemotherapy specimens were evaluated for intratumoral (It-TIL) and stromal (Str-TIL) TIL. Cases were classified as High-TIL if It-TIL and/or Str-TIL >60%. Results TIL were assessable for 278 cases. Continuous It-TIL and Str-TIL variables were strong prognostic factors in the multivariate model, both for metastasis-free [hazard ratio (HR) 0.86, 95% confidence interval (CI) 0.77–0.96, P = 0.01 and HR 0.85, 95% CI 0.75–0.98, P = 0.02 for Str-TIL and It-TIL, respectively] and overall survival (HR 0.86, 95% CI 0.77–0.97, P = 0.01 and HR 0.86, 95% CI 0.75–0.99, P = 0.03 for Str-TIL and It-TIL, respectively). The 5-year overall survival rate was 91% (95% CI 68% to 97%) for High-TIL patients (n = 27) and 55% (95% CI 48% to 61%) for Low-TIL patients (HR 0.19, 95% CI 0.06–0.61, log-rank P = 0.0017). The major prognostic impact of TIL was seen for patients with large tumor burden following NACT (residual tumor >2 cm and/or node metastasis). In all but one High-TIL case, It-TIL and Str-TIL values were lower on the prechemotherapy sample. Conclusions The presence of TIL in residual disease after NACT is associated with better prognosis in TNBC patients. This parameter may represent a new surrogate of drug efficacy to test investigational agents in the neoadjuvant setting and a new prognostic marker to select patients at high risk of relapse. PMID:24401929

In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB.

PubMed

Sarika; Arora, Vasu; Iquebal, Mir Asif; Rai, Anil; Kumar, Dinesh

2013-01-19

Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiation hybrid of buffalo and these reported STR can be used further in final gap plugging and "finishing" expected in de novo genome assembly. QTL and gene mapping needs mining of putative STR from buffalo genome at equal interval on each and every chromosome. Such markers have potential role in improvement of desirable characteristics, such as high milk yields, resistance to diseases, high growth rate. The STR mining from whole genome and development of user friendly database is yet to be done to reap the benefit of whole genome sequence. By in silico microsatellite mining of whole genome, we have developed first STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database (http://cabindb.iasri.res.in/buffsatdb/) which is a web based relational database of 910529 microsatellite markers, developed using PHP and MySQL database. Microsatellite markers have been generated using MIcroSAtellite tool. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes, motif type (mono-hexa), repeat motif and repeat kind (simple and composite). The search may be customised by limiting location of STR on chromosome as well as number of markers in that range. This is a novel approach and not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of the selected markers enabling researcher to select markers of choice at desired interval over the chromosome. The unique add-on of degenerate bases further helps in resolving presence of degenerate bases in current buffalo assembly. Being first buffalo STR database in the world , this would not only pave the way in resolving current assembly problem but shall be of immense use for global community in QTL/gene mapping critically required to increase knowledge in the endeavour to increase buffalo productivity, especially for third world country where rural economy is significantly dependent on buffalo productivity.

AGARD Flight Test Instrumentation Series. Volume 11. Pressure and Flow Measurement

DTIC Science & Technology

1980-07-01

Unempfindlichkeit gegen Schrdg- anstr~ mung . Luftfo-ahrtforschung V (1935), S.75-79. 35. Winternitz, F.A.L. Cantilevered pitot cylinder. The Engineer 199 (1955), pp...cur Str ~mungsmessung. Z.far Instrumentenkunde 71 (1963) 7, 187-197. 42. Davies, P.O.A.L. The behavior of a pitot tube in transverse shear. J. Fluid...Ober den Einflug der Kompressibilitit auf die Druckan-eige eines Prandtl-Rohres bei Str ~mungen mit Unterschallgeschwin- digkeit. Jahrbuch der

LispSEI: The Programmer’s Manual

DTIC Science & Technology

1988-01-01

defun print-entities ( str entities etype) (format t str ) (dolist (entity entities) (format t " -A" (entity-name entity *type)))) (detun entity-name...fields are munged only after the filters are executed. This makes things much easier. ;:Algorithm: (1) get initial list. (2) take out those entitles which...don’t meet all the constraints. 1, 3) pass the entities list through all the filters.(4) munge the appropriate fields (5)u return the result. (defn s

Genetic variation in a compound short tandem repeat/Alu haplotype system at the SB19.3 locus: properties and interpretation.

PubMed

Gaspar, Paulo; Seixas, Susana; Rocha, Jorge

2004-04-01

The genetic variation at a compound nonrecombining haplotype system, consisting of the previously reported SB19.3 Alu insertion polymorphism and a newly identified adjacent short tandem repeat (STR), was studied in population samples from Portugal and São Tomé (Gulf of Guinea, West Africa). Age estimates based on the linked microsatellite variation suggest that the Alu insertion occurred about 190,000 years ago. In accordance with the global patterns of distribution of human genetic variation, the highest haplotype diversity was found in the African sample. This excess in African diversity was due to both a substantial reduction in heterozygosity at the Alu polymorphism and a lower STR variability associated with the predominant Alu insertion allele in the Portuguese sample. The high level of interpopulation differentiation observed at the Alu locus (F(ST) = 0.43) was interpreted under alternative selective and demographic scenarios. The need for compatibility between patterns of variation at the STR and Alu loci could be used to restrict the range of selection coefficients in selection-driven genetic hitchhiking frameworks and to favor demographic scenarios dominated by larger pre-expansion African population sizes. Taken together, the data show that the SB19.3 Alu-STR system is an informative marker that can be included in more extended batteries of compound haplotypes used in human evolutionary studies.

Differential regulation of NMDA receptor-expressing neurons in the rat hippocampus and striatum following bilateral vestibular loss demonstrated using flow cytometry.

PubMed

Benoit, Alice; Besnard, Stephane; Guillamin, Maryline; Philoxene, Bruno; Sola, Brigitte; Le Gall, Anne; Machado, Marie-Laure; Toulouse, Joseph; Hitier, Martin; Smith, Paul F

2018-06-21

There is substantial evidence that loss of vestibular function impairs spatial learning and memory related to hippocampal (HPC) function, as well as increasing evidence that striatal (Str) plasticity is also implicated. Since the N-methyl-D-aspartate (NMDA) subtype of glutamate receptor is considered essential to spatial memory, previous studies have investigated whether the expression of HPC NMDA receptors changes following vestibular loss; however, the results have been contradictory. Here we used a novel flow cytometric method to quantify the number of neurons expressing NMDA receptors in the HPC and Str following bilateral vestibular loss (BVL) in rats. At 7 and 30 days post-op., there was a significant increase in the number of HPC neurons expressing NMDA receptors in the BVL animals, compared to sham controls (P ≤ 0.004 and P ≤ 0.0001, respectively). By contrast, in the Str, at 7 days there was a significant reduction in the number of neurons expressing NMDA receptors in the BVL group (P ≤ 0.05); however, this difference had disappeared by 30 days post-op. These results suggest that BVL causes differential changes in the number of neurons expressing NMDA receptors in the HPC and Str, which may be related to its long-term impairment of spatial memory. Copyright © 2018. Published by Elsevier B.V.

Design and operation of a portable scanner for high performance microchip capillary array electrophoresis.

PubMed

Scherer, James R; Liu, Peng; Mathies, Richard A

2010-11-01

We have developed a compact, laser-induced fluorescence detection scanner, the multichannel capillary array electrophoresis portable scanner (McCAEPs) as a platform for electrophoretic detection and control of high-throughput, integrated microfluidic devices for genetic and other analyses. The instrument contains a confocal optical system with a rotary objective for detecting four different fluorescence signals, a pneumatic system consisting of two pressure/vacuum pumps and 28 individual addressable solenoid valves for control of on-chip microvalves and micropumps, four Polymerase Chain Reaction (PCR) temperature control systems, and four high voltage power supplies for electrophoresis. The detection limit of the instrument is ~20 pM for on-chip capillary electrophoresis of fluorescein dyes. To demonstrate the system performance for forensic short tandem repeat (STR) analysis, two experiments were conducted: (i) electrophoretic separation and detection of STR samples on a 96-lane microfabricated capillary array electrophoresis microchip. Fully resolved PowerPlex(®) 16 STR profiles amplified from 1 ng of 9947A female standard DNA were successfully obtained; (ii) nine-plex STR amplification, sample injection, separation, and fluorescence detection of 100-copy 9948 male standard DNA in a single integrated PCR- capillary electrophoresis microchip. These results demonstrate that the McCAEPs can be used as a versatile control and detection instrument that operates integrated microfluidic devices for high-performance forensic human identification.

Characterization of antimicrobial susceptibility and virulence genes of Salmonella serovars collected at a commercial turkey processing plant.

PubMed

Nde, C W; Logue, C M

2008-01-01

To determine the antimicrobial susceptibility profiles, distribution of class 1 integrons, virulence genes and genes encoding resistance to tetracycline (tetA, tetC, tetD and tetE) and streptomycin (strA, strB and aadA1) in Salmonella recovered from turkeys. The antimicrobial susceptibility of 80 isolates was determined using National Antimicrobial Resistance Monitoring System. The distribution of resistance genes, class 1 integrons and virulence genes was determined using PCR. Resistances to tetracycline (76 x 3%) and streptomycin (40%) were common. Sixty-two (77 x 5%) isolates displayed resistance against one or more antimicrobials and 33 were multi-drug resistant. tetA was detected in 72 x 5% of the isolates, while tetC, tetD and tetE were not detected. The strA and strB genes were detected in 73 x 8% of the isolates. Two isolates possessed class 1 integrons of 1 kb in size, containing the aadA1 gene conferring resistance to streptomycin and spectinomycin. Fourteen of the virulence genes were detected in over 80% of the isolates. This study shows that continuous use of tetracycline and streptomycin in poultry production selects for resistant strains. The Salmonella isolates recovered possess significant ability to cause human illness. Information from this study can be employed in guiding future strategies for the use of antimicrobials in poultry production.

Integrated massively parallel sequencing of 15 autosomal STRs and Amelogenin using a simplified library preparation approach.

PubMed

Xue, Jian; Wu, Riga; Pan, Yajiao; Wang, Shunxia; Qu, Baowang; Qin, Ying; Shi, Yuequn; Zhang, Chuchu; Li, Ran; Zhang, Liyan; Zhou, Cheng; Sun, Hongyu

2018-04-02

Massively parallel sequencing (MPS) technologies, also termed as next-generation sequencing (NGS), are becoming increasingly popular in study of short tandem repeats (STR). However, current library preparation methods are usually based on ligation or two-round PCR that requires more steps, making it time-consuming (about 2 days), laborious and expensive. In this study, a 16-plex STR typing system was designed with fusion primer strategy based on the Ion Torrent S5 XL platform which could effectively resolve the above challenges for forensic DNA database-type samples (bloodstains, saliva stains, etc.). The efficiency of this system was tested in 253 Han Chinese participants. The libraries were prepared without DNA isolation and adapter ligation, and the whole process only required approximately 5 h. The proportion of thoroughly genotyped samples in which all the 16 loci were successfully genotyped was 86% (220/256). Of the samples, 99.7% showed 100% concordance between NGS-based STR typing and capillary electrophoresis (CE)-based STR typing. The inconsistency might have been caused by off-ladder alleles and mutations in primer binding sites. Overall, this panel enabled the large-scale genotyping of the DNA samples with controlled quality and quantity because it is a simple, operation-friendly process flow that saves labor, time and costs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples

PubMed Central

Pérez Santángelo, Agustín; Corti Bielsa, Rodrigo M.; Sala, Andrea; Ginart, Santiago; Corach, Daniel

2017-01-01

Obtaining informative short tandem repeat (STR) profiles from degraded DNA samples is a challenging task usually undermined by locus or allele dropouts and peak-high imbalances observed in capillary electrophoresis (CE) electropherograms, especially for those markers with large amplicon sizes. We hereby show that the current STR assays may be greatly improved for the detection of genetic markers in degraded DNA samples by using long single stranded DNA polynucleotides (ssDNA polynucleotides) as surrogates for PCR primers. These long primers allow a closer annealing to the repeat sequences, thereby reducing the length of the template required for the amplification in fragmented DNA samples, while at the same time rendering amplicons of larger sizes suitable for multiplex assays. We also demonstrate that the annealing of long ssDNA polynucleotides does not need to be fully complementary in the 5’ region of the primers, thus allowing for the design of practically any long primer sequence for developing new multiplex assays. Furthermore, genotyping of intact DNA samples could also benefit from utilizing long primers since their close annealing to the target STR sequences may overcome wrong profiling generated by insertions/deletions present between the STR region and the annealing site of the primers. Additionally, long ssDNA polynucleotides might be utilized in multiplex PCR assays for other types of degraded or fragmented DNA, e.g. circulating, cell-free DNA (ccfDNA). PMID:29099837

Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems.

PubMed

Yao, Yining; Yang, Qinrui; Shao, Chengchen; Liu, Baonian; Zhou, Yuxiang; Xu, Hongmei; Zhou, Yueqin; Tang, Qiqun; Xie, Jianhui

2018-01-01

Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex ® 21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR ® . Identifiler ® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex ® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets. Copyright © 2017 Elsevier B.V. All rights reserved.

Haplotype data for 23 Y-chromosome markers in a reference sample from Bosnia and Herzegovina

PubMed Central

Kovačević, Lejla; Fatur-Cerić, Vera; Hadžić, Negra; Čakar, Jasmina; Primorac, Dragan; Marjanović, Damir

2013-01-01

Aim To detect polymorphisms of 23 Y-chromosomal short tandem repeat (STR) loci, including 6 new loci, in a reference database of male population of Bosnia and Herzegovina, as well as to assess the importance of increasing the number of Y-STR loci utilized in forensic DNA analysis. Methods The reference sample consisted of 100 healthy, unrelated men originating from Bosnia and Herzegovina. Sample collection using buccal swabs was performed in all geographical regions of Bosnia and Herzegovina in the period from 2010 to 2011. DNA samples were typed for 23 Y STR loci, including 6 new loci: DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643, which are included in the new PowerPlex® Y 23 amplification kit. Results The absolute frequency of generated haplotypes was calculated and results showed that 98 samples had unique Y 23 haplotypes, and that only two samples shared the same haplotype. The most polymorphic locus was DYS418, with 14 detected alleles and the least polymorphic loci were DYS389I, DYS391, DYS437, and DYS393. Conclusion This study showed that by increasing the number of highly polymorphic Y STR markers, to include those tested in our analysis, leads to a reduction of repeating haplotypes, which is very important in the application of forensic DNA analysis. PMID:23771760

Mitochondrial and Y-chromosomal profile of the Kazakh population from East Kazakhstan

PubMed Central

Tarlykov, Pavel V.; Zholdybayeva, Elena V.; Akilzhanova, Ainur R.; Nurkina, Zhannur M.; Sabitov, Zhaxylyk M.; Rakhypbekov, Tolebay K.; Ramanculov, Erlan M.

2013-01-01

Aim To study the genetic relationship of Kazakhs from East Kazakhstan to other Eurasian populations by examining paternal and maternal DNA lineages. Methods Whole blood samples were collected in 2010 from 160 unrelated healthy Kazakhs residing in East Kazakhstan. Genomic DNA was extracted with Wizard® genomic DNA Purification Kit. Nucleotide sequence of hypervariable segment I of mitochondrial DNA (mtDNA) was determined and analyzed. Seventeen Y-short tandem repeat (STR) loci were studied in 67 samples with the AmpFiSTR Y-filer PCR Amplification Kit. In addition, mtDNA data for 2701 individuals and Y-STR data for 677 individuals were retrieved from the literature for comparison. Results There was a high degree of genetic differentiation on the level of mitochondrial DNA. The majority of maternal lineages belonged to haplogroups common in Central Asia. In contrast, Y-STR data showed very low genetic diversity, with the relative frequency of the predominant haplotype of 0.612. Conclusion The results revealed different migration patterns in the population sample, showing there had been more migration among women. mtDNA genetic diversity in this population was equivalent to that in other Central Asian populations. Genetic evidence suggests the existence of a single paternal founder lineage in the population of East Kazakhstan, which is consistent with verbal genealogical data of the local tribes. PMID:23444242

Design and operation of a portable scanner for high performance microchip capillary array electrophoresis

NASA Astrophysics Data System (ADS)

Scherer, James R.; Liu, Peng; Mathies, Richard A.

2010-11-01

We have developed a compact, laser-induced fluorescence detection scanner, the multichannel capillary array electrophoresis portable scanner (McCAEPs) as a platform for electrophoretic detection and control of high-throughput, integrated microfluidic devices for genetic and other analyses. The instrument contains a confocal optical system with a rotary objective for detecting four different fluorescence signals, a pneumatic system consisting of two pressure/vacuum pumps and 28 individual addressable solenoid valves for control of on-chip microvalves and micropumps, four Polymerase Chain Reaction (PCR) temperature control systems, and four high voltage power supplies for electrophoresis. The detection limit of the instrument is ˜20 pM for on-chip capillary electrophoresis of fluorescein dyes. To demonstrate the system performance for forensic short tandem repeat (STR) analysis, two experiments were conducted: (i) electrophoretic separation and detection of STR samples on a 96-lane microfabricated capillary array electrophoresis microchip. Fully resolved PowerPlex® 16 STR profiles amplified from 1 ng of 9947A female standard DNA were successfully obtained; (ii) nine-plex STR amplification, sample injection, separation, and fluorescence detection of 100-copy 9948 male standard DNA in a single integrated PCR- capillary electrophoresis microchip. These results demonstrate that the McCAEPs can be used as a versatile control and detection instrument that operates integrated microfluidic devices for high-performance forensic human identification.

Depression of streptomycin production by Streptomyces griseus at elevated growth temperature: studies using gene fusions.

PubMed

Deeble, V J; Lindley, H K; Fazeli, M R; Cove, J H; Baumberg, S

1995-10-01

Streptomyces griseus ATCC 12475 fails to produce streptomycin when grown at 34 degrees C or above, although growth is appreciable up to at least 37 degrees C. This depression of streptomycin production at elevated growth temperature is manifest equally in liquid and on solid, and with complex and minimal, media. We report studies with gene fusions of the reporter genes aph or xyIE to restriction fragments containing the streptomycin biosynthesis promoter PstrB1. aph constructs were in high, and xyIE constructs in low, copy number vectors. Two strB1 promoter fragments were used, one requiring activation by the pathway-specific activator StrR of S. griseus, the other reportedly activator independent. PstrB1 expression in the aph constructs in S. griseus and in S. lividans was significantly reduced at 37 degrees C compared to 30 degrees C. Some of this reduction could be explained by lower plasmid copy number at the higher temperature, but strR-dependent expression was clearly temperature controlled. Using the xyIE reporter system, the temperature dependence of PstrB1 expression was confirmed but, surprisingly, the strR dependence of the two promoter fragments differed from that observed in the multicopy aph constructs. These data identify a temperature-dependent promoter which may contribute to the depressive effect of elevated growth temperature on streptomycin production.

The development and application of a multiplex short tandem repeat (STR) system for identifying subspecies, individuals and sex in tigers.

PubMed

Zou, Zheng-Ting; Uphyrkina, Olga V; Fomenko, Pavel; Luo, Shu-Jin

2015-07-01

Poaching and trans-boundary trafficking of tigers and body parts are threatening the world's last remaining wild tigers. Development of an efficient molecular genetic assay for tracing the origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species. We developed a multiplex genotyping system "tigrisPlex" to simultaneously assess 22 short tandem repeat (STR, or microsatellite) loci and a gender-identifying SRY gene, all amplified in 4 reactions using as little as 1 ng of template DNA. With DNA samples used for between-run calibration, the system generates STR genotypes that are directly compatible with voucher tiger subspecies genetic profiles, hence making it possible to identify subspecies via bi-parentally inherited markers. We applied "tigrisPlex" to 12 confiscated specimens from Russia and identified 6 individuals (3 females and 3 males), each represented by duplicated samples and all designated as Amur tigers (Panthera tigris altaica) with high confidence. This STR multiplex system can serve as an effective and versatile approach for genetic profiling of both wild and captive tigers as well as confiscated tiger products, fulfilling various conservation needs for identifying the origins of tiger samples. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

Absence of subtelomeric rearrangements in selected patients with mental retardation as assessed by multiprobe T FISH

PubMed Central

2012-01-01

Background Mental retardation (MR) is a heterogeneous condition that affects 2-3% of the general population and is a public health problem in developing countries. Chromosomal abnormalities are an important cause of MR and subtelomeric rearrangements (STR) have been reported in 4-35% of individuals with idiopathic MR or an unexplained developmental delay, depending on the screening tests and patient selection criteria used. Clinical checklists such as that suggested by de Vries et al. have been used to improve the predictive value of subtelomeric screening. Findings Fifteen patients (1–20 years old; five females and ten males) with moderate to severe MR from a genetics outpatient clinic of the Gaffrée and Guinle Teaching Hospital (HUGG) of the Federal University of Rio de Janeiro State (UNIRIO) were screened with Multiprobe T FISH after normal high resolution karyotyping. No subtelomeric rearrangements were detected even though the clinical score of the patients ranged from four to seven. Conclusion In developing countries, FISH-based techniques such as Multiprobe T FISH are still expensive. Although Multiprobe T FISH is a good tool for detecting STR, in this study it did not detect STR in patients with unexplained MR/developmental delay even though these patients had a marked chromosomal imbalance. Our findings also show that clinical scores are not reliable predictors of STR. PMID:23259705

A prospective study on gait-related intrinsic risk factors for lower leg overuse injuries.

PubMed

Ghani Zadeh Hesar, N; Van Ginckel, A; Cools, A; Peersman, W; Roosen, P; De Clercq, D; Witvrouw, E

2009-12-01

To determine prospectively gait-related risk factors for lower leg overuse injury (LLOI). A prospective cohort study. Male and female recruits from a start-to-run (STR) programme during a 10-week training period. 131 healthy subjects (20 men and 111 women), without a history of any lower leg complaint, participated in the study. Before the start of the 10-week STR programme, plantar force measurements during running were performed. During STR, lower leg injuries were diagnosed and registered by a sports physician. Plantar force measurements during running were performed using a footscan pressure plate. During the STR, 27 subjects (five men and 22 women) developed a LLOI. Logistic regression analysis revealed that subjects who developed a LLOI had a significantly more laterally directed force distribution at first metatarsal contact and forefoot flat, a more laterally directed force displacement in the forefoot contact phase, foot flat phase and at heel-off. These subjects also had a delayed change of the centre of force (COF) at forefoot flat, a higher force and loading underneath the lateral border of the foot, and a significantly higher directed force displacement of the COF at forefoot flat. These findings suggest that a less pronated heel strike and a more laterally directed roll-off can be considered as risk factors for LLOI. Clinically, the results of this study can be considered important in identifying individuals at risk of LLOI.

Investigator® HDplex (Qiagen) reference population database for forensic use in Argentina.

PubMed

Martínez, Gustavo; Borosky, Alicia; Corach, Daniel; Llull, Cintia; Locarno, Laura; Lojo, Mercedes; Marino, Miguel; Miozzo, María Cecilia; Modesti, Nidia; Pacharoni, Carla; Pilili, Juan Pablo; Ramella, María Isabel; Sala, Andrea; Schaller, Cecilia; Vullo, Carlos; Toscanini, Ulises

2017-01-01

Currently, autosomal Short Tandem Repeat (STR) markers represent the method of election in forensic human identification. Commercial kits of most common use nowadays -e.g. PowerPlex ® Fusion, Promega Corp.; AmpFlSTR GlobalFiler, Thermofisher scientific; Investigator 24Plex QS,Qiagen-, allow the co-amplification of 23 highly polymorphic STR loci providing a high discrimination power in human identity testing. However, in complex kinship analysis and familial database searches involving distant relationships, additional DNA typing is often required in order to achieve well-founded conclusions. The recently developed kit Investigator ® HDplex (Qiagen) co-amplify twelve autosomal STRs markers (D7S1517, D3S1744, D12S391, D2S1360, D6S474, D4S2366, D8S1132, D5S2500, D18S51, D21S2055, D10S2325, SE33), nine of which are not present in the above mentioned kits, providing a set of efficient supplementary markers for human identification purposes. In this study we genotyped a sample of 980 individuals from urban areas of ten Argentinean provinces using the Investigator ® HDplex kit, aiming to provide forensic estimates for use in forensic casework and parentage testing in Argentina. We report reference allelic frequency databases for each of the provinces studied as well as for the combined samples. No deviation of Hardy-Weinberg equilibrium was observed. A reasonable discrimination capacity and power of exclusion was estimated which allowed predicting an acceptable forensic behavior of this kit, either to be used as the main STR panel for simple cases or as an auxiliary tool in complex cases. Additionally, population comparison tests showed that the studied samples are relatively homogeneous across the country for these STR set. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The zeta potential of extended dielectrics and conductors in terms of streaming potential and streaming current measurements.

PubMed

Gallardo-Moreno, Amparo M; Vadillo-Rodríguez, Virginia; Perera-Núñez, Julia; Bruque, José M; González-Martín, M Luisa

2012-07-21

The electrical characterization of surfaces in terms of the zeta potential (ζ), i.e., the electric potential contributing to the interaction potential energy, is of major importance in a wide variety of industrial, environmental and biomedical applications in which the integration of any material with the surrounding media is initially mediated by the physico-chemical properties of its outer surface layer. Among the different existing electrokinetic techniques for obtaining ζ, streaming potential (V(str)) and streaming current (I(str)) are important when dealing with flat-extended samples. Mostly dielectric materials have been subjected to this type of analysis and only a few papers can be found in the literature regarding the electrokinetic characterization of conducting materials. Nevertheless, a standardized procedure is typically followed to calculate ζ from the measured data and, importantly, it is shown in this paper that such a procedure leads to incorrect zeta potential values when conductors are investigated. In any case, assessment of a reliable numerical value of ζ requires careful consideration of the origin of the input data and the characteristics of the experimental setup. In particular, it is shown that the cell resistance (R) typically obtained through a.c. signals (R(a.c.)), and needed for the calculations of ζ, always underestimates the zeta potential values obtained from streaming potential measurements. The consideration of R(EK), derived from the V(str)/I(str) ratio, leads to reliable values of ζ when dielectrics are investigated. For metals, the contribution of conductivity of the sample to the cell resistance provokes an underestimation of R(EK), which leads to unrealistic values of ζ. For the electrical characterization of conducting samples I(str) measurements constitute a better choice. In general, the findings gathered in this manuscript establish a measurement protocol for obtaining reliable zeta potentials of dielectrics and conductors based on the intrinsic electrokinetic behavior of both types of samples.

Strictosidine activation in Apocynaceae: towards a "nuclear time bomb"?

PubMed Central

2010-01-01

Background The first two enzymatic steps of monoterpene indole alkaloid (MIA) biosynthetic pathway are catalysed by strictosidine synthase (STR) that condensates tryptamine and secologanin to form strictosidine and by strictosidine β-D-glucosidase (SGD) that subsequently hydrolyses the glucose moiety of strictosidine. The resulting unstable aglycon is rapidly converted into a highly reactive dialdehyde, from which more than 2,000 MIAs are derived. Many studies were conducted to elucidate the biosynthesis and regulation of pharmacologically valuable MIAs such as vinblastine and vincristine in Catharanthus roseus or ajmaline in Rauvolfia serpentina. However, very few reports focused on the MIA physiological functions. Results In this study we showed that a strictosidine pool existed in planta and that the strictosidine deglucosylation product(s) was (were) specifically responsible for in vitro protein cross-linking and precipitation suggesting a potential role for strictosidine activation in plant defence. The spatial feasibility of such an activation process was evaluated in planta. On the one hand, in situ hybridisation studies showed that CrSTR and CrSGD were coexpressed in the epidermal first barrier of C. roseus aerial organs. However, a combination of GFP-imaging, bimolecular fluorescence complementation and electromobility shift-zymogram experiments revealed that STR from both C. roseus and R. serpentina were localised to the vacuole whereas SGD from both species were shown to accumulate as highly stable supramolecular aggregates within the nucleus. Deletion and fusion studies allowed us to identify and to demonstrate the functionality of CrSTR and CrSGD targeting sequences. Conclusions A spatial model was drawn to explain the role of the subcellular sequestration of STR and SGD to control the MIA metabolic flux under normal physiological conditions. The model also illustrates the possible mechanism of massive activation of the strictosidine vacuolar pool upon enzyme-substrate reunion occurring during potential herbivore feeding constituting a so-called "nuclear time bomb" in reference to the "mustard oil bomb" commonly used to describe the myrosinase-glucosinolate defence system in Brassicaceae. PMID:20723215

Molecular phylogeny and systematics of the Echinostomatoidea Looss, 1899 (Platyhelminthes: Digenea).

PubMed

Tkach, Vasyl V; Kudlai, Olena; Kostadinova, Aneta

2016-03-01

The Echinostomatoidea is a large, cosmopolitan group of digeneans currently including nine families and 105 genera, the vast majority parasitic, as adults, in birds with relatively few taxa parasitising mammals, reptiles and, exceptionally, fish. Despite the complex structure, diverse content and substantial species richness of the group, almost no attempt has been made to elucidate its phylogenetic relationships at the suprageneric level based on molecules due to the lack of data. Herein, we evaluate the consistency of the present morphology-based classification system of the Echinostomatoidea with the phylogenetic relationships of its members based on partial sequences of the nuclear lsrRNA gene for a broad diversity of taxa (80 species, representing eight families and 40 genera), including representatives of five subfamilies of the Echinostomatidae, which currently exhibits the most complex taxonomic structure within the superfamily. This first comprehensive phylogeny for the Echinostomatoidea challenged the current systematic framework based on comparative morphology. A morphology-based evaluation of this new molecular framework resulted in a number of systematic and nomenclatural changes consistent with the phylogenetic estimates of the generic and suprageneric boundaries and a new phylogeny-based classification of the Echinostomatoidea. In the current systematic treatment: (i) the rank of two family level lineages, the former Himasthlinae and Echinochasminae, is elevated to full family status; (ii) Caballerotrema is distinguished at the family level; (iii) the content and diagnosis of the Echinostomatidae (sensu stricto) (s. str.) are revised to reflect its phylogeny, resulting in the abolition of the Nephrostominae and Chaunocephalinae as synonyms of the Echinostomatidae (s. str.); (iv) Artyfechinostomum, Cathaemasia, Rhopalias and Ribeiroia are re-allocated within the Echinostomatidae (s. str.), resulting in the abolition of the Cathaemasiidae, Rhopaliidae and Ribeiroiinae, which become synonyms of the Echinostomatidae (s. str.); and (v) refinements of the generic boundaries within the Echinostomatidae (s. str.), Psilostomidae and Fasciolidae are made. Copyright © 2015 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kanukollu, Saranya; Voget, Sonja; Pohlner, Marion

Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae. The strain was isolated from surface sediment (0-1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase ( mttB) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able tomore » switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. Among the ability to convert other sulfur compounds it has the genetic capacity to produce climatically active dimethyl sulfide. Growth on glutamate as a sole carbon source results in formation of cell-connecting filaments, a putative phenotypic adaptation of the surface-associated strain to the environmental conditions at the seafloor. Genome analysis revealed the presence of a flagellum ( fla1) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. This is also related to genes responsible for signalling such as N-acyl homoserine lactones, as well as quip-genes responsible for quorum quenching and antibiotic biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence similarity to the next relative S. haliotis) and the in silico DNA-DNA hybridization (21.20 % sequence similarity to S. haliotis) indicated Shimia str. SK013 to be considered as a new species. In conclusion, the genome analysis of Shimia str. SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter-affiliated bacteria to the benthic environment.« less

Genetic characterization of an X-STR decaplex system in the State of Mato Grosso, Brazil: distribution, forensic efficiency and population structure.

PubMed

Martins, Joyce A; Martins, Denise P; Oliveira-Brancati, Camila I F; Martinez, Juliana; Cicarelli, Regina M B; Souza, Dorotéia R S

2017-11-01

Studies with X-STR loci show population genetic substructure, which makes necessary the characterization of such markers in the different geographical and/or ethnic populations. Therefore, this study assessed the distribution and forensic efficiency of an X-STR decaplex system in the population of the State of Mato Grosso, as well as analysed the population structure of this State based on the aforementioned system. All X-STR markers were in Hardy-Weinberg equilibrium and linkage equilibrium, and the DXS6809 was the most informative marker. The power of discrimination value in females and males was 0.99999999995 and 0.9999994, respectively. Analysis of molecular variance indicated 1.10% (p < 0.00001) of heterogeneity among Europeans, Africans, Brazilians and other Latin Americans, and in relation to such groups, the population of the State of Mato Grosso showed lower genetic variation when compared with the Brazilian group (-0.10%, p = 0.67327). The genetic distance analysis showed lower values of F ST (0.0004 ≤ F ST  ≤ 0.00331), with non-significant p value (p > 0.00024), between the populations of Mato Grosso and Mato Grosso do Sul, Paraná and the Southeast region of Brazil (except for one sample of Rio de Janeiro). F ST values with significant p values (p ≤ 0.00024) were obtained between the population of Mato Grosso and Iberian, African and some Latin American populations. The X-STR decaplex system proved to be extremely useful in the population of the State of Mato Grosso, and the data obtained does not show the need for a specific forensic database for this State in relation to the Brazilian populations compared in this study, except for population of Rio de Janeiro.

The recombination landscape around forensic STRs: Accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP data.

PubMed

Phillips, C; Ballard, D; Gill, P; Court, D Syndercombe; Carracedo, A; Lareu, M V

2012-05-01

Family studies can be used to measure the genetic distance between same-chromosome (syntenic) STRs in order to detect physical linkage or linkage disequilibrium. However, family studies are expensive and time consuming, in many cases uninformative, and lack a reliable means to infer the phase of the diplotypes obtained. HapMap provides a more comprehensive and fine-scale estimation of recombination rates using high density multi-point SNP data (average inter-SNP distance: 900 nucleotides). Data at this fine scale detects sub-kilobase genetic distances across the whole recombining human genome. We have used the most recent HapMap SNP data release 22 to measure and compare genetic distances, and by inference fine-scale recombination rates, between 29 syntenic STR pairs identified from 39 validated STRs currently available for forensic use. The 39 STRs comprise 23 core loci: SE33, Penta D & E, 13 CODIS and 7 non-CODIS European Standard Set STRs, plus supplementary STRs in the recently released Promega CS-7™ and Qiagen Investigator HDplex™ kits. Also included were D9S1120, a marker we developed for forensic use unique to chromosome 9, and the novel D6S1043 component STR of SinoFiler™ (Applied Biosystems). The data collated provides reliable estimates of recombination rates between each STR pair, that can then be placed into haplotype frequency calculators for short pedigrees with multiple meiotic inputs and which just requires the addition of allele frequencies. This allows all current STR sets or their combinations to be used in supplemented paternity analyses without the need for further adjustment for physical linkage. The detailed analysis of recombination rates made for autosomal forensic STRs was extended to the more than 50 X chromosome STRs established or in development for complex kinship analyses. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment

DOE PAGES

Kanukollu, Saranya; Voget, Sonja; Pohlner, Marion; ...

2016-03-12

Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae. The strain was isolated from surface sediment (0-1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase ( mttB) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able tomore » switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. Among the ability to convert other sulfur compounds it has the genetic capacity to produce climatically active dimethyl sulfide. Growth on glutamate as a sole carbon source results in formation of cell-connecting filaments, a putative phenotypic adaptation of the surface-associated strain to the environmental conditions at the seafloor. Genome analysis revealed the presence of a flagellum ( fla1) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. This is also related to genes responsible for signalling such as N-acyl homoserine lactones, as well as quip-genes responsible for quorum quenching and antibiotic biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence similarity to the next relative S. haliotis) and the in silico DNA-DNA hybridization (21.20 % sequence similarity to S. haliotis) indicated Shimia str. SK013 to be considered as a new species. In conclusion, the genome analysis of Shimia str. SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter-affiliated bacteria to the benthic environment.« less

[The haplomatch program for comparing Y-chromosome STR-haplotypes and its application to the analysis of the origin of Don Cossacks].

PubMed

Chukhryaeva, M I; Ivanov, I O; Frolova, S A; Koshel, S M; Utevska, O M; Skhalyakho, R A; Agdzhoyan, A T; Bogunov, Yu V; Balanovska, E V; Balanovsky, O P

2016-05-01

STR haplotypes of the Y chromosome are widely used as effective genetic markers in studies of human populations and in forensic DNA analysis. The task often arises to compare the spectrum of haplotypes in individuals or entire populations. Performing this task manually is too laborious and thus unrealistic. We propose an algorithm for counting similarity between STR haplotypes. This algorithm is suitable for massive analyses of samples. It is implemented in the computer program Haplomatch, which makes it possible to find haplotypes that differ from the target haplotype by 0, 1, 2, 3, or more mutational steps. The program may operate in two modes: comparison of individuals and comparison of populations. Flexibility of the program (the possibility of using any external database), its usability (MS Excel spreadsheets are used), and the capability of being applied to other chromosomes and other species could make this software a new useful tool in population genetics and forensic and genealogical studies. The Haplomatch software is freely available on our website www.genofond.ru. The program is applied to studying the gene pool of Cossacks. Experimental analysis of Y-chromosomal diversity in a representative set (N = 131) of Upper Don Cossacks is performed. Analysis of the STR haplotypes detects genetic proximity of Cossacks to East Slavic populations (in particular, to Southern and Central Russians, as well as to Ukrainians), which confirms the hypothesis of the origin of the Cossacks mainly due to immigration from Russia and Ukraine. Also, a small genetic influence of Turkicspeaking Nogais is found, probably caused by their occurrence in the Don Voisko as part of the Tatar layer. No similarities between haplotype spectra of Cossacks and Caucasus populations are found. This case study demonstrates the effectiveness of the Haplomatch software in analyzing large sets of STR haplotypes.

Non-Destructive Impermeability Testing of Land-Based Sewage Systems (zerstoerungsfreie dichtheitspruefung con grundstuecksentwaesserungsleitungen)

DTIC Science & Technology

2001-01-01

CYberdeckungsh6he zunehmen. Ffr die Stabilitdt des Str ~mungszustandes ist dagegen ein weniger empfindlicher Ansaugstutzen von Vorteil, weil geringe Schwankungen im...Gerinnestr() mung mit einem Laser-Doppler- Anemometer und einem Pitot-Rohr Ltd. BD Dipl.-Ing. B. Ftirmaier M6glichkeiten der Verwertung von HausmUll und...GrundstticksentwAsserungsleitungen ISBN 3-486-26517-2 * diese Hefte k6nnen beim Oldenbourg Industrieverlag GmbH, Rosenheimer Str . 145, 81671 MUnchen bezogen werden (Preis pro Heft: 35,00 DM, Stand 2001)

Electrochemical energy storage by polyaniline nanofibers: high gravity assisted oxidative polymerization vs. rapid mixing chemical oxidative polymerization.

PubMed

Zhao, Yibo; Wei, Huige; Arowo, Moses; Yan, Xingru; Wu, Wei; Chen, Jianfeng; Wang, Yiran; Guo, Zhanhu

2015-01-14

Polyaniline (PANI) nanofibers prepared by high gravity chemical oxidative polymerization in a rotating packed bed (RPB) have demonstrated a much higher specific capacitance of 667.6 F g(-1) than 375.9 F g(-1) of the nanofibers produced by a stirred tank reactor (STR) at a gravimetric current of 10 A g(-1). Meanwhile, the cycling stability of the electrode is 62.2 and 65.9% for the nanofibers from RPB and STR after 500 cycles, respectively.

Boronated porphyrin compounds

DOEpatents

Kahl, Stephen B.; Koo, Myoung-Seo

1992-01-01

A compound is described having the structure ##STR1## where R preferably is ##STR2## and most preferably R.sup.3 is a closo-carborane and R.sup.2 is --H, an alkyl or aryl having 1 to about 7 carbon atoms, This invention was made with Government support under NIH Grant No. CA-37961 awarded by the Department of Health and Human Services and under the Associated Universities Inc. Contract No. De-AC02-76CH00016 with the U.S. Department of Energy. The Government has rights in this invention.

Boronated porphyrin compounds

DOEpatents

Kahl, S.B.; Koo, M.S.

1992-09-22

A compound is described having the structure ##STR1## where R preferably is ##STR2## and most preferably R.sup.3 is a closo-carborane and R.sup.2 is --H, an alkyl or aryl having 1 to about 7 carbon atoms, This invention was made with Government support under NIH Grant No. CA-37961 awarded by the Department of Health and Human Services and under the Associated Universities Inc. Contract No. De-AC02-76CH00016 with the U.S. Department of Energy. The Government has rights in this invention.

[The inadequacy of using the autosomal STR markers for the establishment of the kinship in the parent-child pairs].

PubMed

Kovtun, P A; Kuklev, M Iu; Lapenkov, M I; Plakhina, N V

2013-01-01

This article is concerned with the management of the disputable situations arising in the course of establishment of the kinship based on the analysis of autosomal STR loci. It is proposed to enhance the accuracy of determining thekinsip relations in the parent-child pairs (in the absence of one of the parents) by using additional sets of genetic markers localized for example on sex chromosomes, mitochondrial DNA (mtDNA) and bi-allele markers.

Genetic data for 26 autosomal STR markers from Brazilian population.

PubMed

Pereira, Tamiris Fátima Correia; Malaghini, Marcelo; Magalhães, João Carlos Maciel; Moura-Neto, Rodrigo; Sotomaior, Vanessa Santos

2018-01-19

The allelic frequency distributions and statistical forensic parameters of 26 mini short tandem repeat (mini-STR) loci in a sample of 1575 unrelated individuals from five different Brazilian regions were obtained. All the analyzed loci showed great diversity and were highly informative. The results were compared with those of the US Caucasian, African American, and Hispanic population studies. This study aimed to contribute to forensic analysis for human identification and inference of the evidential value in familial bond tests.

Cost analysis of initial highly active antiretroviral therapy regimens for managing human immunodeficiency virus-infected patients according to clinical practice in a hospital setting

PubMed Central

Colombo, Giorgio L; Castagna, Antonella; Di Matteo, Sergio; Galli, Laura; Bruno, Giacomo; Poli, Andrea; Salpietro, Stefania; Carbone, Alessia; Lazzarin, Adriano

2014-01-01

Objective In the study reported here, single-tablet regimen (STR) versus (vs) multi-tablet regimen (MTR) strategies were evaluated through a cost analysis in a large cohort of patients starting their first highly active antiretroviral therapy (HAART). Adult human immunodeficiency virus (HIV) 1-naïve patients, followed at the San Raffaele Hospital, Milan, Italy, starting their first-line regimen from June 2008 to April 2012 were included in the analysis. Methods The most frequently used first-line HAART regimens (>10%) were grouped into two classes: 1) STR of tenofovir disoproxil fumarate (TDF) + emtricitabine (FTC) + efavirenz (EFV) and 2) MTR including TDF + FTC + EFV, TDF + FTC + atazanavir/ritonavir (ATV/r), TDF + FTC + darunavir/ritonavir (DRV/r), and TDF + FTC + lopinavir/ritoavir (LPV/r). Data were analyzed from the point of view of the Lombardy Regional Health Service. HAART, hospitalizations, visits, medical examinations, and other concomitant non-HAART drug costs were evaluated and price variations included. Descriptive statistics were calculated for baseline demographic, clinical, and laboratory characteristics; associations between categorical variables and type of antiretroviral strategy (STR vs MTR) were examined using chi-square or Fisher’s exact tests. At multivariate analysis, the generalized linear model was used to identify the predictive factors of the overall costs of the first-line HAART regimens. Results A total of 474 naïve patients (90% male, mean age 42.2 years, mean baseline HIV-RNA 4.50 log 10 copies/mL, and cluster of differentiation 4 [CD4+] count of 310 cells/μL, with a mean follow-up of 28 months) were included. Patients starting an STR treatment were less frequently antibody-hepatitis C virus positive (4% vs 11%, P=0.040), and had higher mean CD4+ values (351 vs 297 cells/μL, P=0.004) than MTR patients. The mean annual cost per patient in the STR group was €9,213.00 (range: €6,574.71–€33,570.00) and €14,277.00 (range: €5,908.89–€82,310.30) among MTR patients. At multivariate analysis, after adjustment for age, sex, antibody-hepatitis C virus status, HIV risk factors, baseline CD4+, and HIV-RNA, the cost analysis was significantly lower among patients starting an STR treatment than those starting an MTR (adjusted mean: €12,096.00 vs €16,106.00, P=0.0001). Conclusion STR was associated with a lower annual cost per patient than MTR, thus can be considered a cost-saving strategy in the treatment of HIV patients. This analysis is an important tool for policy makers and health care professionals to make short- and long-term cost projections and thus assess the impact of these on available budgets. PMID:24379676

Genetic polymorphisms of 15 STR loci within Turkish student population living in Sarajevo, Bosnia and Herzegovina.

PubMed

Dogan, Serkan; Kovacević, Lejla; Marjanović, Damir

2013-12-01

Allele frequencies of 15 STRs included in the PowerPlex 16 System (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA) were calculated from the referent sample of 100 unrelated individuals of both sexes from Turkish student population living in Sarajevo, Bosnia and Herzegovina. Buccal swab, as a source of DNA, was collected from the volunteers from whom the informed consent form was obtained. DNA extraction was performed using QIAamp DNA Micro kit by Qiagen. DNA template ranging from 0.5 to 2 ng was used to amplify 15 STR loci by PCR multiplex amplification which was performed by using the PowerPlex 16 kit (Promega Corp., Madison, WI, USA) according to the manufacturer's protocol. The amplifications were carried out in a PE Gene Amp PCR System thermal cycler (Applied Biosystems) and capillary electrophoresis was carried out in an ABI PRISM 310 Genetic Analyzer (Applied Biosystems) in accordance with the manufacturer's recommendations. The frequency of each locus was calculated from the numbers of each observed genotype. Deviation from Hardy-Weinberg equilibrium and observed heterozygosity were calculated. Data were analyzed by using Microsoft Excel workbook template--Powerstats V12 and the power of discrimination (PD), power of exclusion (PE), as well as other population genetic indices for the 15 STR loci were calculated. Obtained results contribute to existing Turkish DNA database, as well as insight of differences and similarities in comparison to population of Bosnia and Herzegovina. In addition, 13 autosomal STR loci frequencies (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSFIPO, Penta D, VWA, D8S1 179, TPOX, and FGA) were studied in 15 different worldwide populations (Turkish, Bosnian, Croatian, Serbian, Montenegrin, Macedonian, Albanian, Kosovan, Greek, Russian, Japanese, Korean, Lithuanian, Iraqi, Belarusian). For the proof of corresponding data, two different Turkish population STR data obtained from previously published articles were compared with our data and this showed that our data correspond to these 2 previously published data. Further, STR allele frequency data for 13 loci for each population were obtained from previous scientific articles and the allele frequencies and genetic diversity among the 15 sample populations were compared. In addition, even though the populations are from different nationalities, the STR data are similar among the geographically close populations. The phylogenetic tree established among worldwide populations and genetic distance values show a great affinity among the 15populations. Our data is useful for anthropological and further comparative genetic studies of populations.

ASAS 095221-4329.8 und ASAS 123034-7703.9 - zwei R-CrB-Stern-Kandidaten aus der ASAS-Datenbank

NASA Astrophysics Data System (ADS)

Huemmerich, Stefan

2011-04-01

During an examination of ASAS Misc-type objects, the stars ASAS 095221-4329.8 GSC 07706-00560, 09:52:21.38 -43:29:40.5) and ASAS 123034-7703.9 (GSC 09416-00380, 12:30:34.22 -77:03:52.7) - both of which show semi-regular variability - were found to exhibit significant obscuration events in their V-band lightcurves. Both stars are likely to be red giants undergoing fading events, possibly of DY Per-type. However, spectroscopy of both stars is needed for a conclusive classification. The corresponding entries in the International Variable Star Index (VSX) have been revised accordingly; variability type was set to "RCB:".

Genes Involved in Anaerobic Metabolism of Phenol in the Bacterium Thauera aromatica

PubMed Central

Breinig, Sabine; Schiltz, Emile; Fuchs, Georg

2000-01-01

Genes involved in the anaerobic metabolism of phenol in the denitrifying bacterium Thauera aromatica have been studied. The first two committed steps in this metabolism appear to be phosphorylation of phenol to phenylphosphate by an unknown phosphoryl donor (“phenylphosphate synthase”) and subsequent carboxylation of phenylphosphate to 4-hydroxybenzoate under release of phosphate (“phenylphosphate carboxylase”). Both enzyme activities are strictly phenol induced. Two-dimensional gel electrophoresis allowed identification of several phenol-induced proteins. Based on N-terminal and internal amino acid sequences of such proteins, degenerate oligonucleotides were designed to identify the corresponding genes. A chromosomal DNA segment of about 14 kbp was sequenced which contained 10 genes transcribed in the same direction. These are organized in two adjacent gene clusters and include the genes coding for five identified phenol-induced proteins. Comparison with sequences in the databases revealed the following similarities: the gene products of two open reading frames (ORFs) are each similar to either the central part and N-terminal part of phosphoenolpyruvate synthases. We propose that these ORFs are components of the phenylphosphate synthase system. Three ORFs showed similarity to the ubiD gene product, 3-octaprenyl-4-hydroxybenzoate carboxy lyase; UbiD catalyzes the decarboxylation of a 4-hydroxybenzoate analogue in ubiquinone biosynthesis. Another ORF was similar to the ubiX gene product, an isoenzyme of UbiD. We propose that (some of) these four proteins are involved in the carboxylation of phenylphosphate. A 700-bp PCR product derived from one of these ORFs cross-hybridized with DNA from different Thauera and Azoarcus strains, even from those which have not been reported to grow with phenol. One ORF showed similarity to the mutT gene product, and three ORFs showed no strong similarities to sequences in the databases. Upstream of the first gene cluster, an ORF which is transcribed in the opposite direction codes for a protein highly similar to the DmpR regulatory protein of Pseudomonas putida. DmpR controls transcription of the genes of aerobic phenol metabolism, suggesting a similar regulation of anaerobic phenol metabolism by the putative regulator. PMID:11004186

[Population data analysis of miniSTR loci: D10S1248, D14S1434 and D22S1045 in the Pomerania-Kujawy region of Poland].

PubMed

Kodroń, Agata; Rychlicka, Edyta; Milewska, Iwona; Woźniak, Marcin; Grzybowski, Tomasz

2010-01-01

This paper presents the allele frequencies and forensic parameters of the three miniSTR loci D10S1248, D14S1434 and D22S1045 in the Pomerania-Kujawy region of Poland. Genomic DNA was extracted by a standard phenol-chloroform extraction procedure. The three miniSTR loci D10S1248, D14S1434 and D22S1045 were amplified in a triplex polymerase chain reaction with the primer sets designed by Coble and Butler in a GeneAmp PCR System 9700 (Applied Biosystems). The amplified products were separated and detected by capillary electrophoresis on an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems).The genotype frequency distributions showed no deviations from Hardy-Weinberg equilibrium expectations. The values of forensic parameters confirm that D10S1248 and D22S1045 are highly informative genetic markers, whereas D14S1434 is a moderately useful for forensic genetic identification purposes.

A Simple and Efficient Method of Extracting DNA from Aged Bones and Teeth.

PubMed

Liu, Qiqi; Liu, Liyan; Zhang, Minli; Zhang, Qingzhen; Wang, Qiong; Ding, Xiaoran; Shao, Liting; Zhou, Zhe; Wang, Shengqi

2018-05-01

DNA is often difficult to extract from old bones and teeth due to low levels of DNA and high levels of degradation. This study established a simple yet efficient method for extracting DNA from 20 aged bones and teeth (approximately 60 years old). Based on the concentration and STR typing results, the new method of DNA extraction (OM) developed in this study was compared with the PrepFiler™ BTA Forensic DNA Extraction Kit (BM). The total amount of DNA extracted using the OM method was not significantly different from that extracted using the commercial kit (p > 0.05). However, the number of STR loci detected was significantly higher in the samples processed using the OM method than using the BM method (p < 0.05). This study aimed to establish a DNA extraction method for aged bones and teeth to improve the detection rate of STR typing and reduce costs compared to the BM technique. © 2017 American Academy of Forensic Sciences.

Trace DNA Sampling Success from Evidence Items Commonly Encountered in Forensic Casework.

PubMed

Dziak, Renata; Peneder, Amy; Buetter, Alicia; Hageman, Cecilia

2018-05-01

Trace DNA analysis is a significant part of a forensic laboratory's workload. Knowing optimal sampling strategies and item success rates for particular item types can assist in evidence selection and examination processes and shorten turnaround times. In this study, forensic short tandem repeat (STR) casework results were reviewed to determine how often STR profiles suitable for comparison were obtained from "handler" and "wearer" areas of 764 items commonly submitted for examination. One hundred and fifty-five (155) items obtained from volunteers were also sampled. Items were analyzed for best sampling location and strategy. For casework items, headwear and gloves provided the highest success rates. Experimentally, eyeglasses and earphones, T-shirts, fabric gloves and watches provided the highest success rates. Eyeglasses and latex gloves provided optimal results if the entire surfaces were swabbed. In general, at least 10%, and up to 88% of all trace DNA analyses resulted in suitable STR profiles for comparison. © 2017 American Academy of Forensic Sciences.

Y-STR INRA189 polymorphisms in Chinese yak breeds.

PubMed

Ma, Z J; Chen, S M; Sun, Y G; Xi, Y L; Li, R Z; Xu, J T; Lei, C Z

2015-12-29

To further explore Y-STR INRA189 polymorphisms in the yak, and to determine the genetic differences among yak breeds, genotyping analysis of INRA189 in 102 male yak individuals from three yak breeds in Qinghai Province of China was performed. Genotyping revealed the presence of four alleles, with sizes of 149, 155, 157, and 159 bp, respectively. Of these, the 157-bp allele, which was found with the highest frequency in the three yak breeds, was the dominant allele. Interestingly, the 149-bp allele was only detected in the Gaoyuan breed, and the 159-bp allele was only found in the Huanhu and Datong breeds. Only the 157- and 155-bp alleles were found in all three yak breeds. Taking the three yak breeds as a single population, the frequency of these four alleles was 0.0294, 0.0686, 0.8628, and 0.0392, respectively. The average polymorphism information content in the three yak breeds was 0.2379, indicating that the INRA189 was a low polymorphic Y-STR marker in yak.

STR-typing of ancient skeletal remains: which multiplex-PCR kit is the best?

PubMed Central

Harder, Melanie; Renneberg, Rebecca; Meyer, Patrick; Krause-Kyora, Ben; von Wurmb-Schwark, Nicole

2012-01-01

Aim To comparatively test nine commercially available short tandem repeat (STR)-multiplex kits (PowerPlex 16, 16HS, ES, ESI17, ESX17, S5 [all Promega]; AmpFiSTR Identifiler, NGM and SEfiler [all Applied Biosystems]) for their efficiency and applicability to analyze ancient and thus highly degraded DNA samples. Methods Fifteen human skeletal remains from the late medieval age were obtained and analyzed using the nine polymerase chain reaction assays with slightly modified protocols. Data were systematically compared to find the most meaningful and sensitive assay. Results The ESI, ESX, and NGM kits showed the best overall results regarding amplification success, detection rate, identification of heterozygous alleles, sex determination, and reproducibility of the obtained data. Conclusion Since application of these three kits enables the employment of different primer sequences for all the investigated amplicons, a combined application is recommended for best possible and – most importantly – reliable genetic analysis of ancient skeletal material or otherwise highly degraded samples, eg, from forensic cases. PMID:23100203

Allele frequencies of 23 autosomal short tandem repeat loci in the Philippine population.

PubMed

Rodriguez, Jae Joseph Russell Beltran; Salvador, Jazelyn M; Calacal, Gayvelline C; Laude, Rita P; De Ungria, Maria Corazon A

2015-07-01

We characterized diversity and forensic descriptive parameters of 23 autosomal STR loci (CSF1PO, D13S317, D16S539, D5S818, D7S820, TPOX, D18S51, D21S11, D3S1358, D8S1179, FGA, TH01, vWA, D1S1656, D10S1248, D12S391, D2S441, D22S1045, D19S433, D2S1338, D6S1043, Penta D and Penta E) among 167 unrelated Filipinos. The most variable autosomal STR loci observed is Penta E (observed heterozygosity: 0.9222, match probability: 0.0167). Results reveal matching probability of 8.21×10(-28) for 23 autosomal STR loci. This dataset for the Philippine population may now be used in evaluating the weight of DNA evidence for forensic applications such as in human identification, parentage/kinship testing, and interpretation of DNA mixtures. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.

PubMed

Guo, Qingsheng; Bai, Zhixiong; Liu, Yuqian; Sun, Qingjiang

2016-03-15

In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs. Copyright © 2015 Elsevier B.V. All rights reserved.

Similarities and distinctions in Y chromosome gene pool of Western Slavs.

PubMed

Woźniak, Marcin; Malyarchuk, Boris; Derenko, Miroslava; Vanecek, Tomas; Lazur, Jan; Gomolcak, Pavol; Grzybowski, Tomasz

2010-08-01

Analysis of Y chromosome Y-STRs has proven to be a useful tool in the field of population genetics, especially in the case of closely related populations. We collected DNA samples from 169 males of Czech origin, 80 males of Slovakian origin, and 142 males dwelling Northern Poland. We performed Y-STR analysis of 12 loci in the samples collected (PowerPlex Y system from Promega) and compared the Y chromosome haplotype frequencies between the populations investigated. Also, we used Y-STR data available from the literature for comparison purposes. We observed significant differences between Y chromosome pools of Czechs and Slovaks compared to other Slavic and European populations. At the same time we were able to point to a specific group of Y-STR haplotypes belonging to an R1a haplogroup that seems to be shared by Slavic populations dwelling in Central Europe. The observed Y chromosome diversity may be explained by taking into consideration archeological and historical data regarding early Slav migrations. Copyright 2010 Wiley-Liss, Inc.

Genetic distribution of 15 autosomal STR markers in the Punjabi population of Pakistan.

PubMed

Shan, Muhammad Adnan; Hussain, Manzoor; Shafique, Muhammad; Shahzad, Muhammad; Perveen, Rukhsana; Idrees, Muhammad

2016-11-01

Genetic diversity of 15 autosomal short tandem repeat (STR) loci was evaluated in 713 unrelated individual samples of a Punjabi population of Pakistan. These loci were scrutinized to establish allelic frequencies and statistical parameters of forensic and paternity interests. A total of 165 alleles were observed with the corresponding allele frequencies ranging from 0.001 to 0.446. D2S1338 was found as the most informative locus while TPOX (0.611) was the least discriminating locus. The combined power of discrimination (CPD), the combined probability of exclusion (CPE), and cumulative probability of matching (CPM) were found equaled to 0.999999999999999998606227424808, 0.999995777557989, and 1.37543 × 10-18, respectively. All the loci followed the Hardy-Weinberg equilibrium after the Bonferroni correction (p < 0.0033) except one locus D3S1358. The study revealed that these STR loci are highly polymorphic, suitable for forensic and parentage analyses. In comparison to different populations (Asians and non-Asians), significant differences were recorded for these loci.

The hip strength:ankle proprioceptive threshold ratio predicts falls and injury in diabetic neuropathy

PubMed Central

Richardson, James K.; DeMott, Trina; Allet, Lara; Kim; Ashton-Miller, James A.

2014-01-01

Introduction We determined lower limb neuromuscular capacities associated with falls and fall-related injuries in older people with declining peripheral nerve function. Methods Thirty-two subjects (67.4 ± 13.4 years; 19 with type 2 diabetes), representing a spectrum of peripheral neurologic function, were evaluated with frontal plane proprioceptive thresholds at the ankle, frontal plane motor function at the ankle and hip, and prospective follow-up for 1 year. Results Falls and fall-related injuries were reported by 20 (62.5%) and 14 (43.8%) subjects, respectively. The ratio of hip adductor rate of torque development to ankle proprioceptive threshold (HipSTR/AnkPRO) predicted falls (pseudo-R2 = .726) and injury (pseudo-R2 = .382). No other variable maintained significance in the presence of HipSTR/AnkPRO. Discussion Fall and injury risk in the population studied is related inversely to HipSTR/AnkPRO. Increasing rapidly available hip strength in patients with neuropathic ankle sensory impairment may decrease risk of falls and related injuries. PMID:24282041

[Inhibition of osthole for resorption of rats femur tissue in vitro].

PubMed

Zhou, Jian; Ren, Xue-mei; Ma, Xiao-ni; Gao, Yu-hai; Yan, Li-juan; Shi, Wen-gui; Chen, Ke-ming

2015-09-01

To investigate osthole effect on femoral tissue resorption activity of rat in vitro. Six SD rats weighted (80 ± 5) g were used to isolate and culture femoral tissue (diaphyses and metaphysis) in vitro. The cultured tissue were devided into control group, estradiol group and osthole group. The femoral tissue was treated with final concentration of 1 x 10(-5) mol/L osthole and 1 x 10(-8) mol/L estradiol culture in vitro at 48 hours after cultured. Tartrate-resistant acid phosphatase (StrACP) activity, glucose and Lactic acid content, StrACP, MCSF (Macrophage colony stimulating factor) and CTSK (Cathepsin K) mRNA was detected by Real-Time RT-PCR were detected. Concetration of Alkaline phosphatase activity were 2226 and 2498 in 1 x 10(-5) mol/L osthole and 1 x 10(-8) mol/L estradiol respectively. As compared with control group, the activity of StrACP of 1 x 10(-5) mol/L osthole and 1 x 10(-8) mol/L estradiol were inhibited at 6, 9, 12 days (P < 0.05); under treatment of in l x 10(-5) mol/L osthole, the content of Lactic acid were increased and the content of glucose were decreased at 3, 6, 9 days (P < 0.05); StrACP, MCSF and CTSK mRNA expression level were inhibited at 6, 9 days (P < 0.05). Osthole can inhibit bone resorption and raise the level of nutrition metabolism of femurs tissue.

[Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

PubMed

Pesik, V Yu; Fedunin, A A; Agdzhoyan, A T; Utevska, O M; Chukhraeva, M I; Evseeva, I V; Churnosov, M I; Lependina, I N; Bogunov, Yu V; Bogunova, A A; Ignashkin, M A; Yankovsky, N K; Balanovska, E V; Orekhov, V A; Balanovsky, O P

2014-06-01

We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA.

Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing.

PubMed

Phillips, Chris; Fernandez-Formoso, Luis; Gelabert-Besada, Miguel; Garcia-Magariños, Manuel; Santos, Carla; Fondevila, Manuel; Carracedo, Angel; Lareu, Maria Victoria

2013-04-01

There is growing interest in developing additional DNA typing techniques to provide better investigative leads in forensic analysis. These include inference of genetic ancestry and prediction of common physical characteristics of DNA donors. To date, forensic ancestry analysis has centered on population-divergent SNPs but these binary loci cannot reliably detect DNA mixtures, common in forensic samples. Furthermore, STR genotypes, forming the principal DNA profiling system, are not routinely combined with forensic SNPs to strengthen frequency data available for ancestry inference. We report development of a 12-STR multiplex composed of ancestry informative marker STRs (AIM-STRs) selected from 434 tetranucleotide repeat loci. We adapted our online Bayesian classifier for AIM-SNPs: Snipper, to handle multiallele STR data using frequency-based training sets. We assessed the ability of the 12-plex AIM-STRs to differentiate CEPH Human Genome Diversity Panel populations, plus their informativeness combined with established forensic STRs and AIM-SNPs. We found combining STRs and SNPs improves the success rate of ancestry assignments while providing a reliable mixture detection system lacking from SNP analysis alone. As the 12 STRs generally show a broad range of alleles in all populations, they provide highly informative supplementary STRs for extended relationship testing and identification of missing persons with incomplete reference pedigrees. Lastly, mixed marker approaches (combining STRs with binary loci) for simple ancestry inference tests beyond forensic analysis bring advantages and we discuss the genotyping options available. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mutation rates at 42 Y chromosomal short tandem repeats in Chinese Han population in Eastern China.

PubMed

Wu, Weiwei; Ren, Wenyan; Hao, Honglei; Nan, Hailun; He, Xin; Liu, Qiuling; Lu, Dejian

2018-01-31

Mutation analysis of 42 Y chromosomal short tandem repeats (Y-STRs) loci was performed using a sample of 1160 father-son pairs from the Chinese Han population in Eastern China. The results showed that the average mutation rate across the 42 Y-STR loci was 0.0041 (95% CI 0.0036-0.0047) per locus per generation. The locus-specific mutation rates varied from 0.000 to 0.0190. No mutation was found at DYS388, DYS437, DYS448, DYS531, and GATA_H4. DYS627, DYS570, DYS576, and DYS449 could be classified as rapidly mutating Y-STRs, with mutation rates higher than 1.0 × 10 -2 . DYS458, DYS630, and DYS518 were moderately mutating Y-STRs, with mutation rates ranging from 8 × 10 -3 to 1 × 10 -2 . Although the characteristics of the Y-STR mutations were consistent with those in previous studies, mutation rate differences between our data and previous published data were found at some rapidly mutating Y-STRs. The single-copy loci located on the short arm of the Y chromosome (Yp) showed relatively higher mutation rates more frequently than the multi-copy loci. These results will not only extend the data for Y-STR mutations but also be important for kinship analysis, paternal lineage identification, and family relationship reconstruction in forensic Y-STR analysis.

Dietary aspartyl-phenylalanine-1-methyl ester delays osteoarthritis and prevents associated bone loss in STR/ORT mice

PubMed Central

Manion, Carl V.; Hochgeschwender, Ute; Edmundson, Allen B.; Hugli, Tony E.

2011-01-01

Objective. STR/ORT mice provide a well-known model for murine idiopathic OA, with histological joint lesions resembling those of human OA. This model was used to investigate protective effects of the dipeptide aspartyl-phenylalanine-1-methyl ester (Asp-Phe-OMe or aspartame) via the oral route vs a regular diet. Methods. STR/ORT mice were housed individually and fed diets with or without Asp-Phe-OMe (4 mg/kg), after weaning at the age of 3 weeks, until 15 months of age (average of 20 animals per group). The study groups were kept blinded to the investigators, who measured food consumption and body weight and performed gait mobility tests. Radiographic scans were also performed at regular time intervals to evaluate differential radiographic anomalies associated with progress of OA in response to oral Asp-Phe-OMe therapy. Results. The Asp-Phe-OMe-fed animals presented a pattern of significantly delayed disease onset. In addition, their muscle and bone mass were highly preserved, even at later time points after OA was established. Moreover, control animals presented a higher variability in gait motility in comparison with the Asp-Phe-OMe-fed animals, suggesting a protective effect from movement limitations associated with advanced OA. Conclusion. Asp-Phe-OMe, given orally, delays OA in the spontaneous STR/ORT model, improves bone cortical density and muscle mass, and may contribute to a better quality of life for these diseased animals. PMID:21372000

Application of Short Tandem Repeat markers in diagnosis of chromosomal aneuploidies and forensic DNA investigation in Pakistan.

PubMed

Chishti, Hafsah Muhammad; Ansar, Muhammad; Ajmal, Muhammad; Hameed, Abdul

2014-09-15

Short Tandem Repeat (STR) genetic markers hold great potential in forensic investigations, molecular diagnostics and molecular genetics research. AmpFlSTR® Identifiler™ PCR amplification kit is a multiplex system for co-amplification of 15 STR markers used worldwide in forensic investigations. This study attempts to assess forensic validity of these STRs in Pakistani population and to investigate its applicability in quick and simultaneous diagnosis and tracing parental source of common chromosomal aneuploidies. Samples from 554 healthy Pakistani individuals from 5 different ethnicities were analyzed for forensic parameters using Identifiler STRs and 74 patients' samples with different aneuploidies were evaluated for diagnostic strengths of these markers. All STRs hold sufficient forensic applicability in Pakistani population with paternity index between 1.5 and 3.5, polymorphic information content from 0.63 to 0.87 and discrimination power ≥0.9 (except TPOX locus). Variation from Hardy-Weinberg equilibrium was observed at some loci reflecting selective breeding and intermarriages trend in Pakistan. Among aneuploidic samples, all trisomies were precisely detectable while aneuploidies involving sex chromosomes or missing chromosomes were not clearly detectable using Identifiler STRs. Parental origin of aneuploidy was traceable in 92.54% patients. The studied STR markers are valuable tools for forensic application in Pakistan and utilizable for quick and simultaneous identification of some common trisomic conditions. Adding more sex chromosome specific STR markers can immensely increase the diagnostic and forensic potential of this system. Copyright © 2014 Elsevier B.V. All rights reserved.

Enhanced production of poly(3-hydroxybutyrate) in a novel airlift reactor with in situ cell retention using Azohydromonas australica.

PubMed

Gahlawat, Geeta; Sengupta, Bedoshree; Srivastava, Ashok K

2012-09-01

Economic production of biodegradable plastics is a challenge particularly because of high substrate and energy cost inputs for its production. Research efforts are being directed towards innovations to minimize both of the above costs to economize polyhydroxybutyrate (PHB) production. A novel airlift reactor (ALR) with outer aeration and internal settling was utilized in this investigation. Although it featured no power consumption for agitation, it facilitated increased oxygen transfer rate and better cell retention than stirred tank reactor (STR), thereby resulting in enhanced PHB productivity. ALR with in situ cell retention demonstrated a significant improvement in biomass concentration and biopolymer accumulation. The total PHB production rate, specific biomass, and product yield in the ALR were observed to be 0.84 g/h, 0.43 g/g, and 0.32 g/g, respectively. The studies revealed that the volumetric oxygen mass transfer rate and mixing time for ALR were 0.016 s⁻¹ and 3.73 s, respectively, at 2.0 vvm as compared with corresponding values of 0.005 s⁻¹ and 4.95 s, respectively, in STR. This demonstrated that ALR has better oxygen mass transfer and mixing efficiency than STR. Hence, ALR with cell retention would serve as a better bioreactor design for economic biopolymer production than STR, particularly due to its lower cost of operation and simplicity along with its enhanced oxygen and heat transfer rates.

Tenofovir alafenamide (TAF) as the successor of tenofovir disoproxil fumarate (TDF).

PubMed

De Clercq, Erik

2016-11-01

Tenofovir alafenamide (TAF) can be considered a new prodrug of tenofovir (TFV), as successor of tenofovir disoproxil fumarate (TDF). It is in vivo as potent against human immunodeficiency virus (HIV) at a 30-fold lower dose (10mg) than TDF (300mg). TAF has been approved in November 2015 (in the US and EU), as a single-tablet regimen (STR) containing 150mg elvitegravir (E), 150mg cobicistat (C), 200mg emtricitabine [(-)FTC] (F) and 10mg TAF, marketed as Genvoya®, on 01 March 2016 in the US as an STR containing 25mg rilpivirine (R), 200mg F and 25mg TAF, marketed as Odefsey®, and on 4 April 2016 in the US, as an STR containing 200mg F and 25mg TAF, marketed as Descovy®, for the treatment of HIV infections. STR combinations containing TAF and emtricitabine could be paired with a range of third agents, for example, darunavir and cobicistat. TAF has a much lower risk of kidney toxicity or bone density changes than TDF, and also offers long-term potential in the pre-exposure prophylaxis (PrEP) of HIV infections. TAF is specifically accumulated in lymphatic tissue, and in the liver, and hence also holds great potential for the treatment of hepatitis B virus (HBV) infections. Akin to TDF, TAF is converted intracellularly to TFV. Its active diphosphate metabolite (TFVpp) is targeted at the RNA-dependent DNA polymerase (reverse transcriptase) of either HIV or HBV. Copyright © 2016 Elsevier Inc. All rights reserved.

Increased recovery of touch DNA evidence using FTA paper compared to conventional collection methods.

PubMed

Kirgiz, Irina A; Calloway, Cassandra

2017-04-01

Tape lifting and FTA paper scraping methods were directly compared to traditional double swabbing for collecting touch DNA from car steering wheels (n = 70 cars). Touch DNA was collected from the left or right side of each steering wheel (randomized) using two sterile cotton swabs, while the other side was sampled using water-soluble tape or FTA paper cards. DNA was extracted and quantified in duplicate using qPCR. Quantifiable amounts of DNA were detected for 100% of the samples (n = 140) collected independent of the method. However, the DNA collection yield was dependent on the collection method. A statistically significant difference in DNA yield was observed between FTA scraping and double swabbing methods (p = 0.0051), with FTA paper collecting a two-fold higher amount. Statistical analysis showed no significant difference in DNA yields between the double swabbing and tape lifting techniques (p = 0.21). Based on the DNA concentration required for 1 ng input, 47% of the samples collected using FTA paper would be expected to yield a short tandem repeat (STR) profile compared to 30% and 23% using double swabbing or tape, respectively. Further, 55% and 77% of the samples collected using double swabbing or tape, respectively, did not yield a high enough DNA concentration for the 0.5 ng of DNA input recommended for conventional STR kits and would be expected to result in a partial or no profile compared to 35% of the samples collected using FTA paper. STR analysis was conducted for a subset of the higher concentrated samples to confirm that the DNA collected from the steering wheel was from the driver. 32 samples were selected with DNA amounts of at least 1 ng total DNA (100 pg/μl when concentrated if required). A mixed STR profile was observed for 26 samples (88%) and the last driver was the major DNA contributor for 29 samples (94%). For one sample, the last driver was the minor DNA contributor. A full STR profile of the last driver was observed for 21 samples (69%) and a partial profile was observed for nine samples (25%); STR analysis failed for two samples collected using tape (6%). In conclusion, we show that the FTA paper scraping method has the potential to collect higher DNA yields from touch DNA evidence deposited on non-porous surfaces often encountered in criminal cases compared to conventional methods. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Integrative Analysis of Brain Region-specific Shank3 Interactomes for Understanding the Heterogeneity of Neuronal Pathophysiology Related to SHANK3 Mutations

PubMed Central

Lee, Yeunkum; Kang, Hyojin; Lee, Bokyoung; Zhang, Yinhua; Kim, Yoonhee; Kim, Shinhyun; Kim, Won-Ki; Han, Kihoon

2017-01-01

Recent molecular genetic studies have identified 100s of risk genes for various neurodevelopmental and neuropsychiatric disorders. As the number of risk genes increases, it is becoming clear that different mutations of a single gene could cause different types of disorders. One of the best examples of such a gene is SHANK3, which encodes a core scaffold protein of the neuronal excitatory post-synapse. Deletions, duplications, and point mutations of SHANK3 are associated with autism spectrum disorders, intellectual disability, schizophrenia, bipolar disorder, and attention deficit hyperactivity disorder. Nevertheless, how the different mutations of SHANK3 can lead to such phenotypic diversity remains largely unknown. In this study, we investigated whether Shank3 could form protein complexes in a brain region-specific manner, which might contribute to the heterogeneity of neuronal pathophysiology caused by SHANK3 mutations. To test this, we generated a medial prefrontal cortex (mPFC) Shank3 in vivo interactome consisting of 211 proteins, and compared this protein list with a Shank3 interactome previously generated from mixed hippocampal and striatal (HP+STR) tissues. Unexpectedly, we found that only 47 proteins (about 20%) were common between the two interactomes, while 164 and 208 proteins were specifically identified in the mPFC and HP+STR interactomes, respectively. Each of the mPFC- and HP+STR-specific Shank3 interactomes represents a highly interconnected network. Upon comparing the brain region-enriched proteomes, we found that the large difference between the mPFC and HP+STR Shank3 interactomes could not be explained by differential protein expression profiles among the brain regions. Importantly, bioinformatic pathway analysis revealed that the representative biological functions of the mPFC- and HP+STR-specific Shank3 interactomes were different, suggesting that these interactors could mediate the brain region-specific functions of Shank3. Meanwhile, the same analysis on the common Shank3 interactors, including Homer and GKAP/SAPAP proteins, suggested that they could mainly function as scaffolding proteins at the post-synaptic density. Lastly, we found that the mPFC- and HP+STR-specific Shank3 interactomes contained a significant number of proteins associated with neurodevelopmental and neuropsychiatric disorders. These results suggest that Shank3 can form protein complexes in a brain region-specific manner, which might contribute to the pathophysiological and phenotypic diversity of disorders related to SHANK3 mutations. PMID:28469556

Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples.

PubMed

Børsting, Claus; Mogensen, Helle Smidt; Morling, Niels

2013-05-01

Heterozygote imbalances leading to allele drop-outs and disproportionally large stutters leading to allele drop-ins are known stochastic phenomena related to STR typing of low-template DNA (LtDNA). The large stutters and the many drop-ins in typical STR stutter positions are artifacts from the PCR amplification of tandem repeats. These artifacts may be avoided by typing bi-allelic markers instead of STRs. In this work, the SNPforID multiplex assay was used to type LtDNA. A sensitized SNP typing protocol was introduced, that increased signal strengths without increasing noise and without affecting the heterozygote balance. Allele drop-ins were only observed in experiments with 25 pg of DNA and not in experiments with 50 and 100 pg of DNA. The allele drop-in rate in the 25 pg experiments was 0.06% or 100 times lower than what was previously reported for STR typing of LtDNA. A composite model and two different consensus models were used to interpret the SNP data. Correct profiles with 42-49 SNPs were generated from the 50 and 100 pg experiments, whereas a few incorrect genotypes were included in the generated profiles from the 25 pg experiments. With the strict consensus model, between 35 and 48 SNPs were correctly typed in the 25 pg experiments and only one allele drop-out (error rate: 0.07%) was observed in the consensus profiles. A total of 28 crime case samples were selected for typing with the sensitized SNPforID protocol. The samples were previously typed with old STR kits during the crime case investigation and only partial profiles (0-6 STRs) were obtained. Eleven of the samples could not be quantified with the Quantifiler™ Human DNA Quantification kit because of partial or complete inhibition of the PCR. For eight of these samples, SNP typing was only possible when the buffer and DNA polymerase used in the original protocol was replaced with the AmpFℓSTR(®) SEfiler Plus™ Master Mix, which was developed specifically for challenging forensic samples. All the crime case samples were successfully typed with the SNPforID multiplex assay and the match probabilities ranged from 1.1×10(-15) to 7.9×10(-23). In comparison, four of the samples could not be typed with the AmpFℓSTR(®) SEfiler Plus™ kit and the match probabilities were higher than 10(-7) for another six samples. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

THE GALACTIC R CORONAE BOREALIS STARS: THE C{sub 2} SWAN BANDS, THE CARBON PROBLEM, AND THE {sup 12}C/{sup 13}C RATIO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hema, B. P.; Pandey, Gajendra; Lambert, David L., E-mail: hema@iiap.res.in, E-mail: pandey@iiap.res.in, E-mail: dll@astro.as.utexas.edu

2012-03-10

Observed spectra of R Coronae Borealis (RCB) and hydrogen-deficient carbon (HdC) stars are analyzed by synthesizing the C{sub 2} Swan bands (1, 0), (0, 0), and (0, 1) using our detailed line list and the Uppsala model atmospheres. The (0, 1) and (0, 0) C{sub 2} bands are used to derive the {sup 12}C abundance, and the (1, 0) {sup 12}C{sup 13}C band to determine the {sup 12}C/{sup 13}C ratios. The carbon abundance derived from the C{sub 2} Swan bands is about the same for the adopted models constructed with different carbon abundances over the range 8.5 (C/He = 0.1%)more » to 10.5 (C/He = 10%). Carbon abundances derived from C I lines are about a factor of four lower than the carbon abundance of the adopted model atmosphere over the same C/He interval, as reported by Asplund et al., who dubbed the mismatch between adopted and derived C abundance as the 'carbon problem'. In principle, the carbon abundances obtained from C{sub 2} Swan bands and that assumed for the model atmosphere can be equated for a particular choice of C/He that varies from star to star. Then, the carbon problem for C{sub 2} bands is eliminated. However, such C/He ratios are in general less than those of the extreme helium stars, the seemingly natural relatives to the RCB and HdC stars. A more likely solution to the C{sub 2} carbon problem may lie in a modification of the model atmosphere's temperature structure. The derived carbon abundances and the {sup 12}C/{sup 13}C ratios are discussed in light of the double degenerate and the final flash scenarios.« less

Rotordynamic Instability Problems in High-Performance Turbomachinery. Proceedings of a Workshop (1st) Held at Texas A&M University, College Station, Texas, May 12-14, 1980.

DTIC Science & Technology

1980-08-01

Vibrations Stimulated by Lateral Forces in Sealing Gaps," In German, Institut ffir Thermische Str ~mungsmaschinen, Unwersitat Stuttgart. 26. Warner, R. E...investigations at the "Institut fOr Thermische Str ~mungsmaschinen at the Uni- versity of Stuttgart" are performed. This is done with the aim to point out the...Eigenschwingungen von Turbinenlaufern, angefacht durch die Spaltstr~ mung in Stopfbuchsen und Beschauflungen. Bull. de l’AIM 71 (1958) pp. 1039-1063 4

Self-tuning regulator for an interacting CSTR process

NASA Astrophysics Data System (ADS)

Rajendra Mungale, Niraj; Upadhyay, Akshay; Jaganatha Pandian, B.

2017-11-01

In the paper we have laid emphasis on STR that is Self Tuning Regulator and its application for an interacting process. CSTR has a great importance in Chemical Process when we deal with controlling different parameters of a process using CSTR. Basically CSTR is used to maintain a constant liquid temperature in the process. The proposed method called self-tuning regulator, is a different scheme where process parameters are updated and the controller parameters are obtained from the solution of a design problem. The paper deals with STR and methods associated with it.

IkeNet: Social Network Analysis of E-mail Traffic in the Eisenhower Leadership Development Program

DTIC Science & Technology

2007-11-01

8217Create the recipients TO TempArray = Sphit(strTo,") For Each varArrayltem In TemnpArray hextGuy = Chr(34) & CStr (Trim(varArrayltem)) & Chr(34) MsgBox...34next guy = " & nextGuy ’Set oRecipient = Recipients.Add(nextGuy) Set oRecipient = Recipients.Add( CStr (Trim(varArrayItem))) oRecipient.Type = olTo...TempArray = Split(strAttachments, "" For Each varArrayltern In TempArray .Attachments.Add CStr (Trim(varArrayItem)) Next varArrayltern .Send No return value

Amino-siloxane composition and methods of using the same

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Brien, Michael Joseph; Farnum, Rachel Lizabeth; Perry, Robert James

An amino-siloxane composition is presented. The amino-siloxane composition includes structure (I): ##STR00001## wherein R 1 is independently at each occurrence a C 1-C 5 aliphatic radical; R 2 is a C 3-C. 4 aliphatic radical; R 3 is a C 1-C 5 aliphatic radical or R 4, wherein R 4 comprises structure (II): ##STR00002## and X is an electron donating group. Methods of reducing an amount of carbon dioxide in a process stream using the amino-siloxane composition are also presented.

Dynamic Response of Multiphase Porous Media

DTIC Science & Technology

1993-06-16

34"--OIct 5oct, tf1 2fOct, a f s,t,R Linearly Set Parameters Interpolate s = 1.03 from Model Fit s,t,R t = R = 0.0 Parameters Figure 3.3 Extrapolation...nitrogen. To expedite the testing, the system was equipped with solenoid operated valves so that the tests could be conducted by a single operator...incident bar. Figure 6.6 shows the incident bar entering the pressure vessel that contains the test specimen. The hose and valves are for filling and 6-5 I

Haplotype data for 23 Y-chromosome markers in four U.S. population groups.

PubMed

Coble, Michael D; Hill, Carolyn R; Butler, John M

2013-05-01

The PowerPlex Y23 kit contains 23 Y-chromosomal loci including all 17 of the markers in the Yfiler Y-STR kit plus six additional markers: DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643. We have typed 1032 unrelated population samples from four self-declared US groups: African Americans, Asians, Hispanics, and Western European Caucasians. An analysis of the population genetic parameters and the improvement of adding additional Y-STR markers to the dataset are described. Published by Elsevier Ireland Ltd.

Larva and pupa of Megatoma (s. str.) undata (Linnaeus, 1758) with remarks on biology and economic importance (Coleoptera, Dermestidae).

PubMed

Kadej, Marcin

2017-01-01

An updated description of the final larval instar and pupa of Megatoma (s. str.) undata (Linnaeus, 1758) (Coleoptera: Dermestidae) is presented. Several morphological characteristics of M. undata larvae are documented and discussed: antenna, epipharynx, mandibula, maxilla, ligula with labial palpi, hastisetae, terga, and condition of the antecostal suture. The paper is fully illustrated and includes some important additions to extend notes on this species available in the references. Summarised data about biology, economic importance, and distribution of M. undata are also provided.

Mitochondrial DNA and STR analyses for human DNA from maggots crop contents: a forensic entomology case from central-southern China.

PubMed

Li, X; Cai, J F; Guo, Y D; Xiong, F; Zhang, L; Feng, H; Meng, F M; Fu, Y; Li, J B; Chen, Y Q

2011-08-01

Insect larvae and adult insects found on human corpses can provide important forensic evidence however it is useful to be able to prove evidence of association. Without this, it could be claimed that the insect evidence was a contaminant or had been planted on the body. This paper describes how mitochondrial DNA (mtDNA) and STR analysis of the crop contents of larvae of the blowfly Aldrichina grahami collected from separated body parts was used to provide evidence of association.

A comprehensive Y-STR portrait of Yousafzai's population.

PubMed

Tabassum, Sadia; Ilyas, Muhammad; Ullah, Inam; Israr, Muhammad; Ahmad, Habib

2017-09-01

In the current study, 17 Y-Chromosomal short tandem repeats (Y-STRs) included in theAmpFlSTR Y-Filer amplification kit (Applied Biosystems, Foster City, USA) were investigated in 146 unrelated Yousafzai males residing in the Khyber Pakhtunkhwa Province of Pakistan. A total of 94 (89.52%) unique haplotypes were observed. Discrimination capacity was 71.92%. Haplotype diversity ranged from 0.354 (DYS456) to 0.663 (DYS458). Both Rst pairwise analysis and multidimensional scaling plot showed that the genetic structure of the Yousafzais is significantly different from neighbouring populations.

STR-based genetic structure of the Berber population of Bejaia (Northern Algeria) and its relationships to various ethnic groups.

PubMed

Amir, Nadir; Sahnoune, Mohamed; Chikhi, Lounes; Atmani, Djebbar

2015-12-10

Patterns of genetic variation in human populations have been described for decades. However, North Africa has received little attention and Algeria, in particular, is poorly studied, Here we genotyped a Berber-speaking population from Algeria using 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA from the commercially available AmpF/STR Identifiler kit. Altogether 150 unrelated North Algerian individuals were sampled across 10 administrative regions or towns from the Bejaia Wilaya (administrative district). We found that all of the STR loci met Hardy-Weinberg equilibrium expectations, after Bonferroni correction and that the Berber-speaking population of Bejaia presented a high level of observed heterozygosity for the 15 STR system (>0.7). Genetic parameters of forensic interest such as combined power of discrimination (PD) and combined probability of exclusion (PE) showed values higher than 0.999, suggesting that this set of STRs can be used for forensic studies. Our results were also compared to those published for 42 other human populations analyzed with the same set. We found that the Bejaia sample clustered with several North African populations but that some geographically close populations, including the Berber-speaking Mozabite from Algeria were closer to Near-Eastern populations. While we were able to detect some genetic structure among samples, we found that it was not correlated to language (Berber-speaking versus Arab-speaking) or to geography (east versus west). In other words, no significant genetic differences were found between the Berber-speaking and the Arab-speaking populations of North Africa. The genetic closeness of European, North African and Near-Eastern populations suggest that North Africa should be integrated in models aiming at reconstructing the demographic history of Europe. Similarly, the genetic proximity with sub-Saharan Africa is a reminder of the links that connect all African regions. Copyright © 2015 Elsevier B.V. All rights reserved.

[Polymorphism analysis of 20 autosomal short-tandem repeat loci in southern Chinese Han population].

PubMed

Chen, Ling; Lu, Hui-Jie; DU, Wei-An; Qiu, Ping-Ming; Liu, Chao

2016-02-20

To evaluate the value of PowerPlex ® 21 System (Promega) and study the genetic polymorphism of its 20 short-tandem repeat (STR) loci in southern Chinese Han population. We conducted genotyping experiments using PowerPlex ® 21 System on 20 autosomal STR loci (D3S1358, D1S1656, D6S1043, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433 and FGA) in 2367 unrelated Chinese Han individuals living in South China. The allele frequencies and parameters commonly used in forensic science were statistically analyzed in these individuals and compared with the reported data of other populations. The PowerPlex ® 21 System had a power of discrimination (PD) ranging from 0.7839 to 0.9852 and a power of exclusion (PE) ranging from 0.2974 to 0.8099 for the 20 loci. No significant deviation from Hardy-Weinberg expectations was found for all the loci except for D5S818. This southern Chinese Han population had significant differences in the allele frequencies from 8 ethnic groups reported in China, and showed significant differences at 8 to 20 STR foci from 5 foreign populations. The allele frequency at the locus D1S1656 in this southern Chinese Han population differed significantly from those in the 5 foreign populations and from 3 reported Han populations in Beijing, Zhejiang Province and Fujian Province of China. The neighbor-joining phylogenetictree showed clustering of all the Asian populations in one branch, while the northern Italian and Argentina populations clustered in a separate branch. This southern Chinese Han population had the nearest affinity with the Yi ethnic population in Yunnan Province of China. The 20 STR loci are highly polymorphic in this southern Chinese Han population, suggesting the value of this set of STR loci in forensic personal identification, paternity testing and anthropological study.

Differences in 5-HT2A and mGlu2 Receptor Expression Levels and Repressive Epigenetic Modifications at the 5-HT2A Promoter Region in the Roman Low- (RLA-I) and High- (RHA-I) Avoidance Rat Strains.

PubMed

Fomsgaard, Luna; Moreno, Jose L; de la Fuente Revenga, Mario; Brudek, Tomasz; Adamsen, Dea; Rio-Alamos, Cristobal; Saunders, Justin; Klein, Anders Bue; Oliveras, Ignasi; Cañete, Toni; Blazquez, Gloria; Tobeña, Adolf; Fernandez-Teruel, Albert; Gonzalez-Maeso, Javier; Aznar, Susana

2018-03-01

The serotonin 2A (5-HT 2A ) and metabotropic glutamate 2 (mGlu2) receptors regulate each other and are associated with schizophrenia. The Roman high- (RHA-I) and the Roman low- (RLA-I) avoidance rat strains present well-differentiated behavioral profiles, with the RHA-I strain emerging as a putative genetic rat model of schizophrenia-related features. The RHA-I strain shows increased 5-HT 2A and decreased mGlu2 receptor binding levels in prefrontal cortex (PFC). Here, we looked for differences in gene expression and transcriptional regulation of these receptors. The striatum (STR) was included in the analysis. 5-HT 2A , 5-HT 1A , and mGlu2 mRNA and [ 3 H]ketanserin binding levels were measured in brain homogenates. As expected, 5-HT 2A binding was significantly increased in PFC in the RHA-I rats, while no difference in binding was observed in STR. Surprisingly, 5-HT 2A gene expression was unchanged in PFC but significantly decreased in STR. mGlu2 receptor gene expression was significantly decreased in both PFC and STR. No differences were observed for the 5-HT 1A receptor. Chromatin immunoprecipitation assay revealed increased trimethylation of histone 3 at lysine 27 (H3K27me3) at the promoter region of the HTR2A gene in the STR. We further looked at the Akt/GSK3 signaling pathway, a downstream point of convergence of the serotonin and glutamate system, and found increased phosphorylation levels of GSK3β at tyrosine 216 and increased β-catenin levels in the PFC of the RHA-I rats. These results reveal region-specific regulation of the 5-HT 2A receptor in the RHA-I rats probably due to absence of mGlu2 receptor that may result in differential regulation of downstream pathways.

Comprehensive mutation analysis of 17 Y-chromosomal short tandem repeat polymorphisms included in the AmpFlSTR Yfiler PCR amplification kit.

PubMed

Goedbloed, Miriam; Vermeulen, Mark; Fang, Rixun N; Lembring, Maria; Wollstein, Andreas; Ballantyne, Kaye; Lao, Oscar; Brauer, Silke; Krüger, Carmen; Roewer, Lutz; Lessig, Rüdiger; Ploski, Rafal; Dobosz, Tadeusz; Henke, Lotte; Henke, Jürgen; Furtado, Manohar R; Kayser, Manfred

2009-11-01

The Y-chromosomal short tandem repeat (Y-STR) polymorphisms included in the AmpFlSTR Yfiler polymerase chain reaction amplification kit have become widely used for forensic and evolutionary applications where a reliable knowledge on mutation properties is necessary for correct data interpretation. Therefore, we investigated the 17 Yfiler Y-STRs in 1,730-1,764 DNA-confirmed father-son pairs per locus and found 84 sequence-confirmed mutations among the 29,792 meiotic transfers covered. Of the 84 mutations, 83 (98.8%) were single-repeat changes and one (1.2%) was a double-repeat change (ratio, 1:0.01), as well as 43 (51.2%) were repeat gains and 41 (48.8%) repeat losses (ratio, 1:0.95). Medians from Bayesian estimation of locus-specific mutation rates ranged from 0.0003 for DYS448 to 0.0074 for DYS458, with a median rate across all 17 Y-STRs of 0.0025. The mean age (at the time of son's birth) of fathers with mutations was with 34.40 (+/-11.63) years higher than that of fathers without ones at 30.32 (+/-10.22) years, a difference that is highly statistically significant (p < 0.001). A Poisson-based modeling revealed that the Y-STR mutation rate increased with increasing father's age on a statistically significant level (alpha = 0.0294, 2.5% quantile = 0.0001). From combining our data with those previously published, considering all together 135,212 meiotic events and 331 mutations, we conclude for the Yfiler Y-STRs that (1) none had a mutation rate of >1%, 12 had mutation rates of >0.1% and four of <0.1%, (2) single-repeat changes were strongly favored over multiple-repeat ones for all loci but 1 and (3) considerable variation existed among loci in the ratio of repeat gains versus losses. Our finding of three Y-STR mutations in one father-son pair (and two pairs with two mutations each) has consequences for determining the threshold of allelic differences to conclude exclusion constellations in future applications of Y-STRs in paternity testing and pedigree analyses.

Stable Caloric Intake and Continued Virologic Suppression for HIV-Positive Antiretroviral Treatment-Experienced Women After Switching to a Single-Tablet Regimen of Emtricitabine, Rilpivirine, and Tenofovir Disoproxil Fumarate.

PubMed

Menezes, Prema; Mollan, Katie; Hoffman, Erin; Xie, Zimeng; Wills, Jennifer; Marcus, Cheryl; Rublein, John; Hudgens, Michael; Eron, Joseph J

2018-05-02

Benefits of switching to a single-tablet regimen (STR) of emtricitabine/rilpivirine/tenofovir (FTC/RPV/TDF) in virologically suppressed antiretroviral treatment (ART) experienced HIV-positive women include pregnancy category B rating and lack of clinically significant drug interactions between RPV and oral contraceptives. Unfortunately, studies involving switching to FTC/RPV/TDF enrolled fewer than 25% women. We undertook this 48-week study to assess the ability of virologically suppressed HIV-positive women switching to RPV STR to remain virologically suppressed and comply with the caloric intake requirement. HIV-positive women on ART with viral load <50 c/mL for 6 months before study entry and no known resistance to FTC, TDF, or RPV were enrolled and switched to STR RPV/FTC/TDF. Caloric intake (≥400 kcal) compliance and concurrency with oral STR RPV/FTC/TDF were evaluated with a 3-day food diary, which was validated by obtaining participant's caloric consumption through phone calls on randomly chosen dates. For each 3-day food diary, the daily median caloric intake and median value for each macronutrient consumed concurrent with FTC/RPV/TDF were computed. Medication adherence was measured using a visual analog scale. We enrolled 33 women, 73% of whom were African American. At week 48, virologic suppression (HIV RNA <40 c/mL) was maintained in 96% of women, including those (n = 4) who reported imperfect ART adherence. The daily median caloric intake concurrent with FTC/RPV/TDF was 820 kcal by food diary and 677 kcal by random phone call. Median kcal intake (food diary) did not change significantly from baseline (684 kcal) to week 48 (820 kcal); median change 102 kcal, p = .15. Women who reported noncompliance with a ≥400 kcal meal did not experience virologic failure. Significant concordance between caloric adherence and virologic suppression was not detected. Our study demonstrated that HIV-positive women who switched to STR FTC/RPV/TDF continued to experience virologic suppression and were readily able to comply with the recommended caloric intake requirement.

Preservation and rapid purification of DNA from decomposing human tissue samples.

PubMed

Sorensen, Amy; Rahman, Elizabeth; Canela, Cassandra; Gangitano, David; Hughes-Stamm, Sheree

2016-11-01

One of the key features to be considered in a mass disaster is victim identification. However, the recovery and identification of human remains are sometimes complicated by harsh environmental conditions, limited facilities, loss of electricity and lack of refrigeration. If human remains cannot be collected, stored, or identified immediately, bodies decompose and DNA degrades making genotyping more difficult and ultimately decreasing DNA profiling success. In order to prevent further DNA damage and degradation after collection, tissue preservatives may be used. The goal of this study was to evaluate three customized (modified TENT, DESS, LST) and two commercial DNA preservatives (RNAlater and DNAgard ® ) on fresh and decomposed human skin and muscle samples stored in hot (35°C) and humid (60-70% relative humidity) conditions for up to three months. Skin and muscle samples were harvested from the thigh of three human cadavers placed outdoors for up to two weeks. In addition, the possibility of purifying DNA directly from the preservative solutions ("free DNA") was investigated in order to eliminate lengthy tissue digestion processes and increase throughput. The efficiency of each preservative was evaluated based on the quantity of DNA recovered from both the "free DNA" in solution and the tissue sample itself in conjunction with the quality and completeness of downstream STR profiles. As expected, DNA quantity and STR success decreased with time of decomposition. However, a marked decrease in DNA quantity and STR quality was observed in all samples after the bodies entered the bloat stage (approximately six days of decomposition in this study). Similar amounts of DNA were retrieved from skin and muscle samples over time, but slightly more complete STR profiles were obtained from muscle tissue. Although higher amounts of DNA were recovered from tissue samples than from the surrounding preservative, the average number of reportable alleles from the "free DNA" was comparable. Overall, DNAgard ® and the modified TENT buffer were the most successful tissue preservatives tested in this study based on STR profile success from "free DNA" in solution when decomposing tissues were stored for up to three months in hot, humid conditions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Single Nucleotide Polymorphism (SNP)-Based Loss of Heterozygosity (LOH) Testing by Real Time PCR in Patients Suspect of Myeloproliferative Disease

PubMed Central

Huijsmans, Cornelis J. J.; Poodt, Jeroen; Damen, Jan; van der Linden, Johannes C.; Savelkoul, Paul H. M.; Pruijt, Johannes F. M.; Hilbink, Mirrian; Hermans, Mirjam H. A.

2012-01-01

During tumor development, loss of heterozygosity (LOH) often occurs. When LOH is preceded by an oncogene activating mutation, the mutant allele may be further potentiated if the wild-type allele is lost or inactivated. In myeloproliferative neoplasms (MPN) somatic acquisition of JAK2V617F may be followed by LOH resulting in loss of the wild type allele. The occurrence of LOH in MPN and other proliferative diseases may lead to a further potentiating the mutant allele and thereby increasing morbidity. A real time PCR based SNP profiling assay was developed and validated for LOH detection of the JAK2 region (JAK2LOH). Blood of a cohort of 12 JAK2V617F-positive patients (n = 6 25–50% and n = 6>50% JAK2V617F) and a cohort of 81 patients suspected of MPN was stored with EDTA and subsequently used for validation. To generate germ-line profiles, non-neoplastic formalin-fixed paraffin-embedded tissue from each patient was analyzed. Results of the SNP assay were compared to those of an established Short Tandem Repeat (STR) assay. Both assays revealed JAK2LOH in 1/6 patients with 25–50% JAK2V617F. In patients with >50% JAK2V617F, JAK2LOH was detected in 6/6 by the SNP assay and 5/6 patients by the STR assay. Of the 81 patients suspected of MPN, 18 patients carried JAK2V617F. Both the SNP and STR assay demonstrated the occurrence of JAK2LOH in 5 of them. In the 63 JAK2V617F-negative patients, no JAK2LOH was observed by SNP and STR analyses. The presented SNP assay reliably detects JAK2LOH and is a fast and easy to perform alternative for STR analyses. We therefore anticipate the SNP approach as a proof of principle for the development of LOH SNP-assays for other clinically relevant LOH loci. PMID:22768290

Mixed donor chimerism in non-malignant haematological diseases after allogeneic bone marrow transplantation.

PubMed

Shamshad, Ghassan Umair; Ahmed, Suhaib; Bhatti, Farhat Abbas; Ali, Nadir

2012-12-01

To determine the frequency of mixed donor chimerism in patients of non-malignant haematological diseases after allogeneic bone marrow transplant. A cross-sectional, observational study. Department of Haematology, Armed Forces Institute of Pathology (AFIP), Rawalpindi, from July 2010 to June 2011. Donor chimerism was assessed in patients of aplastic anaemia and beta-thalassaemia major who underwent allogeneic bone marrow transplantation (BMT). Peripheral blood samples were used to assess chimerism status by analysis of short tandem repeats (STR). In patients where pre-transplant blood sample was not available, swab of buccal mucosa was used for pre-transplant STR profile. A standard set of primers for STR markers were used and the amplified DNA was resolved by gel electrophoresis and stained with silver nitrate. The percentage of donor origin DNA was estimated by densitometer. Out of 84 patients, 52 (62%) were males, while 32 (38%) were females. In patients of beta-thalassaemia major, 31 (62%) developed mixed donor chimerism (MC), 13 (26%) developed complete donor chimerism (CC) and 6 (12%) had graft failure. In aplastic anaemia, 17 patients (50%) achieved MC, 13 (38.2%) had CC and 4 (11.8%) developed graft failure. The combined frequency of mixed donor chimerism for both the diseases was 58.3%. D3S1358 was the most informative STR marker in these patients. Majority of the studied patients developed mixed donor chimerism following bone marrow transplantation, whereas only a minor percentage of the patients had graft failure. Analysis of D3S1358 was the most informative in assessing donor chimerism in patients who underwent BMT.

Cortical stimulation evokes abnormal responses in the dopamine-depleted rat basal ganglia.

PubMed

Kita, Hitoshi; Kita, Takako

2011-07-13

The motor cortex (MC) sends massive projections to the basal ganglia. Motor disabilities in patients and animal models of Parkinson's disease (PD) may be caused by dopamine (DA)-depleted basal ganglia that abnormally process the information originating from MC. To study how DA depletion alters signal transfer in the basal ganglia, MC stimulation-induced (MC-induced) unitary responses were recorded from the basal ganglia of control and 6-hydroxydopamine-treated hemi-parkinsonian rats anesthetized with isoflurane. This report describes new findings about how DA depletion alters MC-induced responses. MC stimulation evokes an excitation in normally quiescent striatal (Str) neurons projecting to the globus pallidus external segment (GPe). After DA-depletion, the spontaneous firing of Str-GPe neurons increases, and MC stimulation evokes a shorter latency excitation followed by a long-lasting inhibition that was invisible under normal conditions. The increased firing activity and the newly exposed long inhibition generate tonic inhibition and a disfacilitation in GPe. The disfacilitation in GPe is then amplified in basal ganglia circuitry and generates a powerful long inhibition in the basal ganglia output nucleus, the globus pallidus internal segment. Intra-Str injections of a behaviorally effective dose of DA precursor l-3,4-dihydroxyphenylalanine effectively reversed these changes. These newly observed mechanisms also support the generation of pauses and burst activity commonly observed in the basal ganglia of parkinsonian subjects. These results suggest that the generation of abnormal response sequences in the basal ganglia contributes to the development of motor disabilities in PD and that intra-Str DA supplements effectively suppress abnormal signal transfer.

Surgeon and hospital cost variability for septoplasty and inferior turbinate reduction.

PubMed

Thomas, Andrew; Alt, Jeremiah; Gale, Craig; Vijayakumar, Sathya; Padia, Reema; Peters, Matthew; Champagne, Trevor; Meier, Jeremy D

2016-10-01

Septoplasty and turbinate reduction (STR) is a common procedure for which cost reduction efforts may improve value. The purpose of this study was to identify sources of variation in medical facility and surgeon costs associated with STR, and whether these costs correlated with short-term complications. An observational cohort study was performed in a multifacility network using a standardized cost-accounting system to determine costs associated with adult STR from January 1, 2008 to July 31, 2015. A total of 4007 cases, performed at 21 facilities, by 72 different surgeons were included in the study. Total costs, variable costs, operating room (OR) time, and 30-day complications (eg, epistaxis) were compared among surgeons, facilities, and specialties. Total procedure cost: (mean ± standard deviation [SD]) $2503 ± $790 (range, $852 to $10,559). Mean total variable cost: $1147 ± $423 (range, $400 to $5,081). Intersurgeon and interfacility variability was significant for total cost (p < 0.0001) and OR time (p < 0.0001). Intersurgeon OR supply cost variability was also significant (p < 0.0001). Otolaryngologists had less total cost (p < 0.0001), OR time/cost (p < 0.0001), and complications (p = 0.0164), but greater supply cost (p < 0.0001), than other specialties. There is wide variation in cost associated with STR. Significant variance in OR time and supply cost between surgeons suggests these are potential areas for cost reduction. Although no increased 30-day complications were seen with faster and less costly surgeries, further research is needed to evaluate how time and cost relate to quality of care. © 2016 ARS-AAOA, LLC.

Patterns of genetic diversity at the nine forensically approved STR loci in the Indian populations.

PubMed

Dutta, Ranjan; Reddy, B Mohan; Chattopadhyay, P; Kashyap, V K; Sun, Guangyun; Deka, Ranjan

2002-02-01

Genetic diversity at the nine short tandem repeat (STR) loci, which are universally approved and widely used for forensic investigations, has been studied among nine Indian populations with diverse ethnic, linguistic, and geographic backgrounds. The nine STR loci were profiled on 902 individuals using fluorescent detection methods on an ABI377 System, with the aid of an Amp-F1 Profiler Plus Kit. The studied populations include two upper castes, Brahmin and Kayastha; a tribe, Garo, from West Bengal; a Hindu caste, Meitei, with historical links to Bengal Brahmins; a migrant group of Muslims; three tribal groups, Naga, Kuki and Hmar, from Manipur in northeast India; and a middle-ranking caste, Golla, who are seminomadic herders from Andhra Pradesh. Gene diversity analysis suggests that the average heterozygosity is uniformly high (>0.8) in the studied populations, with the coefficient of gene differentiation at 0.050 +/- 0.0054. Both neighbor-joining (NJ) and unweighted pair group method with arithmetic mean (UPGMA) trees based on DA distances bring out distinct clusters that are consistent with ethnic, linguistic, and/or geographic backgrounds of the populations. The fit of the Harpending and Ward model of regression of average heterozygosity on the gene frequency centroid is found to be good, and the observed outliers are consistent with the population structure and history of the studied populations. Our study suggests that the nine STR loci, used so far mostly for forensic investigations, can be used fruitfully for microevolutionary studies as well, and for reconstructing the phylogenetic history of human populations, at least at the local level.

As solid as a rock-comparison of CE- and MPS-based analyses of the petrosal bone as a source of DNA for forensic identification of challenging cranial bones.

PubMed

Kulstein, Galina; Hadrys, Thorsten; Wiegand, Peter

2018-01-01

Short tandem repeat (STR) typing from skeletal remains can be a difficult task. Dependent on the environmental conditions of the provenance of the bones, DNA can be degraded and STR typing inhibited. Generally, dense and compact bones are known to preserve DNA better. Several studies already proved that femora and teeth have high DNA typing success rates. Unfortunately, these elements are not present in all cases involving skeletal remains. Processing partial or singular skeletal elements, it is favorable to select bone areas where DNA preservation is comparably higher. Especially, cranial bones are often accidentally discovered during criminal investigations. The cranial bone is composed of multiple parts. In this examination, we evaluated the potential of the petrous bone for human identification of skeletal remains in forensic case work. Material from different sections of eight unknown cranial bones and-where available-additionally other skeletal elements, collected at the DNA department of the Institute of Legal Medicine in Ulm, Germany, from 2010 to 2017, were processed with an optimized DNA extraction and STR typing strategy. The results highlight that STR typing from the petrous bones leads to reportable profiles in all individuals, even in cases where the analysis of the parietal bone failed. Moreover, the comparison of capillary electrophorese (CE) typing to massively parallel sequencing (MPS) analysis shows that MPS has the potential to analyze degraded human remains and is even capable to provide additional information about phenotype and ancestry of unknown individuals.

Increasing Freshwater Runoff and Tidal Action Influences on Spatial Mixing Patterns in Søndre Strømfjord, West Greenland

NASA Astrophysics Data System (ADS)

Smiley, C. R.; Kamenos, N.; Hoey, T.; Cottier, F.; Ellam, R. M.

2014-12-01

Greenland Ice Sheet melt has the potential to affect global sea levels and the strength of the thermohaline circulation (THC). Investigating spatial mixing patterns of seawater in Greenlandic fjords can help reveal characteristics of changes in runoff from the GrIS; for example higher runoff may be associated with lower salinity within GrIS fjords, which can be recorded by palaeoenvironmental proxies (Kamenos et al 2012). The Kangerlussuaq Drainage Basin mirrors melt patterns of the whole GrIS and drains into Søndre Strømfjord, a 170km long fjord on the west coast of Greenland. Temperature and salinity profiles to 40m depth were obtained at 11 stations along Søndre Strømfjord during the 2014 melt season. Each station was sampled twice once at high KDB runoff and once at low KDB runoff. With increasing freshwater runoff, salinity decreases by 1.65 - 2.91 at each station over a 7 hour time period. Higher salinities occur at low run-off. In addition, with increasing run-off, the disparity between surface and deeper water (30m) becomes greater with a 19.3 difference between the surface and 30m. With higher KDB runoff temperature increases by 0.47oC - 2.34oC. This information will be integrated with oxygen and deuterium isotope patterns to pinpoint the exact source of the runoff causing salinity reductions. Our data show a relationship between KDB runoff and salinity of Søndre Strømfjord, data that will enable further calibration of marine proxies of GrIS melt.

A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers.

PubMed

Santos, Sara; Oliveira, Manuela; Amorim, António; van Asch, Barbara

2014-11-01

The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparative performance evaluation of conventional and two-phase hydrophobic stirred tank reactors for methane abatement: Mass transfer and biological considerations.

PubMed

Cantera, Sara; Estrada, José M; Lebrero, Raquel; García-Encina, Pedro A; Muñoz, Raúl

2016-06-01

This study demonstrated for the first time the capability of methanotrophs to grow inside silicone oil (SO200) and identified the optimum cultivation conditions for enrichment of hydrophobic methanotrophs (high dilution rates (D) and low CH4 transfer rates). The potential of the hydrophobic methanotrophs enriched was assessed in a single-phase stirred tank reactor (1P-STR) and in a two-phase stirred tank reactor (2P-STR). Different operational conditions were systematically evaluated in both reactors (SO200 fractions of 30 and 60 %, stirring rates of 250 and 500 rpm, and D of 0.1-0.35 day(-1) with and without biomass retention). The results showed that the TPPB only supported a superior CH4 abatement performance compared to the 1P-STR (40% enhancement at 250 rpm and 25% enhancement at 500 rpm) at a D of 0.3 day(-1) due to the retention of the biocatalytic activity inside the SO200, while the 1P-STR achieved higher elimination capacities (EC up to ≈3 times) than the TPPB under the rest of conditions tested (ECmax  = 91.1 g m(-3)  h(-1) ). Furthermore, the microscopic examination and DGGE-sequencing of the communities showed that the presence of SO200 influenced the microbial population structure, impacting on bacterial biodiversity and favoring the growth of methanotrophs such as Methylosarcina. Biotechnol. Bioeng. 2016;113: 1203-1212. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

On the Evolution of O(He)-Type Stars

NASA Technical Reports Server (NTRS)

Kruk, Jeffrey W.; Reindl, N.; Rauch, T.; Werner, K.

2012-01-01

O(He) stars represent a small group of four very hot post-AGB stars whose atmospheres are composed of almost pure helium. Their evolution deviates from the hydrogen-deficient post-AGO evolutionary sequence of carbon-dominated stars like e.g. PG 1159 or Wolf- Rayet stars. While (very) late thermal pulse evolutionary models can explain the observed He/C/O abundances in these objects, they do not reproduce He-dominated surface abundances. Currently it seems most likely that the O(He) stars originate from a double helium white dwarf merger and so they could be the successors of the luminous helium-rich sdO-stars. An other possibility is that O(He)-stars could be successors of RCB or EHe stars.

Detection of Heteromers Formed by Cannabinoid CB1, Dopamine D2, and Adenosine A2A G-Protein-Coupled Receptors by Combining Bimolecular Fluorescence Complementation and Bioluminescence Energy Transfer

PubMed Central

Navarro, Gemma; Carriba, Paulina; Gandí, Jorge; Ciruela, Francisco; Casadó, Vicent; Cortés, Antoni; Mallol, Josefa; Canela, Enric I.; Lluis, Carmen; Franco, Rafael

2008-01-01

Functional interactions in signaling occur between dopamine D2 (D2R) and cannabinoid CB1 (CB1R) receptors, between CB1R and adenosine A2A (A2AR) receptors, and between D2R and A2AR. Furthermore, direct molecular interactions have been reported for the pairs CB1R-D2R, A2AR-D2R, and CB1R-A2AR. Here a combination of bimolecular fluorescence complementation and bioluminescence energy transfer techniques was used to identify the occurrence of D2R-CB1R-A2AR hetero-oligomers in living cells. PMID:18956124

Molecular and karyological data confirm that the enigmatic genus Platypholis from Bonin-Islands (SE Japan) is phylogenetically nested within Orobanche (Orobanchaceae).

PubMed

Li, Xi; Jang, Tae-Soo; Temsch, Eva M; Kato, Hidetoshi; Takayama, Koji; Schneeweiss, Gerald M

2017-03-01

Molecular phylogenetic studies have greatly improved our understanding of phylogenetic relationships of non-photosynthetic parasitic broomrapes (Orobanche and related genera, Orobanchaceae), but a few genera have remained unstudied. One of those is Platypholis, whose sole species, Platypholis boninsimae, is restricted to the Bonin-Islands (Ogasawara Islands) about 1000 km southeast of Japan. Based on overall morphological similarity, Platypholis has been merged with Orobanche, but this hypothesis has never been tested with molecular data. Employing maximum likelihood and Bayesian analyses on a family-wide data set (two plastid markers, matK and rps2, and three nuclear markers, ITS, phyA and phyB) as well as on an ITS data set focusing on Orobanche s. str., it is shown that P. boninsimae Maxim. is phylogenetically closely linked to or even nested within Orobanche s. str. This position is supported both by morphological evidence and by the newly obtained chromosome number of 2n = 38, which is characteristic for the genus Orobanche s. str.

A comparison of mass transfer coefficients between trickle-bed, hollow fiber membrane and stirred tank reactors.

PubMed

Orgill, James J; Atiyeh, Hasan K; Devarapalli, Mamatha; Phillips, John R; Lewis, Randy S; Huhnke, Raymond L

2013-04-01

Trickle-bed reactor (TBR), hollow fiber membrane reactor (HFR) and stirred tank reactor (STR) can be used in fermentation of sparingly soluble gasses such as CO and H2 to produce biofuels and bio-based chemicals. Gas fermenting reactors must provide high mass transfer capabilities that match the kinetic requirements of the microorganisms used. The present study compared the volumetric mass transfer coefficient (K(tot)A/V(L)) of three reactor types; the TBR with 3 mm and 6 mm beads, five different modules of HFRs, and the STR. The analysis was performed using O2 as the gaseous mass transfer agent. The non-porous polydimethylsiloxane (PDMS) HFR provided the highest K(tot)A/V(L) (1062 h(-1)), followed by the TBR with 6mm beads (421 h(-1)), and then the STR (114 h(-1)). The mass transfer characteristics in each reactor were affected by agitation speed, and gas and liquid flow rates. Furthermore, issues regarding the comparison of mass transfer coefficients are discussed. Copyright © 2013 Elsevier Ltd. All rights reserved.

Allele frequency distribution for 15 autosomal STR loci in two Muslim populations of Tamilnadu, India.

PubMed

Eaaswarkhanth, M; Roy, Soma; Haque, Ikramul

2007-11-01

Allele frequencies of the 15 autosomal STR loci: D8S1179, D21S11, D7S820, CSF1PO, D19S433, vWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818, and FGA were determined in two endogamous Muslim populations (Dawoodi Bohra Muslims from Shiite Muslims and Sunni Muslims) residing in Tamilnadu, India. The Loci D7S820, CSF1PO, D19S433, vWA, TPOX, D13S317, D16S539, D5S818, and FGA in Dawoodi Bohra Muslims from Shiite Muslims, and CSF1PO, D19S433, TPOX, and D16S539 in Sunni Muslims were found to deviate significantly from Hardy-Weinberg equilibrium. The power of discrimination of the analyzed markers was found to be high for the populations, thereby facilitating the validation and efficiency of these STR markers in human identification.

The association of 22 Y chromosome short tandem repeat loci with initiative-aggressive behavior.

PubMed

Yang, Chun; Ba, Huajie; Zhang, Wei; Zhang, Shuyou; Zhao, Hanqing; Yu, Haiying; Gao, Zhiqin; Wang, Binbin

2018-05-15

Aggressive behavior represents an important public concern and a clinical challenge to behaviorists and psychiatrists. Aggression in humans is known to have an important genetic basis, so to investigate the association of Y chromosome short tandem repeat (Y-STR) loci with initiative-aggressive behavior, we compared allelic and haplotypic distributions of 22 Y-STRs in a group of Chinese males convicted of premeditated extremely violent crimes (n = 271) with a normal control group (n = 492). Allelic distributions of DYS533 and DYS437 loci differed significantly between the two groups (P < 0.05). The case group had higher frequencies of DYS533 allele 14, DYS437 allele 14, and haplotypes 11-14 of DYS533-DYS437 compared with the control group. Additionally, the DYS437 allele 15 frequency was significantly lower in cases than controls. No frequency differences were observed in the other 20 Y-STR loci between these two groups. Our results indicate a genetic role for Y-STR loci in the development of initiative aggression in non-psychiatric subjects. Copyright © 2018 Elsevier B.V. All rights reserved.

Synthesis of [1-.sup.13C]pyruvic acid], [2-.sup.13C]pyruvic acid], [3-.sup.13C]pyruvic acid] and combinations thereof

DOEpatents

Martinez, Rodolfo A. , Unkefer; Clifford J. , Alvarez; Marc, A [Santa Fe, NM

2012-06-12

The present invention is directed to the labeled compounds, ##STR00001## wherein C* is each either .sup.13C and .sup.12C where at least one C* is .sup.13C, each hydrogen of the methylene group is hydrogen or deuterium, the methyl group includes either zero or three deuterium atoms, Q is sulfide, sulfinyl, or sulfone, Z is an aryl group such as 1-naphthyl, substituted 1-naphthyl, 2-naphthyl, substituted 2-naphthyl, or a phenyl group ##STR00002## wherein R.sub.1, R.sub.2, R.sub.3, R.sub.4 and R.sub.5 are each independently either hydrogen, a C.sub.1-C.sub.4 lower alkyl, a halogen, and an amino group such as NH.sub.2, NHR and NRR' where R and R' are each independently either a C.sub.1-C.sub.4 lower alkyl, a phenyl, and an alkoxy group, and the methyl group can include either zero or three deuterium atoms. The present invention is also directed to the labeled compounds ##STR00003##

Evaluation of commercial kits for dual extraction of DNA and RNA from human body fluids.

PubMed

Schweighardt, Andrew J; Tate, Courtney M; Scott, Kristina A; Harper, Kathryn A; Robertson, James M

2015-01-01

STR typing of DNA evidence can identify the donor with a high power of discrimination but cannot identify the tissue origin of a body-fluid stain. Using RNA to attribute a crime scene stain to a particular tissue may aid in reconstruction efforts. With blood from 10 donors, four DNA and RNA coextraction kits were evaluated by measuring yields and STR and mRNA profiles. T tests indicated some significant differences in kit performance. The Zymo Research ZR-Duet(™) kit performed best based on average DNA (41.4 ng) and mRNA (4.07 ng) yields and was the only kit to provide complete DNA/RNA profiles for all samples. The consistency of this kit was challenged by data from additional blood and saliva donors. Further testing is advised before a superior kit is unequivocally chosen. Stand-alone DNA or RNA purification generally offers higher yield, but coextraction may still allow successful STR profiling and tissue source identification. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

An Optimized DNA Analysis Workflow for the Sampling, Extraction, and Concentration of DNA obtained from Archived Latent Fingerprints.

PubMed

Solomon, April D; Hytinen, Madison E; McClain, Aryn M; Miller, Marilyn T; Dawson Cruz, Tracey

2018-01-01

DNA profiles have been obtained from fingerprints, but there is limited knowledge regarding DNA analysis from archived latent fingerprints-touch DNA "sandwiched" between adhesive and paper. Thus, this study sought to comparatively analyze a variety of collection and analytical methods in an effort to seek an optimized workflow for this specific sample type. Untreated and treated archived latent fingerprints were utilized to compare different biological sampling techniques, swab diluents, DNA extraction systems, DNA concentration practices, and post-amplification purification methods. Archived latent fingerprints disassembled and sampled via direct cutting, followed by DNA extracted using the QIAamp® DNA Investigator Kit, and concentration with Centri-Sep™ columns increased the odds of obtaining an STR profile. Using the recommended DNA workflow, 9 of the 10 samples provided STR profiles, which included 7-100% of the expected STR alleles and two full profiles. Thus, with carefully selected procedures, archived latent fingerprints can be a viable DNA source for criminal investigations including cold/postconviction cases. © 2017 American Academy of Forensic Sciences.

The ancient Yakuts: a population genetic enigma

PubMed Central

Keyser, Christine; Hollard, Clémence; Gonzalez, Angela; Fausser, Jean-Luc; Rivals, Eric; Alexeev, Anatoly Nikolayevich; Riberon, Alexandre; Crubézy, Eric; Ludes, Bertrand

2015-01-01

This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages. PMID:25487336

Typeability of PowerPlex Y (Promega) profiles in selected tissue samples incubated in various environments.

PubMed

Niemcunowicz-Janica, Anna; Pepiński, Witold; Janica, Jacek Robert; Janica, Jerzy; Skawrońska, Małgorzata; Koc-Zórawska, Ewa

2007-01-01

In cases of decomposed bodies, Y chromosomal STR markers may be useful in identification of a male relative. The authors assessed typeability of PowerPlex Y (Promega) loci in post mortem tissue material stored in various environments. Kidney, spleen and pancreas specimens were collected during autopsies of five persons aged 20-30 years, whose time of death was determined within the limit of 14 hours. Tissue material was incubated at 21 degrees C and 4 degrees C in various environmental conditions. DNA was extracted by the organic method from tissue samples collected in 7-day intervals and subsequently typed using the PowerPlexY-STR kit and ABI 310. A fast decrease in the typeability rate was seen in specimens incubated in peat soil and in sand. Kidney tissue samples were typeable in all PowerPlexY-STR loci within 63 days of incubation at 4 degrees C. Faster DNA degradation was recorded in spleen and pancreas specimens. In samples with negative genotyping results, no DNA was found by fluorometric quantitation. Decomposed soft tissues are a potential material for DNA typing.

Identification of bodies from the scene of a mass disaster using DNA amplification of short tandem repeat (STR) loci.

PubMed

Clayton, T M; Whitaker, J P; Maguire, C N

1995-11-30

The accompanying paper in this issue describes work conducted during a collaborative effort to identify the victims of a mass disaster that occurred on the 19th of April 1993 near Waco, Texas. The DNA identification programme was also used partly as an exercise to further investigate the robustness and reliability of a recently developed STR quadruplex. The preceding paper provides details of the loci used and also deals with efforts to assess the applicability of STR profiling and its suitability for forensic investigations of this nature. In this paper, we present the results obtained from 61 Waco bodies. Using reference blood samples and family trees 26 positive identifications were made using a 'paternity style' analytical approach. Worked examples, representing a range of casework situations, are used to illustrate the kind of approach taken in interpretation of the data and highlight factors which affected its success. Additionally, we report on the successful application of a PCR-based gender test to 24 of the Waco bodies.

Massively Parallel Sequencing of Forensic STRs Using the Ion Chef™ and the Ion S5™ XL Systems.

PubMed

Wang, Le; Chen, Man; Wu, Bo; Liu, Yi-Cheng; Zhang, Guang-Feng; Jiang, Li; Xu, Xiu-Lan; Zhao, Xing-Chun; Ji, An-Quan; Ye, Jian

2018-03-01

Next-generation sequencing (NGS) has been used to genotype forensic short tandem repeat (STR) markers for individual identification and kinship analysis. STR data from several NGS platforms have been published, but forensic application trials using the Ion S5™ XL system have not been reported. In this work, we report sensitivity, reproducibility, mixture, simulated degradation, and casework sample data on the Ion Chef™ and S5™ XL systems using an early access 25-plex panel. Sensitivity experiments showed that over 97% of the alleles were detectable with down to 62 pg input of genomic DNA. In mixture studies, alleles from minor contributors were correctly assigned at 1:9 and 9:1 ratios. NGS successfully gave 12 full genotype results from 13 challenging casework samples, compared with five full results using the CE platform. In conclusion, the Ion Chef™ and the Ion S5™ XL systems provided an alternative and promising approach for forensic STR genotyping. © 2018 American Academy of Forensic Sciences.

Short tandem repeat DNA typing provides an international reference standard for authentication of human cell lines.

PubMed

Dirks, Wilhelm Gerhard; Faehnrich, Silke; Estella, Isabelle Annick Janine; Drexler, Hans Guenter

2005-01-01

Cell lines have wide applications as model systems in the medical and pharmaceutical industry. Much drug and chemical testing is now first carried out exhaustively on in vitro systems, reducing the need for complicated and invasive animal experiments. The basis for any research, development or production program involving cell lines is the choice of an authentic cell line. Microsatellites in the human genome that harbour short tandem repeat (STR) DNA markers allow individualisation of established cell lines at the DNA level. Fluorescence polymerase chain reaction amplification of eight highly polymorphic microsatellite STR loci plus gender determination was found to be the best tool to screen the uniqueness of DNA profiles in a fingerprint database. Our results demonstrate that cross-contamination and misidentification remain chronic problems in the use of human continuous cell lines. The combination of rapidly generated DNA types based on single-locus STR and their authentication or individualisation by screening the fingerprint database constitutes a highly reliable and robust method for the identification and verification of cell lines.