Musical Practices and Methods in Music Lessons: A Comparative Study of Estonian and Finnish General Music Education

ERIC Educational Resources Information Center

Sepp, Anu; Ruokonen, Inkeri; Ruismäki, Heikki

2015-01-01

This article reveals the results of a comparative study of Estonian and Finnish general music education. The aim was to find out what music teaching practices and approaches/methods were mostly used, what music education perspectives supported those practices. The data were collected using questionnaires and the results of 107 Estonian and 50…

Tracing Assessment Policy Discourses in Neoliberalised Higher Education Settings

ERIC Educational Resources Information Center

Raaper, Rille

2017-01-01

This article explores assessment policy in two European universities with different political, historical and social backgrounds: the University of Glasgow and Tallinn University. The University of Glasgow is a well-established Russell Group university in the UK; Tallinn University is a relatively new university in post-Soviet Estonia, shaped by…

[The Tallinn Charter: health systems for health and wealth].

PubMed

Piotrowicz, Maria; Cianciara, Dorota; Wysocki, Mirosław J

2009-01-01

The article presents main issues of Tallinn Charter (2008) that concerns functioning health systems, theirs influence on health and wealth of society. Health systems are diverse, but share common set of functions. Theirs effective performance contribute, not only to improving health, but also to participation in labour market and socioeconomical development of country.

DefenseLink.mil - Special Report - Travels With Gates

Science.gov Websites

of Estonia Estonia Defense Secretary Robert M. Gates holds a press conference after the Tallinn High . Sgt. Jerry Morrison Defense Secretary Robert M. Gates holds a press conference after the Tallinn High . Sgt. Jerry Morrison Defense Secretary Robert M. Gates walks with the Prime Minister of Estonia Andrus

A rapid situation assessment of the market for surrogate and illegal alcohols in Tallinn, Estonia.

PubMed

Pärna, Kersti; Lang, Katrin; Raju, Kadi; Väli, Marika; McKee, Martin

2007-01-01

To understand the phenomenon of consumption of surrogate and illegal alcohols in Tallinn, capital of Estonia. This study, conducted in Tallinn in May 2006, used rapid situation assessment. Interviews with key informants in relevant settings such as emergency departments of hospitals, accommodation for the homeless, police etc. (n = 22), with alcohol abusers (n = 33), natural observations of surrogate sale and consumption venues (n = 46), and tracking of trade data were carried out. Key informants confirmed that consumption of illegal and surrogate alcohols are widely used by alcohol abusers, a finding confirmed by the alcohol abusers. Availability of surrogates varied by area of the city, mainly sold from street kiosks. Illegally produced spirits were also easily available. Sales of surrogates appear to have increased in recent years. A range of alcohol-containing substances that appear to be easily available at low cost, and that have high concentration of ethanol or contaminants known to be toxic, were identified in Tallinn. Alcohol policies in Estonia should address the consumption and availability of these substances.

Personal control of privacy and data: Estonian experience.

PubMed

Priisalu, Jaan; Ottis, Rain

2017-01-01

The Republic of Estonia leads Europe in the provision of public digital services. The national communications and transactions platform allows for twenty-first century governance by allowing for transparency, e-safety (inter alia privacy), e-security, entrepreneurship and, among other things, rising levels of prosperity, and well-being for all its Citizens. However, a series of Information Infrastructure attacks against the Estonian e-society infrastructure in 2007 became one of best known incidents and experiences that fundamentally changed both Estonian and international discussions about Cyber Security and Privacy. Estonian experience shows that an open and transparent attitude provides a good foundation for trust between the Citizen and the State, and gives more control to the real owner of the data - the Citizen. Another important lesson is that the Citizen needs to be confident in the government's ability to keep their data safe -- in terms of confidentiality, integrity and availability - establishing a strong link between privacy and information security. This paper discusses certain critical choices, context, and events connected to the birth and growth of the Estonian e-society in terms of Privacy.

Hospitalised neonates in Estonia commonly receive potentially harmful excipients

PubMed Central

2012-01-01

Background Information on the neonatal exposure to excipients is limited. Our aim was to describe the extent of excipient intake by Estonian neonates; to classify the excipients according to potential neonatal toxicity and thereby to measure the extent of exposure of neonates to potentially harmful excipients. Methods A prospective cohort study that recorded all medicines prescribed to patients aged below 28 days admitted to Tartu University Hospital from 01.02-01.08 2008 and to Tallinn Children’s Hospital from 01.02- 01.08 2009 was conducted. Excipients were identified from Summaries of Product Characteristics and classified according to toxicity following a literature review. Results 1961 prescriptions comprising 107 medicines were written for 348/490 neonates admitted. A total of 123 excipients were found in 1620 (83%) prescriptions and 93 (87%) medicines. 47 (38%) of these excipients were classified as potentially or known to be harmful to neonates. Most neonates (97%) received at least one medicine (median number 2) with potentially or known to be harmful excipient. Parabens were the most commonly used known to be harmful excipients and sodium metabisulphite the most commonly used potentially harmful excipient, received by 343 (99%) and 297 (85%) of treated neonates, respectively. Conclusions Hospitalised neonates in Estonia are commonly receiving a wide range of excipients with their medication. Quantitative information about excipients should be made available to pharmacists and neonatologists helping them to take into account excipient issues when selecting medicines and to monitor for adverse effects if administration of medicines containing excipients is unavoidable. PMID:22931304

Feasibility of cohort studies in Estonia

PubMed Central

Innos, K.; Rahu, M.; Rahu, K.

1999-01-01

OBJECTIVES: To describe the methodology and feasibility of follow up for vital status in retrospective cohort studies in Estonia. METHODS: A cohort of 7412 workers who had been employed at two factories in Tallinn between 1946 and 1988 was followed up for vital status from the date of first employment until death, emigration, or the end of the study, 31 December 1995, whichever occurred first. The cohort was electronically linked with the National Population Registry of Estonia that was created in 1992 and includes personal identification numbers of Estonian citizens and residents, and the Mortality Database that contains information from death certificates issued in 1983-95. A manual search was carried out on several non-computerised population data sources and archives. RESULTS: By 31 December 1995, the vital status of 6780 (91.5%) subjects could be traced (4495 (60.6%) subjects were alive, 1993 (26.9%) had died, and 292 (3.9%) had emigrated). Analysis by calendar period of leaving work showed that the proportion of subjects traced was lowest in the group of workers who had left work between 1946 and 1955 (58.4%), especially those whose age at leaving work was < 30 (53.2%) or > 60 years (42.3%). Among subjects who left work in 1956-65, 1966-75, and 1976-88, the follow up rate was 84.7%, 94.6%, and 98.2%, respectively. CONCLUSIONS: The findings, which are especially important for occupational epidemiology, confirm the feasibility of conducting retrospective cohort studies in Estonia. Most of the issues discussed in the paper apply to other former Soviet countries.   PMID:10472323

76 FR 68243 - Social Security Rulings, SSR 91-1c and SSR 66-18c; Rescission of Social Security Rulings (SSR) 66...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-03

..., Social Security Online, at http://www.socialsecurity.gov . SUPPLEMENTARY INFORMATION: SSRs make available... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2011-0068] Social Security Rulings, SSR 91-1c and SSR 66-18c; Rescission of Social Security Rulings (SSR) 66-18c and SSR 91-1c AGENCY: Social Security...

Use of Web 2.0 Technologies in LIS Education: Experiences at Tallinn University, Estonia

ERIC Educational Resources Information Center

Virkus, Sirje

2008-01-01

Purpose: The purpose of this paper is to describe the experiences of the Institute of Information Studies of Tallinn University in introducing ICT, including Web 2.0 technologies, in library and information science education, and to explore the role that these can play in new models of learning and teaching. Design/methodology/approach: Web 2.0…

SSR allelic variation in almond (Prunus dulcis Mill.).

PubMed

Xie, Hua; Sui, Yi; Chang, Feng-Qi; Xu, Yong; Ma, Rong-Cai

2006-01-01

Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.

Somatotype in 6-11-year-old Italian and Estonian schoolchildren.

PubMed

Ventrella, A R; Semproli, S; Jürimäe, J; Toselli, S; Claessens, A L; Jürimäe, T; Brasili, P

2008-01-01

The study of somatotypes can contribute to the understanding of variability in human body build. The aim of this study was to compare the somatotypes of Italian and Estonian schoolchildren in order to evaluate factors that might lead to variability in somatotypes. The sample consisted of 762 Italian and 366 Estonian children aged 6-11 years. They were somatotyped by the Heath-Carter anthropometric method. Data on organised extra-curricular physical activity and hours of weekly training were also collected. One-way ANOVA was used to evaluate country-related variations of somatotype in each age/sex group, while factorial ANOVA was used to test the influence of country and organised physical activity on the variability of the anthropometric characteristics and somatotype components. There are significant differences in mean somatotypes between the Italian and Estonian children in many age classes and a different constitutional trend in children from the two different countries is observed. The Italian children are more endomorphic and less mesomorphic and ectomorphic than the Estonian children. On the other hand, it emerges from factorial ANOVA, that the somatotype components do not present significant variations related to organised physical activity and to the interaction between the country of origin and sport practice. Moreover, the results of the forward stepwise discriminant analyses show that mesomorphy is the best discriminator between the two countries, followed by ectomorphy. Our findings suggest that the observed differences between Italian and Estonian children could be related mainly to country rather than to the practice of organised physical activity in the two countries.

Personality traits measured by the Swedish universities Scales of Personality: factor structure and position within the five-factor model in an Estonian sample.

PubMed

Aluoja, Anu; Voogne, Helina; Maron, Eduard; Gustavsson, J Petter; Võhma, Ulle; Shlik, Jakov

2009-01-01

The study aims to test the reliability and validity of the Estonian version of the Swedish universities Scales of Personality (SSP), and to characterize the position of the SSP-measured traits within the basic personality dimensions of the five-factor model. A total of 529 participants completed the Estonian version of the SSP. A subsample of 197 persons completed the SSP together with the Revised NEO Personality Inventory (NEO-PI-R). The internal consistency of the SSP scales was satisfactory. Principal component analysis yielded three factors representing neuroticism, aggression and disinhibition. The factor solution obtained in the Estonian sample was similar to the original SSP study in the Swedish normative sample. NEO-PI-R Neuroticism had highest correlations with SSP neuroticism factor scales. Extraversion had strongest relationship with adventure seeking and low detachment. Agreeableness correlated positively with SSP social desirability and negatively to aggression-irritability scales. Conscientiousness facet Deliberation correlated with Impulsiveness. The Estonian SSP showed acceptable reliability and validity, which confirms that SSP is applicable in different social and cultural background. The SSP measures traits that correspond to the major personality models. The SSP characterizes three broad dimensions of personality, namely neuroticism, disinhibition and aggression, which are useful in assessment of personality correlates of mental disorders.

Evaluation of cryopreserved stallion semen from Tori and Estonian breeds using CASA and flow cytometry.

PubMed

Kavak, A; Johannisson, A; Lundeheim, N; Rodriguez-Martinez, H; Aidnik, M; Einarsson, S

2003-04-15

Methods to evaluate the quality of frozen-thawed stallion semen are still needed, particularly those considering the sperm function. The present study evaluated sperm motility, membrane and acrosome integrity and the capacitation status of frozen-thawed spermatozoa from seven Tori and six Estonian breed stallions by way of computer assisted sperm analysis (CASA), a triple fluorophore stain combination and Merocyanine 540, respectively, the latter ones using flow cytometry. Two ejaculates from each stallion were cryopreserved using the Hannover method in 0.5 ml plastic straws. Two straws per ejaculate per stallion were thawed at 37 degrees C for 30s. Motility was analysed with CASA immediately after thawing, while for flow cytometry spermatozoa were cleansed by 70:40% Percoll discontinuous density gradient separation before analysed for sperm viability, acrosome integrity (stained with SNARF, PI and FITC-PSA) and capacitation status (stained with Merocyanine 540/Yo-Pro-1). Results (as least square means) were as follows: the motility of frozen-thawed semen was 43.4% for Tori stallions and 42.3% for Estonian stallions (P>0.05). After Percoll separation 79.3% of the spermatozoa from Tori stallions had intact acrosomes and 1.7% of them showed early signs of capacitation. The same parameters for Estonian stallions were 84.5 and 2.3%, respectively. There were no statistically significant differences between breeds or ejaculates within breed for any evaluated parameter. We conclude that triple staining and flow cytometry are valuable techniques to evaluate frozen-thawed stallion spermatozoa, and that no differences in quality of frozen semen were registered between Tori and Estonian breed stallions, allowing implementation of this technology in the Estonian horse population.

The contribution of the Estonian Soil Sciences Society to the science, society and education

NASA Astrophysics Data System (ADS)

Rossner, Helis; Reintam, Endla; Astover, Alar; Shanskiy, Merrit

2015-04-01

Predecessor of todays Estonian Soil Science Society was Estonian Branch of All-Union Soil Society of Soil Scientist which acted from 1957 to 1991. In 1957-1964 Estonian Branch was leaded by prof. Osvald Hallik and in 1964-1991 by prof. Loit Reintam. After re-independence of Estonia in 1991 the society acted in informal way and was leaded by prof. L. Reintam. Non-profit organization "Estonian Soil Science Society" was officially (re)established in 10.23.2009. Estonian Soil Science Society (ESSS) is aimed to: • coordinate collaboration between institutions and individuals intrested of soil science, conservation and sustainable use of soils; • promoting soil science education and research, raising awareness of publicity on topics relating to soils in Estonia; • cooperation between local and foreign unions and associations. In recent years the ESSS had managed to reunite the number of soil scientist from different research institutions of Estonia and of related institutions. Also, the ESSS had provided numerous of materials based on later scientific findings. One of most important activity leaded by ESSS is the organizing Soil Day in Estonia with relevant seminar, where the speakers are sharing latest information with target group (researchers, teachers, policy makers, farmers, students etc.). In a frames of Soil Day the Soil of the Year is selected for Estonia. In 2015, the soil of the year is Leptosol. For current, International Year of the Soil ESSS had planned numerous activities to introduce the importance of soils to wider audience. In current presentation we would like to share the soil science researchers experience through- out the decades of soil science research in Estonia, show our latest findings and designed activities for the International Year of SOIL.

PREFACE: Algebra, Geometry, and Mathematical Physics 2010

NASA Astrophysics Data System (ADS)

Stolin, A.; Abramov, V.; Fuchs, J.; Paal, E.; Shestopalov, Y.; Silvestrov, S.

2012-02-01

This proceedings volume presents results obtained by the participants of the 6th Baltic-Nordic workshop 'Algebra, Geometry, and Mathematical Physics (AGMP-6)' held at the Sven Lovén Centre for Marine Sciences in Tjärnö, Sweden on October 25-30, 2010. The Baltic-Nordic Network AGMP 'Algebra, Geometry, and Mathematical Physics' http://www.agmp.eu was created in 2005 on the initiative of two Estonian universities and two Swedish universities: Tallinn University of Technology represented by Eugen Paal (coordinator of the network), Tartu University represented by Viktor Abramov, Lund University represented by Sergei Silvestrov, and Chalmers University of Technology and the University of Gothenburg represented by Alexander Stolin. The goal was to promote international and interdisciplinary cooperation between scientists and research groups in the countries of the Baltic-Nordic region in mathematics and mathematical physics, with special emphasis on the important role played by algebra and geometry in modern physics, engineering and technologies. The main activities of the AGMP network consist of a series of regular annual international workshops, conferences and research schools. The AGMP network also constitutes an important educational forum for scientific exchange and dissimilation of research results for PhD students and Postdocs. The network has expanded since its creation, and nowadays its activities extend beyond countries in the Baltic-Nordic region to universities in other European countries and participants from elsewhere in the world. As one of the important research-dissimilation outcomes of its activities, the network has a tradition of producing high-quality research proceedings volumes after network events, publishing them with various international publishers. The PDF also contains the following: List of AGMP workshops and other AGMP activities Main topics discussed at AGMP-6 Review of AGMP-6 proceedings Acknowledgments List of Conference Participants

The role of gender, values, and culture in adolescent bystanders' strategies.

PubMed

Tamm, Anni; Tulviste, Tiia

2015-02-01

We examined the relationship between adolescent bystanders' strategies for intervening in the bullying-like situation and their gender, values, and cultural origin. The sample consisted of 682 Estonian and Russian-Estonian adolescents (M age = 13.02 years). They were shown a video of a bullying-like situation with a non-intervening adult bystander and asked to describe what they would do if they, instead of the adult, witnessed that situation. Only 10% said that they would not intervene. Girls were more likely than boys to suggest multiple actions. Adolescents who valued conformity were less likely to propose using physical aggression. Doing nothing was less likely suggested by those who placed more importance on conformity and less on power. Estonian adolescents were more likely than their Russian-Estonian peers to suggest finding out what is going on, and less likely to say that they would do nothing. The findings suggest that although most adolescents express willingness to help the victim, they might not actually know how to intervene. © The Author(s) 2014.

[A study of sympathetic skin response to the damage of autonomic nerves function in patients with chronic N-hexane poisoning].

PubMed

Situ, Jie; Wu, Jian; Wang, Jing-lin; Zhu, De-xiang; Zhang, Jian-jie; Liu, Wei-wei; Qin, Zhuo-hui

2012-05-01

To study the sympathetic skin response (SSR) to the effects of N-hexane on autonomic nerves function in patients with chronic N-hexane poisoning. The subjects in present study included 30 controls and 37 cases with chronic N-hexane poisoning. Also 37 patients were divided into 3 subgroups (mild, moderate and severe poisoning) according to diagnostic criteria of occupational diseases. All subjects were examined by SSR test and nerve conduction velocity (NCV) test. All patients were reexamined by SSR and NCV every 1 ∼ 2 months. The differences in SSR parameters (latency, amplitude) among groups were observed. In the severe poisoning subgroup, the changes of SSR and NCV parameters (conduction velocity, amplitude) in different poisoning stages were observed. There were significant differences in SSR latency of upper extremity among groups and the significant differences in SSR amplitude of upper and lower extremity among groups (P < 0.05). No significant differences in SSR parameters were found between the adjacent groups (P > 0.05). There were significant differences in SSR latency of upper extremity during different periods and the significant differences in SSR amplitude of upper and lower extremity during different periods among all groups (P < 0.05). The change of SSR parameters consistent with that in NCV. The longest SSR latency of upper extremity and the smallest SSR amplitudes of upper and lower extremity appears 1 - 2 months earlier than that of the smallest action potential amplitude. The damage of autonomic nerves induced by N-hexane increased with poisoning progresses. The damage of autonomic nerves corresponded with the damage of myelin sheath of large myelinated nerves, but which appeared 1 - 2 months earlier than the damage of axon of large myelinated nerves. SSR test may serve as a method to detect the damage of autonomic nerves function in patients with chronic N-hexane poisoning.

Health-related quality of life of Estonian adolescents: reliability and validity of the PedsQL™ 4.0 Generic Core Scales in Estonia.

PubMed

Viira, Roomet; Koka, Andre

2011-07-01

The main aim of this study was to examine the reliability and validity of the Pediatric Quality of Life Inventory™ 4.0 (PedsQL™ 4.0) Generic Core Scales among Estonian adolescents. Gender differences in health-related quality of life (HRQoL) were also investigated. The 654 adolescents (309 boys and 345 girls) aged 13-14 years (M age = 13.57 years, SD = 0.62) completed Estonian version of the PedsQL™ 4.0. Results of the confirmatory factor analysis for a five-factor model of the Estonian version of PedsQL™ 4.0 approached the criteria of acceptable fit after setting error covariance to be free between some of the items within physical health, emotional functioning and social functioning subscales. Cronbach's alpha coefficients exceeded the minimum criterion of 0.70 for all subscales except for days missed from school because of illness subscale. With regard to gender differences, consistent with previous studies, girls reported lower level on total score of HRQoL as well as its aspects of physical health, emotional functioning and psychosocial health. The present study revealed that after some modifications, the PedsQL™ 4.0 could be considered as suitable instrument to measure HRQoL among Estonian adolescents. © 2011 The Author(s)/Acta Paediatrica © 2011 Foundation Acta Paediatrica.

The Futures of Adult Educator(s): Agency, Identity and Ethos. Joint Conference Proceedings of the 2nd ESREA/ReNAdET Meeting and the 4th TQF Seminar (Tallinn, Estonia, November 9-11, 2011)

ERIC Educational Resources Information Center

Heikkinen, Anja, Ed.; Jogi, Larissa, Ed.; Jutte, Wolfgang, Ed.; Zarifis, Georgios K., Ed.

2012-01-01

This edited volume contains the papers presented in the 2nd ESREA|ReNAdet meeting that was jointly organised with the VET & CULTURE Network in the University of Tallinn (Estonia), 9-11 November 2011. The papers that appear in the volume discuss the future (or the futures) of adult educators in respect to issues of developing their identities…

Early Vocabulary and Gestures in Estonian Children

ERIC Educational Resources Information Center

Schults, Astra; Tulviste, Tiia; Konstabel, Kenn

2012-01-01

Parents of 592 children between the age of 0 ; 8 and 1 ; 4 completed the Estonian adaptation of the MacArthur-Bates Communicative Development Inventory (ECDI Infant Form). The relationships between comprehension and production of different categories of words and gestures were examined. According to the results of regression modelling the…

Value Education in Estonian Preschool Child Care Institutions

ERIC Educational Resources Information Center

Ülavere, Pärje; Tammik, Anu

2017-01-01

For systematic implementation of value education in educational institutions, the national programme "Values Development in Estonian Society 2009-2013" (Ministry of Education and Research 2009) was prepared in Estonia. However, it was launched only in 2010, and the authors intended to ascertain the values of the heads of preschool child…

Assessing Estonian Mothers' Involvement in Their Children's Education and Trust in Teachers

ERIC Educational Resources Information Center

Kikas, Eve; Peets, Katlin; Niilo, Airi

2011-01-01

Questionnaires assessing mothers' involvement in children's education and their trust in teachers were developed for the usage in Estonian kindergartens and elementary schools. The scales were adapted based on the questionnaires by Fantuzzo and colleagues (parental involvement) and Adams and Christenson (trust). Mothers of 454 kindergarten…

Genic and Intergenic SSR Database Generation, SNPs Determination and Pathway Annotations, in Date Palm (Phoenix dactylifera L.).

PubMed

Mokhtar, Morad M; Adawy, Sami S; El-Assal, Salah El-Din S; Hussein, Ebtissam H A

2016-01-01

The present investigation was carried out aiming to use the bioinformatics tools in order to identify and characterize, simple sequence repeats within the third Version of the date palm genome and develop a new SSR primers database. In addition single nucleotide polymorphisms (SNPs) that are located within the SSR flanking regions were recognized. Moreover, the pathways for the sequences assigned by SSR primers, the biological functions and gene interaction were determined. A total of 172,075 SSR motifs was identified on date palm genome sequence with a frequency of 450.97 SSRs per Mb. Out of these, 130,014 SSRs (75.6%) were located within the intergenic regions with a frequency of 499 SSRs per Mb. While, only 42,061 SSRs (24.4%) were located within the genic regions with a frequency of 347.5 SSRs per Mb. A total of 111,403 of SSR primer pairs were designed, that represents 291.9 SSR primers per Mb. Out of the 111,403, only 31,380 SSR primers were in the genic regions, while 80,023 primers were in the intergenic regions. A number of 250,507 SNPs were recognized in 84,172 SSR flanking regions, which represents 75.55% of the total SSR flanking regions. Out of 12,274 genes only 463 genes comprising 896 SSR primers were mapped onto 111 pathways using KEGG data base. The most abundant enzymes were identified in the pathway related to the biosynthesis of antibiotics. We tested 1031 SSR primers using both publicly available date palm genome sequences as templates in the in silico PCR reactions. Concerning in vitro validation, 31 SSR primers among those used in the in silico PCR were synthesized and tested for their ability to detect polymorphism among six Egyptian date palm cultivars. All tested primers have successfully amplified products, but only 18 primers detected polymorphic amplicons among the studied date palm cultivars.

SSR-CE/FD assessment of Guizhou approved sugarcane cultivars and regional materials

USDA-ARS?s Scientific Manuscript database

Twelve sugarcane genotypes (three cultivars and nine clones involved in regional tests) from Guizhou Province, China were analyzed using SSR-capillary electrophoresis/fluorescence detection (SSR-CE/FD) technology to construct the SSR fingerprints and assess the genetic diversity. A total of 131 DNA ...

[SSR loci information analysis in transcriptome of Andrographis paniculata].

PubMed

Li, Jun-Ren; Chen, Xiu-Zhen; Tang, Xiao-Ting; He, Rui; Zhan, Ruo-Ting

2018-06-01

To study the SSR loci information and develop molecular markers, a total of 43 683 Unigenes in transcriptome of Andrographis paniculata were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MicroSAtellite software, SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 14 135 SSR loci were found in the transcriptome of A. paniculata, which distributed in 9 973 Unigenes with a distribution frequency of 32.36%. Di-nucleotide and Tri-nucleotide repeat were the main types, accounted for 75.54% of all SSRs. The repeat motifs of AT/AT and CCG/CGG were the predominant repeat types of Di-nucleotide and Tri-nucleotide, respectively. A total of 4 740 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. Ten pairs of primers in 20 pairs of randomly picked primers produced fragments with expected molecular size. The gene function of Unigenes containing SSR were mostly related to the basic metabolism function of A. paniculata. The SSR markers in transcriptome of A. paniculata show rich type, strong specificity and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. Copyright© by the Chinese Pharmaceutical Association.

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake

USGS Publications Warehouse

Castoe, Todd A.; Poole, Alexander W.; de Koning, A. P. Jason; Jones, Kenneth L.; Tomback, Diana F.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Lance, Stacey L.; Streicher, Jeffrey W.; Smith, Eric N.; Pollock, David D.

2012-01-01

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample – a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.

Rapid microsatellite identification from illumina paired-end genomic sequencing in two birds and a snake

USGS Publications Warehouse

Castoe, T.A.; Poole, A.W.; de Koning, A. P. J.; Jones, K.L.; Tomback, D.F.; Oyler-McCance, S.J.; Fike, J.A.; Lance, S.L.; Streicher, J.W.; Smith, E.N.; Pollock, D.D.

2012-01-01

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample - a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable. ?? 2012 Castoe et al.

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.

PubMed

Castoe, Todd A; Poole, Alexander W; de Koning, A P Jason; Jones, Kenneth L; Tomback, Diana F; Oyler-McCance, Sara J; Fike, Jennifer A; Lance, Stacey L; Streicher, Jeffrey W; Smith, Eric N; Pollock, David D

2012-01-01

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample--a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.

Exploring Constructivist Social Learning Practices in Aiding Russian-Speaking Teachers to Learn Estonian: An Action Research Approach

ERIC Educational Resources Information Center

Kiilo, Tatjana; Kutsar, Dagmar

2012-01-01

Based on appreciative inquiry and threshold concepts from an intercultural learning perspective, the article makes insights into the constructivist social learning practice of Estonian language learning amongst Russian-speaking teachers in Estonia. The application of educational action research methodology, more specifically that of Bridget…

Sociocultural Aspects of Russian-Speaking Parents' Choice of Language of Instruction for Their Children in Estonia

ERIC Educational Resources Information Center

Kemppainen, Raija Pini; Ferrin, Scott Ellis; Hite, Steven J.; Hilton, Sterling C.

2008-01-01

The present research was undertaken to identify sociocultural variables that influence whether Russian-speaking parents living in Estonia choose Russian, Estonian, or bilingual (Russian and Estonian) instruction for their children. To examine which sociocultural variables are related to parents' choice of language of instruction, 346…

Estonian Vocational Teachers' Attitudes towards Inclusive Education for Students with Special Educational Needs

ERIC Educational Resources Information Center

Rose, Richard; Kaikkonen, Leena; Koiv, Kristi

2007-01-01

This paper presents the findings from research conducted with two samples of teachers from Estonian Vocational Schools. The first sample comprised a group of teachers who had received professional development directly related to the management of students with special educational needs in vocational education settings. Their attitudes and…

The Perceived Impact of External Evaluation: The System, Organisation and Individual Levels-Estonian Case

ERIC Educational Resources Information Center

Seema, Riin; Udam, Maiki; Mattisen, Heli; Lauri, Liia

2017-01-01

The purpose of this article is to provide an overview of how the employees of higher education institutions perceive the impact of external evaluations. The study was conducted using the concurrent mixed method and involved 361 employees from Estonian universities and professional higher education institutions. The results indicated that…

Enhancing Teachers' Curriculum Ownership via Teacher Engagement in State-Based Curriculum-Making: The Estonian Case

ERIC Educational Resources Information Center

Mikser, Rain; Kärner, Anita; Krull, Edgar

2016-01-01

Teachers' curriculum ownership is increasingly gaining attention in many countries. It is particularly important that under the conditions of centralized curriculum-making, teachers as final implementers of curricular ideas identify themselves with these ideas. This study investigates Estonian upper secondary school teachers' views on the impact…

Abortion trends from 1996 to 2011 in Estonia: special emphasis on repeat abortion

PubMed Central

2014-01-01

Background The study aimed to describe the overall and age-specific trends of induced abortions from 1996 to 2011 with an emphasis on socio-demographic characteristics and contraceptive use of women having had repeat abortions in Estonia. Methods Data were retrieved from the Estonian Medical Birth and Abortion Registry and Statistics Estonia. Total induced abortion numbers, rates, ratios and age-specific rates are presented for 1996–2011. The percentage change in the number of repeat abortions within selected socio-demographic subgroups, contraception use and distribution of induced abortions among Estonians and non-Estonians for the first, second, third, fourth and subsequent abortions were calculated for the periods 1996–2003 and 2004–2011. Results Observed trends over the 16-year study period indicated a considerable decline in induced abortions with a reduction in abortion rate of 57.1%, which was mainly attributed to younger cohorts. The percentage of women undergoing repeat abortions fell steadily from 63.8% during 1996–2003 to 58.0% during 2004–2011. The percentage of women undergoing repeat abortions significantly decreased over the 16 years within all selected socio-demographic subgroups except among women with low educational attainment and students. Within each time period, a greater percentage of non-Estonians than Estonians underwent repeat abortions and obtained third and subsequent abortions. Most women did not use any contraceptive method prior to their first or subsequent abortion. Conclusion A high percentage of women obtaining repeat abortions reflects a high historical abortion rate. If current trends continue, a rapid decline in repeat abortions may be predicted. To decrease the burden of sexual ill health, routine contraceptive counselling, as standard care in the abortion process, should be seriously addressed with an emphasis on those groups - non-Estonians, women with lower educational attainment, students and women with children - vulnerable with respect to repeat abortion. PMID:25005363

Characterization of EST-derived and non-EST simple sequence repeats in an F₁ hybrid population of Vitis vinifera L.

PubMed

Kayesh, E; Bilkish, N; Liu, G S; Chen, W; Leng, X P; Fang, J G

2014-03-31

Among different classes of molecular markers, expressed sequence tags (ESTs) are a new resource for developing simple sequence repeat (SSR) functional markers for genotyping and genetic mapping in F1 hybrid populations of Vitis vinifera L. Recently, because of the availability of an enormous amount of data for ESTs in the public domain, the emphasis has shifted from genomic SSRs to EST-SSRs, which belong to transcribed regions of the genome and may have a role in gene expression or function. The objective of this study was to assess the polymorphisms among 94 F1 hybrids from "Early Rose" and "Red Globe" using 25 EST-derived and 25 non-EST SSR markers. A total collection of 362,375 grape ESTs that were retrieved from the National Center for Biotechnology Information (NCBI) and 2522 EST-SSR sequences were identified. From them, 205 primer pairs were randomly selected, including 176 pairs that were EST-derived and 29 non-EST SSR primer pairs, for polymerase chain reaction amplification. A total of 131 alleles were amplified using 50 pairs of primers; 78 alleles were amplified using EST-derived SSR primers and 53 were from non-EST SSR primers. At most, 6 and 5 alleles were amplified by EST-derived and non-EST SSR primers, respectively. The EST-derived SSR markers showed a maximum polymorphic information content (PIC) value of 1 and a minimum of 0.33 while non-EST SSR markers had maximum and minimum PIC values of 1 and 0.25, respectively. The average PIC value was 0.56 for EST-derived SSR markers and 0.45 for non-EST SSR markers.

Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species.

PubMed

Gupta, S K; Gopalakrishna, T

2010-07-01

Unigene sequences available in public databases provide a cost-effective and valuable source for the development of molecular markers. In this study, the identification and development of unigene-based SSR markers in cowpea (Vigna unguiculata (L.) Walp.) is presented. A total of 1071 SSRs were identified in 15 740 cowpea unigene sequences downloaded from the National Center for Biotechnology Information. The most frequent SSR motifs present in the unigenes were trinucleotides (59.7%), followed by dinucleotides (34.8%), pentanucleotides (4%), and tetranucleotides (1.5%). The copy number varied from 6 to 33 for dinucleotide, 5 to 29 for trinucleotide, 5 to 7 for tetranucleotide, and 4 to 6 for pentanucleotide repeats. Primer pairs were successfully designed for 803 SSR motifs and 102 SSR markers were finally characterized and validated. Putative function was assigned to 64.7% of the unigene SSR markers based on significant homology to reported proteins. About 31.7% of the SSRs were present in coding sequences and 68.3% in untranslated regions of the genes. About 87% of the SSRs located in the coding sequences were trinucleotide repeats. Allelic variation at 32 SSR loci produced 98 alleles in 20 cowpea genotypes. The polymorphic information content for the SSR markers varied from 0.10 to 0.83 with an average of 0.53. These unigene SSR markers showed a high rate of transferability (88%) across other Vigna species, thereby expanding their utility. Alignment of unigene sequences with soybean genomic sequences revealed the presence of introns in amplified products of some of the SSR markers. This study presents the distribution of SSRs in the expressed portion of the cowpea genome and is the first report of the development of functional unigene-based SSR markers in cowpea. These SSR markers would play an important role in molecular mapping, comparative genomics, and marker-assisted selection strategies in cowpea and other Vigna species.

ESAP plus: a web-based server for EST-SSR marker development.

PubMed

Ponyared, Piyarat; Ponsawat, Jiradej; Tongsima, Sissades; Seresangtakul, Pusadee; Akkasaeng, Chutipong; Tantisuwichwong, Nathpapat

2016-12-22

Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can download all the results through the web interface. ESAP Plus is a comprehensive and convenient web-based bioinformatic tool for SSR marker development. ESAP Plus offers all necessary EST-SSR development processes with various adjustable options that users can easily use to identify SSR markers from a large EST collection. With familiar web interface, users can upload the raw EST using the data submission page and visualize/download the corresponding EST-SSR information from within ESAP Plus. ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/ .

Organizational Commitment in Estonian University Libraries: A Review and Survey

ERIC Educational Resources Information Center

Kont, Kate-Riin; Jantson, Signe

2014-01-01

The data used in this article is based on the reviewing of relevant literature to provide an overview of the concepts of organizational commitment, job security, and interpersonal relations, as well as on the results of the original online survey, conducted by the article's authors, held in 2012 in Estonian university libraries governed by public…

Scenarios of Mentor Education in Romania--Towards Improving Teacher Induction

ERIC Educational Resources Information Center

Stîngu, Mihaela; Eisenschmidt, Eve; Iucu, Romi?a

2016-01-01

The aim of this paper is to examine the induction programme for newly qualified teachers and mentor education in Estonia, providing a comparative analysis of existing Estonian and possible Romanian models of mentoring. While the Estonian induction programme has been in place for more than ten years, induction in Romania is a relatively new and has…

Estonian Preschool Teachers' Views on Learning in Preschool

ERIC Educational Resources Information Center

Ugaste, Aino; Tuul, Maire; Niglas, Katrin; Neudorf, Evelyn

2014-01-01

As in many Western countries, children's learning in the curriculum of Estonian Early Childhood Education is seen as a lifelong process, wherein the teacher is primarily a guide to children's active learning. Thus, a child-centred approach to learning is valued in the national curriculum, but our interest was whether this approach is fixed in the…

Estonian Language Competencies for Peace Corps Volunteers in the Republic of Estonia.

ERIC Educational Resources Information Center

Ets, Tiina K.

This guide is designed for Estonian language training of Peace Corps workers in Estonia, is intended for use in a competency-based language training program, and reflects daily communication needs in that context. It consists of 52 lessons, each addressing a specific language competency, organized in 14 topical units. An introductory section gives…

Tiger in Focus--A National Survey of ICT in Estonian Schools

ERIC Educational Resources Information Center

Toots, Anu; Laanpere, Mart

2004-01-01

Estonia has not participated in international studies of ICT in education, nor have there been any similar studies at the national level up until the year 2000. The first survey of ICT in Estonian schools was conducted after completion of the national school computerization programme called Tiger Leap. This paper focuses on the targeted responses…

Estonian Science and Non-Science Students' Attitudes towards Mathematics at University Level

ERIC Educational Resources Information Center

Kaldo, Indrek; Reiska, Priit

2012-01-01

This article investigates the attitudes and beliefs towards studying mathematics by university level students. A total of 970 randomly chosen, first year, Estonian bachelor students participated in the study (of which 498 were science students). Data were collected using a Likert-type scale questionnaire and analysed with a respect to field of…

Consumer Socialisation and Value Orientations among Estonian and Chinese Young People

ERIC Educational Resources Information Center

Waerdahl, Randi; Kalmus, Veronika; Keller, Margit

2011-01-01

This paper asks if Estonian and Chinese tweens' access to pocket money influences their brand valuation, as well as value orientations in the context of perceived peer popularity and personal well-being. Surveys conducted in autumns 2006 (China n = 188) and 2007 (Estonia n = 111) show an inherent cultural resistance among tweens in both countries…

A Silent Finn, a Silent Finno-Ugric, or a Silent Nordic? A Comparative Study of Estonian, Finnish, and Swedish Mother-Adolescent Interactions.

ERIC Educational Resources Information Center

Tulviste, Tiia; Mizera, Luule; de Geer, Boel; Tryggvason, Marja-Terttu

2003-01-01

Compared verbal characteristics of family interaction in the stereotypically tongue-tied Nordic region of the Western world. Compared mothers' and early adolescents' talkativeness and monologuing and mothers' conversational dominance emerging in real-life video recordings in Estonian, Finnish, and Swedish monolingual and bilingual families. (VWL)

Use of SSR markers for DNA fingerprinting and diversity analysis of Pakistani sugarcane (Saccharum spp. hybrids) cultivars

USDA-ARS?s Scientific Manuscript database

In recent years SSR markers have been used widely for genetic analysis. The objective of this study was to use an SSR-based marker system to develop the molecular fingerprints and analyze the genetic relationship of sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers wer...

A framework linkage map of perennial ryegrass based on SSR markers

Treesearch

G.P. Gill; P.L. Wilcox; D.J. Whittaker; R.A. Winz; P. Bickerstaff; Craig E. Echt; J. Kent; M.O. Humphreys; K.M. Elborough; R.C. Gardner

2006-01-01

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third ( 124) of the SSR markers were developed from GeneThresher libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci...

78 FR 12130 - Social Security Ruling, SSR 13-3p; Appeal of an Initial Medical Disability Cessation...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-21

... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2011-0106] Social Security Ruling, SSR 13-3p; Appeal of an Initial Medical Disability Cessation Determination or Decision AGENCY: Social Security Administration. ACTION: Notice of Social Security Ruling (SSR). SUMMARY: We are giving notice of SSR 13-3p. This...

Impact of land use/land cover change on changes in surface solar radiation in eastern China since the reform and opening up

NASA Astrophysics Data System (ADS)

Qian, Cheng

2016-01-01

Observational evidence of the impacts of land use/land cover change (LULCC) on changes in surface solar radiation (SSR) in eastern China (EC) during 1979-2008 are identified by using diurnal temperature range as a proxy of SSR and by using observation minus reanalysis approach to disentangle these effects. For the period 1979-2008, the impact of LULCC is shown as a reduction in SSR in most stations in EC, whereas SSR in the reanalysis data has increased at nearly every location. The competition of the dimming effect of LULCC with the brightening effect in the reanalysis results in an observed dipole pattern of SSR with slightly decreasing (increasing) trends in most stations north (south) of the Yangtze River and statistically significant decreasing trends in central EC. In terms of EC area mean, this competition has resulted in a slightly dimming trend in the observed SSR during 1979-2008, although a transition from an apparent dimming to a general leveling off near 1990 is identified. For the period 1990-2008, LULCC has significantly reduced SSR in central EC and southern China. This dimming effect of LULCC competes with the apparent brightening effect in the reanalysis to result in the general leveling off in the observed SSR in terms of EC area mean and a sandwich spatial pattern in the observed SSR in EC where parts of central EC show significant dimming. The impact of LULCC on the changes in SSR may be through both biogeophysical and biogeochemical processes.

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

PubMed Central

Jewell, Erica; Robinson, Andrew; Savage, David; Erwin, Tim; Love, Christopher G.; Lim, Geraldine A. C.; Li, Xi; Batley, Jacqueline; Spangenberg, German C.; Edwards, David

2006-01-01

Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at . PMID:16845092

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery.

PubMed

Jewell, Erica; Robinson, Andrew; Savage, David; Erwin, Tim; Love, Christopher G; Lim, Geraldine A C; Li, Xi; Batley, Jacqueline; Spangenberg, German C; Edwards, David

2006-07-01

Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at http://bioinformatics.pbcbasc.latrobe.edu.au/ssrdiscovery.html.

The 2011 Estonian High School Language Reform in the Context of Critical Language Policy and Planning

ERIC Educational Resources Information Center

Skerrett, Delaney Michael

2014-01-01

This paper seeks to situate Estonian language use and policy within the emerging field of critical language policy and planning (CLPP) by investigating the discourses that frame linguistic behaviour. This done by way of an analysis of a series of interviews carried out with key actors in language policy in Estonia. The discourses framing language…

Gender Advantages and Gender Normality in the Views of Estonian Secondary School Students

ERIC Educational Resources Information Center

Kuurme, Tiiu; Kasemaa, Gertrud

2015-01-01

The aim of the study on Estonian secondary school students was to obtain an overview of the gender-related views and experiences of the everyday school life by students, and to analyse the school-related factors in the development of gender roles and gender-related expectations. We view gender equality as a central condition for social…

Working Community-Related Interaction Factors Building Occupational Well-Being--Learning Based Intervention in Finnish and Estonian Schools (2010-2013)

ERIC Educational Resources Information Center

Pertel, Tiia; Laine, Sari; Saaranen, Terhi; Hansen, Siivi; Lepp, Kädi; Liiv, Krystiine; Tossavainen, Kerttu

2018-01-01

This article examines whether a three-year learning-based work community intervention resulted in changes in working community-related interaction factors and occupational well-being among Finnish and Estonian school staff. It reports the types of changes in working community-related interaction factors and their associations to the subjective…

Supervision and Early Career Work Experiences of Estonian Humanities Researchers under the Conditions of Project-Based Funding

ERIC Educational Resources Information Center

Eigi, Jaana; Põiklik, Pille; Lõhkivi, Endla; Velbaum, Katrin

2014-01-01

We analyze a series of interviews with Estonian humanities researchers to explore topics related to the beginning of academic careers and the relationships with supervisors and mentors. We show how researchers strive to have meaningful relationships and produce what they consider quality research in the conditions of a system that is very strongly…

Orthographic Depth and Spelling Acquisition in Estonian and English: A Comparison of Two Diverse Alphabetic Languages

ERIC Educational Resources Information Center

Viise, Neva M.; Richards, Herbert C.; Pandis, Meeli

2011-01-01

In this study, we investigated the link between the orthographic transparency of a language and the ease or difficulty of acquiring spelling proficiency in that language. The two languages compared are English, with a highly irregular sound-to-print correspondence, and Estonian, a Finno-Ugric language that has one of the most highly regular…

Enhancements to PCRSM.

DTIC Science & Technology

1991-03-01

the A parameters; yhatf, to calculate the y-hat statistics; ssrf, to calculate the uncorrected SSR; sstof, to calculate the uncorrected SSTO ; matmulmm...DEGREES OF FREEDOM * int sstocdf, ssrcdf, ssecdf; float ssr, ssto , sse; /* SUM OF SQUARES * float ssrc, sstoc, ssec; float insr, insto, inse; float...Y-HAT STATSISTICS * yhatf(x,beta,stats,n,n); /* CALCULATE UNCORRECTED SSR * ssrf(beta, x, y, mn, n, ss); ssr = ss[l][l]; /* CALCULATE UNCORRECTED SSTO

Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich

PubMed Central

Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

2015-01-01

Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

The Non-Peptide Vasopressin V1b Receptor Antagonist, SSR149415, Ameliorates Spermatogenesis Function in a Mouse Model of Chronic Social Defeat Stress.

PubMed

Wang, Bin; Zhou, Jian; Zhuang, Yan-Yan; Wang, Liang-Liang; Pu, Jin-Xian; Huang, Yu-Hua; Xia, Fei; Lv, Jin-Xing

2017-11-01

To determine the effects of SSR149415 on testis and spermatogenesis in male mice subjected to chronic social defeat stress, C57BL/6 male mice were divided into two groups: Control and Stress. Then Stress group was subdivided into four subgroups administered water, SSR149415 (1 mg/kg/day), SSR149415 (10 mg/kg/day), SSR149415 (30 mg/kg/day), respectively. The behavioral alterations revealed by social interaction test and open field test were measured. The physical indices, including body weight and gonad weight (testis and epididymis) as well as testis/body weight and cauda epididymis/body weight were detected. Serum hormones, including testosterone, luteinizing hormone (LH), and follicle-stimulating hormone (FSH) were determined. Sperm count and abnormality as well as testicular histology structure were assessed. The germ cells apoptosis were also evaluated. Chronic social defeat stress-induced behavioral abnormality, as well as gonad atrophy (testis and epididymis) was significantly alleviated in stressed male mice exposed to SSR149415. Regressed serum testosterone levels and elevated serum FSH and LH levels exhibited by stressed male mice were observably reversed following SSR149415 administration. Chronic social defeat stress-induced damage in testicular histology structure and semen quality were also improved after SSR149415 administration. In addition, SSR149415 significantly reversed chronic social defeat stress-induced germ cells apoptosis. Overall, we provide clear evidence indicating the amelioration of chronic social defeat stress-induced behavioral abnormality and testicular dysfunction via SSR149415, promoting the development of drug-directed therapy against this disease. J. Cell. Biochem. 118: 3891-3898, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species.

PubMed

Huang, Li; Wu, Bei; Zhao, Jiaojiao; Li, Haitao; Chen, Weigang; Zheng, Yanli; Ren, Xiaoping; Chen, Yuning; Zhou, Xiaojing; Lei, Yong; Liao, Boshou; Jiang, Huifang

2016-01-01

Microsatellite or simple sequence repeat (SSR) is one of the most widely distributed molecular markers that have been widely utilized to assess genetic diversity and genetic mapping for important traits in plants. However, the understanding of microsatellite characteristics in Arachis species and the currently available amount of high-quality SSR markers remain limited. In this study, we identified 16,435 genome survey sequences SSRs (GSS-SSRs) and 40,199 expressed sequence tag SSRs (EST-SSRs) in Arachis hypogaea and its wild relative species using the publicly available sequence data. The GSS-SSRs had a density of 159.9-239.8 SSRs/Mb for wild Arachis and 1,015.8 SSR/Mb for cultivated Arachis, whereas the EST-SSRs had the density of 173.5-384.4 SSR/Mb and 250.9 SSRs/Mb for wild and cultivated Arachis, respectively. The trinucleotide SSRs were predominant across Arachis species, except that the dinucleotide accounted for most in A. hypogaea GSSs. From Arachis GSS-SSR and EST-SSR sequences, we developed 2,589 novel SSR markers that showed a high polymorphism in six diverse A. hypogaea accessions. A genetic linkage map that contained 540 novel SSR loci and 105 anchor SSR loci was constructed by case of a recombinant inbred lines F6 population. A subset of 82 randomly selected SSR markers were used to screen 39 wild and 22 cultivated Arachis accessions, which revealed a high transferability of the novel SSRs across Arachis species. Our results provided informative clues to investigate microsatellite patterns across A. hypogaea and its wild relative species and potentially facilitate the germplasm evaluation and gene mapping in Arachis species.

Genetic Diversity in Various Accessions of Pineapple [Ananas comosus (L.) Merr.] Using ISSR and SSR Markers.

PubMed

Wang, Jian-Sheng; He, Jun-Hu; Chen, Hua-Rui; Chen, Ye-Yuan; Qiao, Fei

2017-12-01

Inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers were used to assess the genetic diversity of 36 pineapple accessions that were introduced from 10 countries/regions. Thirteen ISSR primers amplified 96 bands, of which 91 (93.65%) were polymorphic, whereas 20 SSR primers amplified 73 bands, of which 70 (96.50%) were polymorphic. Nei's gene diversity (h = 0.28), Shannon's information index (I = 0.43), and polymorphism information content (PIC = 0.29) generated using the SSR primers were higher than that with ISSR primers (h =  0.23, I = 0.37, PIC = 0.24), thereby suggesting that the SSR system is more efficient than the ISSR system in assessing genetic diversity in various pineapple accessions. Mean genetic similarities were 0.74, 0.61, and 0.69, as determined using ISSR, SSR, and combined ISSR/SSR, respectively. These results suggest that the genetic diversity among pineapple accessions is very high. We clustered the 36 pineapple accessions into three or five groups on the basis of the phylogenetic trees constructed based on the results of ISSR, SSR, and combined ISSR/SSR analyses using the unweighted pair-group with arithmetic averaging (UPGMA) method. The results of principal components analysis (PCA) also supported the UPGMA clustering. These results will be useful not only for the scientific conservation and management of pineapple germplasm but also for the improvement of the current pineapple breeding strategies.

WGSSAT: A High-Throughput Computational Pipeline for Mining and Annotation of SSR Markers From Whole Genomes.

PubMed

Pandey, Manmohan; Kumar, Ravindra; Srivastava, Prachi; Agarwal, Suyash; Srivastava, Shreya; Nagpure, Naresh S; Jena, Joy K; Kushwaha, Basdeo

2018-03-16

Mining and characterization of Simple Sequence Repeat (SSR) markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. Whole genome sequencing (WGS)-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, noncoding RNA (ncRNA), core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic, and core gene region) along with primer identification and mining of cross-species markers. The program also generates a detailed statistical report along with visualization of mapped SSRs, genes, core genes, and RNAs. The features of WGSSAT were demonstrated using Takifugu rubripes data. This yielded a total of 139 057 SSR, out of which 113 703 SSR primer pairs were uniquely amplified in silico onto a T. rubripes (fugu) genome. Out of 113 703 mined SSRs, 81 463 were from coding region (including 4286 exonic and 77 177 intronic), 7 from RNA, 267 from core genes of fugu, whereas 105 641 SSR and 601 SSR primer pairs were uniquely mapped onto the medaka genome. WGSSAT is tested under Ubuntu Linux. The source code, documentation, user manual, example dataset and scripts are available online at https://sourceforge.net/projects/wgssat-nbfgr.

Confamiliar transferability of simple sequence repeat (SSR) markers from cotton (Gossypium hirsutum L.) and jute (Corchorus olitorius L.) to twenty two Malvaceous species.

PubMed

Satya, Pratik; Paswan, Pramod Kumar; Ghosh, Swagata; Majumdar, Snehalata; Ali, Nasim

2016-06-01

Cross-species transferability is a quick and economic method to enrich SSR database, particularly for minor crops where little genomic information is available. However, transferability of SSR markers varies greatly between species, genera and families of plant species. We assessed confamiliar transferability of SSR markers from cotton (Gossypium hirsutum) and jute (Corchorus olitorius) to 22 species distributed in different taxonomic groups of Malvaceae. All the species selected were potential industrial crop species having little or no genomic resources or SSR database. Of the 14 cotton SSR loci tested, 13 (92.86 %) amplified in G. arboreum and 71.43 % exhibited cross-genera transferability. Nine out of 11 jute SSRs (81.81 %) showed cross-transferability across genera. SSRs from both the species exhibited high polymorphism and resolving power in other species. The correlation between transferability of cotton and jute SSRs were highly significant (r = 0.813). The difference in transferability among species was also significant for both the marker groups. High transferability was observed at genus, tribe and subfamily level. At tribe level, transferability of jute SSRs (41.04 %) was higher than that of cotton SSRs (33.74 %). The tribe Byttnerieae exhibited highest SSR transferability (48.7 %). The high level of cross-genera transferability (>50 %) in ten species of Malvaceae, where no SSR resource is available, calls for large scale transferability testing from the enriched SSR databases of cotton and jute.

Long-term series and trends in surface solar radiation in Athens, Greece

NASA Astrophysics Data System (ADS)

Kazadzis, Stelios; Founda, Dimitra; Psiloglou, Basil E.; Kambezidis, Harry; Mihalopoulos, Nickolaos; Sanchez-Lorenzo, Arturo; Meleti, Charikleia; Raptis, Panagiotis I.; Pierros, Fragiskos; Nabat, Pierre

2018-02-01

We present a long-term series of surface solar radiation (SSR) from the city of Athens, Greece. SSR measurements were performed from 1954 to 2012, and before that (1900-1953) sunshine duration (SD) records were used in order to reconstruct monthly SSR. Analysis of the whole data set (1900-2012) mainly showed very small (0.02 %) changes in SSR from 1900 to 1953, including a maximum decrease of -2.9 % decade-1 in SSR during the 1910 to 1940 period, assuming a linear change. For the dimming period 1955-1980, -2 % decade-1 was observed that matches various European long-term SSR-measurement-related studies. This percentage in Athens is in the lower limit, compared to other studies in the Mediterranean area. For the brightening period 1980-2012 we calculated +1.5 % decade-1, which is also in the lower limit of the reported positive changes in SSR around Europe. Comparing the 30-year periods 1954-1983 and 1983-2012, we found a difference of 4.5 %. However, measurements of the first 30-year period are associated with higher uncertainties than those of the second period, especially when looking at year-to-year changes. The difference between the two periods was observed for all seasons except winter. Analyzing SSR calculations of all-sky and clear-sky (cloudless) conditions/days, we report that most of the observed changes in SSR after 1954 can be attributed partly to cloudiness and mostly to aerosol load changes.

Augmentation of the Sympathetic Skin Response after Electrical Train Stimuli

PubMed Central

Emmer, A.; Mangalo, S.; Kornhuber, M. E.

2012-01-01

It is well known that the size of the sympathetic skin response (SSR) depends on the stimulus strength. In the present investigation train stimuli (TS) were employed to study the behavior of the SSR when recruited above the usual level. The SSR was obtained in healthy human subjects over the palm of the hand after supramaximal single stimuli (SS) and trains of three (TS; interstimulus interval 3 ms) over the ipsilateral superficial radial nerve in 15 healthy volunteers. Ipsilateral to the stimulus site SSR amplitudes were 5.7 ± 5.3 (SS) and 7.7 ± 5.9 mV (TS; p < 0.001), and contralateral 6.3 ± 6.3 (SS) and 7.2 ± 4.9 mV (TS; not significant). The relative gain in amplitude after TS vs. SS was negatively correlated with the SSR amplitude after SS ipsilateral (p < 0.0005) and contralateral to the stimulus site (p < 0.01). The increase in SSR amplitudes after TS compared with SS is in line with temporal summation of the excitatory synaptic input in neurons generating the SSR. Driving the SSR with TS is of possible relevance for the investigation of disorders of the peripheral or central autonomic nervous system. PMID:23115555

Dilatation by Soehendra stent retriever is feasible and effective in multiple deployment of metallic stents to malignant hilar biliary strictures.

PubMed

Kato, Hironari; Kawamoto, Hirofumi; Noma, Yasuhiro; Sonoyama, Takayuki; Tsutsumi, Koichiro; Fujii, Masakuni; Okada, Hiroyuki; Yamamoto, Kazuhide

2013-01-01

The endoscopic management of malignant hilar biliary strictures using multiple metallic stents (MS) is technically demanding, in the initial deployment of MS and the recovery from MS occlusion with deployment of multiple plastic stents (PS). We evaluated the outcomes of the application of a Soehendra stent retriever (SSR) as a dilator of intractable strictures. Fifty-nine patients with malignant hilar biliary strictures had multiple MS inserted using a partial stent-in-stent procedure. When we encountered intractable strictures, we adopted SSR to dilate the stricture and the interstice of the MS. We evaluated the success rate of MS or PS deployment after SSR application and procedural complications. Five of 59 patients (8%) were subjected to SSR application for the initial MS deployment. MS were successfully deployed in all of these patients (100%). MS occlusion was noted in 27 patients. We applied SSR to seven patients (26%) for the deployment of multiple PS after MS occlusion. In five patients (71%), successful PS deployment was achieved after the SSR application. No complications related to dilatation using SSR occurred in any patient. SSR proved to be a potent dilator of difficult strictures in the management of malignant hilar biliary strictures.

Proficiency Assessment of Male Volleyball Teams of the 13-15-Year Age Group at Estonian Championships

ERIC Educational Resources Information Center

Stamm, Meelis; Stamm, Raini; Koskel, Sade

2008-01-01

Study aim: Assessment of feasibility of using own computer software "Game" at competitions. Material and methods: The data were collected during Estonian championships in 2006 for male volleyball teams of the 13-15-years age group (n = 8). In all games, the performance of both teams was recorded in parallel with two computers. A total of…

University Language Policies and Language Choice among Ph.D. Graduates in Estonia: The (Unbalanced) Interplay between English and Estonian

ERIC Educational Resources Information Center

Soler-Carbonell, Josep

2014-01-01

The role of English as a global language and its consequences for the internationalization of higher education are matters that have increasingly drawn the attention of researchers from different fields of language and communication. In this paper, an overview of the situation in Estonia is presented. The Estonian context has not previously been…

Puolin ja toisin: Suomalais-virolaista kielentutkimusta. AFinLAn vuosikirja 1998 (On Both Sides: Finnish-Estonian Research on Language. AFinLA Yearbook 1998).

ERIC Educational Resources Information Center

Luukka, Minna-Riitta, Ed.; Salla, Sigrid, Ed.; Dufva, Hannele, Ed.

The papers included in this yearbook of the Finnish Society of Applied Linguistics (AFinLA) were presented at the 1998 AFinLA conference "Linguistics and Finland: Crossing the Gulf." Papers are in Finnish, Estonian, or English, but all have accompanying English abstracts. The topics discussed in the papers include the following: speed…

Changes in Estonian General Education from the Collapse of the Soviet Union to EU Entry

ERIC Educational Resources Information Center

Krull, Edgar; Trasberg, Karmen

2006-01-01

This article introduces and discusses the nature and development of Estonian system of general education in the period of last thirty years. The main focus is paid on the changes resulting from the collapse of the Soviet Union and the period of integration leading up to EU entry. Also changes in other spheres of education and social life are…

USSR Report, Political and Sociological Affairs, No. 1437.

DTIC Science & Technology

1983-08-02

to Christian Jaak Peterson, the first Estonian lyric poet, now stands in old Vyshgorod, under the ancient lindens and oaks. Estonian poetry began...world. I. R. Grigulevich has also devoted many articles, surveys, and essays to the activity of the Catho- lic Church. These works examine such...issledovaniya za rubezhom. Kritiches- kiye ocherki" /Ethnological Studies Abroad: Critical Essays /, Moscow, 1973; "Kontseptsii zarubezhnoy etnografii

Changes in Learning Process Caused by the Implementation of ICT in Education in Estonian In-Service and Pre-Service Teachers Perceptions

ERIC Educational Resources Information Center

Luik, Piret; Kukemelk, Hasso

2008-01-01

The current paper reports on a qualitative study examining in-service and pre-service teachers perceptions about changes in the learning process caused by the involvement of ICT (Information and Communication Technology) in Estonian schools. Based on five in-service and five pre-service teachers' interviews, findings indicate some positive, some…

Composition of Estonian Infants' Expressive Lexicon According to the Adaptation of CDI/Words and Gestures

ERIC Educational Resources Information Center

Schults, Astra; Tulviste, Tiia

2016-01-01

The growth rate and the composition of expressive lexicon was studied in a sample of 903 infants between the age of 0;8 and 1;4 whose parents completed the Estonian adaptation of the MacArthur-Bates Communicative Development Inventory-Words and Gestures. As expected, older children had on average larger vocabularies compared to younger children.…

Attitudes of Academic Staff towards Their Own Work and towards External Evaluation, from the Perspective of Self-Determination Theory: Estonian Case

ERIC Educational Resources Information Center

Seema, Riin; Udam, Maiki; Mattisen, Heli

2016-01-01

The purpose of this study was to ascertain the attitudes of academic staff towards their own work as well as towards external evaluations. The study was based on (1) an analysis of assessment reports of institutional accreditations conducted by the Estonian Quality Agency for Higher and Vocational Education and (2) self-determination theory on…

Height Connections and Land Uplift Rates in West-Estonian Archipelago

NASA Astrophysics Data System (ADS)

Jürgenson, H.; Liibusk, A.; Kall, T.

2012-04-01

Land uplift rates are largest in the western part of Estonia. The uplift is due to post-glacial rebound. In 2001-2011, the Estonian national high-precision levelling network was completely renewed and levelled. This was the third precise levelling campaign in the re-gion. The first one had taken place before the Second World War and the second one in the 1950s. The Estonian mainland was connected with the two largest islands (Saaremaa and Hiiumaa) in the west-Estonian archipelago using the water level monitoring (hydrody-namic levelling) method. Three pairs of automatic tide gauges were installed on opposite coasts of each waterway. The tide gauges were equipped with piezoresistive pressure sen-sors. This represented the first use of such kind of equipment in Estonia. The hydrodynamic levelling series span up to two calendar years. Nevertheless, the obtained hydrodynamic levelling results need to be additionally verified using alternative geodetic methods. The obtained results were compared with the previous high-precision levelling data from the 1960s and 1970s. As well, the new Estonian gravimetric geoid model and the GPS survey were used for GPS-levelling. All the three methods were analyzed, and the preliminary results coincided within a 1-2 cm margin. Additionally, the tide gauges on the mainland and on both islands were connected using high-precision levelling. In this manner, three hydrodynamic and three digital levelling height differences formed a closed loop with the length of 250 km. The closing error of the loop was less than 1 cm. Finally, the Fennoscandian post-glacial rebound was determined from repeated levelling as well as from repeated GPS survey. The time span between the two campaigns of the first-order GPS survey was almost 13 years. According to new calculations, the relative land uplift rates within the study area reached up to +2 mm/year. This is an area with a rela-tively small amount of input data for the Nordic models. In addition, a comparison with the Fennoscandian land uplift model NKG2005LU is presented. The results coincided with this model within a 1-mm range. Keywords: hydrodynamic levelling, post-glacial land uplift, GPS-levelling, West-Estonian archipelago.

Development and use of EST-SSR markers for assessing genetic diversity in the brown planthopper (Nilaparvata lugens Stål).

PubMed

Jing, S; Liu, B; Peng, L; Peng, X; Zhu, L; Fu, Q; He, G

2012-02-01

To assess genetic diversity in populations of the brown planthopper (Nilaparvata lugens Stål) (Homoptera: Delphacidae), we have developed and applied microsatellite, or simple sequence repeat (SSR), markers from expressed sequence tags (ESTs). We found that the brown planthopper clusters of ESTs were rich in SSRs with unique frequencies and distributions of SSR motifs. Three hundred and fifty-one EST-SSR markers were developed and yielded clear bands from samples of four brown planthopper populations. High cross-species transferability of these markers was detected in the closely related planthopper N. muiri. The newly developed EST-SSR markers provided sufficient resolution to distinguish within and among biotypes. Analyses based on SSR data revealed host resistance-based genetic differentiation among different brown planthopper populations; the genetic diversity of populations feeding on susceptible rice varieties was lower than that of populations feeding on resistant rice varieties. This is the first large-scale development of brown planthopper SSR markers, which will be useful for future molecular genetics and genomics studies of this serious agricultural pest.

First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

PubMed

Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

2016-08-04

Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.

Mutational analysis of COL1A1 and COL1A2 genes among Estonian osteogenesis imperfecta patients.

PubMed

Zhytnik, Lidiia; Maasalu, Katre; Reimann, Ene; Prans, Ele; Kõks, Sulev; Märtson, Aare

2017-08-15

Osteogenesis imperfecta (OI) is a rare bone disorder. In 90% of cases, OI is caused by mutations in the COL1A1/2 genes, which code procollagen α1 and α2 chains. The main aim of the current research was to identify the mutational spectrum of COL1A1/2 genes in Estonian patients. The small population size of Estonia provides a unique chance to explore the collagen I mutational profile of 100% of OI families in the country. We performed mutational analysis of peripheral blood gDNA of 30 unrelated Estonian OI patients using Sanger sequencing of COL1A1 and COL1A2 genes, including all intron-exon junctions and 5'UTR and 3'UTR regions, to identify causative OI mutations. We identified COL1A1/2 mutations in 86.67% of patients (26/30). 76.92% of discovered mutations were located in the COL1A1 (n = 20) and 23.08% in the COL1A2 (n = 6) gene. Half of the COL1A1/2 mutations appeared to be novel. The percentage of quantitative COL1A1/2 mutations was 69.23%. Glycine substitution with serine was the most prevalent among missense mutations. All qualitative mutations were situated in the chain domain of pro-α1/2 chains. Our study shows that among the Estonian OI population, the range of collagen I mutations is quite high, which agrees with other described OI cohorts of Northern Europe. The Estonian OI cohort differs due to the high number of quantitative variants and simple missense variants, which are mostly Gly to Ser substitutions and do not extend the chain domain of COL1A1/2 products.

Soviet Material on Internal Wave Effects, No. 3, April 1975,

DTIC Science & Technology

1975-04-01

telemekhanika Acta phyfica polonica Akademiya naiik Armyanskoy SSR. Doklady Akademiya nauk Aserbaydzhanskoy SSR. Doklady Akademiya nauk Belorusskoy SSR... Physica status solid! Pribory i sistemy upravleniya Pribery I tekhnika eksperimenta Radietskhnika Radliotakhnika i elektronika Rafarativnyy zhurnal

Field of genes: the politics of science and identity in the Estonian Genome Project.

PubMed

Fletcher, Amy L

2004-04-01

This case study of the Estonian Genome Project (EGP) analyses the Estonian policy decision to construct a national human gene bank. Drawing upon qualitative data from newspaper articles and public policy documents, it focuses on how proponents use discourse to link the EGP to the broader political goal of securing Estonia's position within the Western/European scientific and cultural space. This dominant narrative is then situated within the analytical notion of the "brand state", which raises potentially negative political consequences for this type of market-driven genomic research. Considered against the increasing number of countries engaging in gene bank and/or gene database projects, this analysis of Estonia elucidates issues that cross national boundaries, while also illuminating factors specific to this small, post-Soviet state as it enters the global biocybernetic economy.

Vibrio vulnificus typing based on simple sequence repeats: insights into the biotype 3 group.

PubMed

Broza, Yoav Y; Danin-Poleg, Yael; Lerner, Larisa; Broza, Meir; Kashi, Yechezkel

2007-09-01

Vibrio vulnificus is an opportunistic, highly invasive human pathogen with worldwide distribution. V. vulnificus strains are commonly divided into three biochemical groups (biotypes), most members of which are pathogenic. Simple sequence repeats (SSR) provide a source of high-level genomic polymorphism used in bacterial typing. Here, we describe the use of variations in mutable SSR loci for accurate and rapid genotyping of V. vulnificus. An in silico screen of the genomes of two V. vulnificus strains revealed thousands of SSR tracts. Twelve SSR with core motifs longer than 5 bp in a panel of 32 characterized and 56 other V. vulnificus isolates, including both clinical and environmental isolates from all three biotypes, were tested for polymorphism. All tested SSR were polymorphic, and diversity indices ranged from 0.17 to 0.90, allowing a high degree of discrimination among isolates (27 of 32 characterized isolates). Genetic analysis of the SSR data resulted in the clear distinction of isolates that belong to the highly virulent biotype 3 group. Despite the clonal nature of this new group, SSR analysis demonstrated high-level discriminatory power within the biotype 3 group, as opposed to other molecular methods that failed to differentiate these isolates. Thus, SSR are suitable for rapid typing and classification of V. vulnificus strains by high-throughput capillary electrophoresis methods. SSR (>/=5 bp) by their nature enable the identification of variations occurring on a small scale and, therefore, may provide new insights into the newly emerged biotype 3 group of V. vulnificus and may be used as an efficient tool in epidemiological studies.

Meeting the Objectives of the Curriculum at the First Stage of Basic School by the Child Having Left the Language Immersion Kindergarten

ERIC Educational Resources Information Center

Kukk, Airi; Õun, Tiia

2014-01-01

Year after year, the interest in early learning of the state language by non-Estonian children has increased. In Estonia, the course has been directed that non-Estonian learners have to reach functional bilingualism by the time they leave basic school and thus to become competitive in labour and education markets in Estonia. The objective of the…

HIV testing and counselling in Estonian prisons, 2012 to 2013: aims, processes and impacts.

PubMed

Kivimets, K; Uuskula, A

2014-11-27

We present data from an observational cohort study on human immunodeficiency virus (HIV) prevention and control measures in prisons in Estonia to assess the potential for HIV transmission in this setting. HIV testing and retesting data from the Estonian prison health department were used to estimate HIV prevalence and incidence in prison. Since 2002, voluntary HIV counselling and testing has routinely been offered to all prisoners and has been part of the new prisoners health check. At the end of 2012, there were 3,289 prisoners in Estonia, including 170 women: 28.5% were drug users and 15.6% were infected with HIV. Of the HIV-positive inmates, 8.3% were newly diagnosed on prison entry. In 2012, 4,387 HIV tests (including retests) were performed in Estonian prisons. Among 1,756 initially HIV-negative prisoners who were in prison for more than one year and therefore tested for HIV twice within 12 months (at entry and annual testing), one new HIV infection was detected, an incidence of 0.067 per 100 person-years (95% confidence interval (CI): 0.025–5.572). This analysis indicates low risk of HIV transmission in Estonian prisons. Implementation of HIV management interventions could impact positively on the health of prisoners and the communities to which they return.

Comparison of knowledge, attitudes and behaviour regarding smoking among Estonian and Finnish physicians.

PubMed

Pärna, Kersti; Rahu, Kaja; Barengo, Noël C; Rahu, Mati; Sandström, Patrick H; Jormanainen, Vesa J; Myllykangas, Markku T

2005-01-01

To compare smoking behaviour, attitudes and opinions towards smoking and smoking cessation among Estonian and Finnish physicians. A cross-sectional postal survey using a self-administered questionnaire was carried out among 2,480 Estonian and 2,075 Finnish physicians. Daily smoking prevalence was higher among Estonian physicians than among their Finnish counterparts in both male (18.6% and 6.7%) and female (6.6% and 3.6%). Compared to Estonia, physicians in Finland more often agreed that smoking is very harmful to their health, that trying to convince people to stop smoking is their responsibility and that smoking prevention should be part of the normal and special training of health professionals. In both countries, non-smoking physicians held more unfavourable attitudes towards smoking than those who were smoking. Physicians' own smoking patterns and quitting behaviour are important because physicians serve as models for their patients and play a key role in the reinforcement of smoke-free health facilities. These results remain a challenge to medical educators, especially in Estonia. Estonia needs to improve medical education in terms of motivating physicians to ask about the smoking patterns of their patients and of training medical students and resident physicians to counsel their patients to stop smoking.

Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.).

PubMed

Wang, Zan; Yan, Hongwei; Fu, Xinnian; Li, Xuehui; Gao, Hongwen

2013-04-01

Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di-(26.1 %), tetra-(11.5 %), penta-(9.7 %), and hexanucleotide (3.9 %). One hundred EST-SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST-SSR markers. Based on the 29 EST-SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST-SSR markers was also found for relative species.

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

PubMed Central

Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R. K.; Singh, N. K.; Singh, Rakesh

2013-01-01

Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis. PMID:24367635

First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers

PubMed Central

Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

2016-01-01

Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future. PMID:27488242

ssrA (tmRNA) Plays a Role in Salmonella enterica Serovar Typhimurium Pathogenesis

PubMed Central

Julio, Steven M.; Heithoff, Douglas M.; Mahan, Michael J.

2000-01-01

Escherichia coli ssrA encodes a small stable RNA molecule, tmRNA, that has many diverse functions, including tagging abnormal proteins for degradation, supporting phage growth, and modulating the activity of DNA binding proteins. Here we show that ssrA plays a role in Salmonella enterica serovar Typhimurium pathogenesis and in the expression of several genes known to be induced during infection. Moreover, the phage-like attachment site, attL, encoded within ssrA, serves as the site of integration of a region of Salmonella-specific sequence; adjacent to the 5′ end of ssrA is another region of Salmonella-specific sequence with extensive homology to predicted proteins encoded within the unlinked Salmonella pathogenicity island SPI4. S. enterica serovar Typhimurium ssrA mutants fail to support the growth of phage P22 and are delayed in their ability to form viable phage particles following induction of a phage P22 lysogen. These data indicate that ssrA plays a role in the pathogenesis of Salmonella, serves as an attachment site for Salmonella-specific sequences, and is required for the growth of phage P22. PMID:10692360

Sympathetic skin responses in patients with hyperthyroidism.

PubMed

Gozke, E; Ozyurt, Z; Dortcan, N; Ore, O; Kocer, A; Ozer, E

2007-01-01

The aim of this study was to investigate the disorders of sympathetic nervous system in patients with hyperthyroidism using sympathetic skin response (SSR). Twenty-two newly diagnosed cases with hyperthyroidism were included in the study. The results were compared with those of 20 healthy controls. SSR was recorded with the contralateral electrical stimulation of the median nerve (of the upper extremities) and tibial nerve (of the lower extremities) with active electrodes placed on palms and soles and reference electrodes attached on the dorsal aspects of hands and feet. Ages of the cases with hyperthyroidism and controls ranged between 15-65 years (mean: 46.7 +/- 15.0 years) and 24-62 years (mean: 39.6 +/- 9.8 years) respectively (p > 0.05). In all the control subjects SSR could be obtained, while from the lower extremities of 4 cases with hyperthyroidism (18.0%) SSR could not be elicited. Mean SSR latencies of lower extremities were found significantly longer than control group (p < 0. 05). No difference was detected between mean amplitudes of SSR in upper and lower extremities. These findings suggest that SSR is useful for investigation of sympathetic nervous system involvement in cases with hyperthyroidism.

DNA profiling of pineapple cultivars in Japan discriminated by SSR markers

PubMed Central

Shoda, Moriyuki; Urasaki, Naoya; Sakiyama, Sumisu; Terakami, Shingo; Hosaka, Fumiko; Shigeta, Narumi; Nishitani, Chikako; Yamamoto, Toshiya

2012-01-01

We developed 18 polymorphic simple sequence repeat (SSR) markers in pineapple (Ananas comosus) by using genomic libraries enriched for GA and CA motifs. The markers were used to genotype 31 pineapple accessions, including seven cultivars and 11 breeding lines from Okinawa Prefecture, 12 foreign accessions and one from a related species. These SSR loci were highly polymorphic: the 31 accessions contained three to seven alleles per locus, with an average of 4.1. The values of expected heterozygosity ranged from 0.09 to 0.76, with an average of 0.52. All 31 accessions could be successfully differentiated by the 18 SSR markers, with the exception of ‘N67-10’ and ‘Hawaiian Smooth Cayenne’. A single combination of three markers TsuAC004, TsuAC010 and TsuAC041, was enough to distinguish all accessions with one exception. A phenogram based on the SSR genotypes did not show any distinct groups, but it suggested that pineapples bred in Japan are genetically diversed. We reconfirmed the parentage of 14 pineapple accessions by comparing the SSR alleles at 17 SSR loci in each accession and its reported parents. The obtained information will contribute substantially to protecting plant breeders’ rights. PMID:23341750

Cultivar identification and genetic relationship of pineapple (Ananas comosus) cultivars using SSR markers.

PubMed

Lin, Y S; Kuan, C S; Weng, I S; Tsai, C C

2015-11-25

The genetic relationships among 27 pineapple [Ananas comosus (L.) Merr.] cultivars and lines were examined using 16 simple sequence repeat (SSR) markers. The number of alleles per locus of the SSR markers ranged from 2 to 6 (average 3.19), for a total of 51 alleles. Similarity coefficients were calculated on the basis of 51 amplified bands. A dendrogram was created according to the 16 SSR markers by the unweighted pair-group method. The banding patterns obtained from the SSR primers allowed most of the cultivars and lines to be distinguished, with the exception of vegetative clones. According to the dendrogram, the 27 pineapple cultivars and lines were clustered into three main clusters and four individual clusters. As expected, the dendrogram showed that derived cultivars and lines are closely related to their parental cultivars; the genetic relationships between pineapple cultivars agree with the genealogy of their breeding history. In addition, the analysis showed that there is no obvious correlation between SSR markers and morphological characters. In conclusion, SSR analysis is an efficient method for pineapple cultivar identification and can offer valuable informative characters to identify pineapple cultivars in Taiwan.

Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

PubMed

Rauscher, Gilda; Simko, Ivan

2013-01-22

Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.

Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes

PubMed Central

2013-01-01

Background Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Results Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. Conclusions The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes. PMID:23339733

Retrieving high-resolution surface solar radiation with cloud parameters derived by combining MODIS and MTSAT data

NASA Astrophysics Data System (ADS)

Tang, Wenjun; Qin, Jun; Yang, Kun; Liu, Shaomin; Lu, Ning; Niu, Xiaolei

2016-03-01

Cloud parameters (cloud mask, effective particle radius, and liquid/ice water path) are the important inputs in estimating surface solar radiation (SSR). These parameters can be derived from MODIS with high accuracy, but their temporal resolution is too low to obtain high-temporal-resolution SSR retrievals. In order to obtain hourly cloud parameters, an artificial neural network (ANN) is applied in this study to directly construct a functional relationship between MODIS cloud products and Multifunctional Transport Satellite (MTSAT) geostationary satellite signals. In addition, an efficient parameterization model for SSR retrieval is introduced and, when driven with MODIS atmospheric and land products, its root mean square error (RMSE) is about 100 W m-2 for 44 Baseline Surface Radiation Network (BSRN) stations. Once the estimated cloud parameters and other information (such as aerosol, precipitable water, ozone) are input to the model, we can derive SSR at high spatiotemporal resolution. The retrieved SSR is first evaluated against hourly radiation data at three experimental stations in the Haihe River basin of China. The mean bias error (MBE) and RMSE in hourly SSR estimate are 12.0 W m-2 (or 3.5 %) and 98.5 W m-2 (or 28.9 %), respectively. The retrieved SSR is also evaluated against daily radiation data at 90 China Meteorological Administration (CMA) stations. The MBEs are 9.8 W m-2 (or 5.4 %); the RMSEs in daily and monthly mean SSR estimates are 34.2 W m-2 (or 19.1 %) and 22.1 W m-2 (or 12.3 %), respectively. The accuracy is comparable to or even higher than two other radiation products (GLASS and ISCCP-FD), and the present method is more computationally efficient and can produce hourly SSR data at a spatial resolution of 5 km.

Retrieving high-resolution surface solar radiation with cloud parameters derived by combining MODIS and MTSAT data

NASA Astrophysics Data System (ADS)

Tang, W.; Qin, J.; Yang, K.; Liu, S.; Lu, N.; Niu, X.

2015-12-01

Cloud parameters (cloud mask, effective particle radius and liquid/ice water path) are the important inputs in determining surface solar radiation (SSR). These parameters can be derived from MODIS with high accuracy but their temporal resolution is too low to obtain high temporal resolution SSR retrievals. In order to obtain hourly cloud parameters, the Artificial Neural Network (ANN) is applied in this study to directly construct a functional relationship between MODIS cloud products and Multi-functional Transport Satellite (MTSAT) geostationary satellite signals. Meanwhile, an efficient parameterization model for SSR retrieval is introduced and, when driven with MODIS atmospheric and land products, its root mean square error (RMSE) is about 100 W m-2 for 44 Baseline Surface Radiation Network (BSRN) stations. Once the estimated cloud parameters and other information (such as aerosol, precipitable water, ozone and so on) are input to the model, we can derive SSR at high spatio-temporal resolution. The retrieved SSR is first evaluated against hourly radiation data at three experimental stations in the Haihe River Basin of China. The mean bias error (MBE) and RMSE in hourly SSR estimate are 12.0 W m-2 (or 3.5 %) and 98.5 W m-2 (or 28.9 %), respectively. The retrieved SSR is also evaluated against daily radiation data at 90 China Meteorological Administration (CMA) stations. The MBEs are 9.8 W m-2 (5.4 %); the RMSEs in daily and monthly-mean SSR estimates are 34.2 W m-2 (19.1 %) and 22.1 W m-2 (12.3 %), respectively. The accuracy is comparable or even higher than other two radiation products (GLASS and ISCCP-FD), and the present method is more computationally efficient and can produce hourly SSR data at a spatial resolution of 5 km.

Sparse signal representation and its applications in ultrasonic NDE.

PubMed

Zhang, Guang-Ming; Zhang, Cheng-Zhong; Harvey, David M

2012-03-01

Many sparse signal representation (SSR) algorithms have been developed in the past decade. The advantages of SSR such as compact representations and super resolution lead to the state of the art performance of SSR for processing ultrasonic non-destructive evaluation (NDE) signals. Choosing a suitable SSR algorithm and designing an appropriate overcomplete dictionary is a key for success. After a brief review of sparse signal representation methods and the design of overcomplete dictionaries, this paper addresses the recent accomplishments of SSR for processing ultrasonic NDE signals. The advantages and limitations of SSR algorithms and various overcomplete dictionaries widely-used in ultrasonic NDE applications are explored in depth. Their performance improvement compared to conventional signal processing methods in many applications such as ultrasonic flaw detection and noise suppression, echo separation and echo estimation, and ultrasonic imaging is investigated. The challenging issues met in practical ultrasonic NDE applications for example the design of a good dictionary are discussed. Representative experimental results are presented for demonstration. Copyright © 2011 Elsevier B.V. All rights reserved.

The Role of Parents and Parental Mediation on 0-3-Year Olds' Digital Play with Smart Devices: Estonian Parents' Attitudes and Practices

ERIC Educational Resources Information Center

Nevski, Elyna; Siibak, Andra

2016-01-01

In this manuscript, we analyse the attitudes and practices of Estonian parents (N = 198) who allowed their 0-3-year olds to use smart devices. We aimed to discover if there was an interaction between parental use of smart technologies, parents' attitudes and the child's age that would predict young children's usage of smart devices. We also wanted…

Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel.

PubMed

Mitt, Mario; Kals, Mart; Pärn, Kalle; Gabriel, Stacey B; Lander, Eric S; Palotie, Aarno; Ripatti, Samuli; Morris, Andrew P; Metspalu, Andres; Esko, Tõnu; Mägi, Reedik; Palta, Priit

2017-06-01

Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF)≥5% and low-frequency variants (0.5≤MAF<5%) across diverse populations, but the imputation of rare variation (MAF<0.5%) is still rather limited. In the current study, we evaluate imputation accuracy achieved with reference panels from diverse populations with a population-specific high-coverage (30 ×) whole-genome sequencing (WGS) based reference panel, comprising of 2244 Estonian individuals (0.25% of adult Estonians). Although the Estonian-specific panel contains fewer haplotypes and variants, the imputation confidence and accuracy of imputed low-frequency and rare variants was significantly higher. The results indicate the utility of population-specific reference panels for human genetic studies.

Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel

PubMed Central

Mitt, Mario; Kals, Mart; Pärn, Kalle; Gabriel, Stacey B; Lander, Eric S; Palotie, Aarno; Ripatti, Samuli; Morris, Andrew P; Metspalu, Andres; Esko, Tõnu; Mägi, Reedik; Palta, Priit

2017-01-01

Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF)≥5% and low-frequency variants (0.5≤MAF<5%) across diverse populations, but the imputation of rare variation (MAF<0.5%) is still rather limited. In the current study, we evaluate imputation accuracy achieved with reference panels from diverse populations with a population-specific high-coverage (30 ×) whole-genome sequencing (WGS) based reference panel, comprising of 2244 Estonian individuals (0.25% of adult Estonians). Although the Estonian-specific panel contains fewer haplotypes and variants, the imputation confidence and accuracy of imputed low-frequency and rare variants was significantly higher. The results indicate the utility of population-specific reference panels for human genetic studies. PMID:28401899

The growth of IQ among Estonian schoolchildren from ages 7 to 19.

PubMed

Pullmann, Helle; Allik, Jüri; Lynn, Richard

2004-11-01

The Standard Progressive Matrices test was standardized in Estonia on a representative sample of 4874 schoolchildren aged from 7 to 19 years. When the IQ of Estonian children was expressed in relation to British and Icelandic norms, both demonstrated a similar sigmoid relationship. The youngest Estonian group scored higher than the British and Icelandic norms: after first grade, the score fell below 100 and remained lower until age 12, and after that age it increased above the mean level of these two comparison countries. The difference between the junior school children and the secondary school children may be due to schooling, sampling error or different trajectories of intellectual maturation in different populations. Systematic differences in the growth pattern suggest that the development of intellectual capacities proceeds at different rates and the maturation process can take longer in some populations than in others.

M-learning in a geography lesson

NASA Astrophysics Data System (ADS)

Mirski, Katri

2014-05-01

We live in rapidly advancing world. Our homes and offices are invaded by new technological achievements. School is a part of the society and many students nowadays use smartphones and table pc's daily. Therefore it's important that schoolteachers advise them on how to manage in such a complex world of engineering miracles and show how to use this kind of equipment in their studies and everyday life. Geography is a natural substance and the best way to study nature is to see, touch and feel it directly. It's important to link the theoretical knowledge that students acquire in a classroom with a practical work in the nature. M-learning gives a great opportunity for that. M-learning, shortened from mobile learning is defined as learning across multiple contexts, through social and content interactions, using personal electronic devices. The main goal of M-learning is to bring new technological equipment to the studies for the purpose of diversifying the learning process. You can use M-learning whether students are doing individual or teamwork. By doing the practical work and thinking all the steps through the students are more actively involved in the learning process and can acquire and fix the knowledge more effectively. Personal electronic devices give the freedom to study anytime and anywhere. This means M-learning is really good for trails and other outdoor activities. In spring 2012 I did my Master's thesis about M-learning. For it I compiled a geographical trail in Tallinn city centre. There were many different geographical tasks that students had to solve. The trail included whether observation, practical work on a slope (measuring the height and the inclination of a slope), drawing a plan, questions about rocks, trees and many other tasks. The students had worksheets, where there were only geographical coordinates. They used GPS devices to get to the designated points. In every point they had a task to take a photo. After the exercises the students formed their work in Google Earth where they did a tour of their journey. In the feedback students said that it was a very interesting and an educational practical task. A new opportunity in M-learning is to use QR codes. This means that you don't have to print out worksheets with questions. You can hide question in the code and students can read them with their own devices on site. From the Master's thesis I also developed a tutorial material named "M-learning in a geography lesson" (in Estonian: M-õpe geograafiatunnis), you can see it in the webpage katrimope@wordpress.com. The tutorial received a second place on the Estonian study material contest in 2013. This is only one example on how to use M-learning. In Gustav Adolf Grammar School we use M-learning in lots of different subjects because it's really important in modern school to link new technologies, surrounding environment and learning for the purpose of better obtainment of knowledge.

Development and validation of new SSR markers from expressed regions in the garlic genome

USDA-ARS?s Scientific Manuscript database

Limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) although SSR markers have become one of the most preferred marker systems because they are typically co-dominant, reproducible, cross species transferable and highly polymorphic. In this ...

Differential transferability of EST-SSR primers developed from diploid species Pseudoroegneria spicata, Thinopyrum bessarabicum, and Th. elongatum

USDA-ARS?s Scientific Manuscript database

Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid T...

Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane

USDA-ARS?s Scientific Manuscript database

Though sugarcane cultivars (Saccharum spp. hybrids) are complex aneu-polyploid hybrids, genetic evaluation and tracking of clone- or cultivar-specific alleles become possible due to capillary electrophoregrams (CE) using fluorescence-labeled SSR primer pairs. Twenty-four sugarcane cultivars, 12 each...

Suicide in Greece 1992-2012: A time-series analysis.

PubMed

Papaslanis, Theodoros; Kontaxakis, Vassilis; Christodoulou, Christos; Konstantakopoulos, George; Kontaxaki, Maria-Irini; Papadimitriou, George N

2016-08-01

Since 2008, Greece has entered a long period of economic crisis with adverse effects on various aspects of daily life. In this frame, it is quite important to examine the suicide trends in Greece. Our analysis covered the period 1992-2012. 2012 was the last year for which official suicide data were available. The inclusion of data for pre-crisis period enabled us to assess trends in suicide preceding the economic crisis, starting in 2008. Trends in sex- and age-adjusted standardized suicide rates (SSR) were analyzed using joinpoint regression. Total SSR presented statistically significant annual decrease of 0.89% (95% confidence interval (CI): -1.7, -0.1) during the period 1992-2008. After 2009, the trend in total SSR increased statistically significant annual increase (12.48%; 95% CI: 0.3%, 26.1%). SSR in males presented an initial period of modest annual decrease (-0.84%; 95% CI: -1.6%, -0.1%), during the period 1992-2008. After 2009, an annual increase by 9.25% (95% CI: 2.7%, 16.3%) was revealed. No change in female SSR trend was observed during the studied period. According to the results of this study, there is clear evidence of an increase in the overall SSR and male SSR in Greece during the period of the current financial crisis. © The Author(s) 2016.

Loblolly pine SSR markers for shortleaf pine genetics

Treesearch

C. Dana Nelson; Sedley Josserand; Craig S. Echt; Jeff Koppelman

2007-01-01

Simple sequence repeats (SSR) are highly informative DNA-based markers widely used in population genetic and linkage mapping studies. We have been developing PCR primer pairs for amplifying SSR markers for loblolly pine (Pinus taeda L.) using loblolly pine DNA and EST sequence data as starting materials. Fifty primer pairs known to reliably amplify...

Causes of the sharp increase in the time series of surface solar radiation in China between 1990 and 1993

NASA Astrophysics Data System (ADS)

Wang, Yawen; Wild, Martin

2017-02-01

During 1990-1993, a nation-wide replacement of the instruments measuring surface solar radiation (SSR) and a restructuring of SSR stations took place in China. Meanwhile, a sudden upward jump was noted in published composite time series of observed SSR records in this period. This study clarifies that about 1/3 of the magnitude of the SSR jump in China was accidentally caused by the abandonment/establishment of 51 stations (˜39% of total) during the period of 1990-1993. The remaining 2/3 of the SSR jump was only caused by 22 stations detected by the methods of the accumulated deviation curve and the Mann-Whitney U test. Out of these 22 stations, about 1/4 of the SSR jump were caused by 6 stations due to natural factors, as similar variations were recorded by sunshine duration. The other 3/4 were caused by the remaining 16 stations as a result of artificial factors such as instrument replacement, changes in the classification or location of stations, or potential operational errors.

Genetic variation assessment of acid lime accessions collected from south of Iran using SSR and ISSR molecular markers.

PubMed

Sharafi, Ata Allah; Abkenar, Asad Asadi; Sharafi, Ali; Masaeli, Mohammad

2016-01-01

Iran has a long history of acid lime cultivation and propagation. In this study, genetic variation in 28 acid lime accessions from five regions of south of Iran, and their relatedness with other 19 citrus cultivars were analyzed using Simple Sequence Repeat (SSR) and Inter-Simple Sequence Repeat (ISSR) molecular markers. Nine primers for SSR and nine ISSR primers were used for allele scoring. In total, 49 SSR and 131 ISSR polymorphic alleles were detected. Cluster analysis of SSR and ISSR data showed that most of the acid lime accessions (19 genotypes) have hybrid origin and genetically distance with nucellar of Mexican lime (9 genotypes). As nucellar of Mexican lime are susceptible to phytoplasma, these acid lime genotypes can be used to evaluate their tolerance against biotic constricts like lime "witches' broom disease".

The combination of energy-dependent internal adaptation mechanisms and external factors enables Listeria monocytogenes to express a strong starvation survival response during multiple-nutrient starvation.

PubMed

Lungu, Bwalya; Saldivar, Joshua C; Story, Robert; Ricke, Steven C; Johnson, Michael G

2010-05-01

The goal of this study was to characterize the starvation survival response (SSR) of a wild-type Listeria monocytogenes 10403S and an isogenic DeltasigB mutant strain during multiple-nutrient starvation conditions over 28 days. This study examined the effects of inhibitors of protein synthesis, the proton motive force, substrate level phosphorylation, and oxidative phosphorylation on the SSR of L. monocytogenes 10403S and a DeltasigB mutant during multiple-nutrient starvation. The effects of starvation buffer changes on viability were also examined. During multiple-nutrient starvation, both strains expressed a strong SSR, suggesting that L. monocytogenes possesses SigB-independent mechanism(s) for survival during multiple-nutrient starvation. Neither strain was able to express an SSR following starvation buffer changes, indicating that the nutrients/factors present in the starvation buffer could be a source of energy for cell maintenance and survival. Neither the wild-type nor the DeltasigB mutant strain was able to elicit an SSR when exposed to the protein synthesis inhibitor chloramphenicol within the first 4 h of starvation. However, both strains expressed an SSR when exposed to chloramphenicol after 6 h or more of starvation, suggesting that the majority of proteins required to elicit an effective SSR in L. monocytogenes are likely produced somewhere between 4 and 6 h of starvation. The varying SSRs of both strains to the different metabolic inhibitors under aerobic or anaerobic conditions suggested that (1) energy derived from the proton motive force is important for an effective SSR, (2) L. monocytogenes utilizes an anaerobic electron transport during multiple-nutrient starvation conditions, and (3) the glycolytic pathway is an important energy source during multiple-nutrient starvation when oxygen is available, and less important under anaerobic conditions. Collectively, the data suggest that the combination of energy-dependent internal adaptation mechanisms of cells and external nutrients/factors enables L. monocytogenes to express a strong SSR.

Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.].

PubMed

Jia, Xiaoping; Zhang, Zhongbao; Liu, Yinghui; Zhang, Chengwei; Shi, Yunsu; Song, Yanchun; Wang, Tianyu; Li, Yu

2009-02-01

SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F(2) population, i.e. "B100" of cultivated S. italica and "A10" of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces' grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together.

An Application of Interactive Computer Graphics to the Study of Inferential Statistics and the General Linear Model

DTIC Science & Technology

1991-09-01

matrix, the Regression Sum of Squares (SSR) and Error Sum of Squares (SSE) are also displayed as a percentage of the Total Sum of Squares ( SSTO ...vector when the student compares the SSR to the SSE. In addition to the plot, the actual values of SSR, SSE, and SSTO are also provided. Figure 3 gives the...Es ainSpace = E 3 Error- Eor Space =n t! L . Pro~cio q Yonto Pro~rct on of Y onto the simaton, pac ror Space SSR SSEL0.20 IV = 14,1 +IErrorI 2 SSTO

Data of 10 SSR markers for genomes of homo sapiens and monkeys.

PubMed

Reddy, K K V V V S; Raju, S Viswanadha; Someswara Rao, Chinta

2017-06-01

In this data, we present 10 Simple Sequence Repeat(SSR) markers TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA which are extracted from the genomes of homo sapiens and monkeys using string matching mechanism [1]. All loci showed 4 Base Pair(bp) in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that maybe useful for the detection of similarity among the genotypes. Collectively, these data show that the SSR extraction is a valuable method to illustrate genetic variation of genomes.

Attitudes of Major Soviet Nationalities. Volume II. The Baltics. Estonia, Latvia, Lithuania.

DTIC Science & Technology

1973-06-01

acquired wide popularity (and probably snob appeal ). Kafka, Ionesco and Dostoyevsky were available to Soviet Estonians earlier than to the Russian reading...Estonia . chided as snob appeal ). Of Estonia’s 757 general schools, 556 (i.e. 71) use Estonian, 90 use Russian and 60 are mixed. 2 The same applies to...novels whicr combine literary quality with national appeal ro 2 ’), collective farm realism at its best (M. Traatl), realisti> lezcription of city life

Construction of an Integrated High Density Simple Sequence Repeat Linkage Map in Cultivated Strawberry (Fragaria × ananassa) and its Applicability

PubMed Central

Isobe, Sachiko N.; Hirakawa, Hideki; Sato, Shusei; Maeda, Fumi; Ishikawa, Masami; Mori, Toshiki; Yamamoto, Yuko; Shirasawa, Kenta; Kimura, Mitsuhiro; Fukami, Masanobu; Hashizume, Fujio; Tsuji, Tomoko; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Tsuruoka, Hisano; Minami, Chiharu; Takahashi, Chika; Wada, Tsuyuko; Ono, Akiko; Kawashima, Kumiko; Nakazaki, Naomi; Kishida, Yoshie; Kohara, Mitsuyo; Nakayama, Shinobu; Yamada, Manabu; Fujishiro, Tsunakazu; Watanabe, Akiko; Tabata, Satoshi

2013-01-01

The cultivated strawberry (Fragaria× ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA′A′BBB′B′ model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers. PMID:23248204

Microsatellite DNA as shared genetic markers among conifer species

Treesearch

C.S. Echt; G.G. Vendramin; C. D. Nelson; Paula E. Marquardt

1999-01-01

Polymerase chain reaction (PCR) primer pairs for 21 simple sequence repeat (SSR) loci in Pinus strobus L, and 6 in Pinus radiata D. Don were evaluated to determine whether SSR marker amplification could be achieved in 1O other conifer species. Eighty percent of SSR primer pairs for (AC) loci that were polymorphic in P. ...

Microsatellite DNA in genomic survey sequences and UniGenes of loblolly pine

Treesearch

Craig S Echt; Surya Saha; Dennis L Deemer; C Dana Nelson

2011-01-01

Genomic DNA sequence databases are a potential and growing resource for simple sequence repeat (SSR) marker development in loblolly pine (Pinus taeda L.). Loblolly pine also has many expressed sequence tags (ESTs) available for microsatellite (SSR) marker development. We compared loblolly pine SSR densities in genome survey sequences (GSSs) to those in non-redundant...

Effects of High Power Lasers, Number 5, September 1974 - February 1975

DTIC Science & Technology

1975-05-01

EOM J AiO FG1V FiKhOM F-KhMM FMiM FTP FTT FZh GiA GiK IAN Arm D\\.N Az SOURCE AB13Ri:viATIONS Avtomatika i tclcmekhanika Acta physica ... polonica Akadcniya nauk Armyanskoy SSR. Doklady Akadcrniya nauk Azerbaydzhanskoy SSR. Doklady Akadcrniya nauk Belorusskoy SSR. Doklady Ak

Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait

Treesearch

Craig S. Echt; L.L. DeVerno; M. Anzidei; G.G. Vendramin

1998-01-01

Variation in paternally inherited chloroplast microsatellite (cpSSR) DNA was used to study population genetic structure in red pine (Pinus resinosa Ait.), a species characterized by morphological uniformity, no allozyme variation, and limited RAPD variation. Using nine cpSSR loci, a total of 23 chloroplast haplotypes and 25 cpSSR alleles were were...

Microsatellite DNA as shared genetic markers among conifer species

Treesearch

Craig S. Echt; G.G. Vendramin; C.D. Nelson; P. Marquardt

1999-01-01

Polymerase chain reaction (PCR) primer pairs for 21 simple sequence repeat (SSR) loci in Pinus strobus L. and 6 in Pinus radiata D. Don. were evaluated to determine whether SSR marker amplification could be achieved in 10 other conifer species. Eighty percent of SSR primer pairs for (AC)n loci that were polymorphic in P. ...

Numerical simulation of surface solar radiation over Southern Africa. Part 1: Evaluation of regional and global climate models

NASA Astrophysics Data System (ADS)

Tang, Chao; Morel, Béatrice; Wild, Martin; Pohl, Benjamin; Abiodun, Babatunde; Bessafi, Miloud

2018-02-01

This study evaluates the performance of climate models in reproducing surface solar radiation (SSR) over Southern Africa (SA) by validating five Regional Climate Models (RCM, including CCLM4, HIRHAM5, RACMO22T, RCA4 and REMO2009) that participated in the Coordinated Regional Downscaling Experiment program over Africa (CORDEX-Africa) along with their ten driving General Circulation Models (GCMs) from the Coupled Model Intercomparison Project Phase 5 over SA. The model simulated SSR was thereby compared to reference data from ground-based measurements, satellite-derived products and reanalyses over the period 1990-2005. Results show that (1) the references obtained from satellite retrievals and reanalyses overall overestimate SSR by up to 10 W/m2 on average when compared to ground-based measurements from the Global Energy Balance Archive, which are located mainly over the eastern part of the southern African continent. (2) Compared to one of the satellite products (Surface Solar Radiation Data Set—Heliosat Edition 2; SARAH-2): GCMs overestimate SSR over SA in terms of their multi-model mean by about 1 W/m2 (compensation of opposite biases over sub-regions) and 7.5 W/m2 in austral summer and winter respectively; RCMs driven by GCMs show in their multimodel mean underestimations of SSR in both seasons with Mean Bias Errors (MBEs) of about - 30 W/m2 in austral summer and about - 14 W/m2 in winter compared to SARAH-2. This multi-model mean low bias is dominated by the simulations of the CCLM4, with negative biases up to - 76 W/m2 in summer and - 32 W/m2 in winter. (3) The discrepancies in the simulated SSR over SA are larger in the RCMs than in the GCMs. (4) In terms of trend during the "brightening" period 1990-2005, both GCMs and RCMs (driven by European Centre for Medium-Range Weather Forecasts Reanalysis ERA-Interim, short as ERAINT and GCMs) simulate an SSR trend of less than 1 W/m2 per decade. However, variations of SSR trend exist among different references data. (5) For individual RCM models, their SSR bias fields seem rather insensitive with respect to the different lateral forcings provided by ERAINT and various GCMs, in line with previous findings over Europe. (6) Biases in SSR are overall qualitatively consistent with those in total cloud cover. The information obtained in present study is of crucial importance for understanding future climate projections of SSR and for relevant impact studies.

Development and characterization of genomic SSR markers in Cynodon transvaalensis Burtt-Davy.

PubMed

Tan, Chengcheng; Wu, Yanqi; Taliaferro, Charles M; Bell, Greg E; Martin, Dennis L; Smith, Mike W

2014-08-01

Simple sequence repeat (SSR) markers are a major molecular tool for genetic and genomic research that have been extensively developed and used in major crops. However, few are available in African bermudagrass (Cynodon transvaalensis Burtt-Davy), an economically important warm-season turfgrass species. African bermudagrass is mainly used for hybridizations with common bermudagrass [C. dactylon var. dactylon (L.) Pers.] in the development of superior interspecific hybrid turfgrass cultivars. Accordingly, the major objective of this study was to develop and characterize a large set of SSR markers. Genomic DNA of C. transvaalensis '4200TN 24-2' from an Oklahoma State University (OSU) turf nursery was extracted for construction of four SSR genomic libraries enriched with [CA](n), [GA](n), [AAG](n), and [AAT](n) as core repeat motifs. A total of 3,064 clones were sequenced at the OSU core facility. The sequences were categorized into singletons and contiguous sequences to exclude redundancy. From the two sequence categories, 1,795 SSR loci were identified. After excluding duplicate SSRs by comparison with previously developed SSR markers using a nucleotide basic local alignment tool, 1,426 unique primer pairs (PPs) were designed. Out of the 1,426 designed PPs, 981 (68.8 %) amplified alleles of the expected size in the donor DNA. Polymorphisms of the SSR PPs tested in eight C. transvaalensis plants were 93 % polymorphic with 544 markers effective in all genotypes. Inheritance of the SSRs was examined in six F(1) progeny of African parents 'T577' × 'Uganda', indicating 917 markers amplified heritable alleles. The SSR markers developed in the study are the first large set of co-dominant markers in African bermudagrass and should be highly valuable for molecular and traditional breeding research.

Traffic at the tmRNA Gene

PubMed Central

Williams, Kelly P.

2003-01-01

A partial screen for genetic elements integrated into completely sequenced bacterial genomes shows more significant bias in specificity for the tmRNA gene (ssrA) than for any type of tRNA gene. Horizontal gene transfer, a major avenue of bacterial evolution, was assessed by focusing on elements using this single attachment locus. Diverse elements use ssrA; among enterobacteria alone, at least four different integrase subfamilies have independently evolved specificity for ssrA, and almost every strain analyzed presents a unique set of integrated elements. Even elements using essentially the same integrase can be very diverse, as is a group with an ssrA-specific integrase of the P4 subfamily. This same integrase appears to promote damage routinely at attachment sites, which may be adaptive. Elements in arrays can recombine; one such event mediated by invertible DNA segments within neighboring elements likely explains the monophasic nature of Salmonella enterica serovar Typhi. One of a limited set of conserved sequences occurs at the attachment site of each enterobacterial element, apparently serving as a transcriptional terminator for ssrA. Elements were usually found integrated into tRNA-like sequence at the 3′ end of ssrA, at subsites corresponding to those used in tRNA genes; an exception was found at the non-tRNA-like 3′ end produced by ssrA gene permutation in cyanobacteria, suggesting that, during the evolution of new site specificity by integrases, tropism toward a conserved 3′ end of an RNA gene may be as strong as toward a tRNA-like sequence. The proximity of ssrA and smpB, which act in concert, was also surveyed. PMID:12533482

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

PubMed Central

Tong, Helin; Chen, You; Wang, Jingyi; Chen, Yeyuan; Sun, Guangming; He, Junhu; Wu, Yaoting

2013-01-01

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region. PMID:24024187

Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae.

PubMed

Wang, Yi; Yang, Chao; Jin, Qiaojun; Zhou, Dongjie; Wang, Shuangshuang; Yu, Yuanjie; Yang, Long

2015-02-15

The Poaceae family is of great importance to human beings since it comprises the cereal grasses which are the main sources for human food and animal feed. With the rapid growth of genomic data from Poaceae members, comparative genomics becomes a convinent method to study genetics of diffierent species. The SSRs (Simple Sequence Repeats) are widely used markers in the studies of Poaceae for their high abundance and stability. In this study, using the genomic sequences of 9 Poaceae species, we detected 11,993,943 SSR loci and developed 6,799,910 SSR primer pairs. The results show that SSRs are distributed on all the genomic elements in grass. Hexamer is the most frequent motif and AT/TA is the most frequent motif in dimer. The abundance of the SSRs has a positive linear relationship with the recombination rate. SSR sequences in the coding regions involve a higher GC content in the Poaceae than that in the other species. SSRs of 70-80 bp in length showed the highest AT/GC base ratio among all of these loci. The result shows the highest polymorphism rate belongs to the SSRs ranged from 30 bp to 40 bp. Using all the SSR primers of Japonica, nineteen universal primers were selected and located on the genome of the grass family. The information of SSR loci, the SSR primers and the tools of mining and analyzing SSR are provided in the PSSRD (Poaceae SSR Database, http://biodb.sdau.edu.cn/pssrd/). Our study and the PSSRD database provide a foundation for the comparative study in the Poaceae and it will accelerate the study on markers application, gene mapping and molecular breeding.

Association of SSR markers with contents of fatty acids in olive oil and genetic diversity analysis of an olive core collection.

PubMed

Ipek, M; Ipek, A; Seker, M; Gul, M K

2015-03-27

The purpose of this research was to characterize an olive core collection using some agronomic characters and simple sequence repeat (SSR) markers and to determine SSR markers associated with the content of fatty acids in olive oil. SSR marker analysis demonstrated the presence of a high amount of genetic variation between the olive cultivars analyzed. A UPGMA dendrogram demonstrated that olive cultivars did not cluster on the basis of their geographic origin. Fatty acid components of olive oil in these cultivars were determined. The results also showed that there was a great amount of variation between the olive cultivars in terms of fatty acid composition. For example, oleic acid content ranged from 57.76 to 76.9% with standard deviation of 5.10%. Significant correlations between fatty acids of olive oil were observed. For instance, a very high negative correlation (-0.812) between oleic and linoleic acids was detected. A structured association analysis between the content of fatty acids in olive oil and SSR markers was performed. STRUCTURE analysis assigned olive cultivars to two gene pools (K = 2). Assignment of olive cultivars to these gene pools was not based on geographical origin. Association between fatty acid traits and SSR markers was evaluated using the general linear model of TASSEL. Significant associations were determined between five SSR markers and stearic, oleic, linoleic, and linolenic acids of olive oil. Very high associations (P < 0.001) between ssrOeUA-DCA14 and stearic acid and between GAPU71B and oleic acid indicated that these markers could be used for marker-assisted selection in olive.

DNA Profiles of MTG (Moderat Tahan Gano) Oil Palm Variety Based on SSR Marker

NASA Astrophysics Data System (ADS)

Putri, L. A. P.; Setiado, H.; Hardianti, R.

2017-03-01

The oil palm, an economically important tree in Indonesia, has been one of the world’s major sources of edible oil and a significant precursor of biodiesel fuel. The objectives of this study were to know DNA profile of commercial MTG (Moderat Tahan Gano) oil palm variety collections. A total of 10 trees MTG oil palm variety were used for analysis. In this experiment, the DNA profile diversity was assessed using mEgCIR0174 and SSR-1 loci of oil palm’s specific SSR markers. The results of the experiment indicated out of 3 alleles of pcr product of mEgCIR0174 (198, 203 and 208 bp) and SSR-1 (201, 217 and 232 bp). These preliminary results demonstrated SSR marker can be used to evaluate genetic relatedness among trees of MTG (Moderat Tahan Gano) oil palm variety derived from different crossing or difference to desease resistance trait or misslabeled.

Development and Molecular Characterization of Novel Polymorphic Genomic DNA SSR Markers in Lentinula edodes.

PubMed

Moon, Suyun; Lee, Hwa-Yong; Shim, Donghwan; Kim, Myungkil; Ka, Kang-Hyeon; Ryoo, Rhim; Ko, Han-Gyu; Koo, Chang-Duck; Chung, Jong-Wook; Ryu, Hojin

2017-06-01

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

Use of Simple Sequence Repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot

USDA-ARS?s Scientific Manuscript database

In recent years SSR markers have been used widely for the genetic analysis. The objective of present research was to use SSR markers to develop DNA-based genetic identification and analyze genetic relationship of sugarcane cultivars grown in Pakistan either resistant or susceptible to red rot. Twent...

Use of suprathreshold stochastic resonance in cochlear implant coding

NASA Astrophysics Data System (ADS)

Allingham, David; Stocks, Nigel G.; Morse, Robert P.

2003-05-01

In this article we discuss the possible use of a novel form of stochastic resonance, termed suprathreshold stochastic resonance (SSR), to improve signal encoding/transmission in cochlear implants. A model, based on the leaky-integrate-and-fire (LIF) neuron, has been developed from physiological data and use to model information flow in a population of cochlear nerve fibers. It is demonstrated that information flow can, in principle, be enhanced by the SSR effect. Furthermore, SSR was found to enhance information transmission for signal parameters that are commonly encountered in cochlear implants. This, therefore, gives hope that SSR may be implemented in cochlear implants to improve speech comprehension.

Breast milk cytokine and IgA composition differ in Estonian and Swedish mothers-relationship to microbial pressure and infant allergy.

PubMed

Tomicić, Sara; Johansson, Git; Voor, Tiia; Björkstén, Bengt; Böttcher, Malin Fagerås; Jenmalm, Maria C

2010-10-01

The immune system of the neonate is influenced by maternal immunity during pregnancy and lactation. An altered microbial exposure, possibly underlying the increase of allergic diseases in affluent societies, may affect maternal breast milk immune composition. Secretory IgA (SIgA), IL-4, IL-10, IL-13, IFN-[gamma], TGF-[beta]1, and TGF-[beta]2 were analyzed with ELISA in colostrum and 1-mo mature milk from mothers from Estonia (n = 39) and Sweden (n = 60), the two geographically adjacent countries with different living conditions and allergy incidence. The IL-10 and IFN-[gamma] levels were higher in colostrum from Estonian than Swedish mothers, whereas the opposite was true for TGF-[beta]2. In mature milk, higher SIgA and IFN-[gamma] levels but lower TGF-[beta]1 and TGF-[beta]2 levels were observed in Estonian than Swedish mothers. Interestingly, in Sweden but not Estonia, the TGF-[beta]1 and TGF-[beta]2 levels correlated inversely with environmental endotoxin concentrations, whereas positive correlations to microbial load were observed for IL-4, IL-10, and IFN-[gamma]. High colostral IL-13 levels were associated with allergic sensitization during infancy in Sweden. In conclusion, Estonian mothers have lower breast milk levels of TGF-[beta], particularly TGF-[beta]2, but higher levels of SIgA, IL-10, and IFN-[gamma] than Swedish mothers, possibly because of differences in microbial load.

Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism.

PubMed

Gur-Arie, R; Cohen, C J; Eitan, Y; Shelef, L; Hallerman, E M; Kashi, Y

2000-01-01

Computer-based genome-wide screening of the DNA sequence of Escherichia coli strain K12 revealed tens of thousands of tandem simple sequence repeat (SSR) tracts, with motifs ranging from 1 to 6 nucleotides. SSRs were well distributed throughout the genome. Mononucleotide SSRs were over-represented in noncoding regions and under-represented in open reading frames (ORFs). Nucleotide composition of mono- and dinucleotide SSRs, both in ORFs and in noncoding regions, differed from that of the genomic region in which they occurred, with 93% of all mononucleotide SSRs proving to be of A or T. Computer-based analysis of the fine position of every SSR locus in the noncoding portion of the genome relative to downstream ORFs showed SSRs located in areas that could affect gene regulation. DNA sequences at 14 arbitrarily chosen SSR tracts were compared among E. coli strains. Polymorphisms of SSR copy number were observed at four of seven mononucleotide SSR tracts screened, with all polymorphisms occurring in noncoding regions. SSR polymorphism could prove important as a genome-wide source of variation, both for practical applications (including rapid detection, strain identification, and detection of loci affecting key phenotypes) and for evolutionary adaptation of microbes.

Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers

PubMed Central

Li, Hui; Li, Defang; Chen, Anguo; Tang, Huijuan; Li, Jianjun; Huang, Siqi

2016-01-01

Kenaf (Hibiscus cannabinus L.) is an economically important natural fiber crop grown worldwide. However, only 20 expressed tag sequences (ESTs) for kenaf are available in public databases. The aim of this study was to develop large-scale simple sequence repeat (SSR) markers to lay a solid foundation for the construction of genetic linkage maps and marker-assisted breeding in kenaf. We used Illumina paired-end sequencing technology to generate new EST-simple sequences and MISA software to mine SSR markers. We identified 71,318 unigenes with an average length of 1143 nt and annotated these unigenes using four different protein databases. Overall, 9324 complementary pairs were designated as EST-SSR markers, and their quality was validated using 100 randomly selected SSR markers. In total, 72 primer pairs reproducibly amplified target amplicons, and 61 of these primer pairs detected significant polymorphism among 28 kenaf accessions. Thus, in this study, we have developed large-scale SSR markers for kenaf, and this new resource will facilitate construction of genetic linkage maps, investigation of fiber growth and development in kenaf, and also be of value to novel gene discovery and functional genomic studies. PMID:26960153

Fingerprinting and genetic purity assessment of F1 barley hybrids and their salt-tolerant parental lines using nSSR molecular markers.

PubMed

Ben Romdhane, Mériam; Riahi, Leila; Jardak, Rahma; Ghorbel, Abdelwahed; Zoghlami, Nejia

2018-01-01

Hybridity and the genuineness of hybrids are prominent characteristics for quality control of seeds and thereby for varietal improvement. In the current study, the cross between two local barley genotypes (Ardhaoui: female; Testour: male) previously identified as susceptible/tolerant to salt stress in Tunisia was achieved. The hybrid genetic purity of the generated F 1 putative hybrids and the fingerprinting of the parents along with their offspring were assessed using a set of 17 nuclear SSR markers. Among the analyzed loci, 11 nSSR were shown polymorphic among the parents and their offspring. Based on the applied 11 polymorphic SSR loci, a total of 28 alleles were detected with an average of 2.54 alleles per locus. The locus HVM33 presented the highest number of alleles. The highest polymorphism information content value was detected for the locus HVM33 (0.6713) whereas the lowest PIC value (0.368) was revealed by the loci BMAC0156 , EBMAC0970 and BMAG0013 with a mean value of 0.4619. The probabilities of identical genotypes PI for the 11 microsatellite markers were 8.63 × 10 -7 . Banding patterns among parents and hybrids showed polymorphic fragments. The 11 SSR loci had produced unique fingerprints for each analyzed genotype and segregate between the two parental lines and their four hybrids. Parentage analysis confirms the hybrid purity of the four analyzed genotypes. Six Tunisian barley accessions were used as an outgroup in the multivariate analysis to confirm the efficiency of the employed 11 nSSR markers in genetic differentiation among various barley germplasms. Thus, neighbor joining and factorial analysis revealed clearly the discrimination among the parental lines, the four hybrids and the outgroup accessions. Out of the detected polymorphic 11 nuclear SSR markers, a set of five markers ( HVM33 , WMC1E8 , BMAC0154 , BMAC0040 and BMAG0007 ) were shown to be sufficient and informative enough to discriminate among the six genotypes representing the two parental lines and the four hybrids from each others. These five nSSR markers presented the highest number of alleles per locus ( A n ), expected heterozygosity ( H e ), PIC values and the lowest probabilities of identity (PI). These nSSR loci may be used as referral SSR markers for unambiguous discrimination and genetic purity assessment in barley breeding programs.

SSR126768A (4-chloro-3-[(3R)-(+)-5-chloro-1-(2,4-dimethoxybenzyl)-3-methyl-2-oxo-2,3-dihydro-1H-indol-3-yl]-N-ethyl-N-(3-pyridylmethyl)-benzamide, hydrochloride): a new selective and orally active oxytocin receptor antagonist for the prevention of preterm labor.

PubMed

Serradeil-Le Gal, Claudine; Valette, Gérard; Foulon, Loïc; Germain, Guy; Advenier, Charles; Naline, Emmanuel; Bardou, Marc; Martinolle, Jean-Pierre; Pouzet, Brigitte; Raufaste, Danielle; Garcia, Corinne; Double-Cazanave, Eléonore; Pauly, Maxime; Pascal, Marc; Barbier, Alain; Scatton, Bernard; Maffrand, Jean-Pierre; Le Fur, Gérard

2004-04-01

4-chloro-3-[(3R)-(+)-5-chloro-1-(2,4-dimethoxybenzyl)-3-methyl-2-oxo-2,3-dihydro-1H-indol-3-yl]-N-ethyl-N-(3-pyridylmethyl)benzamide, hydrochloride (SSR126768A), a new potent and selective, orally active oxytocin (OT) receptor antagonist was characterized in several biochemical and pharmacological models. In binding studies, SSR126768A showed nanomolar affinity for rat and human recombinant and native OT receptors (K(i) = 0.44 nM) and exhibited much lower affinity for V(1a), V(1b), and V(2) receptors. In addition, it did not interact with a large number of other receptors, enzymes, and ion channels (1 microM). In autoradiographic experiments performed on at-term human pregnant uterus sections, SSR126768A dose dependently displaced [I(125)]d(CH(2))(5)[Tyr(Me)(2), Thr(4), Orn(8) (125)I-Tyr-NH(2)(9)]VT in situ labeling to OT receptors highly expressed in these tissues. In functional studies, SSR126768A behaved as a full antagonist and potently antagonized OT-induced intracellular Ca(2+) increase (K(i) = 0.50 nM) and prostaglandin release (K(i) = 0.45 nM) in human uterine smooth muscle cells. In rat isolated myometrium, OT-induced uterine contractions were competitively antagonized by SSR126768A (pA(2) = 8.47). Similarly, in human pregnant myometrial strips, SSR126768A inhibited the contractile uterine response to OT. In conscious telemetrated rats, oral administration of SSR126768A (1-10 mg/kg) produced a competitive inhibition of the dose response to OT on uterine contractions up to 24 h at 3 mg/kg p.o.; no tachyphylaxis was observed after 4-day repeated treatment. Finally, SSR126768A (30 mg/kg p.o.) significantly delayed parturition in pregnant rats in labor similar to ritodrine (10 mg/kg p.o.). Thus, SSR126768A is a potent, highly selective, orally active OT receptor antagonist with a long duration of action. This molecule could find therapeutic application as a tocolytic agent for acute and chronic oral management of preterm labor.

Experimental considerations in metal mobilization from soil by chelating ligands: The influence of soil-solution ratio and pre-equilibration - A case study on Fe acquisition by phytosiderophores.

PubMed

Schenkeveld, W D C; Kimber, R L; Walter, M; Oburger, E; Puschenreiter, M; Kraemer, S M

2017-02-01

The efficiency of chelating ligands in mobilizing metals from soils and sediments is generally examined under conditions remote from those under which they are exuded or applied in the field. This may lead to incorrect estimations of the mobilizing efficiency. The aim of this study was to establish the influence of the soil solution ratio (SSR) and pre-equilibration with electrolyte solution on metal mobilization and metal displacement. For this purpose a series of interaction experiments with a calcareous clay soil and a biogenic chelating agent, the phytosiderophore 2'-deoxymugineic acid (DMA) were carried out. For a fixed ligand concentration, the SSR had a strong influence on metal mobilization and displacement. Metal complexation was faster at higher SSR. Reactive pools of metals that were predominantly mobilized at SSR 6 (in this case Cu), became depleted at SSR 0.1, whereas metals that were marginally mobilized at SSR 6, were dominantly mobilized at SSR 0.1 (in this case Fe), because of large soil reactive pools. For a fixed "amount of ligand"-to-"amount of soil"-ratio, metal complexation scaled linearly with the SSR. The efficiency of ligands in mobilizing metals under field conditions can be predicted with batch experiments, as long as the ligand-to-soil-ratio is matched. In most previously reported studies this criterion was not met. Equivalent metal-complex concentrations under field conditions can be back-calculated using adsorption isotherms for the respective metal-complexes. Drying and dry storage created labile pools of Fe, Cu and Zn, which were rapidly mobilized upon addition of DMA solution to dry soil. Pre-equilibration decreased these labile pools, leading to smaller concentrations of these metals during initial mobilization, but did not reduce the lag time between ligand addition and onset of microbial degradation of the metal-complexes. Hence SSR and pre-equilibration should be carefully considered when testing the metal mobilizing efficiency of chelating ligands. Copyright © 2016. Published by Elsevier B.V.

Structural Characterization of the Interaction of the Fibroblast Growth Factor Receptor with a Small Molecule Allosteric Inhibitor.

PubMed

Kappert, Franziska; Sreeramulu, Sridhar; Jonker, Hendrik R A; Richter, Christian; Rogov, Vladimir V; Proschak, Ewgenij; Hargittay, Bruno; Saxena, Krishna; Schwalbe, Harald

2018-06-04

The interaction of fibroblast growth factors (FGFs) with their fibroblast growth factor receptors (FGFRs) are important in the signaling network of cell growth and development. SSR128129E (SSR), a ligand of small molecular weight with potential anti-cancer properties, acts allosterically on the extracellular domains of FGFRs. Up to now, the structural basis of SSR binding to the D3 domain of FGFR remained elusive. This work reports the structural characterization of the interaction of SSR with one specific receptor, FGFR3, by NMR spectroscopy. This information provides a basis for rational drug design for allosteric FGFR inhibitors. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pain Processing and Vegetative Dysfunction in Fibromyalgia: A Study by Sympathetic Skin Response and Laser Evoked Potentials

PubMed Central

Ricci, Katia; Libro, Giuseppe; Vecchio, Eleonora; Delussi, Marianna; Montemurno, Anna; Iannone, Florenzo

2017-01-01

Background A dysfunction of pain processing at central and peripheral levels was reported in fibromyalgia (FM). We aimed to correlate laser evoked potentials (LEPs), Sympathetic Skin Response (SSR), and clinical features in FM patients. Methods Fifty FM patients and 30 age-matched controls underwent LEPs and SSR by the right hand and foot. The clinical evaluation included FM disability (FIQ) and severity scores (WPI), anxiety (SAS) and depression (SDS) scales, and questionnaires for neuropathic pain (DN4). Results The LEP P2 latency and amplitude and the SSR latency were increased in FM group. This latter feature was more evident in anxious patients. The LEPs habituation was reduced in FM patients and correlated to pain severity scores. In a significant number of patients (32%) with higher DN4 and FIQ scores, SSR or LEP responses were absent. Conclusions LEPs and SSR might contribute to clarifying the peripheral and central nervous system involvement in FM patients. PMID:29093972

Pain Processing and Vegetative Dysfunction in Fibromyalgia: A Study by Sympathetic Skin Response and Laser Evoked Potentials.

PubMed

de Tommaso, Marina; Ricci, Katia; Libro, Giuseppe; Vecchio, Eleonora; Delussi, Marianna; Montemurno, Anna; Lopalco, Giuseppe; Iannone, Florenzo

2017-01-01

A dysfunction of pain processing at central and peripheral levels was reported in fibromyalgia (FM). We aimed to correlate laser evoked potentials (LEPs), Sympathetic Skin Response (SSR), and clinical features in FM patients. Fifty FM patients and 30 age-matched controls underwent LEPs and SSR by the right hand and foot. The clinical evaluation included FM disability (FIQ) and severity scores (WPI), anxiety (SAS) and depression (SDS) scales, and questionnaires for neuropathic pain (DN4). The LEP P2 latency and amplitude and the SSR latency were increased in FM group. This latter feature was more evident in anxious patients. The LEPs habituation was reduced in FM patients and correlated to pain severity scores. In a significant number of patients (32%) with higher DN4 and FIQ scores, SSR or LEP responses were absent. LEPs and SSR might contribute to clarifying the peripheral and central nervous system involvement in FM patients.

Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing.

PubMed

Wu, Jianzhong; Zhao, Qian; Wu, Guangwen; Zhang, Shuquan; Jiang, Tingbo

2016-01-01

Flax ( Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1574 microsatellites from Linum usitatissimum L. obtained using reduced representation genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5-8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in this study show potential value for selection of varieties for use in flax breeding programs.

Development and validation of the first SSR markers for Mimosa scabrella Benth.

PubMed

Saiki, F A; Bernardi, A P; Reis, M S; Faoro, H; Souza, E M; Pedrosa, F O; Mantovani, A; Guidolin, A F

2017-02-16

Mimosa scabrella Benth., popularly known as ''bracatinga'', is a pioneer and endemic species of Brazil, occurring in Mixed Ombrophilous Forest associated with Brazilian Atlantic Rainforest biomes. It is a fast-growing tree of the Fabaceae family that facilitates the dynamics of ecological succession. SSR development, when there is no genome sequence, is time and labor intensive and there are no molecular markers for M. scabrella. We developed and validated the first microsatellite markers for this tetraploid species, evaluating mother trees and progenies. Using Illumina sequencing, we identified 290 SSR loci and 211 primer pairs. After 31 SSR loci PCR/agarose electrophoresis selection, a subset of 11 primer pairs was synthetized with fluorescence in the forward primer for PCR and capillary electrophoresis validation with leaf DNA of 33 adult and 411 progeny individuals. Polymorphic locus percentage was 36, 4 in 11 loci, 3 chloroplast SSRs, and 1 nuclear SSR. Allele number of polymorphic loci ranged from 2 to 11 alleles considering all sampling. All 11 primer pairs were also tested for cross-species amplification for five Fabaceae-Mimosoideae species, ranging from 2 loci transferred to Calliandra tweedii Benth. and all 11 loci transferred to Mimosa taimbensis Burkart. The assessed and validated SSR markers for M. scabrella are suitable and useful for analysis and population genetic studies.

A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.

PubMed

Cheng, Jiaowen; Zhao, Zicheng; Li, Bo; Qin, Cheng; Wu, Zhiming; Trejo-Saavedra, Diana L; Luo, Xirong; Cui, Junjie; Rivera-Bustamante, Rafael F; Li, Shuaicheng; Hu, Kailin

2016-01-07

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.

A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum

PubMed Central

Cheng, Jiaowen; Zhao, Zicheng; Li, Bo; Qin, Cheng; Wu, Zhiming; Trejo-Saavedra, Diana L.; Luo, Xirong; Cui, Junjie; Rivera-Bustamante, Rafael F.; Li, Shuaicheng; Hu, Kailin

2016-01-01

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum. PMID:26739748

EST-SSR marker revealed effective over biochemical and morphological scepticism towards identification of specific turmeric (Curcuma longa L.) cultivars.

PubMed

Sahoo, Ambika; Jena, Sudipta; Kar, Basudeba; Sahoo, Suprava; Ray, Asit; Singh, Subhashree; Joshi, Raj Kumar; Acharya, Laxmikanta; Nayak, Sanghamitra

2017-05-01

Turmeric (Curcuma longa L., family Zingiberaceae) is one of the most economically important plants for its use in food, medicine, and cosmetic industries. Cultivar identification is a major constraint in turmeric, owing to high degree of morphological similarity that in turn, affects its commercialization. The present study addresses this constraint, using EST-SSR marker based, molecular identification of 8 elite cultivars and 88 accessions in turmeric. Fifty EST-SSR primers were screened against eight cultivars of turmeric (Suroma, Roma, Lakadong, Megha, Alleppey Supreme, Kedaram, Pratibha, and Suvarna); out of which 11 primers showed polymorphic banding pattern. The polymorphic information content (PIC) of these primers ranged from 0.13 to 0.48. However, only three SSR loci (CSSR 14, CSSR 15, and CSSR 18) gave reproducible unique banding pattern clearly distinguishing the cultivars 'Lakadong' and 'Suvarna' from other cultivars tested. These three unique SSR markers also proved to be effective in identification of 'Lakadong' cultivars when analysed with 88 accessions of turmeric collected from different agro-climatic regions. Furthermore, two identified cultivars (Lakadong and Suvarna) could also be precisely differentiated when analysed and based on phylogenetic tree, with other 94 genotypes of turmeric. The novel SSR markers can be used for identification and authentication of two commercially important turmeric cultivars 'Lakadong' and 'Suvarna'.

Understanding scaling through history-dependent processes with collapsing sample space.

PubMed

Corominas-Murtra, Bernat; Hanel, Rudolf; Thurner, Stefan

2015-04-28

History-dependent processes are ubiquitous in natural and social systems. Many such stochastic processes, especially those that are associated with complex systems, become more constrained as they unfold, meaning that their sample space, or their set of possible outcomes, reduces as they age. We demonstrate that these sample-space-reducing (SSR) processes necessarily lead to Zipf's law in the rank distributions of their outcomes. We show that by adding noise to SSR processes the corresponding rank distributions remain exact power laws, p(x) ~ x(-λ), where the exponent directly corresponds to the mixing ratio of the SSR process and noise. This allows us to give a precise meaning to the scaling exponent in terms of the degree to which a given process reduces its sample space as it unfolds. Noisy SSR processes further allow us to explain a wide range of scaling exponents in frequency distributions ranging from α = 2 to ∞. We discuss several applications showing how SSR processes can be used to understand Zipf's law in word frequencies, and how they are related to diffusion processes in directed networks, or aging processes such as in fragmentation processes. SSR processes provide a new alternative to understand the origin of scaling in complex systems without the recourse to multiplicative, preferential, or self-organized critical processes.

Identification of molecular performance from oil palm clones based on SSR markers

NASA Astrophysics Data System (ADS)

Putri, Lollie Agustina P.; Basyuni, M.; Bayu, Eva S.; Arvita, D.; Arifiyanto, D.; Syahputra, I.

2018-03-01

In Indonesia, the oil palms are an important economic crop, producing food and raw materials for the food, confectionary, cosmetics and oleo-chemical industrial demands of oil palm products. Clonal oil palm offers the potential for greater productivity because it is possible to establish uniform tree stands comprising identical copies (clones) of a limited number of highly productive oil palms. Unfortunately, tissue culture sometimes accentuates the expression of detects in oil palm, particularly when embryogenesis is induced in particullar callus for prolonged periods. This research is conducted by taking individual tree sample of clone germplasm two years old. The purpose of this research is to molecular performance analysis of some oil palm clones based on SSR markers. A total of 30 trees oil palm clones were used for analysis. In this experiment, the DNA profile diversity was assessed using five loci of oil palm’s specific SSR markers. The results of the experiment indicated out of 3 SSR markers (FR-0779, FR-3663 and FR-0782) showed monomorphic of PCR product and 2 SSR markers (FR-0783 and FR- 3745) showed polymorphic of PCR product. There are 10 total number of PCR product. These preliminary results demonstrated SSR marker can be used to evaluate genetic relatedness among trees of oil palm clones.

The selective reversible FAAH inhibitor, SSR411298, restores the development of maladaptive behaviors to acute and chronic stress in rodents.

PubMed

Griebel, Guy; Stemmelin, Jeanne; Lopez-Grancha, Mati; Fauchey, Valérie; Slowinski, Franck; Pichat, Philippe; Dargazanli, Gihad; Abouabdellah, Ahmed; Cohen, Caroline; Bergis, Olivier E

2018-02-05

Enhancing endogenous cannabinoid (eCB) signaling has been considered as a potential strategy for the treatment of stress-related conditions. Fatty acid amide hydrolase (FAAH) represents the primary degradation enzyme of the eCB anandamide (AEA), oleoylethanolamide (OEA) and palmitoylethanolamide (PEA). This study describes a potent reversible FAAH inhibitor, SSR411298. The drug acts as a selective inhibitor of FAAH, which potently increases hippocampal levels of AEA, OEA and PEA in mice. Despite elevating eCB levels, SSR411298 did not mimic the interoceptive state or produce the behavioral side-effects (memory deficit and motor impairment) evoked by direct-acting cannabinoids. When SSR411298 was tested in models of anxiety, it only exerted clear anxiolytic-like effects under highly aversive conditions following exposure to a traumatic event, such as in the mouse defense test battery and social defeat procedure. Results from experiments in models of depression showed that SSR411298 produced robust antidepressant-like activity in the rat forced-swimming test and in the mouse chronic mild stress model, restoring notably the development of inadequate coping responses to chronic stress. This preclinical profile positions SSR411298 as a promising drug candidate to treat diseases such as post-traumatic stress disorder, which involves the development of maladaptive behaviors.

Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae.

PubMed

Barboza, Karina; Beretta, Vanesa; Kozub, Perla C; Salinas, Cecilia; Morgenfeld, Mauro M; Galmarini, Claudio R; Cavagnaro, Pablo F

2018-04-28

Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related Allium (A. cepa, A. fistulosum, and A. tuberosum) and non-Allium monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized-along with 112 previously developed SSRs-at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the Allium species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of Allium species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across Allium species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2-5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of Allium transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other Allium.

Autonomic dysfunction and osteoporosis after electrical burn.

PubMed

Roshanzamir, Sharareh; Dabbaghmanesh, Mohammad Hossein; Dabbaghmanesh, Alireza; Nejati, Solmaz

2016-05-01

Several studies have shown the importance of the sympathetic nervous system in bone metabolism. There is an evidence of sympathetic skin response (SSR) impairment in electrical burn patients up to 2 years after their injuries. The acute phase of burn is accompanied by increased bone resorption. Whether the prolonged dysfunction of sympathetic nervous system may result in bone metabolism derangement even after the acute phase of electrical burn is the inspiring question for this study. And we tried to find correlation between SSR abnormality and areal bone mineral density (BMD) in electrical burn patients 6 months or more after the incidents. 42 electrical burn patients (≥6 months prior to study) who did not have a known joint or bone disease, history of neuropathy (central or peripheral), diabetes mellitus or consumption of any drug affecting the autonomic nervous system or evidence of neuropathy in nerve conduction study were recruited. We also gathered a control group of 50 healthy subjects (without electrical burn or the exclusion criteria). They went under dual energy X-ray absorptiometry and SSR study. Data were analyzed statistically with SPSS 16.0 making use of independent t-test and Pearson correlation coefficient. P<0.05 was considered significant statistically. Areal BMD was significantly lower in electrical burn patients than control group (P<0.001). SSR latency was significantly prolonged and its amplitude was significantly reduced in burn patients compared to control group (P<0.001). In burn patients there was an inverse correlation of areal BMD of lumbar vertebrae, left femur neck and total femur with SSR latency and a direct correlation of areal BMD with SSR amplitude. In control group there was just direct correlation of areal BMD of lumbar vertebrae and left femur neck with SSR amplitude. Electrical burn patients are at risk of reduced areal BMD long after their injuries. Sympathetic derangement and impaired SSR are correlated with reduction in areal BMD in these patients. Copyright © 2015 Elsevier Ltd and ISBI. All rights reserved.

Molecular mapping and candidate gene analysis for resistance to powdery mildew in Cucumis sativus stem.

PubMed

Liu, P N; Miao, H; Lu, H W; Cui, J Y; Tian, G L; Wehner, T C; Gu, X F; Zhang, S P

2017-08-31

Powdery mildew (PM) of cucumber (Cucumis sativus), caused by Podosphaera xanthii, is a major foliar disease worldwide and resistance is one of the main objectives in cucumber breeding programs. The resistance to PM in cucumber stem is important to the resistance for the whole plant. In this study, genetic analysis and gene mapping were implemented with cucumber inbred lines NCG-122 (with resistance to PM in the stem) and NCG-121 (with susceptibility in the stem). Genetic analysis showed that resistance to PM in the stem of NCG-122 was qualitative and controlled by a single-recessive nuclear gene (pm-s). Susceptibility was dominant to resistance. In the initial genetic mapping of the pm-s gene, 10 SSR markers were discovered to be linked to pm-s, which was mapped to chromosome 5 (Chr.5) of cucumber. The pm-s gene's closest flanking markers were SSR20486 and SSR06184/SSR13237 with genetic distances of 0.9 and 1.8 cM, respectively. One hundred and fifty-seven pairs of new SSR primers were exploited by the sequence information in the initial mapping region of pm-s. The analysis on the F 2 mapping population using the new molecular markers showed that 17 SSR markers were confirmed to be linked to the pm-s gene. The two closest flanking markers, pmSSR27and pmSSR17, were 0.1 and 0.7 cM from pm-s, respectively, confirming the location of this gene on Chr.5. The physical length of the genomic region containing pm-s was 135.7 kb harboring 21 predicted genes. Among these genes, the gene Csa5G623470 annotated as encoding Mlo-related protein was defined as the most probable candidate gene for the pm-s. The results of this study will provide a basis for marker-assisted selection, and make the benefit for the cloning of the resistance gene.

Understanding Scaling Relations in Fracture and Mechanical Deformation of Single Crystal and Polycrystalline Silicon by Performing Atomistic Simulations at Mesoscale

DTIC Science & Technology

2009-07-16

0.25 0.26 -0.85 1 SSR SSE R SSTO SSTO = = − 2 2 ˆ( ) : Regression sum of square, ˆwhere : mean value, : value from the fitted line ˆ...Error sum of square : Total sum of square i i i i SSR Y Y Y Y SSE Y Y SSTO SSE SSR = − = − = + ∑ ∑ Statistical analysis: Coefficient of correlation

Simulation of Autonomic Logistics System (ALS) Sortie Generation

DTIC Science & Technology

2003-03-01

84 Appendix B. ANOVA Assumptions Mission Capable Rate ANOVA Assumptions Constant Variance SSR # X cols SSE n Breusch - Pagan Chi-square 3.57E...85 Flying Scheduling Effectiveness ANOVA Assumptions Constant Variance SSR # X cols SSE n Breusch - Pagan Chi-square 2.12E-10 3 0.000816 270...Constant Variance SSR # X cols SSE n Breusch - Pagan Chi-square 1.86E-09 3 0.003758 270 3.20308814 0.9556957 Independence Durbin-Watson

Characterization and multiplexing of EST-SSR primers in Cynodon (Poaceae) species1.

PubMed

Jewell, Margaret C; Frere, Celine H; Prentis, Peter J; Lambrides, Christopher J; Godwin, Ian D

2010-10-01

Cynodon species are multiple-use grasses that display varying levels of adaptation to biotic and abiotic stress. Previously identified EST-SSR primers were characterized and multiplexed to assess the level of genetic diversity present within a collection of almost 1200 Cynodon accessions from across Australia. • Two multiplex reactions were developed comprising a total of 16 EST-SSR markers. All SSR markers amplified across different Cynodon species and different levels of ploidy. The number of alleles ranged from one to eight per locus and the total number of alleles for the germplasm collection was 79. • The 16 markers show sufficient variation for the characterization of Cynodon core collections and analysis of population genetic diversity in Cynodon grasses.

Cocarcinogenicity of phenols from Estonian shale tars (oils).

PubMed Central

Bogovski, P A; Mirme, H I

1979-01-01

Many phenols have carcinogenic activity. The Estonian shale oils contain up to 40 vol % phenols. The promoting activity after initiation of phenols of Estonian shale oils was tested in mice with a single subthreshold dose (0.36 mg) of benzo(a)pyrene. C57Bl and CC57Br mice were used in skin painting experiments. Weak carcinogenic activity was found in the total crude water-soluble phenols recovered from the wastewater of a shale processing plant. In two-stage experiments a clear promoting action of the total crude phenols was established, whereas the fractions A and B (training reagents), obtained by selective crystallization of the total phenols exerted a considerably weaker promoting action. Epo-glue, a commercial epoxy product produced from unfractionated crude phenols, had no promoting activity, which may be due to the processing of the phenols involving polymerization. The mechanism of action of phenols is not clear. According to some data from the literature, phenol and 5-methylresorcinol reduce the resorption speed of BP in mouse skin, causing prolongation of the action fo the carcinogen. PMID:446449

Cocarcinogenicity of phenols from Estonian shale tars (oils).

PubMed

Bogovski, P A; Mirme, H I

1979-06-01

Many phenols have carcinogenic activity. The Estonian shale oils contain up to 40 vol % phenols. The promoting activity after initiation of phenols of Estonian shale oils was tested in mice with a single subthreshold dose (0.36 mg) of benzo(a)pyrene. C57Bl and CC57Br mice were used in skin painting experiments. Weak carcinogenic activity was found in the total crude water-soluble phenols recovered from the wastewater of a shale processing plant. In two-stage experiments a clear promoting action of the total crude phenols was established, whereas the fractions A and B (training reagents), obtained by selective crystallization of the total phenols exerted a considerably weaker promoting action. Epo-glue, a commercial epoxy product produced from unfractionated crude phenols, had no promoting activity, which may be due to the processing of the phenols involving polymerization. The mechanism of action of phenols is not clear. According to some data from the literature, phenol and 5-methylresorcinol reduce the resorption speed of BP in mouse skin, causing prolongation of the action fo the carcinogen.

Estonian greenhouse gas emissions inventory report

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

Punning, J.M.; Ilomets, M.; Karindi, A.

1996-07-01

It is widely accepted that the increase of greenhouse gas concentrations in the atmosphere due to human activities would result in warming of the Earth`s surface. To examine this effect and better understand how the GHG increase in the atmosphere might change the climate in the future, how ecosystems and societies in different regions of the World should adapt to these changes, what must policymakers do for the mitigation of that effect, the worldwide project within the Framework Convention on Climate Change was generated by the initiative of United Nations. Estonia is one of more than 150 countries, which signedmore » the Framework Convention on Climate Change at the United Nations Conference on Environment and Development held in Rio de Janeiro in June 1992. In 1994 a new project, Estonian Country Study was initiated within the US Country Studies Program. The project will help to compile the GHG inventory for Estonia, find contemporary trends to investigate the impact of climate change on the Estonian ecosystems and economy and to formulate national strategies for Estonia addressing to global climate change.« less

The use of teetaimed in Estonia, 1880s-1990s.

PubMed

Sõukand, Renata; Kalle, Raivo

2012-10-01

This research contributes to a better understanding of the criteria used for the selection of plants for making beverages. Worldwide, not only the leaves of Camellia sinensis, but also various other plants are used for making tea. We argue that the selection of plants for making tea (in Estonian teetaimed) depends on specific features possessed by or attributed to the plants. 54 plant taxa and one lichen were identified as being used for making tea, based on the analysis of Estonian historical handwritten archival records on plant use for the period from 1887 to 1994. The influence of popular literature on the use of plants for making tea was also assessed. The suitability of a plant for making tea depends on a combination of factors like multifunctional use, mild taste and attributed medicinal properties. The variety of medicinal properties attributed to teetaimed in folk medicine allowed herbal tea drinking to be considered as mild disease prevention. Hence, the roots of the Estonian tea tradition lie in the medicinal use of the plants, not oriental ceremonial tea drinking. Copyright © 2012 Elsevier Ltd. All rights reserved.

Smoking habits and attitudes towards smoking among Estonian physicians.

PubMed

Pärna, K; Rahu, K; Rahu, M

2005-05-01

This study examined the smoking habits and attitudes towards smoking among Estonian physicians. Cross-sectional data for 2668 physicians were gathered by a self-administered postal survey. The current smoking prevalence was 24.9% for male physicians and 10.8% for female physicians. The percentages of ex-smokers were 32.9 and 16.8%, respectively. Smoking prevalence among physicians was below the levels reported for the highest educational bracket of the total population in Estonia. Non-smoking physicians had more unfavourable views towards smoking than those who smoked. The majority of physicians were aware of the association between smoking and various diseases, with significant differences between smokers and non-smokers. Non-smoking physicians were more active in asking patients about smoking habits than those who smoked. Most Estonian physicians, especially those who smoked, failed to perceive themselves as positive role models. This study found a lower prevalence of smoking among physicians compared with the general population, and demonstrated the impact of personal smoking on physicians' attitudes towards smoking. The results provide an important challenge to medical education in Estonia.

On the ability of RegCM4 to simulate surface solar radiation patterns over Europe: An assessment using satellite-based observations

NASA Astrophysics Data System (ADS)

Alexandri, Georgia; Georgoulias, Aristeidis K.; Zanis, Prodromos; Tsikerdekis, Athanasios; Katragkou, Eleni; Kourtidis, Konstantinos; Meleti, Charikleia

2015-04-01

We assess here the ability of RegCM4 to simulate the surface solar radiation (SSR) patterns over the European domain. For the needs of this work, a decadal (1999-2009) simulation was implemented at a horizontal resolution of 50km using the first year as a spin-up. The model is driven by emissions from CMIP5 while ERA-interim data were used as lateral boundary conditions. The RegCM4 SSR fields were validated against satellite-based SSR observations from Meteosat First Generation (MFG) and Meteosat Second Generation (MSG) sensors (CM SAF SIS product). The RegCM4 simulations slightly overestimate SSR compared to CM SAF over Europe with the bias being +1.54% in case of MFG (2000-2005) and +3.34% in case of MSG (2006-2009). SSR from RegCM4 is much closer to SSR from CM SAF over land (bias of -1.59% for MFG and +0.66% for MSG) than over ocean (bias of +7.20% for MFG and 8.07% for MSG). In order to understand the reasons of this bias, we proceeded to a detailed assessment of various parameters that define the SSR levels (cloud fractional cover - CFC, cloud optical thickness - COT, cloud droplet effective radius - Re, aerosol optical thickness - AOD, asymmetry factor - ASY, single scattering albedo - SSA, water vapor - WV and surface albedo - ALB). We validated the simulated CFC, COT and Re from RegCM4 against satellite-based observations from MSG and we found that RegCM4 significantly underestimates CFC and Re, and overestimates COT over Europe. The aerosol-related parameters from RegCM4 were compared with values from the aerosol climatology taken into account within CM SAF SSR estimates. AOD is significantly underestimated in our simulations which leads to a positive SSR bias. The RegCM4 WV and ALB were compared with WV values from ERA-interim and ALB climatological observations from CERES which are also taken into account within CM SAF SSR estimates. Finally, with the use of a radiative transfer model (SBDART) we manage to quantify the relative contribution of each of the above mentioned parameters to the total bias appearing between RegCM4 and CM SAF SSR. The research leading to these results has received funding from the European Social Fund (ESF) and national resources under the operational programme Education and Lifelong Learning (EdLL) within the framework of the Action "Supporting Postdoctoral Researchers" (QUADIEEMS project), from EPAN II and PEP under the national action "Bilateral, multilateral and regional R&T cooperations" (AEROVIS Sino-Greek project) and from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 226144 (C8 project).

SSR240612 [(2R)-2-[((3R)-3-(1,3-benzodioxol-5-yl)-3-[[(6-methoxy-2-naphthyl)sulfonyl]amino]propanoyl)amino]-3-(4-[[2R,6S)-2,6-dimethylpiperidinyl]methyl]phenyl)-N-isopropyl-N-methylpropanamide hydrochloride], a new nonpeptide antagonist of the bradykinin B1 receptor: biochemical and pharmacological characterization.

PubMed

Gougat, Jean; Ferrari, Bernard; Sarran, Lionel; Planchenault, Claudine; Poncelet, Martine; Maruani, Jeanne; Alonso, Richard; Cudennec, Annie; Croci, Tiziano; Guagnini, Fabio; Urban-Szabo, Katalin; Martinolle, Jean-Pierre; Soubrié, Philippe; Finance, Olivier; Le Fur, Gérard

2004-05-01

The biochemical and pharmacological properties of a novel non-peptide antagonist of the bradykinin (BK) B(1) receptor, SSR240612 [(2R)-2-[((3R)-3-(1,3-benzodioxol-5-yl)-3-[[(6-methoxy-2-naphthyl)sulfonyl]amino]propanoyl)amino]-3-(4-[[2R,6S)-2,6-dimethylpiperidinyl]methyl]phenyl)-N-isopropyl-N-methylpropanamide hydrochloride] were evaluated. SSR240612 inhibited the binding of [(3)H]Lys(0)-des-Arg(9)-BK to the B(1) receptor in human fibroblast MRC5 and to recombinant human B(1) receptor expressed in human embryonic kidney cells with inhibition constants (K(i)) of 0.48 and 0.73 nM, respectively. The compound selectivity for B(1) versus B(2) receptors was in the range of 500- to 1000-fold. SSR240612 inhibited Lys(0)-desAr(9)-BK (10 nM)-induced inositol monophosphate formation in human fibroblast MRC5, with an IC(50) of 1.9 nM. It also antagonized des-Arg(9)-BK-induced contractions of isolated rabbit aorta and mesenteric plexus of rat ileum with a pA(2) of 8.9 and 9.4, respectively. Antagonistic properties of SSR240612 were also demonstrated in vivo. SSR240612 inhibited des-Arg(9)-BK-induced paw edema in mice (3 and 10 mg/kg p.o. and 0.3 and 1 mg/kg i.p.). Moreover, SSR240612 reduced capsaicin-induced ear edema in mice (0.3, 3 and 30 mg/kg p.o.) and tissue destruction and neutrophil accumulation in the rat intestine following splanchnic artery occlusion/reperfusion (0.3 mg/kg i.v.). The compound also inhibited thermal hyperalgesia induced by UV irradiation (1 and 3 mg/kg p.o.) and the late phase of nociceptive response to formalin in rats (10 and 30 mg/kg p.o.). Finally, SSR240612 (20 and 30 mg/kg p.o.) prevented neuropathic thermal pain induced by sciatic nerve constriction in the rat. In conclusion, SSR240612 is a new, potent, and orally active specific non-peptide bradykinin B(1) receptor antagonist.

Impact of economic conditions on the secondary sex ratio in a post-communist economy.

PubMed

Ządzińska, E; Rosset, I; Mikulec, A; Domański, C; Pawłowski, B

2011-06-01

According to the Trivers-Willard hypothesis the secondary sex ratio (SSR, the ratio of male to female newborns [M/F]) should be positively related to the parents' living conditions. This also means that if in some population parents experience environmental (e.g. economic) stress, the SSR should be relatively low. If this holds true, the fluctuations in the SSR of offspring could be one of the ways the human population reacts to environmental (and also socio-economic) changes. Although confirmed for many human populations, such a relationship was not observed in the populations living in the communist-era planned-economy countries until recently. We test the hypothesis that economic stress in Poland after the communist era is also related to the SSR decrease. Using quarterly data from the years 1995-2007 about the total number of live male (M) and female (F) newborns born in central Poland (sample size=310,532), we calculated the time series of the SSR. The quarterly economic conditions of the studied population within the period under consideration constituted the time series of the percentage change in private consumption at constant prices of the year 2000. The relationship between the SSR and the economic conditions in the analyzed 47 quarters of the year was tested with the use of the ARMA models. We have found that four quarters (one year) after the occurrence of economic stress there was a decline in the SSR. This result is consistent with the Trivers-Willard hypothesis at the population level in a modern free-trade economy of a post-communist country. Copyright © 2011 Elsevier GmbH. All rights reserved.

Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica.

PubMed

Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

2015-01-01

Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the "candidate genes" and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops.

Solar-simulated radiation and heat treatment induced metalloproteinase-1 expression in cultured dermal fibroblasts via distinct pathways: implications on reduction of sun-associated aging.

PubMed

Lan, Cheng-Che E; Wu, Ching-Shang; Yu, Hsin-Su

2013-12-01

Sun exposure is an important environmental factor affecting human beings. Most knowledge regarding solar aging focused on light radiation (photoaging), and little emphasis has been placed on heat, a factor that is also closely associated with sun exposure. This study was launched to evaluate the effects of simulated solar radiation (SSR) and environmental heat on skin fibroblasts in terms of dermal aging. Cultured human dermal fibroblasts were treated with moderate amount of SSR (200J/cm(2)) and heat (+2°C). The metalloproteinase-1 (MMP-1) expression was used as a surrogate marker for dermal aging and the involved regulatory mechanisms were explored. Both treatment conditions did not affect viability but significantly increased the expressions of MMP-1. In parallel, both treatments increased the intracellular levels of reactive oxygen species (ROS), but the increase induced by SSR is much greater than heat. In contrast, transient receptor potential vanilloid 1 (TRPV-1), the sensor of environmental heat, was upregulated by heat but not SSR treatment. Pretreating fibroblasts with antioxidant abrogated the SSR-induced MMP-1 but has limited effect on heat-induced MMP-1. On the other hand, TRPV-1 antagonist pretreatment reduced heat-induced MMP-1 in fibroblasts but not their SSR-treated counterparts. Both SSR and heat induced MMP-1 expression in dermal fibroblasts but through different pathways. As current strategies for reducing sun-related aging focused on filtering of light and use of antioxidants, future strategies design to reduce solar aging should also incorporate heat-induced aging into consideration. Copyright © 2013 Japanese Society for Investigative Dermatology. Published by Elsevier Ireland Ltd. All rights reserved.

Laser damage threshold measurements of microstructure-based high reflectors

NASA Astrophysics Data System (ADS)

Hobbs, Douglas S.

2008-10-01

In 2007, the pulsed laser induced damage threshold (LIDT) of anti-reflecting (AR) microstructures built in fused silica and glass was shown to be up to three times greater than the LIDT of single-layer thin-film AR coatings, and at least five times greater than multiple-layer thin-film AR coatings. This result suggested that microstructure-based wavelength selective mirrors might also exhibit high LIDT. Efficient light reflection over a narrow spectral range can be produced by an array of sub-wavelength sized surface relief microstructures built in a waveguide configuration. Such surface structure resonant (SSR) filters typically achieve a reflectivity exceeding 99% over a 1-10nm range about the filter center wavelength, making SSR filters useful as laser high reflectors (HR). SSR laser mirrors consist of microstructures that are first etched in the surface of fused silica and borosilicate glass windows and subsequently coated with a thin layer of a non-absorbing high refractive index dielectric material such as tantalum pent-oxide or zinc sulfide. Results of an initial investigation into the LIDT of single layer SSR laser mirrors operating at 532nm, 1064nm and 1573nm are described along with data from SEM analysis of the microstructures, and spectral reflection measurements. None of the twelve samples tested exhibited damage thresholds above 3 J/cm2 when illuminated at the resonant wavelength, indicating that the simple single layer, first order design will need further development to be suitable for high power laser applications. Samples of SSR high reflectors entered in the Thin Film Damage Competition also exhibited low damage thresholds of less than 1 J/cm2 for the ZnS coated SSR, and just over 4 J/cm2 for the Ta2O5 coated SSR.

Genome-Wide Characterization and Linkage Mapping of Simple Sequence Repeats in Mei (Prunus mume Sieb. et Zucc.)

PubMed Central

Sun, Lidan; Yang, Weiru; Zhang, Qixiang; Cheng, Tangren; Pan, Huitang; Xu, Zongda; Zhang, Jie; Chen, Chuguang

2013-01-01

Because of its popularity as an ornamental plant in East Asia, mei (Prunus mume Sieb. et Zucc.) has received increasing attention in genetic and genomic research with the recent shotgun sequencing of its genome. Here, we performed the genome-wide characterization of simple sequence repeats (SSRs) in the mei genome and detected a total of 188,149 SSRs occurring at a frequency of 794 SSR/Mb. Mononucleotide repeats were the most common type of SSR in genomic regions, followed by di- and tetranucleotide repeats. Most of the SSRs in coding sequences (CDS) were composed of tri- or hexanucleotide repeat motifs, but mononucleotide repeats were always the most common in intergenic regions. Genome-wide comparison of SSR patterns among the mei, strawberry (Fragaria vesca), and apple (Malus×domestica) genomes showed mei to have the highest density of SSRs, slightly higher than that of strawberry (608 SSR/Mb) and almost twice as high as that of apple (398 SSR/Mb). Mononucleotide repeats were the dominant SSR motifs in the three Rosaceae species. Using 144 SSR markers, we constructed a 670 cM-long linkage map of mei delimited into eight linkage groups (LGs), with an average marker distance of 5 cM. Seventy one scaffolds covering about 27.9% of the assembled mei genome were anchored to the genetic map, depending on which the macro-colinearity between the mei genome and Prunus T×E reference map was identified. The framework map of mei constructed provides a first step into subsequent high-resolution genetic mapping and marker-assisted selection for this ornamental species. PMID:23555708

Genetic diversity and identification of Chinese-grown pecan using ISSR and SSR markers.

PubMed

Jia, Xiao-Dong; Wang, Tao; Zhai, Min; Li, Yong-Rong; Guo, Zhong-Ren

2011-12-06

Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140-1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50-350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species

PubMed Central

Misra, Gopal; Gupta, Sarika; Subramanian, Alagesan; Parida, Swarup Kumar; Chattopadhyay, Debasis; Prasad, Manoj

2013-01-01

Foxtail millet ( Setaria italica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02–0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%), maize (~61%) and rice (~42%) chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species. PMID:23805325

Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica

PubMed Central

Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

2015-01-01

Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the “candidate genes” and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops. PMID:26388887

Follow-up of the air pollution and the human male-to-female ratio analysis in São Paulo, Brazil: a times series study

PubMed Central

Miraglia, Simone Georges El Khouri; Veras, Mariana Matera; Amato-Lourenço, Luis Fernando; Rodrigues-Silva, Fernando; Saldiva, Paulo Hilário Nascimento

2013-01-01

Objectives In order to assess if ambient air pollution in urban areas could be related to alterations in male/female ratio this study objectives to evaluate changes in ambient particulate matter (PM10) concentrations after implementation of pollution control programmes in São Paulo city and the secondary sex ratio (SRR). Design and methods A time series study was conducted. São Paulo’s districts were stratified according to the PM10 concentrations levels and were used as a marker of overall air pollution. The male ratio was chosen to represent the secondary sex ratio (SSR=total male birth/total births). The SSR data from each area was analysed according to the time variation and PM10 concentration areas using descriptive statistics. The strength association between annual average of PM10 concentration and SSR was performed through exponential regression, and it was adopted as a statistical significance level of p<0.05. Results The exponential regression showed a negative and significant association between PM10 and SSR. SSR varied from 51.4% to 50.7% in São Paulo in the analysed period (2000–2007). Considering the PM10 average concentration in São Paulo city of 44.72 μg/m3 in the study period, the SSR decline reached almost 4.37%, equivalent to 30 934 less male births. Conclusions Ambient levels of PM10 are negatively associated with changes in the SSR. Therefore, we can speculate that higher levels of particulate pollution could be related to increased rates of female births. PMID:23892420

In vivo and in vitro antiarrhythmic effects of SSR149744C in animal models of atrial fibrillation and ventricular arrhythmias.

PubMed

Gautier, Patrick; Serre, Martine; Cosnier-Pucheu, Sylvie; Djandjighian, Laurent; Roccon, Alain; Herbert, Jean-Marc; Nisato, Dino

2005-02-01

SSR149744C (2-butyl-3-{4-[3-(dibutylamino)propyl]benzoyl}-1-benzofuran-5-carboxylate isopropyl fumarate) is a new noniodinated benzofuran derivative structurally related to amiodarone and dronedarone that is currently undergoing clinical trials as an antiarrhythmic agent. As SSR149744C exhibits electrophysiological and hemodynamic properties of class I, II, III, and IV antiarrhythmic agents, the aim of this study was to evaluate its acute intravenous (IV) or oral (PO) antiarrhythmic activities in in vitro and in vivo animal models of atrial and ventricular arrhythmias. In vagally induced atrial fibrillation (AF) in anesthetized dogs, SSR149744C (3 and 10 mg/kg IV) terminated AF in all 7 dogs and prevented reinduction in 4 out of 7 dogs; effective refractory periods of right atrium were dose-dependently and frequency-independently lengthened. In low-K+ medium-induced AF models, SSR149744C (0.1 to 1 microM) prevented AF in isolated guinea pig hearts in a concentration-dependent manner. At the ventricular level, SSR149744C (0.1 to 10 mg/kg IV and 3 to 90 mg/kg PO) prevented reperfusion-induced arrhythmias in anesthetized rats with a dose-effect relationship, and, at doses of 30 to 90 mg/kg PO, it reduced early (0-24 hours) mortality following permanent left coronary artery ligature in conscious rats. The present results show that SSR149744C is an effective antiarrhythmic agent in atrial fibrillation and in ventricular arrhythmias. Like amiodarone and dronedarone, its efficiency in these animal models of arrhythmias is likely be related to its multifactorial mechanism of action.

The use of suction blisters to measure sunscreen protection against UVR-induced DNA damage.

PubMed

Josse, Gwendal; Douki, Thierry; Le Digabel, Jimmy; Gravier, Eleonore; Questel, Emmanuel

2018-02-01

The formation of DNA photoproducts caused by solar UVR exposure needs to be investigated in-vivo and in particular in order to assess sunscreens' level of protection against solar genotoxicity. The study's purposes were: i) to evaluate if the roof of suction blisters is an appropriate sampling method for measuring photoproducts, and ii) to measure in-vivo sunscreen protection against cyclobutane pyrimidine dimers. Skin areas on the interior forearms of eight healthy volunteers were exposed in-vivo to 2 MED of simulated solar radiation (SSR) and to 15 MED on a sunscreen protected area. After irradiation, six suction blisters were induced and the blister roofs were collected. Analysis of SSR-induced CPDs was performed by two independent methods: a chromatography coupled to mass spectroscopy (HPLC-MS/MS) approach and a 3D-imaging of CPD immunostaining by multiphoton microscopy on floating epidermal sheets. HPLC-MS/MS analyses showed that SSR-unexposed skin presented no CPD dimers, whereas 2 MED SSR-exposed skin showed a significant number of TT-CPD. The sunscreen covered skin exposed to 15 MED appeared highly protected from DNA damage, as the amount of CPD-dimers remained below the detection limit. The multiphoton-immunostaining analysis consistently showed that no CPD staining was observed on the non-SSR-exposed skin. A significant increase of CPD staining intensity and number of CPD-positive cells were observed on the 2 MED SSR-exposed skin. Sunscreen protected skin presented a very low staining intensity and the number of CPD-positive cells remained very close to non-SSR-exposed skin. This study showed that suction blister samples are very appropriate for measuring CPD dimers in-vivo, and that sunscreens provide high protection against UVR-induced DNA damage. Copyright © 2017 Elsevier B.V. All rights reserved.

Treatment of Facial Photodamage With Mass Market Topical Products vs Non-ablative Fractional Laser.

PubMed

Reich, Hilary; Wallander, Irmina; Schulte, Lacie; Goodier, Molly; Zelickson, Brian

2016-11-01

In this split-face, evaluator-blinded study, 18 subjects were randomly assigned to receive either the SSR or NFL treatments on each side of the face. For the SSR facial sides subjects followed two morning-evening regimens. On the NFL sides subjects were treated 3 times with the 1927-nm laser at 4-week intervals. Three physician evaluators were asked to rate hyperpigmentation, global photoaging, and ne lines and wrinkles for each side of the face at baseline and at 3 months using a 5-point scale. The SSR and NFL treatments provided comparable results for each skin attribute. Improvement from baseline was signi - cant in both treatment programs for each skin attribute. The greatest 3-month improvement for both programs was in hyperpigmen- tation. For global photoaging and ne lines and wrinkles, positive responses were slightly greater in the NFL than in the SSR facial sides. Subject preference for the SSR over the NFL was greatest for ne lines around the eyes, ne lines around the mouth, smooth texture, radiant complexion, and overall improvement while the NFL was preferred for skin rmness and evenness. When the study was completed5 of 18 split-face subjects decided to undergo NFR laser treatment on the non laser treated side along with using the SSR product and 13 of the 18 subjects continued to use the SSR products to their full face after the study. The mass market skin care system of the present study provides improvement in hyperpigmentation, global photoaging, and ne lines and wrinkles comparable to that of a series of treatments with a non-ablative fractional laser. J Drugs Dermatol. 2016;15(11):1366-1372..

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species.

PubMed

Kumari, Kajal; Muthamilarasan, Mehanathan; Misra, Gopal; Gupta, Sarika; Subramanian, Alagesan; Parida, Swarup Kumar; Chattopadhyay, Debasis; Prasad, Manoj

2013-01-01

Foxtail millet (Setariaitalica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02-0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%), maize (~61%) and rice (~42%) chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.

Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species

PubMed Central

Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

2014-01-01

Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species. PMID:24130371

Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety 'Amrapali' (Mangifera indica L.).

PubMed

Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

2016-01-01

Mango (Mangifera indica L.) is called "king of fruits" due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties 'Neelam', 'Dashehari' and their hybrid 'Amrapali' using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.

Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)

PubMed Central

Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

2016-01-01

Mango (Mangifera indica L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango. PMID:27736892

Development of highly polymorphic EST-SSR markers and segregation in F₁ hybrid population of Vitis vinifera L.

PubMed

Kayesh, E; Zhang, Y Y; Liu, G S; Bilkish, N; Sun, X; Leng, X P; Fang, J G

2013-09-23

The objectives of this investigation were to develop and validate the expressed sequence tag (EST)-simple sequence repeat (SSR) markers from large EST sequences, and to study the segregation and distribution of SSRs within two grapevine parental lines. In total, 94 F₁ lines crossed between "Early Rose" and "Red Globe" were studied. Approximately 2100 EST-SSR sequences of Vitis vinifera L. were searched for SSRs and analyzed for the design of polymerase chain reaction (PCR) primers amplifying the SSR-rich regions. Trinucleotide repeats were found to be the most abundant, followed by other nucleotide repeats. A total of 182 SSR primer pairs were first developed for the study on the parental polymorphism. Among the 182 SSR primers, 142 primer pairs (78%) could amplify the anticipated PCR products, among which only 52 primer pairs (36.62%) showed polymorphism between the two parents. These polymorphic bands were further surveyed among the 94 F₁ lines, and the results showed that a total of 162 bands were amplified, and 98 of them were polymorphic in both parents (60.86% polymorphism), with an average of 1.88 polymorphic DNA bands for each primer pair. After testing with the chi-square test, 33 of the clearly amplified polymorphic bands followed a 3:1 ratio, and 37 followed a 1:1 ratio. The rest showed distorted segregation ratios.

Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species.

PubMed

Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

2014-02-01

Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.

Simple Sequence Repeats in Escherichia coli: Abundance, Distribution, Composition, and Polymorphism

PubMed Central

Gur-Arie, Riva; Cohen, Cyril J.; Eitan, Yuval; Shelef, Leora; Hallerman, Eric M.; Kashi, Yechezkel

2000-01-01

Computer-based genome-wide screening of the DNA sequence of Escherichia coli strain K12 revealed tens of thousands of tandem simple sequence repeat (SSR) tracts, with motifs ranging from 1 to 6 nucleotides. SSRs were well distributed throughout the genome. Mononucleotide SSRs were over-represented in noncoding regions and under-represented in open reading frames (ORFs). Nucleotide composition of mono- and dinucleotide SSRs, both in ORFs and in noncoding regions, differed from that of the genomic region in which they occurred, with 93% of all mononucleotide SSRs proving to be of A or T. Computer-based analysis of the fine position of every SSR locus in the noncoding portion of the genome relative to downstream ORFs showed SSRs located in areas that could affect gene regulation. DNA sequences at 14 arbitrarily chosen SSR tracts were compared among E. coli strains. Polymorphisms of SSR copy number were observed at four of seven mononucleotide SSR tracts screened, with all polymorphisms occurring in noncoding regions. SSR polymorphism could prove important as a genome-wide source of variation, both for practical applications (including rapid detection, strain identification, and detection of loci affecting key phenotypes) and for evolutionary adaptation of microbes.[The sequence data described in this paper have been submitted to the GenBank data library under accession numbers AF209020–209030 and AF209508–209518.] PMID:10645951

Large-scale development of SSR markers in tobacco and construction of a linkage map in flue-cured tobacco

PubMed Central

Tong, Zhijun; Xiao, Bingguang; Jiao, Fangchan; Fang, Dunhuang; Zeng, Jianmin; Wu, Xingfu; Chen, Xuejun; Yang, Jiankang; Li, Yongping

2016-01-01

Tobacco (Nicotiana tabacum L.), particularly flue-cured tobacco, is one of the most economically important nonfood crops and is also an important model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available for genome analysis, genetic mapping, and breeding. Simple sequence repeats (SSR) are one of the most widely-used molecular markers, having significant advantages including that they are generally co-dominant, easy to use, abundant in eukaryotic organisms, and produce highly reproducible results. In this study, based on the genome sequence data of flue-cured tobacco (K326), we developed a total of 13,645 mostly novel SSR markers, which were working in a set of eighteen tobacco varieties of four different types. A mapping population of 213 backcross (BC1) individuals, which were derived from an intra-type cross between two flue-cured tobacco varieties, Y3 and K326, was selected for mapping. Based on the newly developed SSR markers as well as published SSR markers, we constructed a genetic map consisting of 626 SSR loci distributed across 24 linkage groups and covering a total length of 1120.45 cM with an average distance of 1.79 cM between adjacent markers, which is the highest density map of flue-cured tobacco till date. PMID:27436948

Global Performance of a Fast Parameterization Scheme for Estimating Surface Solar Radiation from MODIS data

NASA Astrophysics Data System (ADS)

Tang, W.; Yang, K.; Sun, Z.; Qin, J.; Niu, X.

2016-12-01

A fast parameterization scheme named SUNFLUX is used in this study to estimate instantaneous surface solar radiation (SSR) based on products from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor onboard both Terra and Aqua platforms. The scheme mainly takes into account the absorption and scattering processes due to clouds, aerosols and gas in the atmosphere. The estimated instantaneous SSR is evaluated against surface observations obtained from seven stations of the Surface Radiation Budget Network (SURFRAD), four stations in the North China Plain (NCP) and 40 stations of the Baseline Surface Radiation Network (BSRN). The statistical results for evaluation against these three datasets show that the relative root-mean-square error (RMSE) values of SUNFLUX are less than 15%, 16% and 17%, respectively. Daily SSR is derived through temporal upscaling from the MODIS-based instantaneous SSR estimates, and is validated against surface observations. The relative RMSE values for daily SSR estimates are about 16% at the seven SURFRAD stations, four NCP stations, 40 BSRN stations and 90 China Meteorological Administration (CMA) radiation stations.

Sympathetic skin response and R-R interval variation in cases with rheumatoid arthritis.

PubMed

Gozke, E; Erdogan, N; Akyuz, G; Turan, B; Akyuz, E; Us, O

2003-03-01

To investigate the autonomic nervus system involvement in cases with rheumatoid arthritis (RA) by assesing sympathetic skin response (SSR) and R-R interval variation (RRIV), 14 healthy women and 10 women with RA, all of them without clinic dysautonomies were examined. SSR's were recorded palmar surface of both hands and soles of both feet, after stimulating median and tibial nerves individually. RRIV's were assessed at rest and during six deep breathing in one minute with electrodes placed on dorsal surfaces of both hands. SSR could not be obtained from lower extremities of one case with RA. We could not find any significant difference between two groups in terms of SSR latencies. RRIV values obtained during deep breathing to those recorded at rest (D%/R%) was found to be significantly lower in RA cases than healthy controls. RRIV values increased with deep breathing in healthy subjects, while they decreased in 50% of the RA cases. We conclude that assessment of SSR and RRIV are valuble methods for revelation of subclinical autonomic involvement in cases with RA.

Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing

PubMed Central

Wu, Jianzhong; Zhao, Qian; Wu, Guangwen; Zhang, Shuquan; Jiang, Tingbo

2017-01-01

Flax (Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1574 microsatellites from Linum usitatissimum L. obtained using reduced representation genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5–8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in this study show potential value for selection of varieties for use in flax breeding programs. PMID:28133461

A high resolution satellite view of surface solar radiation over the climatically sensitive region of Eastern Mediterranean

NASA Astrophysics Data System (ADS)

Alexandri, G.; Georgoulias, A. K.; Meleti, C.; Balis, D.; Kourtidis, K. A.; Sanchez-Lorenzo, A.; Trentmann, J.; Zanis, P.

2017-05-01

In this work, the spatiotemporal variability of surface solar radiation (SSR) is examined over the Eastern Mediterranean region for a 31-year period (1983-2013). The CM SAF SARAH (Satellite Application Facility on Climate Monitoring Solar surfAce RAdiation Heliosat) satellite-based product was found to be homogeneous (based on relative Standard Normal Homogeneity Tests - SNHTs, 95% confidence level) as compared to ground-based observations, and hence appropriate for climatological studies. Specifically, the dataset shows good agreement with monthly observations from five quality assured stations in the region with a mean bias of 7.1 W/m2 or 3.8% and a strong correlation. This high resolution (0.05° × 0.05°) product is capable of revealing various local features. Over land, the SSR levels are highly dependent on the topography, while over the sea, they exhibit a smooth latitudinal variability. SSR varies significantly over the region on a seasonal basis being three times higher in summer (309.6 ± 26.5 W/m2) than in winter (100.2 ± 31.4 W/m2). The CM SAF SARAH product was compared against three satellite-based and one reanalysis products. The satellite-based data from CERES (Cloud and the Earth's Radiant Energy System), GEWEX (Global Energy and Water Cycle Experiment) and ISCCP (International Satellite Cloud Climatology Project) underestimate SSR while the reanalysis data from the ERA-Interim overestimate SSR compared to CM SAF SARAH. Using a radiative transfer model and a set of ancillary data, these biases are attributed to the atmospheric parameters that drive the transmission of solar radiation in the atmosphere, namely, clouds, aerosols and water vapor. It is shown that the bias between CERES and CM SAF SARAH SSR can be explained through the cloud fractional cover and aerosol optical depth biases between these datasets. The CM SAF SARAH SSR trend was found to be positive (brightening) and statistically significant at the 95% confidence level (0.2 ± 0.05 W/m2/year or 0.1 ± 0.02%/year) being almost the same over land and sea. The CM SAF SARAH SSR trends are closer to the ground-based ones than the CERES, GEWEX, ISCCP and ERA-Interim trends. The use of an aerosol climatology for the production of CM SAF SARAH, that neglects the trends of aerosol loads, leads to an underestimation of the SSR trends. It is suggested here, that the inclusion of changes of the aerosol load and composition within CM SAF SARAH would allow for a more accurate reproduction of the SSR trends.

Security Sector Reform in Liberia: Mixed Results from Humble Beginnings

DTIC Science & Technology

2008-03-01

require enhanced efforts to produce reliable crime statistics and the conduct of victimization surveys among the population of Monrovia and the rural...action. SSR IN CONTEXT The concept of SSR was first put forward to a larger public in a speech by Clare Short, the first minister of the United...earlier, but it was speeches by Short and the policy statements by her department from 1998 to 2002 that made SSR prominent as a term and as a

Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.)

PubMed Central

2013-01-01

Background Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. Results We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. Conclusions The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs. PMID:24160306

Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.).

PubMed

Yagi, Masafumi; Yamamoto, Toshiya; Isobe, Sachiko; Hirakawa, Hideki; Tabata, Satoshi; Tanase, Koji; Yamaguchi, Hiroyasu; Onozaki, Takashi

2013-10-26

Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.

Simulated Space Radiation: Murine Skeletal Responses During Recovery and with Mechanical Stimulation

NASA Technical Reports Server (NTRS)

Shirazi-Fard, Yasaman; Zaragoza, Josergio; Schreurs, Ann-Sofie; Truong, Tiffany; Tahimic, Candice; Alwood, Joshua S.; Castillo, Alesha B.; Globus, R. K.

2016-01-01

Simulated space radiation at doses similar to those of solar particle events or a round-trip sojourn to Mars (1-2Gy) may cause skeletal tissue degradation and deplete stem/progenitor cell pools throughout the body. We hypothesized that simulated space radiation (SSR) causes late, time-dependent deficits in bone structure and bone cell function reflected by changes in gene expression in response to anabolic stimuli. We used a unique sequential dual ion exposure (proton and iron) for SSR to investigate time-dependence of responses in gene expression, cell function, and microarchitecture with respect to radiation and an anabolic stimulus of axial loading (AL). Male 16-wk C57BL6/J mice (n=120 total) were exposed to 0Gy (Sham, n=10), 56Fe (2Gy, positive control dose, n=10), or sequential ions for SSR (1Gy 1H/56Fe/1H, n=10) by total body irradiation (IR), and the tissues were harvested 2 or 6 mo. later. Further, to assess the response to anabolic stimuli, we subjected additional Sham-AL (n=15) and SSR-AL (n=15) groups to rest-inserted tibial axial loading (AL) starting at 1 and 5 months post-IR (-9N, 60 cycles/day, 3 days/wk, 4 wks). Exposure to 56Fe caused a significant reduction in cancellous bone volume fraction (BV/TV) compared to Sham (-34%) and SSR (-20%) in the proximal tibia metaphysis at 2-months post-IR; however BV/TV for SSR group was not different than Sham. Both 56Fe and SSR caused significant reduction in trabecular number (Tb.N) compared to Sham (-33% and -16%, respectively). Further, Tb.N for 56Fe (2Gy) was significantly lower than SSR (-21%). Ex vivo culture of marrow cells to assess growth and differentiation of osteoblast lineage cells 6 months post-IR showed that both 56Fe and SSR exposures significantly impaired colony formation compared to Sham (-66% and -54%, respectively), as well as nodule mineralization (-90% and -51%, respectively). Two-way analysis of variance showed that both mechanical loading and radiation reduced BV/TV, mechanical loading reduced trabecular thickness (Tb.Th), and radiation reduced Tb.N, at both time points. To assess acute response to mechanical stimuli, samples were harvested from a subset of Sham-AL (n=5) and SSR-AL (n=5) to measure changes in gene expression levels. Preliminary results indicate that axial loading increased expression of the antioxidant response gene Nfe2l2 and the osteoprogenitor-associated marker Runx2 in the bone marrow cells, and there was an interaction effect between axial loading and radiation at 2-months post-IR. Additional analyses of gene expression levels in the mineralized tissue are in progress. Results indicate that SSR caused persistent impairment of osteoblast colony formation and nodule mineralization 6-mo post-IR. Contrary to our hypothesis, simulated space radiation did not impair the ability of cancellous bone to respond to a mechanical anabolic stimulus, consistent with our previous findings [1]. Hence, compressive loading may be a potential countermeasure against spaceflight-induced bone loss.

Simulated Space Radiation: Murine Skeletal Responses During Recovery and with Mechanical Stimulation

NASA Technical Reports Server (NTRS)

Shirazi-Fard, Yasaman; Zaragoza, Josergio; Schreurs, Ann-Sofie; Truong, Tiffany; Tahimic, Candice; Alwood, Joshua S.; Globus, R. K.

2016-01-01

Simulated space radiation at doses similar to those of solar particle events or a round-trip sojourn to Mars (1-2Gy) may cause skeletal tissue degradation and deplete stem/progenitor cell pools throughout the body. We hypothesized that simulated space radiation (SSR) causes late, time-dependent deficits in bone structure and bone cell function reflected by changes in gene expression in response to anabolic stimuli. We used a unique sequential dual ion exposure (proton and iron) for SSR to investigate time-dependence of responses in gene expression, cell function, and microarchitecture with respect to radiation and an anabolic stimulus of axial loading (AL). Male 16-wk C57BL6/J mice (n=120 total) were exposed to 0Gy (Sham, n=10), 56Fe (2Gy, positive control dose, n=10), or sequential ions for SSR (1Gy 1H/56Fe/1H, n=10) by total body irradiation (IR), and the tissues were harvested 2 or 6 mo. later. Further, to assess the response to anabolic stimuli, we subjected additional Sham-AL (n=15) and SSR-AL (n=15) groups to rest-inserted tibial axial loading (AL) starting at 1 and 5 months post-IR (-9N, 60 cycles/day, 3 days/wk, 4 wks). Exposure to 56Fe caused a significant reduction in cancellous bone volume fraction (BV/TV) compared to Sham (-34%) and SSR (-20%) in the proximal tibia metaphysis at 2-months post-IR; however BV/TV for SSR group was not different than Sham. Both 56Fe and SSR caused significant reduction in trabecular number (Tb.N) compared to Sham (-33% and -16%, respectively). Further, Tb.N for 56Fe (2Gy) was significantly lower than SSR (-21%). Ex vivo culture of marrow cells to assess growth and differentiation of osteoblast lineage cells 6 months post-IR showed that both 56Fe and SSR exposures significantly impaired colony formation compared to Sham (-66% and -54%, respectively), as well as nodule mineralization (-90% and -51%, respectively). Two-way analysis of variance showed that both mechanical loading and radiation reduced BV/TV, mechanical loading reduced trabecular thickness (Tb.Th), and radiation reduced Tb.N, at both time points. To assess acute response to mechanical stimuli, samples were harvested from a subset of Sham-AL (n=5) and SSR-AL (n=5) to measure changes in gene expression levels. Preliminary results indicate that axial loading increased expression of the antioxidant response gene Nfe2l2 and the osteoprogenitor-associated marker Runx2 in the bone marrow cells, and there was an interaction effect between axial loading and radiation at 2-months post-IR. Additional analyses of gene expression levels in the mineralized tissue are in progress. Results indicate that SSR caused persistent impairment of osteoblast colony formation and nodule mineralization 6-mo post-IR. Contrary to our hypothesis, simulated space radiation did not impair the ability of cancellous bone to respond to a mechanical anabolic stimulus, consistent with our previous findings. Hence, compressive loading may be a potential countermeasure against spaceflight-induced bone loss.

A set of tetra-nucleotide core motif SSR markers for efficient identification of potato (Solanum tuberosum) cultivars.

PubMed

Kishine, Masahiro; Tsutsumi, Katsuji; Kitta, Kazumi

2017-12-01

Simple sequence repeat (SSR) is a popular tool for individual fingerprinting. The long-core motif (e.g. tetra-, penta-, and hexa-nucleotide) simple sequence repeats (SSRs) are preferred because they make it easier to separate and distinguish neighbor alleles. In the present study, a new set of 8 tetra-nucleotide SSRs in potato ( Solanum tuberosum ) is reported. By using these 8 markers, 72 out of 76 cultivars obtained from Japan and the United States were clearly discriminated, while two pairs, both of which arose from natural variation, showed identical profiles. The combined probability of identity between two random cultivars for the set of 8 SSR markers was estimated to be 1.10 × 10 -8 , confirming the usefulness of the proposed SSR markers for fingerprinting analyses of potato.

Development and characterization of EST-SSR markers for Ottelia acuminata var. jingxiensis (Hydrocharitaceae).

PubMed

Li, Zhi-Zhong; Lu, Meng-Xue; Saina, Josphat K; Gichira, Andrew W; Wang, Qing-Feng; Chen, Jin-Ming

2017-11-01

Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis . One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively. Interestingly, in cross-varietal amplification, 13 out of the 16 loci were successfully amplified in O. acuminata var. acuminata , and 12 amplified in each of the other three varieties of O. acuminata . These newly developed SSR markers will facilitate further study of genetic variation and provide important genetic data needed for appropriate conservation of natural populations of all varieties of O. acuminata .

Elaeis oleifera Genomic-SSR Markers: Exploitation in Oil Palm Germplasm Diversity and Cross-Amplification in Arecaceae

PubMed Central

Zaki, Noorhariza Mohd; Singh, Rajinder; Rosli, Rozana; Ismail, Ismanizan

2012-01-01

Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (Ho) (0.164) and highly positive fixation indices (Fis) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family. PMID:22605966

Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database

PubMed Central

2012-01-01

Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L.) genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5%) within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5%) was the most abundant followed by AAG (12.1%), AAT (10.9%), and AT (10.3%).The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders. PMID:22818284

The Use of a Binary Composite Endpoint and Sample Size Requirement: Influence of Endpoints Overlap.

PubMed

Marsal, Josep-Ramon; Ferreira-González, Ignacio; Bertran, Sandra; Ribera, Aida; Permanyer-Miralda, Gaietà; García-Dorado, David; Gómez, Guadalupe

2017-05-01

Although composite endpoints (CE) are common in clinical trials, the impact of the relationship between the components of a binary CE on the sample size requirement (SSR) has not been addressed. We performed a computational study considering 2 treatments and a CE with 2 components: the relevant endpoint (RE) and the additional endpoint (AE). We assessed the strength of the components' interrelation by the degree of relative overlap between them, which was stratified into 5 groups. Within each stratum, SSR was computed for multiple scenarios by varying the events proportion and the effect of the therapy. A lower SSR using CE was defined as the best scenario for using the CE. In 25 of 66 scenarios the degree of relative overlap determined the benefit of using CE instead of the RE. Adding an AE with greater effect than the RE leads to lower SSR using the CE regardless of the AE proportion and the relative overlap. The influence of overlapping decreases when the effect on RE increases. Adding an AE with lower effect than the RE constitutes the most uncertain situation. In summary, the interrelationship between CE components, assessed by the relative overlap, can help to define the SSR in specific situations and it should be considered for SSR computation. © The Author 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular genetic variation and structure of Southeast Asian crocodile (Tomistoma schlegelii): Comparative potentials of SSRs versus ISSRs.

PubMed

Shafiei-Astani, Behnam; Ong, Alan Han Kiat; Valdiani, Alireza; Tan, Soon Guan; Yien, Christina Yong Seok; Ahmady, Fatemeh; Alitheen, Noorjahan Banu; Ng, Wei Lun; Kuar, Taranjeet

2015-10-15

Tomistoma schlegelii, also referred to as the "false gharial", is one of the most exclusive and least known of the world's fresh water crocodilians, limited to Southeast Asia. Indeed, lack of economic value for its skin has led to neglect the biodiversity of the species. The current study aimed to investigate the mentioned case using 40 simple sequence repeat (SSR) primer pairs and 45 inter-simple sequence repeat (ISSR) primers. DNA analysis of 17 T. schlegelii samples using the SSR and ISSR markers resulted in producing a total of 49 and 108 polymorphic bands, respectively. Furthermore, the SSR- and ISSR-based cluster analyses both generated two main clusters. However, the SSR based results were found to be more in line with the geographical distributions of the crocodile samples collected across the country as compared with the ISSR-based results. The observed heterozygosity (HO) and expected heterozygosity (HE) of the polymorphic SSRs ranged between 0.588-1 and 0.470-0.891, respectively. The present results suggest that the Malaysian T. schlegelii populations had originated from a core population of crocodiles. In cooperation with the SSR markers, the ISSRs showed high potential for studying the genetic variation of T. schlegelii, and these markers are suitable to be employed in conservation genetic programs of this endangered species. Both SSR- and ISSR-based STRUCTURE analyses suggested that all the individuals of T. schlegelii are genetically similar with each other. Copyright © 2015 Elsevier B.V. All rights reserved.

Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.).

PubMed

Zhu, H; Senalik, D; McCown, B H; Zeldin, E L; Speers, J; Hyman, J; Bassil, N; Hummer, K; Simon, P W; Zalapa, J E

2012-01-01

The American cranberry (Vaccinium macrocarpon Ait.) is a major commercial fruit crop in North America, but limited genetic resources have been developed for the species. Furthermore, the paucity of codominant DNA markers has hampered the advance of genetic research in cranberry and the Ericaceae family in general. Therefore, we used Roche 454 sequencing technology to perform low-coverage whole genome shotgun sequencing of the cranberry cultivar 'HyRed'. After de novo assembly, the obtained sequence covered 266.3 Mb of the estimated 540-590 Mb in cranberry genome. A total of 107,244 SSR loci were detected with an overall density across the genome of 403 SSR/Mb. The AG repeat was the most frequent motif in cranberry accounting for 35% of all SSRs and together with AAG and AAAT accounted for 46% of all loci discovered. To validate the SSR loci, we designed 96 primer-pairs using contig sequence data containing perfect SSR repeats, and studied the genetic diversity of 25 cranberry genotypes. We identified 48 polymorphic SSR loci with 2-15 alleles per locus for a total of 323 alleles in the 25 cranberry genotypes. Genetic clustering by principal coordinates and genetic structure analyzes confirmed the heterogeneous nature of cranberries. The parentage composition of several hybrid cultivars was evident from the structure analyzes. Whole genome shotgun 454 sequencing was a cost-effective and efficient way to identify numerous SSR repeats in the cranberry sequence for marker development.

[DNA marker-assisted selection of medicinal plants (Ⅰ) .Breeding research of disease-resistant cultivars of Panax notoginseng].

PubMed

Li, Qing; Li, Biao; Guo, Shun-Xing

2017-01-01

SSR is one of the most important molecular markers used in molecular identification and genetic diversity research of Dendrobium nobile. In order to enrich the library of SSR and establish a method for rapid identification of D. nobile, the SSR information was analyzed in the transcriptome of D. nobile. A total of 32 709 SSRs were obtained from the transcriptome of D. nobile, distributed in 26 742 unigenes with the distribution frequency of 12.90%. SSR loci occurred every 3 748 bp. Mono-nucleotide repeat was the main type, account for as much as 72.18% of all SSRs, followed by di-nucleotide (15.97%) and tri-nucleotide (11.19%). Among all repeat types, A/T was the predominant one followed by AG/CT. Finally a total of 62 157 primer pairs were designed for marker development. Randomly 20 pairs of primers were selected for PCR amplification, 17 amplified on clear and reproducible bands, the amplification rate was 85.0%.Thirteen pairs were polymorphic among the 3 Dendrobium plants. The results indicated that the unigenes generated from transcriptome sequencing in D. nobile can be used as effective source to develop SSR markers. The SSR loci in the transcriptome of D. nobile have the characteristics of type riches, high density and high potential of polymorphism, and these characteristics might applied in the study of molecular identification, genetic diversity and marker-assisted breeding of D. nobile and its closely related species. Copyright© by the Chinese Pharmaceutical Association.

Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes.

PubMed

An, Jianyu; Yin, Mengqi; Zhang, Qin; Gong, Dongting; Jia, Xiaowen; Guan, Yajing; Hu, Jin

2017-09-11

Luffa cylindrica (L.) Roem. is an economically important vegetable crop in China. However, the genomic information on this species is currently unknown. In this study, for the first time, a genome survey of L. cylindrica was carried out using next-generation sequencing (NGS) technology. In total, 43.40 Gb sequence data of L. cylindrica , about 54.94× coverage of the estimated genome size of 789.97 Mb, were obtained from HiSeq 2500 sequencing, in which the guanine plus cytosine (GC) content was calculated to be 37.90%. The heterozygosity of genome sequences was only 0.24%. In total, 1,913,731 contigs (>200 bp) with 525 bp N 50 length and 1,410,117 scaffolds (>200 bp) with 885.01 Mb total length were obtained. From the initial assembled L. cylindrica genome, 431,234 microsatellites (SSRs) (≥5 repeats) were identified. The motif types of SSR repeats included 62.88% di-nucleotide, 31.03% tri-nucleotide, 4.59% tetra-nucleotide, 0.96% penta-nucleotide and 0.54% hexa-nucleotide. Eighty genomic SSR markers were developed, and 51/80 primers could be used in both "Zheda 23" and "Zheda 83". Nineteen SSRs were used to investigate the genetic diversity among 32 accessions through SSR-HRM analysis. The unweighted pair group method analysis (UPGMA) dendrogram tree was built by calculating the SSR-HRM raw data. SSR-HRM could be effectively used for genotype relationship analysis of Luffa species.

Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.).

PubMed

Mornkham, T; Wangsomnuk, P P; Mo, X C; Francisco, F O; Gao, L Z; Kurzweil, H

2016-10-24

Jerusalem artichoke (Helianthus tuberosus L.) is a perennial tuberous plant and a traditional inulin-rich crop in Thailand. It has become the most important source of inulin and has great potential for use in chemical and food industries. In this study, expressed sequence tag (EST)-based simple sequence repeat (SSR) markers were developed from 40,362 Jerusalem artichoke ESTs retrieved from the NCBI database. Among 23,691 non-redundant identified ESTs, 1949 SSR motifs harboring 2 to 6 nucleotides with varied repeat motifs were discovered from 1676 assembled sequences. Seventy-nine primer pairs were generated from EST sequences harboring SSR motifs. Our results show that 43 primers are polymorphic for the six studied populations, while the remaining 36 were either monomorphic or failed to amplify. These 43 SSR loci exhibited a high level of genetic diversity among populations, with allele numbers varying from 2 to 7, with an average of 3.95 alleles per loci. Heterozygosity ranged from 0.096 to 0.774, with an average of 0.536; polymorphic index content ranged from 0.096 to 0.854, with an average of 0.568. Principal component analysis and neighbor-joining analysis revealed that the six populations could be divided into six clusters. Our results indicate that these newly characterized EST-SSR markers may be useful in the exploration of genetic diversity and range expansion of the Jerusalem artichoke, and in cross-species application for the genus Helianthus.

Molecular mapping and genetic analysis of a rice brown planthopper (Nilaparvata lugens Stål) resistance gene.

PubMed

Yang, Haiyuan; Ren, Xiang; Weng, Qingmei; Zhu, Lili; He, Guangcun

2002-01-01

The brown planthopper (BPH), Nilaparvata lugens Stål, is a serious insect pest of rice (Oryza saliva L.). We have determined the chromosomal location of a BPH resistance gene in rice using SSR and RFLP techniques. A rice line 'B14', derived from the wild rice Oryza latifolia, showed high resistance to BPH. For tagging the resistance gene in 'B14X', an F2 population and a recombinant inbred (RI) population from a cross between Taichung Native 1 and 'B14' were developed and evaluated for BPH resistance. The results showed that a single dominant gene controlled the resistance of 'B14' to BPH. Bulked segregant SSR analysis was employed for identification of DNA markers linked to the resistance gene. From the survey of 302 SSR primer pairs, three SSR (RM335, RM261, RM185) markers linked to the resistance gene were identified. The closest SSR marker RM261 was linked to the resistance gene at a distance of 1.8 cM. Regions surrounding the resistance gene and the SSR markers were examined with additional RFLP markers on chromosome 4 to define the location of the resistance gene. Linkage of RFLP markers C820, R288, C946 with the resistance gene further confirmed its location on the short arm of chromosome 4. Closely linked DNA markers will facilitate selection for resistant lines in breeding programs and provide the basis for map-based cloning of this resistance gene.

A Study on the Effects of Sympathetic Skin Response Parameters in Diagnosis of Fibromyalgia Using Artificial Neural Networks.

PubMed

Ozkan, Ozhan; Yildiz, Murat; Arslan, Evren; Yildiz, Sedat; Bilgin, Suleyman; Akkus, Selami; Koyuncuoglu, Hasan R; Koklukaya, Etem

2016-03-01

Fibromyalgia syndrome (FMS), usually observed commonly in females over age 30, is a rheumatic disease accompanied by extensive chronic pain. In the diagnosis of the disease non-objective psychological tests and physiological tests and laboratory test results are evaluated and clinical experiences stand out. However, these tests are insufficient in differentiating FMS with similar diseases that demonstrate symptoms of extensive pain. Thus, objective tests that would help the diagnosis are needed. This study analyzes the effect of sympathetic skin response (SSR) parameters on the auxiliary tests used in FMS diagnosis, the laboratory tests and physiological tests. The study was conducted in Suleyman Demirel University, Faculty of Medicine, Physical Medicine and Rehabilitation Clinic in Turkey with 60 patients diagnosed with FMS for the first time and a control group of 30 healthy individuals. In the study all participants underwent laboratory tests (blood tests), certain physiological tests (pulsation, skin temperature, respiration) and SSR measurements. The test data and SSR parameters obtained were classified using artificial neural network (ANN). Finally, in the ANN framework, where only laboratory and physiological test results were used as input, a simulation result of 96.51 % was obtained, which demonstrated diagnostic accuracy. This data, with the addition of SSR parameter values obtained increased to 97.67 %. This result including SSR parameters - meaning a higher diagnostic accuracy - demonstrated that SSR could be a new auxillary diagnostic method that could be used in the diagnosis of FMS.

The vasopressin V(1b) receptor antagonist SSR149415 in the treatment of major depressive and generalized anxiety disorders: results from 4 randomized, double-blind, placebo-controlled studies.

PubMed

Griebel, Guy; Beeské, Sandra; Stahl, Stephen M

2012-11-01

These studies were designed to evaluate the efficacy and tolerability of the first nonpeptide vasopressin V(1b) receptor antagonist, SSR149415, in the treatment of major depressive disorder (MDD) and generalized anxiety disorder (GAD). Studies were randomized 8-week, double-blind, placebo-controlled trials evaluating 100- and 250-mg twice daily doses of SSR149415, placebo, and escitalopram 10 mg/day or paroxetine 20 mg/day, conducted from August 2006 through February 2008. Participants met the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision criteria for MDD or GAD. Baseline Montgomery-Asberg Depression Rating Scale (MADRS) and Hamilton Depression Rating Scale (HDRS) total scores were ≥ 24 and 18, respectively, and in the GAD trial baseline Hamilton Anxiety Rating Scale (HARS) score was ≥ 22. Primary efficacy variables included changes from baseline in total score on HDRS or HARS and MADRS, and the secondary variable included changes in the Clinical Global Impressions-Severity of Illness score (CGI-S). A 4-week, double-blind, placebo-controlled study evaluating the effect of 100- and 250-mg twice daily doses of SSR149415 on the hypothalamic-pituitary-adrenal (HPA) axis in MDD patients was also conducted. In the GAD trial, SSR149415 did not separate from placebo on the primary (HARS-100 mg: P = .29; 250 mg: P = .21) and secondary (CGI-S-100 mg: P = .18; 250 mg: P = .24) outcome measures, while paroxetine demonstrated efficacy (HARS: P = .003; CGI-S: P = .01). In 2 MDD trials, SSR149415-treated patients did not show significant improvement from baseline on any outcome measure compared with placebo-treated patients (HDRS-100 mg: P = .21 and .48, respectively; 250 mg: P = .22 and P = .46, respectively; CGI-S-100 mg: P = .64 and P = .82, respectively; 250 mg: P = .33 and P = .08, respectively). In the third MDD study, SSR149415 250 mg (P = .04), but not escitalopram (P = .15), demonstrated significant improvement compared to placebo on the HDRS total score at week 8. SSR149415 had no deleterious effects on the HPA axis. These studies demonstrate that SSR149415 may not be useful for the treatment of GAD and that its antidepressant potential needs to be further evaluated. ClinicalTrials.gov identifiers: NCT00374166 (Sanofi ID number: DFI5880), NCT00361491 (Sanofi ID number: DFI5879), NCT00358631 (Sanofi ID number: DFI5878), NCT01606384 (Sanofi ID number: PDY5467). © Copyright 2012 Physicians Postgraduate Press, Inc.

Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus

PubMed Central

Singh, Swati; Gupta, Sanchita; Mani, Ashutosh; Chaturvedi, Anoop

2012-01-01

Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function. PMID:22368382

Novel and highly informative Capsicum SSR markers and their cross-species transferability.

PubMed

Buso, G S C; Reis, A M M; Amaral, Z P S; Ferreira, M E

2016-09-23

This study was undertaken primarily to develop new simple sequence repeat (SSR) markers for Capsicum. As part of this project aimed at broadening the use of molecular tools in Capsicum breeding, two genomic libraries enriched for AG/TC repeat sequences were constructed for Capsicum annuum. A total of 475 DNA clones were sequenced from both libraries and 144 SSR markers were tested on cultivated and wild species of Capsicum. Forty-five SSR markers were randomly selected to genotype a panel of 48 accessions of the Capsicum germplasm bank. The number of alleles per locus ranged from 2 to 11, with an average of 6 alleles. The polymorphism information content was on average 0.60, ranging from 0.20 to 0.83. The cross-species transferability to seven cultivated and wild Capsicum species was tested with a set of 91 SSR markers. We found that a high proportion of the loci produced amplicons in all species tested. C. frutescens had the highest number of transferable markers, whereas the wild species had the lowest. Our results indicate that the new markers can be readily used in genetic analyses of Capsicum.

A suggestion for computing objective function in model calibration

USGS Publications Warehouse

Wu, Yiping; Liu, Shuguang

2014-01-01

A parameter-optimization process (model calibration) is usually required for numerical model applications, which involves the use of an objective function to determine the model cost (model-data errors). The sum of square errors (SSR) has been widely adopted as the objective function in various optimization procedures. However, ‘square error’ calculation was found to be more sensitive to extreme or high values. Thus, we proposed that the sum of absolute errors (SAR) may be a better option than SSR for model calibration. To test this hypothesis, we used two case studies—a hydrological model calibration and a biogeochemical model calibration—to investigate the behavior of a group of potential objective functions: SSR, SAR, sum of squared relative deviation (SSRD), and sum of absolute relative deviation (SARD). Mathematical evaluation of model performance demonstrates that ‘absolute error’ (SAR and SARD) are superior to ‘square error’ (SSR and SSRD) in calculating objective function for model calibration, and SAR behaved the best (with the least error and highest efficiency). This study suggests that SSR might be overly used in real applications, and SAR may be a reasonable choice in common optimization implementations without emphasizing either high or low values (e.g., modeling for supporting resources management).

Modernizing the Estonian farmhouse, redefining the family, 1880s-1930s.

PubMed

L'Heureux, Marie-Alice

2010-01-01

In the nineteenth century, the transition from a Baltic-German-controlled manor-and-serf economy to individually owned farmsteads transformed all aspects of life including the spatial organization and form of farmhouses in the western provinces of Tsarist Russia. Agricultural experts and social reformers discussed how to update the traditional threshing-room dwelling house (rehielamu) into a healthy dwelling for successful farmers and, after the Estonian War of Independence, for new settlers. Using material culture such as contemporary plans, I show that changing household relationships, in addition to economic and technological factors, helped to transform the ancient rehielamu into a modern dwelling.

Mental health and alcohol problems among Estonian cleanup workers 24 years after the Chernobyl accident.

PubMed

Laidra, Kaia; Rahu, Kaja; Tekkel, Mare; Aluoja, Anu; Leinsalu, Mall

2015-11-01

To study the long-term mental health consequences of the 1986 Chernobyl nuclear accident among cleanup workers from Estonia. In 2010, 614 Estonian Chernobyl cleanup workers and 706 geographically and age-matched population-based controls completed a mail survey that included self-rated health, the Posttraumatic Stress Disorder Checklist (PCL), alcohol symptoms (AUDIT), and scales measuring depressive, anxiety, agoraphobia, fatigue, insomnia, and somatization symptoms. Respondents were dichotomized into high (top quartile) and low symptom groups on each measure. Logistic regression analysis detected significant differences between cleanup workers and controls on all measures even after adjustment for ethnicity, education, marital status, and employment status. The strongest difference was found for somatization, with cleanup workers being three times more likely than controls to score in the top quartile (OR = 3.28, 95% CI 2.39-4.52), whereas for alcohol problems the difference was half as large (OR = 1.52, 95% CI 1.16-1.99). Among cleanup workers, arrival at Chernobyl in 1986 (vs. later) was associated with sleep problems, somatization, and symptoms of agoraphobia. The toll of cleanup work was evident 24 years after the Chernobyl accident among Estonian cleanup workers indicating the need for focused mental health interventions.

Modelling nutrient fluxes from diffuse and point emissions to river loads: the Estonian part of the transboundary Lake Peipsi/Chudskoe drainage basin (Russia/Estonia/Latvia).

PubMed

Mourad, D; van der Perk, M

2004-01-01

First results are presented of a large-scale GIS-based nutrient transport modelling for the 1985-1999 period in the Estonian part of the transboundary drainage basin of Lake Peipsi (Estonian)/Chudskoe (Russian), one of the largest lakes in Europe, shared by Russia and Estonia. Although the lake is relatively undisturbed by human pollution, it is vulnerable for eutrophication by increased river loads, as shown in the past, when the north-eastern part of the former Soviet Union suffered from intensive agriculture. The collapse of the Soviet Union caused a dramatic decline in fertilizer application rates and widespread abandonment of agricultural land. Although concentration measurements and modelling results indicate a general decrease in nutrient loads, modelling is complicated by the transfer of nutrients from diffuse emissions, which is strongly governed by retention and assumed periodic release from storages within the river basin, like the root zone, tile drains, ditches, channels, bed sediments, floodplains and lakes. Modelling diffuse emission contribution to river loads can be improved by better knowledge about the spatial and temporal distribution of this retention and release within the drainage basin.

Two Enhancements of the Logarithmic Least-Squares Method for Analyzing Subjective Comparisons

DTIC Science & Technology

1989-03-25

error term. 1 For this model, the total sum of squares ( SSTO ), defined as n 2 SSTO = E (yi y) i=1 can be partitioned into error and regression sums...of the regression line around the mean value. Mathematically, for the model given by equation A.4, SSTO = SSE + SSR (A.6) A-4 where SSTO is the total...sum of squares (i.e., the variance of the yi’s), SSE is error sum of squares, and SSR is the regression sum of squares. SSTO , SSE, and SSR are given

Protein Degradation in a TX-TL Cell-free Expression System Using ClpXP Protease

DTIC Science & Technology

2014-07-14

function in TX-TL, as well as bacteriophage assembly [2, 6]. Circuits can also be prototyped from basic parts within 8 hours, avoiding cloning and...mRFP, and Venus and variants eGFP-ssrA, mRFP-ssrA, and Venus-ssrA, coding sequences were cloned into a T7-lacO inducible vector containing a N...12672L12677.! 6.! Shin,!J.,!P.!Jardine,!and!V.!Noireaux,!Genome(Replication,(Synthesis,(and( Assembly(of(the( Bacteriophage (T7(in(a(Single(Cell9Free

M13-Tailed Simple Sequence Repeat (SSR) Markers in Studies of Genetic Diversity and Population Structure of Common Oat Germplasm.

PubMed

Onyśk, Agnieszka; Boczkowska, Maja

2017-01-01

Simple Sequence Repeat (SSR) markers are one of the most frequently used molecular markers in studies of crop diversity and population structure. This is due to their uniform distribution in the genome, the high polymorphism, reproducibility, and codominant character. Additional advantages are the possibility of automatic analysis and simple interpretation of the results. The M13 tagged PCR reaction significantly reduces the costs of analysis by the automatic genetic analyzers. Here, we also disclose a short protocol of SSR data analysis.

Genetic variation and DNA fingerprinting of durian types in Malaysia using simple sequence repeat (SSR) markers.

PubMed

Siew, Ging Yang; Ng, Wei Lun; Tan, Sheau Wei; Alitheen, Noorjahan Banu; Tan, Soon Guan; Yeap, Swee Keong

2018-01-01

Durian ( Durio zibethinus ) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity, H E  = 0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10 -3 . Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called "clones", "varieties", or "cultivars". Such matters have a direct impact on the regulation and management of durian genetic resources in the region.

Genetic variation and DNA fingerprinting of durian types in Malaysia using simple sequence repeat (SSR) markers

PubMed Central

Siew, Ging Yang; Tan, Sheau Wei; Tan, Soon Guan; Yeap, Swee Keong

2018-01-01

Durian (Durio zibethinus) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity, HE = 0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10−3. Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called “clones”, “varieties”, or “cultivars”. Such matters have a direct impact on the regulation and management of durian genetic resources in the region. PMID:29511604

A Genome-Wide Survey of the Microsatellite Content of the Globe Artichoke Genome and the Development of a Web-Based Database

PubMed Central

Portis, Ezio; Portis, Flavio; Valente, Luisa; Moglia, Andrea; Barchi, Lorenzo; Lanteri, Sergio; Acquadro, Alberto

2016-01-01

The recently acquired genome sequence of globe artichoke (Cynara cardunculus var. scolymus) has been used to catalog the genome’s content of simple sequence repeat (SSR) markers. More than 177,000 perfect SSRs were revealed, equivalent to an overall density across the genome of 244.5 SSRs/Mbp, but some 224,000 imperfect SSRs were also identified. About 21% of these SSRs were complex (two stretches of repeats separated by <100 nt). Some 73% of the SSRs were composed of dinucleotide motifs. The SSRs were categorized for the numbers of repeats present, their overall length and were allocated to their linkage group. A total of 4,761 perfect and 6,583 imperfect SSRs were present in 3,781 genes (14.11% of the total), corresponding to an overall density across the gene space of 32,5 and 44,9 SSRs/Mbp for perfect and imperfect motifs, respectively. A putative function has been assigned, using the gene ontology approach, to the set of genes harboring at least one SSR. The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. Certain species-specific SSR motifs were identified, along with a hexa-nucleotide motif shared only with the other two Compositae species (sunflower (Helianthus annuus) and horseweed (Conyza canadensis)) included in the study. Finally, a database, called “Cynara cardunculus MicroSatellite DataBase” (CyMSatDB) was developed to provide a searchable interface to the SSR data. CyMSatDB facilitates the retrieval of SSR markers, as well as suggested forward and reverse primers, on the basis of genomic location, genomic vs genic context, perfect vs imperfect repeat, motif type, motif sequence and repeat number. The SSR markers were validated via an in silico based PCR analysis adopting two available assembled transcriptomes, derived from contrasting globe artichoke accessions, as templates. PMID:27648830

High resolution melting analysis is a more sensitive and effective alternative to gel-based platforms in analysis of SSR--an example in citrus.

PubMed

Distefano, Gaetano; Caruso, Marco; La Malfa, Stefano; Gentile, Alessandra; Wu, Shu-Biao

2012-01-01

High resolution melting curve analysis (HRM) has been used as an efficient, accurate and cost-effective tool to detect single nucleotide polymorphisms (SNPs) or insertions or deletions (INDELs). However, its efficiency, accuracy and applicability to discriminate microsatellite polymorphism have not been extensively assessed. The traditional protocols used for SSR genotyping include PCR amplification of the DNA fragment and the separation of the fragments on electrophoresis-based platform. However, post-PCR handling processes are laborious and costly. Furthermore, SNPs present in the sequences flanking repeat motif cannot be detected by polyacrylamide-gel-electrophoresis based methods. In the present study, we compared the discriminating power of HRM with the traditional electrophoresis-based methods and provided a panel of primers for HRM genotyping in Citrus. The results showed that sixteen SSR markers produced distinct polymorphic melting curves among the Citrus spp investigated through HRM analysis. Among those, 10 showed more genotypes by HRM analysis than capillary electrophoresis owing to the presence of SNPs in the amplicons. For the SSR markers without SNPs present in the flanking region, HRM also gave distinct melting curves which detected same genotypes as were shown in capillary electrophoresis (CE) analysis. Moreover, HRM analysis allowed the discrimination of most of the 15 citrus genotypes and the resulting genetic distance analysis clustered them into three main branches. In conclusion, it has been approved that HRM is not only an efficient and cost-effective alternative of electrophoresis-based method for SSR markers, but also a method to uncover more polymorphisms contributed by SNPs present in SSRs. It was therefore suggested that the panel of SSR markers could be used in a variety of applications in the citrus biodiversity and breeding programs using HRM analysis. Furthermore, we speculate that the HRM analysis can be employed to analyse SSR markers in a wide range of applications in all other species.

Sustained Silent Reading: Try It, You'll Like It!

ERIC Educational Resources Information Center

Anderson, Cynthia

2000-01-01

Recommends Sustained Silent Reading (SSR) in grades 2-12 to improve students' reading and to teach them to love to read. Outlines rules for SSR, and offers notes to the teacher on its implementation. (SR)

Selection of high heterozygosity popcorn varieties in Brazil based on SSR markers.

PubMed

Eloi, I B O; Mangolin, C A; Scapim, C A; Gonçalves, C S; Machado, M F P S

2012-07-19

We analyzed genetic structure and diversity among eight populations of popcorn, using SSR loci as genetic markers. Our objectives were to select SSR loci that could be used to estimate genetic diversity within popcorn populations, and to analyze the genetic structure of promising populations with high levels of heterozygosity that could be used in breeding programs. Fifty-seven alleles (3.7 alleles per locus) were detected; the highest effective number of alleles (4.21) and the highest gene diversity (0.763) were found for the Umc2226 locus. A very high level of population differentiation was found (F(ST) = 0.3664), with F(ST) for each locus ranging from 0.1029 (Umc1664) to 0.6010 (Umc2350). This analysis allowed us to identify SSR loci with high levels of heterozygosity and heterozygous varieties, which could be selected for production of inbred lines and for developing new cultivars.

Efficiency of RAPD versus SSR markers for determining genetic diversity among popcorn lines.

PubMed

Leal, A A; Mangolin, C A; do Amaral, A T; Gonçalves, L S A; Scapim, C A; Mott, A S; Eloi, I B O; Cordovés, V; da Silva, M F P

2010-01-05

Using only one type of marker to quantify genetic diversity generates results that have been questioned in terms of reliability, when compared to the combined use of different markers. To compare the efficiency of the use of single versus multiple markers, we quantified genetic diversity among 10 S(7) inbred popcorn lines using both RAPD and SSR markers, and we evaluated how well these two types of markers discriminated the popcorn genotypes. These popcorn genotypes: "Yellow Pearl Popcorn" (P1-1 and P1-5), "Zélia" (P1-2 and P1-4), "Curagua" (P1-3), "IAC 112" (P9-1 and P9-2), "Avati Pichinga" (P9-3 and P9-5), and "Pisankalla" (P9-4) have different soil and climate adaptations. Using RAPD marker analysis, each primer yielded bands of variable intensities that were easily detected, as well as non-specific bands, which were discarded from the analysis. The nine primers used yielded 126 bands, of which 104 were classified as polymorphic, giving an average of 11.6 polymorphisms per primer. Using SSR procedures, the number of alleles per locus ranged from two to five, giving a total of 47 alleles for the 14 SSR loci. When comparing the groups formed using SSR and RAPD markers, there were similarities in the combinations of genotypes from the same genealogy. Correlation between genetic distances obtained through RAPD and SSR markers was relatively high (0.5453), indicating that both techniques are efficient for evaluating genetic diversity in the genotypes of popcorn that we evaluated, though RAPDs yielded more polymorphisms.

Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential

PubMed Central

Biswas, Manosh Kumar; Liu, Yuxuan; Li, Chunyu; Sheng, Ou; Mayer, Christoph; Yi, Ganjun

2015-01-01

The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species. PMID:26121637

RAPD and SSR Polymorphisms in Mutant Lines of Transgenic Wheat Mediated by Low Energy Ion Beam

NASA Astrophysics Data System (ADS)

Wang, Tiegu; Huang, Qunce; Feng, Weisen

2007-10-01

Two types of markers-random amplified polymorphic DNA (RAPD) and simple sequence repeat DNA (SSR)-have been used to characterize the genetic diversity among nine mutant lines of transgenic wheat intermediated by low energy ion beam and their four receptor cultivars. The objectives of this study were to analyze RAPD-based and SSR-based genetic variance among transgenic wheat lines and with their receptors, and to find specific genetic markers of special traits of transgenic wheat lines. 170 RAPD primers were amplified to 733 fragments in all the experimental materials. There were 121 polymorphic fragments out of the 733 fragments with a ratio of polymorphic fragments of 16.5%. 29 SSR primer pairs were amplified to 83 fragments in all the experiment materials. There were 57 polymorphic fragments out of the 83 fragments with a ratio of polymorphic fragments of 68.7%. The dendrograms were prepared based on a genetic distance matrix using the UPGMA (Unweighted Pair-group Method with Arithmetic averaging) algorithm, which corresponded well to the results of the wheat pedigree analysis and separated the 13 genotypes into four groups. Association analysis between RAPD and SSR markers with the special traits of transgenic wheat mutant lines discovered that three RAPD markers, s1, opt-16, and f14, were significantly associated with the muticate trait, while three SSR markers, Rht8 (Xgwm261), Rht-B1b, and Rht-D1b, highly associated with the dwarf trait. These markers will be useful for marker-assistant breeding and can be used as candidate markers for further gene mapping and cloning.

Dependence of particle concentration effect on pH and redox for arsenic removal by FeS-coated sand under anoxic conditions.

PubMed

Han, Young-Soo; Demond, Avery H; Gallegos, Tanya J; Hayes, Kim F

2015-09-01

FeS has been recognized as a good scavenger for arsenic under anoxic conditions. To create a suitable adsorbent for flow-through reactors such as permeable reactive barriers, it has been suggested that this material may be coated onto sand. However, previous work on FeS-coated sand has focused on batch reactors, while flow-through reactors usually have higher solid-solution ratios. To ascertain whether differences in the solid-solution ratio (SSR) are important in this system, batch sorption experiments were conducted as a function of pH using As(III) and FeS-coated sands at various solid-solution ratios. The results showed little variation in the distribution coefficient with SSR at pH 7 and 9. However, at pH 5, the results showed lower values of the distribution coefficient at lower SSRs, the reverse of typically reported SSR effects. Measured pe values showed a dependence on SSR, which, when coupled with chemical modeling of the Fe-As-S-H2O system, suggested a change in the removal mechanism with SSR, from adsorption to a reduced Fe(II) oxyhydroxide phase (represented by Fe2(OH)5) to precipitation as As2S3 or AsS. On the other hand, at pH 7 and 9, arsenite adsorption is the most probable removal mechanism regardless of the pe. Thus, this study identified variations in pH and redox conditions, and the removal mechanisms that these parameters govern, as the reason for the apparent SSR effect. Copyright © 2014 Elsevier Ltd. All rights reserved.

Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes

PubMed Central

An, Jianyu; Yin, Mengqi; Zhang, Qin; Gong, Dongting; Jia, Xiaowen; Guan, Yajing; Hu, Jin

2017-01-01

Luffa cylindrica (L.) Roem. is an economically important vegetable crop in China. However, the genomic information on this species is currently unknown. In this study, for the first time, a genome survey of L. cylindrica was carried out using next-generation sequencing (NGS) technology. In total, 43.40 Gb sequence data of L. cylindrica, about 54.94× coverage of the estimated genome size of 789.97 Mb, were obtained from HiSeq 2500 sequencing, in which the guanine plus cytosine (GC) content was calculated to be 37.90%. The heterozygosity of genome sequences was only 0.24%. In total, 1,913,731 contigs (>200 bp) with 525 bp N50 length and 1,410,117 scaffolds (>200 bp) with 885.01 Mb total length were obtained. From the initial assembled L. cylindrica genome, 431,234 microsatellites (SSRs) (≥5 repeats) were identified. The motif types of SSR repeats included 62.88% di-nucleotide, 31.03% tri-nucleotide, 4.59% tetra-nucleotide, 0.96% penta-nucleotide and 0.54% hexa-nucleotide. Eighty genomic SSR markers were developed, and 51/80 primers could be used in both “Zheda 23” and “Zheda 83”. Nineteen SSRs were used to investigate the genetic diversity among 32 accessions through SSR-HRM analysis. The unweighted pair group method analysis (UPGMA) dendrogram tree was built by calculating the SSR-HRM raw data. SSR-HRM could be effectively used for genotype relationship analysis of Luffa species. PMID:28891982

Test Plan for SSR Antenna Rotation Rate Stabilization

DOT National Transportation Integrated Search

1981-10-01

A comprehensive test plan is presented to evaluate the impact of wind and ice loading on the rotation rate stability of a Secondary Surveillance Radar (SSR) antenna used for air traffic control surveillance. Antenna rotation rate variations may intro...

Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers

PubMed Central

Julier, Bernadette; Flajoulot, Sandrine; Barre, Philippe; Cardinet, Gaëlle; Santoni, Sylvain; Huguet, Thierry; Huyghe, Christian

2003-01-01

Background Alfalfa (Medicago sativa) is a major forage crop. The genetic progress is slow in this legume species because of its autotetraploidy and allogamy. The genetic structure of this species makes the construction of genetic maps difficult. To reach this objective, and to be able to detect QTLs in segregating populations, we used the available codominant microsatellite markers (SSRs), most of them identified in the model legume Medicago truncatula from EST database. A genetic map was constructed with AFLP and SSR markers using specific mapping procedures for autotetraploids. The tetrasomic inheritance was analysed in an alfalfa mapping population. Results We have demonstrated that 80% of primer pairs defined on each side of SSR motifs in M. truncatula EST database amplify with the alfalfa DNA. Using a F1 mapping population of 168 individuals produced from the cross of 2 heterozygous parental plants from Magali and Mercedes cultivars, we obtained 599 AFLP markers and 107 SSR loci. All but 3 SSR loci showed a clear tetrasomic inheritance. For most of the SSR loci, the double-reduction was not significant. For the other loci no specific genotypes were produced, so the significant double-reduction could arise from segregation distortion. For each parent, the genetic map contained 8 groups of four homologous chromosomes. The lengths of the maps were 2649 and 3045 cM, with an average distance of 7.6 and 9.0 cM between markers, for Magali and Mercedes parents, respectively. Using only the SSR markers, we built a composite map covering 709 cM. Conclusions Compared to diploid alfalfa genetic maps, our maps cover about 88–100% of the genome and are close to saturation. The inheritance of the codominant markers (SSR) and the pattern of linkage repulsions between markers within each homology group are consistent with the hypothesis of a tetrasomic meiosis in alfalfa. Except for 2 out of 107 SSR markers, we found a similar order of markers on the chromosomes between the tetraploid alfalfa and M. truncatula genomes indicating a high level of colinearity between these two species. These maps will be a valuable tool for alfalfa breeding and are being used to locate QTLs. PMID:14683527

Highly Informative Simple Sequence Repeat (SSR) Markers for Fingerprinting Hazelnut

USDA-ARS?s Scientific Manuscript database

Simple sequence repeat (SSR) or microsatellite markers have many applications in breeding and genetic studies of plants, including fingerprinting of cultivars and investigations of genetic diversity, and therefore provide information for better management of germplasm collections. They are repeatab...

Heritable variation in seed sex ratio of the stinging nettle (Urtica dioica).

PubMed

de Jong, T J; Nell, H W; Glawe, G A

2005-03-01

Male and female flowering plants of the dioecious Urtica dioica occur in approximately equal numbers in our study area on the coastal sand dunes of Meijendel. The seed sex ratio (SSR, fraction of males) collected from female plants in the field varied between 0.05 and 0.76, and differed significantly between maternal parents. After one generation of selection for either high or low SSR, female plants produced seed batches with sex ratios as extreme as 0.08 and 0.73. Natural populations of U. dioica harbour considerable genetic variation in SSR.

Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data.

PubMed

Cömertpay, G; Baloch, F S; Derya, M; Andeden, E E; Alsaleh, A; Sürek, H; Özkan, H

2016-02-19

Effective breeding programs based on genetic diversity are needed to broaden the genetic basis of rice (Oryza sativa L.) in Turkey. In this study, 81 commercial varieties from seven countries were studied in order to estimate the genomic relationships among them using nine inter-primer binding site (iPBS)-retrotransposon and 17 simple-sequence repeat (SSR) markers. A total of 59 alleles for the SSR markers and 96 bands for the iPBS-retrotransposon markers were detected, with an average of 3.47 and 10.6 per locus, respectively. Each of the varieties could be unequivocally identified by the SSR and iPBS-retrotransposon profiles. The iPBS-retrotransposon- and SSR-based clustering were identical and closely mirrored each other, with a significantly high correlation (r = 0.73). A neighbor-joining cluster based on the combined SSR and iPBS-retrotransposon data divided the rice varieties into three clusters. The population structure was determined using the STRUCTURE software, and three populations (K = 3) were identified among the varieties studied, showing that the diversity harbored by Turkish rice varieties is low. The results indicate that iPBS-retrotransposon markers are a very powerful technique to determine the genetic diversity of rice varieties.

Effect of the bradykinin 1 receptor antagonist SSR240612 after oral administration in Mycobacterium tuberculosis-infected mice.

PubMed

Rodrigues-Junior, Valnês S; Pail, Priscilla B; Villela, Anne D; Falcão, Virgínia C A; Dadda, Adílio S; Abbadi, Bruno L; Pesquero, João B; Santos, Diógenes S; Basso, Luiz A; Campos, Maria M

2018-03-01

The role, if any, played by the kinin system in tuberculosis infection models, either in vivo or in vitro, was investigated. The effects of Mycobacterium tuberculosis infection on C57BL/6 wild type, B 1 R-/-, B 2 R-/- and double B 1 R/B 2 R knockout mice were evaluated. Immunohistochemistry analysis was carried out to assess B 1 R and B 2 R expression in spleens and lungs of M. tuberculosis-infected mice. In addition, in vitro experiments with M. tuberculosis-infected macrophages were performed. The in vivo effects of HOE-140 and SSR240612 on the mice model of infection were also evaluated. Infected B 2 R-/- mice exhibited increased splenomegaly, whereas decreased spleen weight in infected double B 1 R/B 2 R knockout mice was observed. The bacterial load, determined as colony-forming units, did not differ in the spleens and lungs of the studied mouse strains. Importantly, immunohistochemical analysis revealed that B 1 R was upregulated in both spleens and lungs of infected mice. M. tuberculosis-infected macrophages incubated with SSR240612, alone or in combination with des-Arg 9 -BK, for four days, displayed a marked inhibitory effect on CFU counts. However, the pre-incubation of the selective B 1 R (des-Arg 9 -BK and SSR240612) and B 2 R (BK and HOE-140) agonists and antagonists, respectively, did not significantly affect the bacterial loads. A statistically significant reduction in the CFU of M. tuberculosis in lungs and spleens of animals treated with SSR240612, but not with HOE-140, was observed. Further efforts should be pursued to clarify whether or not SSR240612 might be considered an option for the treatment of tuberculosis. Copyright © 2018. Published by Elsevier Ltd.

The CRF₁ receptor antagonist SSR125543 prevents stress-induced long-lasting sleep disturbances in a mouse model of PTSD: comparison with paroxetine and d-cycloserine.

PubMed

Philbert, Julie; Beeské, Sandra; Belzung, Catherine; Griebel, Guy

2015-02-15

The selective CRF₁ (corticotropin releasing factor type 1) receptor antagonist SSR125543 has been previously shown to attenuate the long-term behavioral and electrophysiological effects produced by traumatic stress exposure in mice. Sleep disturbances are one of the most commonly reported symptoms by people with post-traumatic stress disorder (PTSD). The present study aims at investigating whether SSR125543 (10 mg/kg/day/i.p. for 2 weeks) is able to attenuate sleep/wakefulness impairment induced by traumatic stress exposure in a model of PTSD in mice using electroencephalographic (EEG) analysis. Effects of SSR125543 were compared to those of the 5-HT reuptake inhibitor, paroxetine (10 mg/kg/day/i.p.), and the partial N-methyl-d-aspartate (NMDA) receptor agonist, d-cycloserine (10 mg/kg/day/i.p.), two compounds which have demonstrated clinical efficacy against PTSD. Baseline EEG recording was performed in the home cage for 6h prior to the application of two electric foot-shocks of 1.5 mA. Drugs were administered from day 1 post-stress to the day preceding the second EEG recording session, performed 14 days later. Results showed that at day 14 post-stress, shocked mice displayed sleep fragmentation as shown by an increase in the occurrence of both non-rapid eye movement (NREM) sleep and wakefulness bouts. The duration of wakefulness, NREM and REM sleep were not significantly affected. The stress-induced effects were prevented by repeated administration of SSR125543, paroxetine and D-cycloserine. These findings confirm further that the CRF₁ receptor antagonist SSR125543 is able to attenuate the deleterious effects of traumatic stress exposure. Copyright © 2014 Elsevier B.V. All rights reserved.

Optimization of sequence alignment for simple sequence repeat regions.

PubMed

Jighly, Abdulqader; Hamwieh, Aladdin; Ogbonnaya, Francis C

2011-07-20

Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs) mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs).SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type.When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic phylogenic relationship.

Increased sensitivity to protein synthesis inhibitors in cells lacking tmRNA.

PubMed Central

de la Cruz, J; Vioque, A

2001-01-01

tmRNA (also known as SsrA or 10Sa RNA) is involved in a trans-translation reaction that contributes to the recycling of stalled ribosomes at the 3' end of an mRNA lacking a stop codon or at an internal mRNA cluster of rare codons. Inactivation of the ssrA gene in most bacteria results in viable cells bearing subtle phenotypes, such as temperature-sensitive growth. Herein, we report on the functional characterization of the ssrA gene in the cyanobacterium Synechocystis sp. strain PCC6803. Deletion of the ssrA gene in Synechocystis resulted in viable cells with a growth rate identical to wild-type cells. However, null ssrA cells (deltassrA) were not viable in the presence of the protein synthesis inhibitors chloramphenicol, lincomycin, spiramycin, tylosin, erythromycin, and spectinomycin at low doses that do not significantly affect the growth of wild-type cells. Sensitivity of deltassrA cells similar to wild-type cells was observed with kasugamycin, fusidic acid, thiostrepton, and puromycin. Antibiotics unrelated to protein synthesis, such as ampicillin or rifampicin, had no differential effect on the deltassrA strain. Furthermore, deletion of the ssrA gene is sufficient to impair global protein synthesis when chloramphenicol is added at sublethal concentrations for the wild-type strain. These results indicate that ribosomes stalled by some protein synthesis inhibitors can be recycled by tmRNA. In addition, this suggests that the first elongation cycle with tmRNA, which incorporates a noncoded alanine on the growing peptide chain, may have mechanistic differences with the normal elongation cycles that bypasses the block produced by these specific antibiotics. tmRNA inactivation could be an useful therapeutic target to increase the sensitivity of pathogenic bacteria against antibiotics. PMID:11780628

Spatial Representativeness of Surface-Measured Variations of Downward Solar Radiation

NASA Astrophysics Data System (ADS)

Schwarz, M.; Folini, D.; Hakuba, M. Z.; Wild, M.

2017-12-01

When using time series of ground-based surface solar radiation (SSR) measurements in combination with gridded data, the spatial and temporal representativeness of the point observations must be considered. We use SSR data from surface observations and high-resolution (0.05°) satellite-derived data to infer the spatiotemporal representativeness of observations for monthly and longer time scales in Europe. The correlation analysis shows that the squared correlation coefficients (R2) between SSR times series decrease linearly with increasing distance between the surface observations. For deseasonalized monthly mean time series, R2 ranges from 0.85 for distances up to 25 km between the stations to 0.25 at distances of 500 km. A decorrelation length (i.e., the e-folding distance of R2) on the order of 400 km (with spread of 100-600 km) was found. R2 from correlations between point observations and colocated grid box area means determined from satellite data were found to be 0.80 for a 1° grid. To quantify the error which arises when using a point observation as a surrogate for the area mean SSR of larger surroundings, we calculated a spatial sampling error (SSE) for a 1° grid of 8 (3) W/m2 for monthly (annual) time series. The SSE based on a 1° grid, therefore, is of the same magnitude as the measurement uncertainty. The analysis generally reveals that monthly mean (or longer temporally aggregated) point observations of SSR capture the larger-scale variability well. This finding shows that comparing time series of SSR measurements with gridded data is feasible for those time scales.

Sympathetic skin response in multiple sclerosis: a meta-analysis of case-control studies.

PubMed

Margaritella, Nicolò; Mendozzi, Laura; Garegnani, Massimo; Gilardi, Elisabetta; Nemni, Raffaello; Pugnetti, Luigi

2018-01-01

The usefulness of sympathetic skin responses (SSR) in multiple sclerosis (MS) has been advocated by several studies in the last 20 years; however, due to a great heterogeneity of findings, a comprehensive meta-analysis of case-control studies is in order to pinpoint consistencies and investigate the causes of discrepancies. We searched MEDLINE, EMBASE and Cochrane databases for case-control studies comparing SSR absence frequency and latency between patients with MS and healthy controls. Thirteen eligible studies including 415 MS patients and 331 healthy controls were identified. The pooled analysis showed that SSR can be always obtained in healthy controls while 34% of patients had absent SSRs in at least one limb (95% CI 22-47%; p < 0.0001) but with considerable heterogeneity across studies (I 2  = 90.3%). Patients' age explained 22% of the overall variability and positive correlations were found with Expanded Disability Status Scale and disease duration. The pooled mean difference of SSR latency showed a significant increase in patients on both upper (193 ms; 95% CI 120-270 ms) and lower (350 ms; 95% CI 190-510 ms) extremities. We tested the discriminatory value of SSR latency thresholds defined as the 95% confidence interval (CI) upper bound of the healthy controls, and validated the results on a new dataset. The lower limb threshold of 1.964 s produces the best results in terms of sensitivity 0.86, specificity 0.67, positive predicted value 0.75 and negative predicted value 0.80. Despite a considerable heterogeneity of findings, there is evidence that SSR is a useful tool in MS.

Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa).

PubMed

Nagano, Soichiro; Shirasawa, Kenta; Hirakawa, Hideki; Maeda, Fumi; Ishikawa, Masami; Isobe, Sachiko N

2017-05-12

The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S 1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers. The 'Reikou' linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

Site response and attenuation in the Puget Lowland, Washington State

USGS Publications Warehouse

Pratt, T.L.; Brocher, T.M.

2006-01-01

Simple spectral ratio (SSR) and horizontal-to-vertical (HN) site-response estimates at 47 sites in the Puget Lowland of Washington State document significant attenuation of 1.5- to 20-Hz shear waves within sedimentary basins there. Amplitudes of the horizontal components of shear-wave arrivals from three local earthquakes were used to compute SSRs with respect to the average of two bedrock sites and H/V spectral ratios with respect to the vertical component of the shear-wave arrivals at each site. SSR site-response curves at thick basin sites show peak amplifications of 2 to 6 at frequencies of 3 to 6 Hz, and decreasing spectra amplification with increasing frequency above 6 Hz. SSRs at nonbasin sites show a variety of shapes and larger resonance peaks. We attribute the spectral decay at frequencies above the amplification peak at basin sites to attenuation within the basin strata. Computing the frequency-independent, depth-dependent attenuation factor (Qs,int) from the SSR spectral decay between 2 and 20 Hz gives values of 5 to 40 for shallow sedimentary deposits and about 250 for the deepest sedimentary strata (7 km depth). H/V site responses show less spectral decay than the SSR responses but contain many of the same resonance peaks. We hypothesize that the H/V method yields a flatter response across the frequency spectrum than SSRs because the H/V reference signal (vertical component of the shear-wave arrivals) has undergone a degree of attenuation similar to the horizontal component recordings. Correcting the SSR site responses for attenuation within the basins by removing the spectral decay improves agreement between SSR and H/V estimates.

Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.

PubMed Central

2014-01-01

Background Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species. Result A total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1’ by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei’s genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective. Conclusions A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species. PMID:24472631

Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv].

PubMed

Zhang, Shuo; Tang, Chanjuan; Zhao, Qiang; Li, Jing; Yang, Lifang; Qie, Lufeng; Fan, Xingke; Li, Lin; Zhang, Ning; Zhao, Meicheng; Liu, Xiaotong; Chai, Yang; Zhang, Xue; Wang, Hailong; Li, Yingtao; Li, Wen; Zhi, Hui; Jia, Guanqing; Diao, Xianmin

2014-01-28

Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species. A total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1' by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei's genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective. A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species.

Development and Identification of SSR Markers Associated with Starch Properties and β-Carotene Content in the Storage Root of Sweet Potato (Ipomoea batatas L.)

PubMed Central

Zhang, Kai; Wu, Zhengdan; Tang, Daobin; Lv, Changwen; Luo, Kai; Zhao, Yong; Liu, Xun; Huang, Yuanxin; Wang, Jichun

2016-01-01

Sweet potato (Ipomoea batatas L.) is a nutritious food crop and, based on the high starch content of its storage root, a potential bioethanol feedstock. Enhancing the nutritional value and starch quantity of storage roots are important goals of sweet potato breeding programs aimed at developing improved varieties for direct consumption, processing, and industrial uses. However, developing improved lines of sweet potato is challenging due to the genetic complexity of this plant and the lack of genome information. Short sequence repeat (SSR) markers are powerful molecular tools for tracking important loci in crops and for molecular-based breeding strategies; however, few SSR markers and marker-trait associations have hitherto been identified in sweet potato. In this study, we identified 1824 SSRs by using a de novo assembly of publicly available ESTs and mRNAs in sweet potato, and designed 1476 primer pairs based on SSR-containing sequences. We mapped 214 pairs of primers in a natural population comprised of 239 germplasms, and identified 1278 alleles with an average of 5.972 alleles per locus and a major allele frequency of 0.7702. Population structure analysis revealed two subpopulations in this panel of germplasms, and phenotypic characterization demonstrated that this panel is suitable for association mapping of starch-related traits. We identified 32, 16, and 17 SSR markers associated with starch content, β-carotene content, and starch composition in the storage root, respectively, using association analysis and further evaluation of a subset of sweet potato genotypes with various characteristics. The SSR markers identified here can be used to select varieties with desired traits and to investigate the genetic mechanism underlying starch and carotenoid formation in the starchy roots of sweet potato. PMID:26973669

Strategic purchasing reform in Estonia: Reducing inequalities in access while improving care concentration and quality.

PubMed

Habicht, Triin; Habicht, Jarno; van Ginneken, Ewout

2015-08-01

As of 2014, the Estonian Health Insurance Fund has adopted new purchasing procedures and criteria, which it now has started to implement in specialist care. Main changes include (1) redefined access criteria based on population need rather than historical supply, which aim to achieve more equal access of providers and specialties; (2) stricter definition and use of optimal workload criteria to increase the concentration of specialist care (3) better consideration of patient movement; and (4) an increased emphasis on quality to foster quality improvement. The new criteria were first used in the contract cycle that started in 2014 and resulted in fewer contracted providers for a similar volume of care compared to the previous contract cycle. This implies that provision of specialized care has become concentrated at fewer providers. It is too early to draw firm conclusions on the impact on care quality or on actors, but the process has sparked debate on the role of selective contracting and the role of public and private providers in Estonian health care. Lastly, the Estonian experience may hold important lessons for other countries looking to overcome inequalities in access while concentrating care and improving care quality. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

High levels of heterozygosity found for 15 SSR loci in Solanum chacoense

USDA-ARS?s Scientific Manuscript database

Genetic variation is a necessary prerequisite for improving domesticated plants through breeding; without it, breeding progress would be impossible. Genetic variation can be readily ascertained with co-dominant DNA markers, such as simple sequence repeats (SSRs). Twenty-four SSR markers specifically...

Synthesis-Spectroscopy Roadmap Problems: Discovering Organic Chemistry

ERIC Educational Resources Information Center

Kurth, Laurie L.; Kurth, Mark J.

2014-01-01

Organic chemistry problems that interrelate and integrate synthesis with spectroscopy are presented. These synthesis-spectroscopy roadmap (SSR) problems uniquely engage second-year undergraduate organic chemistry students in the personal discovery of organic chemistry. SSR problems counter the memorize-or-bust strategy that many students tend to…

Genetic differentiation and geographical relationship of Asian barley landraces using SSRs

USDA-ARS?s Scientific Manuscript database

Genetic diversity in 403 morphologically distinctive landraces of barley (Hordeum vulgare L. subsp. vulgare) originating from seven geographical zones of Asia was studied using simple sequence repeat (SSR) markers. The seven polymorphic SSR markers representing each chromosome chosen for this study ...

Construction of a genetic map using EST-SSR markers and QTL analysis of major agronomic characters in hexaploid sweet potato (Ipomoea batatas (L.) Lam).

PubMed

Kim, Jin-Hee; Chung, Il Kyung; Kim, Kyung-Min

2017-01-01

The Sweet potato, Ipomoea batatas (L.) Lam, is difficult to study in genetics and genomics because it is a hexaploid. The sweet potato study not have been performed domestically or internationally. In this study was performed to construct genetic map and quantitative trait loci (QTL) analysis. A total of 245 EST-SSR markers were developed, and the map was constructed by using 210 of those markers. The total map length was 1508.1 cM, and the mean distance between markers was 7.2 cM. Fifteen characteristics were investigated for QTLs analysis. According to those, the Four QTLs were identified, and The LOD score was 3.0. Further studies need to develop molecular markers in terms of EST-SSR markers for doing to be capable of efficient breeding. The genetic map created here using EST-SSR markers will facilitate planned breeding of sweet potato cultivars with various desirable traits.

Polymorphic SSR Markers for Plasmopara obducens (Peronosporaceae), the Newly Emergent Downy Mildew Pathogen of Impatiens (Balsaminaceae)

DOE PAGES

Salgado-Salazar, Catalina; Rivera, Yazmín; Veltri, Daniel; ...

2015-11-10

Premise of the study: Simple sequence repeat (SSR) markers were developed for Plasmopara obducens, the causal agent of the newly emergent downy mildew disease of Impatiens walleriana. Methods and Results: A 202-Mb draft genome assembly was generated from P. obducens using Illumina technology and mined to identify 13,483 SSR motifs. Primers were synthesized for 62 marker candidates, of which 37 generated reliable PCR products. Testing of the 37 markers using 96 P. obducens samples showed 96% of the markers were polymorphic, with 2-6 alleles observed. Observed and expected heterozygosity ranged from 0.000-0.892 and 0.023-0.746, respectively. Just 17 markers were sufficientmore » to identify all multilocus genotypes. Conclusions: These are the first SSR markers available for this pathogen, and one of the first molecular resources. These markers will be useful in assessing variation in pathogen populations and determining the factors contributing to the emergence of destructive impatiens downy mildew disease.« less

Simple sequence repeat marker loci discovery using SSR primer.

PubMed

Robinson, Andrew J; Love, Christopher G; Batley, Jacqueline; Barker, Gary; Edwards, David

2004-06-12

Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. With the increase in the availability of DNA sequence information, an automated process to identify and design PCR primers for amplification of SSR loci would be a useful tool in plant breeding programs. We report an application that integrates SPUTNIK, an SSR repeat finder, with Primer3, a PCR primer design program, into one pipeline tool, SSR Primer. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. The results are parsed to Primer3 for locus-specific primer design. The script makes use of a Web-based interface, enabling remote use. This program has been written in PERL and is freely available for non-commercial users by request from the authors. The Web-based version may be accessed at http://hornbill.cspp.latrobe.edu.au/

Field trial on glucose-induced insulin and metabolite responses in Estonian Holstein and Estonian Red dairy cows in two herds

PubMed Central

2010-01-01

Background Insulin secretion and tissue sensitivity to insulin is considered to be one of the factors controlling lipid metabolism post partum. The objective of this study was to compare glucose-induced blood insulin and metabolite responses in Estonian Holstein (EH, n = 14) and Estonian Red (ER, n = 14) cows. Methods The study was carried out using the glucose tolerance test (GTT) performed at 31 ± 1.9 days post partum during negative energy balance. Blood samples were obtained at -15, -5, 5, 10, 20, 30, 40, 50 and 60 min relative to infusion of 0.15 g/kg BW glucose and analysed for glucose, insulin, triglycerides (TG), non-esterified fatty acids (NEFA), cholesterol and β-hydroxybutyrate (BHB). Applying the MIXED Procedure with the SAS System the basal concentration of cholesterol, and basal concentration and concentrations at post-infusion time points for other metabolites, area under the curve (AUC) for glucose and insulin, clearance rate (CR) for glucose, and maximum increase from basal concentration for glucose and insulin were compared between breeds. Results There was a breed effect on blood NEFA (P < 0.05) and a time effect on all metabolites concentration (P < 0.01). The following differences were observed in EH compared to ER: lower blood insulin concentration 5 min after glucose infusion (P < 0.05), higher glucose concentration 20 (P < 0.01) and 30 min (P < 0.05) after infusion, and higher NEFA concentration before (P < 0.01) and 5 min after infusion (P < 0.05). Blood TG concentration in ER remained stable, while in EH there was a decrease from the basal level to the 40th min nadir (P < 0.01), followed by an increase to the 60th min postinfusion (P < 0.01). Conclusion Our results imply that glucose-induced changes in insulin concentration and metabolite responses to insulin differ between EH and ER dairy cows. PMID:20089161

Development of Cymbidium ensifolium genic-SSR markers and their utility in genetic diversity and population structure analysis in cymbidiums.

PubMed

Li, Xiaobai; Jin, Feng; Jin, Liang; Jackson, Aaron; Huang, Cheng; Li, Kehu; Shu, Xiaoli

2014-12-05

Cymbidium is a genus of 68 species in the orchid family, with extremely high ornamental value. Marker-assisted selection has proven to be an effective strategy in accelerating plant breeding for many plant species. Analysis of cymbidiums genetic background by molecular markers can be of great value in assisting parental selection and breeding strategy design, however, in plants such as cymbidiums limited genomic resources exist. In order to obtain efficient markers, we deep sequenced the C. ensifolium transcriptome to identify simple sequence repeats derived from gene regions (genic-SSR). The 7,936 genic-SSR markers were identified. A total of 80 genic-SSRs were selected, and primers were designed according to their flanking sequences. Of the 80 genic-SSR primer sets, 62 were amplified in C. ensifolium successfully, and 55 showed polymorphism when cross-tested among 9 Cymbidium species comprising 59 accessions. Unigenes containing the 62 genic-SSRs were searched against Non-redundant (Nr), Gene Ontology database (GO), eukaryotic orthologous groups (KOGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The search resulted in 53 matching Nr sequences, of which 39 had GO terms, 18 were assigned to KOGs, and 15 were annotated with KEGG. Genetic diversity and population structure were analyzed based on 55 polymorphic genic-SSR data among 59 accessions. The genetic distance averaged 0.3911, ranging from 0.016 to 0.618. The polymorphic index content (PIC) of 55 polymorphic markers averaged 0.407, ranging from 0.033 to 0.863. A model-based clustering analysis revealed that five genetic groups existed in the collection. Accessions from the same species were typically grouped together; however, C. goeringii accessions did not always form a separate cluster, suggesting that C. goeringii accessions were polyphyletic. The genic-SSR identified in this study constitute a set of markers that can be applied across multiple Cymbidium species and used for the evaluation of genetic relationships as well as qualitative and quantitative trait mapping studies. Genic-SSR's coupled with the functional annotations provided by the unigenes will aid in mapping candidate genes of specific function.

The ESASSI-08 cruise in the South Scotia Ridge region: Water masses, currents, and the ASF

NASA Astrophysics Data System (ADS)

Palmer, M.; Gomis, D.; Flexas, M. M.; Jordà, G.; Orsi, A. H.

2009-04-01

The ESASSI-08 oceanographic cruise carried out in January 2008 was the major milestone of ESASSI, the Spanish component of SASSI (a core project of the International Polar Year devoted to study the shelf-slope exchanges in different locations of Antarctica). The specific objectives of ESASSI, the sampling strategy and the overall distribution of the main variables across the 11 sections covered by the cruise are presented in a poster. Here we focus on three specific issues: i) the observation of strong tidal currents over some of the sampled slopes; ii) the path of the Antarctic Slope Front (ASF) over the SSR; and iii) the outflow of dense, ventilated water from the Weddell Sea into the South Scotia Sea. The main results are: i) Strong tidal currents with a significant diurnal component were observed over the southern slope of the SSR. Three tidal models are compared with the observations and used to de-tide ADCP currents. ii) The signature of the ASF is clearly detected on the southern slopes of the SSR (on the Weddell Sea flank). Over the northern slopes (the Scotia Sea flank), however, only weak signatures of frontal structures are observed; an in-depth biochemical analysis will be required to link the structures observed over the two flanks of the SSR. What seems clear is that the ASF does not extend further than Elephant Island, since southwestward of that island the shelf and the slope are fully occupied by Circumpolar Deep Water (CDW) from the Antarctic Circumpolar Current. iii) The shallower component of Weddell Sea Deep Water (Upper WSDW) flows over the SSR and pours into the Scotia Sea except to the east of Elephant Island, where the channels are less than 1500 m deep. The densest component of WSDW (Lower WSDW) is observed at both flanks of the SSR, but again a more detailed analysis of biochemical data will be required to prove a direct flux of this water mass across the SSR. Weddell Sea Bottom Water (WSBW) is not observed in any of the sampled sections.

Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea)

PubMed Central

Zhao, Chuanzhi; Qiu, Jingjing; Agarwal, Gaurav; Wang, Jiangshan; Ren, Xuezhen; Xia, Han; Guo, Baozhu; Ma, Changle; Wan, Shubo; Bertioli, David J.; Varshney, Rajeev K.; Pandey, Manish K.; Wang, Xingjun

2017-01-01

Despite several efforts in the last decade toward development of simple sequence repeat (SSR) markers in peanut, there is still a need for more markers for conducting different genetic and breeding studies. With the effort of the International Peanut Genome Initiative, the availability of reference genome for both the diploid progenitors of cultivated peanut allowed us to identify 135,529 and 199,957 SSRs from the A (Arachis duranensis) and B genomes (Arachis ipaensis), respectively. Genome sequence analysis showed uneven distribution of the SSR motifs across genomes with variation in parameters such as SSR type, repeat number, and SSR length. Using the flanking sequences of identified SSRs, primers were designed for 51,354 and 60,893 SSRs with densities of 49 and 45 SSRs per Mb in A. duranensis and A. ipaensis, respectively. In silico PCR analysis of these SSR markers showed high transferability between wild and cultivated Arachis species. Two physical maps were developed for the A genome and the B genome using these SSR markers, and two reported disease resistance quantitative trait loci (QTLs), qF2TSWV5 for tomato spotted wilt virus (TSWV) and qF2LS6 for leaf spot (LS), were mapped in the 8.135 Mb region of chromosome A04 of A. duranensis. From this genomic region, 719 novel SSR markers were developed, which provide the possibility for fine mapping of these QTLs. In addition, this region also harbors 652 genes and 49 of these are defense related genes, including two NB-ARC genes, three LRR receptor-like genes and three WRKY transcription factors. These disease resistance related genes could contribute to resistance to viral (such as TSWV) and fungal (such as LS) diseases in peanut. In summary, this study not only provides a large number of molecular markers for potential use in peanut genetic map development and QTL mapping but also for map-based gene cloning and molecular breeding. PMID:28769940

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh].

PubMed

Dutta, Sutapa; Kumawat, Giriraj; Singh, Bikram P; Gupta, Deepak K; Singh, Sangeeta; Dogra, Vivek; Gaikwad, Kishor; Sharma, Tilak R; Raje, Ranjeet S; Bandhopadhya, Tapas K; Datta, Subhojit; Singh, Mahendra N; Bashasab, Fakrudin; Kulwal, Pawan; Wanjari, K B; K Varshney, Rajeev; Cook, Douglas R; Singh, Nagendra K

2011-01-20

Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥ 18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh

PubMed Central

2011-01-01

Background Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. Results In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. Conclusion We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea. PMID:21251263

Installation Restoration Program. Phase 2. Confirmation/Quantification. Stage 1. Air Force Plant 4, Fort Worth, Texas. Volume 5. Appendix A-2.

DTIC Science & Technology

1987-12-01

Limit Spiked Samale Samole ISailced C" auod R sIus’lt (SSR) esult. (SR) A-dded ( .SA) Iels: I. I 1. A.luminum 75-125 - I Z. Antimony - 3. Arsenic " I...UntKtarix *s %Control Limit Spiked Samale Sample SieiCm.,ound _ _R R esult (SSR) Re t,.- (SR) Added (SA) Z,10 1. AUlunu m 7 I I I 2. Antimonyj ____ 3...No. DATE Lab Sample) ;S4 No Katrix waot, " . n ...Central L imi Spiked Samale Samale Spiked Comnpound M Rsult: (SSR) Result (SR) jAdded (SA) XR

Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

USDA-ARS?s Scientific Manuscript database

Although the microsatellite (SSR) DNA markers have been extensively used in sugarcane breeding research, little is known about its inheritance mechanism. To address this problem, a high throughput molecular genotyping experiment was conducted on 964 single pollen grains and a 288-self progeny S1 map...

UPIC: Perl scripts to determine the number of SSR markers to run

USDA-ARS?s Scientific Manuscript database

We have developed Perl Scripts for the cost-effective planning of fingerprinting and genotyping experiments. The UPIC scripts detect the best combination of polymorphic simple sequence repeat (SSR) markers and provide coefficients of the amount of information obtainable (number of alleles of patter...

The art of attrition: development of robust oat microsatellites

USDA-ARS?s Scientific Manuscript database

Microsatellite or simple sequence repeat (SSR) markers are important tools for genetic analyses, especially those targeting diversity, based on the fact that multiple alleles can occur at a given locus. Currently, only 160 genomic-based SSR markers are publicly available for oat, most of which have...

Independently segregating simple sequence repeats (SSR) alleles in polyploid sugarcane

USDA-ARS?s Scientific Manuscript database

The complex nuclear genomic and flower structures of sugarcane cultivars (Saccharum hybrids spp., 2n = 10x = 100 – 130) render sugarcane a difficult subject for genetics research. Using a capillary electrophoresis- and fluorescence-labeling-based SSR genotyping platform, the segregation of a multi-a...

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations

PubMed Central

Szczecińska, Monika

2016-01-01

Background Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction). Methods The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers. Results SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and ΦPT for SSR (20%) and ΦPT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations of P. patens for ISJ markers, but not for SSR markers. Conclusions The results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs. PMID:27833793

Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species

PubMed Central

Liang, Xuanqiang; Chen, Xiaoping; Hong, Yanbin; Liu, Haiyan; Zhou, Guiyuan; Li, Shaoxiong; Guo, Baozhu

2009-01-01

Background Lack of sufficient molecular markers hinders current genetic research in peanuts (Arachis hypogaea L.). It is necessary to develop more molecular markers for potential use in peanut genetic research. With the development of peanut EST projects, a vast amount of available EST sequence data has been generated. These data offered an opportunity to identify SSR in ESTs by data mining. Results In this study, we investigated 24,238 ESTs for the identification and development of SSR markers. In total, 881 SSRs were identified from 780 SSR-containing unique ESTs. On an average, one SSR was found per 7.3 kb of EST sequence with tri-nucleotide motifs (63.9%) being the most abundant followed by di- (32.7%), tetra- (1.7%), hexa- (1.0%) and penta-nucleotide (0.7%) repeat types. The top six motifs included AG/TC (27.7%), AAG/TTC (17.4%), AAT/TTA (11.9%), ACC/TGG (7.72%), ACT/TGA (7.26%) and AT/TA (6.3%). Based on the 780 SSR-containing ESTs, a total of 290 primer pairs were successfully designed and used for validation of the amplification and assessment of the polymorphism among 22 genotypes of cultivated peanuts and 16 accessions of wild species. The results showed that 251 primer pairs yielded amplification products, of which 26 and 221 primer pairs exhibited polymorphism among the cultivated and wild species examined, respectively. Two to four alleles were found in cultivated peanuts, while 3–8 alleles presented in wild species. The apparent broad polymorphism was further confirmed by cloning and sequencing of amplified alleles. Sequence analysis of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the microsatellite regions. In addition, a few single base mutations were observed in the microsatellite flanking regions. Conclusion This study gives an insight into the frequency, type and distribution of peanut EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated peanut. These EST-SSR markers could enrich the current resource of molecular markers for the peanut community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, and genetic diversity studies in cultivated peanut as well as related Arachis species. All of the 251 working primer pairs with names, motifs, repeat types, primer sequences, and alleles tested in cultivated and wild species are listed in Additional File 1. PMID:19309524

Development of Genic and Genomic SSR Markers of Robusta Coffee (Coffea canephora Pierre Ex A. Froehner)

PubMed Central

Hendre, Prasad S.; Aggarwal, Ramesh K.

2014-01-01

Coffee breeding and improvement efforts can be greatly facilitated by availability of a large repository of simple sequence repeats (SSRs) based microsatellite markers, which provides efficiency and high-resolution in genetic analyses. This study was aimed to improve SSR availability in coffee by developing new genic−/genomic-SSR markers using in-silico bioinformatics and streptavidin-biotin based enrichment approach, respectively. The expressed sequence tag (EST) based genic microsatellite markers (EST-SSRs) were developed using the publicly available dataset of 13,175 unigene ESTs, which showed a distribution of 1 SSR/3.4 kb of coffee transcriptome. Genomic SSRs, on the other hand, were developed from an SSR-enriched small-insert partial genomic library of robusta coffee. In total, 69 new SSRs (44 EST-SSRs and 25 genomic SSRs) were developed and validated as suitable genetic markers. Diversity analysis of selected coffee genotypes revealed these to be highly informative in terms of allelic diversity and PIC values, and eighteen of these markers (∼27%) could be mapped on a robusta linkage map. Notably, the markers described here also revealed a very high cross-species transferability. In addition to the validated markers, we have also designed primer pairs for 270 putative EST-SSRs, which are expected to provide another ca. 200 useful genetic markers considering the high success rate (88%) of marker conversion of similar pairs tested/validated in this study. PMID:25461752

High-Throughput Development of SSR Markers from Pea (Pisum sativum L.) Based on Next Generation Sequencing of a Purified Chinese Commercial Variety

PubMed Central

Zhang, Xiaoyan; Hu, Jinguo; Bao, Shiying; Hao, Junjie; Li, Ling; He, Yuhua; Jiang, Junye; Wang, Fang; Tian, Shufang; Zong, Xuxiao

2015-01-01

Pea (Pisum sativum L.) is an important food legume globally, and is the plant species that J.G. Mendel used to lay the foundation of modern genetics. However, genomics resources of pea are limited comparing to other crop species. Application of marker assisted selection (MAS) in pea breeding has lagged behind many other crops. Development of a large number of novel and reliable SSR (simple sequence repeat) or microsatellite markers will help both basic and applied genomics research of this crop. The Illumina HiSeq 2500 System was used to uncover 8,899 putative SSR containing sequences, and 3,275 non-redundant primers were designed to amplify these SSRs. Among the 1,644 SSRs that were randomly selected for primer validation, 841 yielded reliable amplifications of detectable polymorphisms among 24 genotypes of cultivated pea (Pisum sativum L.) and wild relatives (P. fulvum Sm.) originated from diverse geographical locations. The dataset indicated that the allele number per locus ranged from 2 to 10, and that the polymorphism information content (PIC) ranged from 0.08 to 0.82 with an average of 0.38. These 1,644 novel SSR markers were also tested for polymorphism between genotypes G0003973 and G0005527. Finally, 33 polymorphic SSR markers were anchored on the genetic linkage map of G0003973 × G0005527 F2 population. PMID:26440522

[EST-SSR identification, markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences].

PubMed

Yuan, Can; Peng, Fang; Yang, Ze-Mao; Zhong, Wen-Juan; Mou, Fang-Sheng; Gong, Yi-Yun; Ji, Pei-Cheng; Pu, De-Qiang; Huang, Hai-Yan; Yang, Xiao; Zhang, Chao

2017-09-01

Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently, genetic diversity analysis, UPGMA cluster analysis, PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results, L. chuanxiong resources were clustered into two groups, which are believed to be partial related to their geographical distribution. In this study, EST-SSRs in L. chuanxiong was firstly identified, and newly developed molecular markers would contribute significantly to further genetic diversity study, the purity detection, gene mapping, and molecular breeding. Copyright© by the Chinese Pharmaceutical Association.

The determinants of employee participation in occupational health and safety management.

PubMed

Masso, Märt

2015-01-01

This article focuses on employee direct participation in occupational health and safety (OHS) management. The article explains what determines employee opportunities to participate in OHS management. The explanatory framework focuses on safety culture and safety management at workplaces. The framework is empirically tested using Estonian cross-sectional, multilevel data of organizations and their employees. The analysis indicates that differences in employee participation in OHS management in the Estonian case could be explained by differences in OHS management practices rather than differences in safety culture. This indicates that throughout the institutional change and shift to the European model of employment relations system, change in management practices has preceded changes in safety culture which according to theoretical argument is supposed to follow culture change.

A SSR-based genetic linkage map of cultivated peanut (Arachis hypogaea L.)

USDA-ARS?s Scientific Manuscript database

The objective of this study was to construct a molecular linkage map of cultivated tetraploid peanut using simple sequence repeat (SSR) markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs), and by "data mining" sequences released in GenBank. Three recombinant inbre...

Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

USDA-ARS?s Scientific Manuscript database

The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers ...

Analyses of Thinopyrum bessarabicum, Th. elongation and Th. junceum chromosomes using EST-SSR markers

USDA-ARS?s Scientific Manuscript database

Wild Thinopyrum grasses serve as important gene pools for forage and cereal crops. Knowledge of their chromosome organizations is pivotal for efficient utilization of this important gene pool in germplasm enhancement programs. EST-SSR markers for Th. bessarabicum, Th. elongatum and Th. junceum chr...

A Glance at Microsatellite Motifs from 454 Sequencing Reads of Watermelon Genomic DNA

USDA-ARS?s Scientific Manuscript database

A single 454 (Life Sciences Sequencing Technology) run of Charleston Gray watermelon (Citrullus lanatus var. lanatus) genomic DNA was performed and sequence data were assembled. A large scale identification of simple sequence repeat (SSR) was performed and SSR sequence data were used for the develo...

Development of core SSR markers for Gossypium germplasm characterization

USDA-ARS?s Scientific Manuscript database

A set of 105 portable DNA markers were carefully developed to provide a common basis for systematic characterization of cotton germplasm collections in the U.S. and throughout the world. The 105 PCR-based SSR markers of different origins were evenly distributed on each of the 26 cotton chromosomes ...

Sequence analysis reveals genomic factors affecting EST-SSR primer performance and polymorphism

USDA-ARS?s Scientific Manuscript database

Search for simple sequence repeat (SSR) motifs and design of flanking primers in expressed sequence tag (EST) sequences can be easily done at a large scale using bioinformatics programs. However, failed amplification and/or detection, along with lack of polymorphism, is often seen among randomly sel...

78 FR 22361 - Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-15

... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2012-0071] Social Security Ruling, SSR 13-1p..., Misconduct, or Discrimination by Administrative Law Judges (ALJs); Correction AGENCY: Social Security Administration. ACTION: Notice of Social Security Ruling; Correction. SUMMARY: The Social Security Administration...

78 FR 8217 - Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-05

... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2012-0071] Social Security Ruling, SSR 13-1p..., Misconduct, or Discrimination by Administrative Law Judges (ALJs); Correction AGENCY: Social Security Administration. ACTION: Notice of Social Security Ruling; Correction. SUMMARY: The Social Security Administration...

Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

USDA-ARS?s Scientific Manuscript database

A mapping population developed from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum), segregating for a number of important phenotypic traits, has been utilized to produce a genetic linkage map. Data on 233 single sequence repeat (SSR) markers and 1794 sing...

78 FR 9987 - Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-12

... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2012-0071] Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations of Unfairness, Prejudice, Partiality, Bias, Misconduct, or Discrimination by Administrative Law Judges (ALJs); Correction AGENCY: Social Security...

Empowering Secondary Students to Promote Sustained Silent Reading

ERIC Educational Resources Information Center

Grant, Raymond Mead, III

2012-01-01

This study examines the efforts of student volunteers to motivate participation in a school-wide Sustained Silent Reading (SSR) program at a large urban high school. The researcher recruited a group of twenty student volunteers to visit classrooms and implement activities aimed at motivating their peers to read during SSR. Such activities help…

Development of polymorphic genic-SSR markers by cDNA library sequencing in boxwood, Buxus spp. (Buxaceae)

USDA-ARS?s Scientific Manuscript database

Genic microsatellites or simple sequence repeat (genic-SSR) markers were developed in boxwood (Buxus taxa) for genetic diversity analysis, identification of taxa, and to facilitate breeding. cDNA libraries were developed from mRNA extracted from leaves of Buxus sempervirens ‘Vardar Valley’ and seque...

Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil

USDA-ARS?s Scientific Manuscript database

Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes w...

The latest progress in sugarcane molecular genetics research at the USDA-ARS, Sugarcane Research Laboratory

USDA-ARS?s Scientific Manuscript database

In 2005, two sugar molecular genetics tools were developed in the USDA-ARS, Southeast Area, Sugarcane Research Laboratory at Houma, LA. One is the high throughput fluorescence- and capillary electrophoregrams (CE)-based SSR genotyping tool and the other is single pollen collection and SSR genotyping...

Making Data-Driven Decisions: Silent Reading

ERIC Educational Resources Information Center

Trudel, Heidi

2007-01-01

Due in part to conflicting opinions and research results, the practice of sustained silent reading (SSR) in schools has been questioned. After a frustrating experience with SSR, the author of this article began a data-driven decision-making process to gain new insights on how to structure silent reading in a classroom, including a comparison…

Fluorescence- and capillary electrophoresis (CE)-based SSR DNA fingerprinting and a molecular identity database for the Louisiana sugarcane industry

USDA-ARS?s Scientific Manuscript database

A database of Louisiana sugarcane molecular identity has been constructed and is being updated annually using FAM or HEX or NED fluorescence- and capillary electrophoresis (CE)-based microsatellite (SSR) fingerprinting information. The fingerprints are PCR-amplified from leaf DNA samples of current ...

Development and characterization of simple sequence repeats for Bipolaris sokiniana and cross transferability to related species

USDA-ARS?s Scientific Manuscript database

Simple sequence repeats (SSR) markers were developed from a small insert genomic library for Bipolaris sorokiniana, a mitosporic fungal pathogen that causes spot blotch and root rot in switchgrass. About 59% of sequenced clones (n=384) harbored various SSR motifs. After eliminating the redundant seq...

Impacts of wind stilling on solar radiation variability in China

PubMed Central

Lin, Changgui; Yang, Kun; Huang, Jianping; Tang, Wenjun; Qin, Jun; Niu, Xiaolei; Chen, Yingying; Chen, Deliang; Lu, Ning; Fu, Rong

2015-01-01

Solar dimming and wind stilling (slowdown) are two outstanding climate changes occurred in China over the last four decades. The wind stilling may have suppressed the dispersion of aerosols and amplified the impact of aerosol emission on solar dimming. However, there is a lack of long-term aerosol monitoring and associated study in China to confirm this hypothesis. Here, long-term meteorological data at weather stations combined with short-term aerosol data were used to assess this hypothesis. It was found that surface solar radiation (SSR) decreased considerably with wind stilling in heavily polluted regions at a daily scale, indicating that wind stilling can considerably amplify the aerosol extinction effect on SSR. A threshold value of 3.5 m/s for wind speed is required to effectively reduce aerosols concentration. From this SSR dependence on wind speed, we further derived proxies to quantify aerosol emission and wind stilling amplification effects on SSR variations at a decadal scale. The results show that aerosol emission accounted for approximately 20% of the typical solar dimming in China, which was amplified by approximately 20% by wind stilling. PMID:26463748

Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites.

PubMed

Li, Muwang; Shen, Li; Xu, Anying; Miao, Xuexia; Hou, Chengxiang; Sun, Pingjiang; Zhang, Yuehua; Huang, Yongping

2005-10-01

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2-17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12-0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.

[Detection of the introgression of genome elements of the Aegilops cylindrica host. into the Triticum aestivum L. genome by ISSR and SSR analysis].

PubMed

Galaev, A V; Babaiants, L T; Sivolap, Iu M

2004-12-01

To reveal sites of the donor genome in wheat crossed with Aegilops cylindrica, which acquired conferred resistance to fungal diseases, a comparative analysis of introgressive and parental forms was conducted. Two systems of PCR analysis, ISSR and SSR-PCR, were employed. Upon use of 7 ISSR primers in genotypes of 30 individual plants BC1 F9 belonging to lines 5/55-91 and 5/20-91, 19 ISSR loci were revealed and assigned to introgressive fragments of Aegilops cylindrica genome in Triticum aestivum. The 40 pairs of SSR primers allowed the detection of seven introgressive alleles; three of these alleles were located on common wheat chromosomes in the B genome, while four alleles, in the D genome. Based on data of microsatellite analysis, it was assumed that the telomeric region of the long arm of common wheat chromosome 6A also changed. ISSR and SSR methods were shown to be effective for detecting variability caused by introgression of foreign genetic material into the genome of common wheat.

Climate change and forest fires.

PubMed

Flannigan, M D; Stocks, B J; Wotton, B M

2000-11-15

This paper addresses the impacts of climate change on forest fires and describes how this, in turn, will impact on the forests of the United States. In addition to reviewing existing studies on climate change and forest fires we have used two transient general circulation models (GCMs), namely the Hadley Centre and the Canadian GCMs, to estimate fire season severity in the middle of the next century. Ratios of 2 x CO2 seasonal severity rating (SSR) over present day SSR were calculated for the means and maximums for North America. The results suggest that the SSR will increase by 10-50% over most of North America; although, there are regions of little change or where the SSR may decrease by the middle of the next century. Increased SSRs should translate into increased forest fire activity. Thus, forest fires could be viewed as an agent of change for US forests as the fire regime will respond rapidly to climate warming. This change in the fire regime has the potential to overshadow the direct effects of climate change on species distribution and migration.

Textpresso site-specific recombinases: A text-mining server for the recombinase literature including Cre mice and conditional alleles.

PubMed

Urbanski, William M; Condie, Brian G

2009-12-01

Textpresso Site Specific Recombinases (http://ssrc.genetics.uga.edu/) is a text-mining web server for searching a database of more than 9,000 full-text publications. The papers and abstracts in this database represent a wide range of topics related to site-specific recombinase (SSR) research tools. Included in the database are most of the papers that report the characterization or use of mouse strains that express Cre recombinase as well as papers that describe or analyze mouse lines that carry conditional (floxed) alleles or SSR-activated transgenes/knockins. The database also includes reports describing SSR-based cloning methods such as the Gateway or the Creator systems, papers reporting the development or use of SSR-based tools in systems such as Drosophila, bacteria, parasites, stem cells, yeast, plants, zebrafish, and Xenopus as well as publications that describe the biochemistry, genetics, or molecular structure of the SSRs themselves. Textpresso Site Specific Recombinases is the only comprehensive text-mining resource available for the literature describing the biology and technical applications of SSRs. (c) 2009 Wiley-Liss, Inc.

Rapid identification of red-flesh loquat cultivars using EST-SSR markers based on manual cultivar identification diagram strategy.

PubMed

Li, X Y; Xu, H X; Chen, J W

2014-04-29

Manual cultivar identification diagram is a new strategy for plant cultivar identification based on DNA markers, providing information to efficiently separate cultivars. We tested 25 pairs of apple EST-SSR primers for amplification of PCR products from loquat cultivars. These EST-SSR primers provided clear amplification products from the loquat cultivars, with a relatively high transferability rate of 84% to loquat; 11 pairs of primers amplified polymorphic products. After analysis of 24 red-fleshed loquat accessions, we found that only 7 pairs of primers could clearly separate all of them. A cultivar identification diagram of the 24 cultivars was constructed using polymorphic bands from the DNA fingerprints and EST-SSR primers. Any two of the 24 cultivars could be rapidly separated from each other, according to the polymorphic bands from the cultivars; the corresponding primers were marked in the correct position on the cultivar identification diagram. This red-flesh loquat cultivar identification diagram can separate the 24 red-flesh loquat cultivars, which is of benefit for loquat cultivar identification for germplasm management and breeding programs.

Evaluation on newly developed high resolution of surface solar radiation from MTSAT observations for the Tibetan Plateau

NASA Astrophysics Data System (ADS)

Niu, X.; Yang, K.; Tang, W.; Qin, J.

2015-12-01

Neither surface measurement nor existing remote sensing products of the Surface Solar Radiation (SSR) can meet the application requirements of hydrological and land process modeling in the Tibetan Plateau (TP). High resolution (hourly; 0.1⁰) of SSR estimates have been derived recently from the geostationary satellite observations - the Multi-functional Transport Satellite (MTSAT). This SSR estimation is based on updating an existing physical model, the UMD-SRB (University of Maryland Surface Radiation Budget) which is the basis of the well-known GEWEX-SRB model. In the updated framework introduced is the high-resolution Global Land Surface Broadband Albedo Product (GLASS) with spatial continuity. The developed SSR estimates are demonstrated at different temporal resolutions over the TP and are evaluated against ground observations and other satellite products from: (1) China Meteorological Administration (CMA) radiation stations in TP; (2) three TP radiation stations contributed from the Institute of Tibetan Plateau Research; (3) and the universal used satellite products (i.e. ISCCP-FD, GEWEX-SRB) in relatively low spatial resolution (0.5º-2.5º) and temporal resolution (3-hourly, daily, or monthly).

Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae.

PubMed

Awasthi, Praveen; Singh, Ashish; Sheikh, Gulfam; Mahajan, Vidushi; Gupta, Ajai Prakash; Gupta, Suphla; Bedi, Yashbir S; Gandhi, Sumit G

2017-10-01

Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons. SSRs were searched in the unigenes and 515 SSR-containing ESTs were identified with a frequency of 1 SSR per 25.21 kb of the genome. These ESTs were also annotated using BLAST2GO. Primers were designed for 349 EST-SSRs and 25 primer pairs were randomly picked for EST SSR study. Out of these, 16 primer pairs could be optimized for amplification in different accessions of Z. officinale as well as other species belonging to Zingiberaceae. GES454, GES466, GES480 and GES486 markers were found to exhibit 100% cross-transferability among different members of Zingiberaceae.

Why is a “Good Abortion Law” Not Enough? The Case of Estonia

PubMed Central

2017-01-01

Abstract There are various ways to critically discuss abortion. Constructing or finding the most suitable analytical framework—whether rooted in legal formalism, socio-legal considerations, or comparativism—always depends on the country of subject and whether the analysis is for litigation, advocacy, or more theoretical purposes. This paper offers a model for analyzing abortion in Estonia in order to connect it as a thought-provoking case study to the ongoing transnational abortion discussions. I set out by describing the Estonian Abortion Act as a “good abortion law”: a regulation that guarantees in practice women’s legal access to safe abortion. Despite this functioning law, I carve a space for criticism by expanding the conversation to the broader power relations and gender dynamics present in Estonian society. Accordingly, I explain the state of the Estonian feminist movement and gender research, the local legal community’s minimal engagement with the reproductive rights discourse, and the lingering Soviet-era narratives of reproduction and health, which were not fully extinguished by the combination of human rights commitments and neoliberalism upon restoration of independence in the early 1990s. I consequently show that Estonia’s liberal abortion regulation is not grounded in a sufficiently deep understanding of human rights-based approaches to reproductive health, therefore leaving the door open for micro-aggressions toward women and for conservative political winds to gain ground. PMID:28630549

The influence of performance-based payment on childhood immunisation coverage.

PubMed

Merilind, Eero; Salupere, Rauno; Västra, Katrin; Kalda, Ruth

2015-06-01

Pay-for-performance, also called the quality system (QS) in Estonia, was implemented in 2006 and one indicator for achievement is the childhood immunisation coverage rate. The WHO vaccination coverage in Europe for diphtheria, tetanus and pertussis, and measles in children aged around one year old should meet or exceed 90 per cent. The study was conducted using a database from the Estonian Health Insurance Fund. The study compared childhood immunisation coverage rates of all Estonian family physicians in two groups, joined and not joined to the quality system during the observation period 2006-2012. Immunisation coverage was calculated as the percentage of persons in the target age group who received a vaccine dose by a given age. The target level of immunisations in Estonia is set at 90 per cent and higher. Immunisation coverage rates of family doctors (FD) in Estonia showed significant differences between two groups of doctors: joined to the quality system and not joined. Doctors joined to the quality system met the 90 per cent vaccination criterion more frequently compared to doctors not joined to the quality system. Doctors not joined to the quality system were below the 90 per cent vaccination criterion in all vaccinations listed in the Estonian State Immunisation Schedule. Pay-for-performance as a financial incentive encourages higher levels of childhood immunisations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Outbreak of Salmonella enteritidis phage type 1B associated with frozen pre-cooked chicken cubes, Finland 2012.

PubMed

Huusko, S; Pihlajasaari, A; Salmenlinna, S; Sõgel, J; Dontšenko, I; DE Pinna, E; Lundström, H; Toikkanen, S; Rimhanen-Finne, R

2017-10-01

In August to October 2012, a nationwide outbreak of Salmonella enteritidis phase type (PT) 1B with 53 cases occurred in Finland. Hypothesis generating interviews pointed toward ready-to-eat chicken salad from a Finnish company and at the same time Estonian authorities informed of a S. enteritidis PT 1B outbreak linked to chicken wrap prepared at an Estonian restaurant. We found that chicken salad was associated with the infection (odds ratio (OR) 16·1, 95% confidence interval (CI) 1·7-148·7 for consumption and OR 17·5. 95% CI 4·0-76·0 for purchase). The frozen pre-cooked chicken cubes used in Finnish salad and in Estonian wraps were traced back to a production plant in China. Great Britain made two Rapid Alert Systems for Food and Feed notifications on chicken cubes imported to the UK from the same Chinese production plant. Microbiological investigation confirmed that the patient isolates in Estonia and in Finland were indistinguishable from the strains isolated from chicken cubes in Estonia and in the UK. We recommend that despite certificates for tested Salmonella, food items should be analyzed when Salmonella contamination in outbreak investigations is suspected. In outbreak investigations, electronically implemented case-case study saves time, effort, and money compared with case-control study.

Why is a "Good Abortion Law" Not Enough? The Case of Estonia.

PubMed

Oja, Liiri

2017-06-01

There are various ways to critically discuss abortion. Constructing or finding the most suitable analytical framework-whether rooted in legal formalism, socio-legal considerations, or comparativism-always depends on the country of subject and whether the analysis is for litigation, advocacy, or more theoretical purposes. This paper offers a model for analyzing abortion in Estonia in order to connect it as a thought-provoking case study to the ongoing transnational abortion discussions. I set out by describing the Estonian Abortion Act as a "good abortion law": a regulation that guarantees in practice women's legal access to safe abortion. Despite this functioning law, I carve a space for criticism by expanding the conversation to the broader power relations and gender dynamics present in Estonian society. Accordingly, I explain the state of the Estonian feminist movement and gender research, the local legal community's minimal engagement with the reproductive rights discourse, and the lingering Soviet-era narratives of reproduction and health, which were not fully extinguished by the combination of human rights commitments and neoliberalism upon restoration of independence in the early 1990s. I consequently show that Estonia's liberal abortion regulation is not grounded in a sufficiently deep understanding of human rights-based approaches to reproductive health, therefore leaving the door open for micro-aggressions toward women and for conservative political winds to gain ground.

In silico search, characterization and validation of new EST-SSR markers in the genus Prunus.

PubMed

Sorkheh, Karim; Prudencio, Angela S; Ghebinejad, Azim; Dehkordi, Mehrana Kohei; Erogul, Deniz; Rubio, Manuel; Martínez-Gómez, Pedro

2016-07-07

Simple sequence repeats (SSRs) are defined as sequence repeat units between 1 and 6 bp that occur in both coding and non-coding regions abundant in eukaryotic genomes, which may affect the expression of genes. In this study, expressed sequence tags (ESTs) of eight Prunus species were analyzed for in silico mining of EST-SSRs, protein annotation, and open reading frames (ORFs), and the identification of codon repetitions. A total of 316 SSRs were identified using MISA software. Dinucleotide SSR motifs (26.31 %) were found to be the most abundant type of repeats, followed by tri- (14.58 %), tetra- (0.53 %), and penta- (0.27 %) nucleotide motifs. An attempt was made to design primer pairs for 316 identified SSRs but these were successful for only 175 SSR sequences. The positions of SSRs with respect to ORFs were detected, and annotation of sequences containing SSRs was performed to assign function to each sequence. SSRs were also characterized (in terms of position in the reference genome and associated gene) using the two available Prunus reference genomes (mei and peach). Finally, 38 SSR markers were validated across peach, almond, plum, and apricot genotypes. This validation showed a higher transferability level of EST-SSR developed in P. mume (mei) in comparison with the rest of species analyzed. Findings will aid analysis of functionally important molecular markers and facilitate the analysis of genetic diversity.

Lung function after cold-water dives with a standard scuba regulator or full-face-mask during wintertime.

PubMed

Uhlig, Florian; Muth, Claus-Martin; Tetzlaff, Kay; Koch, Andreas; Leberle, Richard; Georgieff, Michael; Winkler, Bernd E

2014-06-01

Full-face-masks (FFM) prevent the diver's face from cold and can support nasal breathing underwater. The aim of the study was to evaluate the effect of the use of FFMs on lung function and wellbeing. Twenty-one, healthy, non-asthmatic divers performed two cold-water dives (4⁰C, 25 min, 10 metres' depth) - one with a FFM and the other with a standard scuba regulator (SSR). Spirometry was performed before and after each dive and well-being and cold sensation were assessed after the dives. Significant decreases in forced vital capacity (FVC), forced expiratory volume in one second (FEV₁) and midexpiratory flow at 75% of FVC (MEF₇₅) occurred after both FFM and SSR dives. Changes in FVC and FEV₁ did not differ significantly between FFM and SSR dives. However, the mid-expiratory flows measured at 50% and 25% of FVC (MEF₅₀ and MEF₂₅) were significantly lower 10 minutes after the FFM dive compared to 10 minutes after the SSR dive. The wellbeing and cold sensation of the divers were significantly improved with FFM dives compared to SSR dives. Cold-water dives during wintertime can be associated with airway narrowing. During cold-water dives, the use of a FFM appears to reduce the cold sensation and enhance the well-being of the divers. However, a FFM does not appear to prevent airway narrowing in healthy, non-asthmatic subjects.

Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers.

PubMed

Korir, N K; Diao, W; Tao, R; Li, X; Kayesh, E; Li, A; Zhen, W; Wang, S

2014-01-08

The genetic diversity and relationship of 42 tomato varieties sourced from different geographic regions was examined with EST-SSR markers. The genetic diversity was between 0.18 and 0.77, with a mean of 0.49; the polymorphic information content ranged from 0.17 to 0.74, with a mean of 0.45. This indicates a fairly high degree of diversity among these tomato varieties. Based on the cluster analysis using unweighted pair-group method with arithmetic average (UPGMA), all the tomato varieties fell into 5 groups, with no obvious geographical distribution characteristics despite their diverse sources. The principal component analysis (PCA) supported the clustering result; however, relationships among varieties were more complex in the PCA scatterplot than in the UPGMA dendrogram. This information about the genetic relationships between these tomato lines helps distinguish these 42 varieties and will be useful for tomato variety breeding and selection. We confirm that the EST-SSR marker system is useful for studying genetic diversity among tomato varieties. The high degree of polymorphism and the large number of bands obtained per assay shows that SSR is the most informative marker system for tomato genotyping for purposes of rights/protection and for the tomato industry in general. It is recommended that these varieties be subjected to identification using an SSR-based manual cultivar identification diagram strategy or other easy-to-use and referable methods so as to provide a complete set of information concerning genetic relationships and a readily usable means of identifying these varieties.

Molecular discrimination of tall fescue morphotypes in association with Festuca relatives

PubMed Central

Chekhovskiy, Konstantin

2018-01-01

Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species used as forage and turf, and in conservation plantings. There are three morphotypes in hexaploid tall fescue: Continental, Mediterranean and Rhizomatous. This study was conducted to develop morphotype-specific molecular markers to distinguish Continental and Mediterranean tall fescues, and establish their relationships with other species of the Festuca genus for genomic inference. Chloroplast sequence variation and simple sequence repeat (SSR) polymorphism were explored in 12 genotypes of three tall fescue morphotypes and four Festuca species. Hypervariable chloroplast regions were retrieved by using 33 specifically designed primers followed by sequencing the PCR products. SSR polymorphism was studied using 144 tall fescue SSR primers. Four chloroplast (NFTCHL17, NFTCHL43, NFTCHL45 and NFTCHL48) and three SSR (nffa090, nffa204 and nffa338) markers were identified which can distinctly differentiate Continental and Mediterranean morphotypes. A primer pair, NFTCHL45, amplified a 47 bp deletion between the two morphotypes is being routinely used in the Noble Research Institute’s core facility for morphotype discrimination. Both chloroplast sequence variation and SSR diversity showed a close association between Rhizomatous and Continental morphotypes, while the Mediterranean morphotype was in a distant clade. F. pratensis and F. arundinacea var. glaucescens, the P and G1G2 genome donors, respectively, were grouped with the Continental clade, and F. mairei (M1M2 genome) grouped with the Mediterranean clade in chloroplast sequence variation, while both F. pratensis and F. mairei formed independent clade in SSR analysis. Age estimation based on chloroplast sequence variation indicated that the Continental and Mediterranean clades might have been colonized independently during 0.65 ± 0.06 and 0.96 ± 0.1 million years ago (Mya) respectively. The findings of the study will enhance tall fescue breeding for persistence and productivity. PMID:29342197

Impact of pioglitazone and bradykinin type 1 receptor antagonist on type 2 diabetes in high-fat diet-fed C57BL/6J mice.

PubMed

El Akoum, S; Haddad, Y; Couture, R

2017-09-01

Type 2 diabetes (T2D) is a major complication of obesity and a leading cause of morbidity and mortality. Antagonizing bradykinin type 1 receptor (B1R) improved body and tissue fat mass and reversed vascular and adipose tissue inflammation in a rat model of insulin resistance. This study aimed at evaluating further the role of B1R in a mouse model of T2D by comparing the antidiabetic and anti-inflammatory effects of the B1R antagonist SSR240612 (SSR) in adipose tissue with those of pioglitazone (TZD), an activator of peroxisome proliferator-activated receptor gamma. C57BL/6J mice were fed with high-fat diet (HFD) or standard diet (control) for 20 weeks. Yet, during the last 4 weeks, HFD-fed mice were administered SSR and TZD (10 mg kg -1  d -1 each) as monotherapy or combined therapy subcutaneously. The impact of treatments was measured on metabolic hormones levels (ELISA), adipose tissue inflammatory status and the expression of candidate genes involved in T2D (quantitative real-time polymerase chain reaction and western blot). SSR240612 and TZD treatments improved hyperglycaemia, hyperinsulinaemia, insulin resistance, adipose tissue inflammation (expression of B1R, chemokine ligand 2, F4/80 and tumour necrosis factor) and modulated adipogenesis (peroxisome proliferator-activated receptor gamma, adipocytes' protein 2 and CD40 expressions) in HFD-fed mice. Yet, SSR was more effective than TZD to reduce visceral fat mass and resistin. TZD/SSR combined treatment had an additive effect to improve insulin sensitivity and glucose intolerance. Bradykinin type 1 receptor antagonism could represent a promising therapeutic tool in combination with TZD for the treatment of T2D, obesity and insulin resistance.

Putative Microsatellite DNA Marker-Based Wheat Genomic Resource for Varietal Improvement and Management.

PubMed

Jaiswal, Sarika; Sheoran, Sonia; Arora, Vasu; Angadi, Ulavappa B; Iquebal, Mir A; Raghav, Nishu; Aneja, Bharti; Kumar, Deepender; Singh, Rajender; Sharma, Pradeep; Singh, G P; Rai, Anil; Tiwari, Ratan; Kumar, Dinesh

2017-01-01

Wheat fulfills 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs) being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/physical location. Previously associated markers with different wheat trait are also not available in any database. Limitations of in vitro SSR discovery can be overcome by genome-wide in silico mining of SSR. Triticum aestivum SSR database ( TaSSRDb ) is an integrated online database with three-tier architecture, developed using PHP and MySQL and accessible at http://webtom.cabgrid.res.in/wheatssr/. For genotyping, Primer3 standalone code computes primers on user request. Chromosome-wise SSR calling for all the three sub genomes along with choice of motif types is provided in addition to the primer generation for desired marker. We report here a database of highest number of SSRs (476,169) from complex, hexaploid wheat genome (~17 GB) along with previously reported 268 SSR markers associated with 11 traits. Highest (116.93 SSRs/Mb) and lowest (74.57 SSRs/Mb) SSR densities were found on 2D and 3A chromosome, respectively. To obtain homozygous locus, e-PCR was done. Such 30 loci were randomly selected for PCR validation in panel of 18 wheat Advance Varietal Trial (AVT) lines. TaSSRDb can be a valuable genomic resource tool for linkage mapping, gene/QTL (Quantitative trait locus) discovery, diversity analysis, traceability and variety identification. Varietal specific profiling and differentiation can supplement DUS (Distinctiveness, Uniformity, and Stability) testing, EDV (Essentially Derived Variety)/IV (Initial Variety) disputes, seed purity and hybrid wheat testing. All these are required in germplasm management as well as also in the endeavor of wheat productivity.

Putative Microsatellite DNA Marker-Based Wheat Genomic Resource for Varietal Improvement and Management

PubMed Central

Jaiswal, Sarika; Sheoran, Sonia; Arora, Vasu; Angadi, Ulavappa B.; Iquebal, Mir A.; Raghav, Nishu; Aneja, Bharti; Kumar, Deepender; Singh, Rajender; Sharma, Pradeep; Singh, G. P.; Rai, Anil; Tiwari, Ratan; Kumar, Dinesh

2017-01-01

Wheat fulfills 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs) being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/physical location. Previously associated markers with different wheat trait are also not available in any database. Limitations of in vitro SSR discovery can be overcome by genome-wide in silico mining of SSR. Triticum aestivum SSR database (TaSSRDb) is an integrated online database with three-tier architecture, developed using PHP and MySQL and accessible at http://webtom.cabgrid.res.in/wheatssr/. For genotyping, Primer3 standalone code computes primers on user request. Chromosome-wise SSR calling for all the three sub genomes along with choice of motif types is provided in addition to the primer generation for desired marker. We report here a database of highest number of SSRs (476,169) from complex, hexaploid wheat genome (~17 GB) along with previously reported 268 SSR markers associated with 11 traits. Highest (116.93 SSRs/Mb) and lowest (74.57 SSRs/Mb) SSR densities were found on 2D and 3A chromosome, respectively. To obtain homozygous locus, e-PCR was done. Such 30 loci were randomly selected for PCR validation in panel of 18 wheat Advance Varietal Trial (AVT) lines. TaSSRDb can be a valuable genomic resource tool for linkage mapping, gene/QTL (Quantitative trait locus) discovery, diversity analysis, traceability and variety identification. Varietal specific profiling and differentiation can supplement DUS (Distinctiveness, Uniformity, and Stability) testing, EDV (Essentially Derived Variety)/IV (Initial Variety) disputes, seed purity and hybrid wheat testing. All these are required in germplasm management as well as also in the endeavor of wheat productivity. PMID:29234333

Alteration of Cardiac Deformation in Acute Rejection in Pediatric Heart Transplant Recipients.

PubMed

Chanana, Nitin; Van Dorn, Charlotte S; Everitt, Melanie D; Weng, Hsin Yi; Miller, Dylan V; Menon, Shaji C

2017-04-01

The objective of this study is to assess changes in cardiac deformation during acute cellular- and antibody-mediated rejection in pediatric HT recipients. Pediatric HT recipients aged ≤18 years with at least one episode of biopsy-diagnosed rejection from 2006 to 2013 were included. Left ventricular systolic S (SS) and SR (SSr) data were acquired using 2D speckle tracking on echocardiograms obtained within 12 h of right ventricular endomyocardial biopsy. A mixed effect model was used to compare cardiac deformation during CR (Grade ≥ 1R), AMR (pAMR ≥ 2), and mixed rejection (CR and AMR positive) versus no rejection (Grade 0R and pAMR 0 or 1). A total of 20 subjects (10 males, 50%) with 71 rejection events (CR 35, 49%; AMR 21, 30% and mixed 15, 21%) met inclusion criteria. The median time from HT to first biopsy used for analysis was 5 months (IQR 0.25-192 months). Average LV longitudinal SS and SSr were reduced significantly during rejection (SS: -17.2 ± 3.4% vs. -10.7 ± 4.5%, p < 0.001 and SSr: -1.2 ± 0.2 s - 1 vs. -0.9 ± 0.3 s - 1 ; p < 0.001) and in all rejection types. Average LV short-axis radial SS was reduced only in CR compared to no rejection (p = 0.04), while average LV circumferential SS and SSr were reduced significantly in AMR compared to CR (SS: 18.9 ± 4.2% vs. 20.8 ± 8.8%, p = 0.03 and SSr: 1.35 ± 0.8 s - 1 vs. 1.54 ± 0.9 s - 1 ; p = 0.03). In pediatric HT recipients, LV longitudinal SS and SSr were reduced in all rejection types, while LV radial SS was reduced only in CR. LV circumferential SS and SSr further differentiated between CR and AMR with a significant reduction seen in AMR as compared to CR. This novel finding suggests mechanistic differences between AMR- and CR-induced myocardial injury which may be useful in non-invasively predicting the type of rejection in pediatric HT recipients.

Identification of QTL regions and SSR markers associated with resistance to reniform nematode in Gossypium barbadense L. accession GB713.

PubMed

Gutiérrez, Osman A; Robinson, Arin F; Jenkins, Johnie N; McCarty, Jack C; Wubben, Martin J; Callahan, Franklin E; Nichols, Robert L

2011-02-01

The identification of molecular markers that are closely linked to gene(s) in Gossypium barbadense L. accession GB713 that confer a high level of resistance to reniform nematode (RN), Rotylenchulus reniformis Linford & Oliveira, would be very useful in cotton breeding programs. Our objectives were to determine the inheritance of RN resistance in the accession GB713, to identify SSR markers linked with RN resistance QTLs, and to map these linked markers to specific chromosomes. We grew and scored plants for RN reproduction in the P(1), P(2), F(1), F(2), BC(1)P(1), and BC(1)P(2) generations from the cross of GB713 × Acala Nem-X. The generation means analysis using the six generations indicated that one or more genes were involved in the RN resistance of GB713. The interspecific F(2) population of 300 plants was genotyped with SSR molecular markers that covered most of the chromosomes of Upland cotton (G. hirsutum L.). Results showed two QTLs on chromosome 21 and one QTL on chromosome 18. One QTL on chromosome 21 was at map position 168.6 (LOD 28.0) flanked by SSR markers, BNL 1551_162 and GH 132_199 at positions 154.2 and 177.3, respectively. A second QTL on chromosome 21 was at map position 182.7 (LOD 24.6) flanked by SSR markers BNL 4011_155 and BNL 3279_106 at positions 180.6 and 184.5, respectively. Our chromosome 21 map had 61 SSR markers covering 219 cM. One QTL with smaller genetic effects was localized to chromosome 18 at map position 39.6 (LOD 4.0) and flanked by SSR markers BNL 1721_178 and BNL 569_131 at positions 27.6 and 42.9, respectively. The two QTLs on chromosome 21 had significant additive and dominance effects, which were about equal for each QTL. The QTL on chromosome 18 showed larger additive than dominance effects. Following the precedent set by the naming of the G. longicalyx Hutchinson & Lee and G. aridum [(Rose & Standley) Skovsted] sources of resistance, we suggest the usage of Ren (barb1) and Ren (barb2) to designate these QTLs on chromosome 21 and Ren (barb3) on chromosome 18.

Pearl millet [Pennisetum glaucum (L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs.

PubMed

Rajaram, Vengaldas; Nepolean, Thirunavukkarasu; Senthilvel, Senapathy; Varshney, Rajeev K; Vadez, Vincent; Srivastava, Rakesh K; Shah, Trushar M; Supriya, Ambawat; Kumar, Sushil; Ramana Kumari, Basava; Bhanuprakash, Amindala; Narasu, Mangamoori Lakshmi; Riera-Lizarazu, Oscar; Hash, Charles Thomas

2013-03-09

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a widely cultivated drought- and high-temperature tolerant C4 cereal grown under dryland, rainfed and irrigated conditions in drought-prone regions of the tropics and sub-tropics of Africa, South Asia and the Americas. It is considered an orphan crop with relatively few genomic and genetic resources. This study was undertaken to increase the EST-based microsatellite marker and genetic resources for this crop to facilitate marker-assisted breeding. Newly developed EST-SSR markers (99), along with previously mapped EST-SSR (17), genomic SSR (53) and STS (2) markers, were used to construct linkage maps of four F7 recombinant inbred populations (RIP) based on crosses ICMB 841-P3 × 863B-P2 (RIP A), H 77/833-2 × PRLT 2/89-33 (RIP B), 81B-P6 × ICMP 451-P8 (RIP C) and PT 732B-P2 × P1449-2-P1 (RIP D). Mapped loci numbers were greatest for RIP A (104), followed by RIP B (78), RIP C (64) and RIP D (59). Total map lengths (Haldane) were 615 cM, 690 cM, 428 cM and 276 cM, respectively. A total of 176 loci detected by 171 primer pairs were mapped among the four crosses. A consensus map of 174 loci (899 cM) detected by 169 primer pairs was constructed using MergeMap to integrate the individual linkage maps. Locus order in the consensus map was well conserved for nearly all linkage groups. Eighty-nine EST-SSR marker loci from this consensus map had significant BLAST hits (top hits with e-value ≤ 1E-10) on the genome sequences of rice, foxtail millet, sorghum, maize and Brachypodium with 35, 88, 58, 48 and 38 loci, respectively. The consensus map developed in the present study contains the largest set of mapped SSRs reported to date for pearl millet, and represents a major consolidation of existing pearl millet genetic mapping information. This study increased numbers of mapped pearl millet SSR markers by >50%, filling important gaps in previously published SSR-based linkage maps for this species and will greatly facilitate SSR-based QTL mapping and applied marker-assisted selection programs.

Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)

PubMed Central

2011-01-01

Background Pigeonpea [Cajanus cajan (L.) Millsp.] is an important legume crop of rainfed agriculture. Despite of concerted research efforts directed to pigeonpea improvement, stagnated productivity of pigeonpea during last several decades may be accounted to prevalence of various biotic and abiotic constraints and the situation is exacerbated by availability of inadequate genomic resources to undertake any molecular breeding programme for accelerated crop improvement. With the objective of enhancing genomic resources for pigeonpea, this study reports for the first time, large scale development of SSR markers from BAC-end sequences and their subsequent use for genetic mapping and hybridity testing in pigeonpea. Results A set of 88,860 BAC (bacterial artificial chromosome)-end sequences (BESs) were generated after constructing two BAC libraries by using HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes. Clustering based on sequence identity of BESs yielded a set of >52K non-redundant sequences, comprising 35 Mbp or >4% of the pigeonpea genome. These sequences were analyzed to develop annotation lists and subdivide the BESs into genome fractions (e.g., genes, retroelements, transpons and non-annotated sequences). Parallel analysis of BESs for microsatellites or simple sequence repeats (SSRs) identified 18,149 SSRs, from which a set of 6,212 SSRs were selected for further analysis. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, we identified 842 polymorphic SSR markers that will have utility in pigeonpea improvement. Based on these markers, the first SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. Utility of developed SSR markers was also demonstrated by identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment in commercial hybrid breeding programme. Conclusion In summary, while BAC libraries and BESs should be useful for genomics studies, BES-SSR markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in pigeonpea. PMID:21447154

On the ability of RegCM4 regional climate model to simulate surface solar radiation patterns over Europe: an assessment using satellite-based observations

NASA Astrophysics Data System (ADS)

Alexandri, G.; Georgoulias, A. K.; Zanis, P.; Katragkou, E.; Tsikerdekis, A.; Kourtidis, K.; Meleti, C.

2015-11-01

In this work, we assess the ability of RegCM4 regional climate model to simulate surface solar radiation (SSR) patterns over Europe. A decadal RegCM4 run (2000-2009) was implemented and evaluated against satellite-based observations from the Satellite Application Facility on Climate Monitoring (CM SAF), showing that the model simulates adequately the SSR patterns over the region. The SSR bias between RegCM4 and CM SAF is +1.5 % for MFG (Meteosat First Generation) and +3.3 % for MSG (Meteosat Second Generation) observations. The relative contribution of parameters that determine the transmission of solar radiation within the atmosphere to the deviation appearing between RegCM4 and CM SAF SSR is also examined. Cloud macrophysical and microphysical properties such as cloud fractional cover (CFC), cloud optical thickness (COT) and cloud effective radius (Re) from RegCM4 are evaluated against data from CM SAF. Generally, RegCM4 underestimates CFC by 24.3 % and Re for liquid/ice clouds by 36.1 %/28.3 % and overestimates COT by 4.3 %. The same procedure is repeated for aerosol optical properties such as aerosol optical depth (AOD), asymmetry factor (ASY) and single-scattering albedo (SSA), as well as other parameters, including surface broadband albedo (ALB) and water vapor amount (WV), using data from MACv1 aerosol climatology, from CERES satellite sensors and from ERA-Interim reanalysis. It is shown here that the good agreement between RegCM4 and satellite-based SSR observations can be partially attributed to counteracting effects among the above mentioned parameters. The potential contribution of each parameter to the RegCM4-CM SAF SSR deviations is estimated with the combined use of the aforementioned data and a~radiative transfer model (SBDART). CFC, COT and AOD are the major determinants of these deviations on a monthly basis; however, the other parameters also play an important role for specific regions and seasons. Overall, for the European domain, CFC, COT and AOD are the most important factors, since their underestimations and overestimations by RegCM4 cause an annual RegCM4-CM SAF SSR absolute deviation of 8.4, 3.8 and 4.5 %, respectively.

Science Planning for the Solar Probe Plus NASA Mission

NASA Astrophysics Data System (ADS)

Kusterer, M. B.; Fox, N. J.; Turner, F. S.; Vandegriff, J. D.

2015-12-01

With a planned launch in 2018, there are a number of challenges for the Science Planning Team (SPT) of the Solar Probe Plus mission. The geometry of the celestial bodies and the spacecraft during some of the Solar Probe Plus mission orbits cause limited uplink and downlink opportunities. The payload teams must manage the volume of data that they write to the spacecraft solid-state recorders (SSR) for their individual instruments for downlink to the ground. The aim is to write the instrument data to the spacecraft SSR for downlink before a set of data downlink opportunities large enough to get the data to the ground and before the start of another data collection cycle. The SPT also intend to coordinate observations with other spacecraft and ground based systems. To add further complexity, two of the spacecraft payloads have the capability to write a large volumes of data to their internal payload SSR while sending a smaller "survey" portion of the data to the spacecraft SSR for downlink. The instrument scientists would then view the survey data on the ground, determine the most interesting data from their payload SSR, send commands to transfer that data from their payload SSR to the spacecraft SSR for downlink. The timing required for downlink and analysis of the survey data, identifying uplink opportunities for commanding data transfers, and downlink opportunities big enough for the selected data within the data collection period is critical. To solve these challenges, the Solar Probe Plus Science Working Group has designed a orbit-type optimized data file priority downlink scheme to downlink high priority survey data quickly. This file priority scheme would maximize the reaction time that the payload teams have to perform the survey and selected data method on orbits where the downlink and uplink availability will support using this method. An interactive display and analysis science planning tool is being designed for the SPT to use as an aid to planning. The tool will integrate the data file priority downlink scheme, payload data volume allocations, spacecraft ephemeris, attitude, downlink and uplink schedules, spacecraft and payload activities, and other spacecraft ephemeris. A prototype of the tool is in development using notional inputs obtained from the spacecraft engineering teams.

R [to the Fifth Power]: The Sustained Silent Reading Makeover that Transformed Readers

ERIC Educational Resources Information Center

Kelley, Michelle; Clausen-Grace, Nicki

2006-01-01

This article reports on a retooled Sustained Silent Reading (SSR) block in an intermediate classroom designed to meet the needs of all students. The authors discuss the benefits and obstacles to SSR and include the framework and classroom management tips that aided their successful implementation of an independent reading block. Students engaged…

Language Policy, Tacit Knowledge, and Institutional Learning: The Case of the Swiss Public Service Broadcaster SRG SSR

ERIC Educational Resources Information Center

Perrin, Daniel

2011-01-01

"Promoting public understanding" is what the programming mandate asks the Swiss public broadcasting company SRG SSR to do. From a sociolinguistic perspective, this means linking speech communities with other speech communities, both between and within the German-, French-, Italian-, and Romansh-speaking parts of Switzerland. In the…

The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia Formosa

Treesearch

Brandon Schlautman; Vera Pfeiffer; Juan Zalapa; Johanne Brunet

2014-01-01

Numerous microsatellite markers were developed for Aquilegia formosafrom sequences deposited within the Expressed Sequence Tag (EST), Genomic Survey Sequence (GSS), and Nucleotide databases in NCBI. Microsatellites (SSRs) were identified and primers were designed for 9 SSR containing sequences in the Nucleotide database, 3803 sequences in the EST...

Development and Characterization of Novel SSR Markers in Carrot (Daucus Carota L.) and Their Application for Mapping and Diversity Analysis in Apiaceae

USDA-ARS?s Scientific Manuscript database

Genomic resources in carrot and other Apiaceae are relatively underdeveloped. The availability of a large set of pcr-based codominant markers, such as simple sequence repeats (SSR), would allow integration of the different carrot genetic maps constructed to date (mainly using anonymous dominant mark...

78 FR 17744 - Social Security Ruling, SSR 13-2p; Titles II and XVI: Evaluating Cases Involving Drug Addiction...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-22

... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2012-0006] Social Security Ruling, SSR 13-2p...: Social Security Administration. ACTION: Notice of Social Security Ruling; Correction. SUMMARY: The Social..., Social Security Administration. [FR Doc. 2013-06594 Filed 3-21-13; 8:45 am] BILLING CODE 4191-02-P ...

[Statistical surveys].

PubMed

1981-01-01

Data are included on territory and population in Czechoslovakia; population development, 1869-1980; number of women aged 15-49 and 15-29, 1970-1979; live births, 1970-1979; reproduction rates, 1970-1979; fertility of women by five-year age group, 1970-1979; fertility of women by age for Czechoslovakia, the Czech SSR, and the Slovak SSR; and natural growth of population, 1975-1980

Development of SSR markers for Chionanthus retusus (Oleaceae) and effective discrimination of closely related taxa

USDA-ARS?s Scientific Manuscript database

We have developed 384 simple sequence repeat (SSR) markers for the identification of accessions of Chionanthus retusus and four related species. The bark of C. retusus and C. virginicus is used in the industry of natural product to treat inflammation, fever and other illnesses, and with the use of ...

An integrated genetic linkage map of watermelon and genetic diversity based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers

USDA-ARS?s Scientific Manuscript database

Watermelon (Citrullus lanatus var. lanatus) is an important vegetable fruit throughout the world. A high number of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers should provide large coverage of the watermelon genome and high phylogenetic resolution of germplasm acces...

75 FR 18848 - Preparation for International Conference on Harmonisation Steering Committee and Expert Working...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-13

...] Preparation for International Conference on Harmonisation Steering Committee and Expert Working Group Meetings... entitled ``Preparation for ICH Steering Committee and Expert Working Group Meetings in Tallinn, Estonia... by April 30, 2010. Interested persons may present data, information, or views orally or in writing...

Nuclear and cytoplasmic genome components of Solanum tuberosum + S. chacoense somatic hybrids and three SSR alleles related to bacterial wilt resistance.

PubMed

Chen, Lin; Guo, Xianpu; Xie, Conghua; He, Li; Cai, Xingkui; Tian, Lingli; Song, Botao; Liu, Jun

2013-07-01

The somatic hybrids were derived previously from protoplast fusion between Solanum tuberosum and S. chacoense to gain the bacterial wilt resistance from the wild species. The genome components analysis in the present research was to clarify the nuclear and cytoplasmic composition of the hybrids, to explore the molecular markers associated with the resistance, and provide information for better use of these hybrids in potato breeding. One hundred and eight nuclear SSR markers and five cytoplasmic specific primers polymorphic between the fusion parents were used to detect the genome components of 44 somatic hybrids. The bacterial wilt resistance was assessed thrice by inoculating the in vitro plants with a bacterial suspension of race 1. The disease index, relative disease index, and resistance level were assigned to each hybrid, which were further analyzed in relation to the molecular markers for elucidating the potential genetic base of the resistance. All of the 317 parental unique nuclear SSR alleles appeared in the somatic hybrids with some variations in the number of bands detected. Nearly 80 % of the hybrids randomly showed the chloroplast pattern of one parent, and most of the hybrids exhibited a fused mitochondrial DNA pattern. One hundred and nine specific SSR alleles of S. chacoense were analyzed for their relationship with the disease index of the hybrids, and three alleles were identified to be significantly associated with the resistance. Selection for the resistant SSR alleles of S. chacoense may increase the possibility of producing resistant pedigrees.

Influence of Salmonella enterica Serovar Typhimurium ssrB on Colonization of Eastern Oysters (Crassostrea virginica) as Revealed by a Promoter Probe Screen

PubMed Central

Cox, Clayton E.; Wright, Anita C.; McClelland, Michael

2015-01-01

Although Salmonella has been isolated from 7.4 to 8.6% of domestic raw oysters, representing a significant risk for food-borne illness, little is known about the factors that influence their initial colonization by Salmonella. This study tested the hypothesis that specific regulatory changes enable a portion of the invading Salmonella population to colonize oysters. An in vivo promoter probe library screen identified 19 unique regions as regulated during colonization. The mutants in the nearest corresponding downstream genes were tested for colonization defects in oysters. Only one mutation, in ssrB, resulted in a significantly reduced ability to colonize oysters compared to that of wild-type Salmonella. Because ssrB regulates Salmonella pathogenicity island 2 (SPI-2)-dependent infections in vertebrate macrophages, the possibility that ssrB mediated colonization of oyster hemocytes in a similar manner was examined. However, no difference in hemocyte colonization was observed. The complementary hypothesis that signal exchange between Salmonella and the oyster's native microbial community aids colonization was also tested. Signals that triggered responses in quorum sensing (QS) reporters were shown to be produced by oyster-associated bacteria and present in oyster tissue. However, no evidence for signal exchange was observed in vivo. The sdiA reporter responded to salinity, suggesting that SdiA may also have a role in environmental sensing. Overall, this study suggests the initial colonization of live oysters by Salmonella is controlled by a limited number of regulators, including ssrB. PMID:26497459

Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers.

PubMed

Van Inghelandt, Delphine; Melchinger, Albrecht E; Lebreton, Claude; Stich, Benjamin

2010-05-01

Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (c) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. Our study was based on 1,537 elite maize inbred lines genotyped with 359 SSR and 8,244 SNP markers. The average number of alleles per locus, of group specific alleles, and the gene diversity (D) were higher for SSRs than for SNPs. Modified Roger's distance (MRD) estimates and membership probabilities of the STRUCTURE matrices were higher for SSR than for SNP markers but the germplasm organization in four heterotic pools was consistent with STRUCTURE results based on SSRs and SNPs. MRD estimates calculated for the two marker systems were highly correlated (0.87). Our results suggested that the same conclusions regarding the structure and the diversity of heterotic pools could be drawn from both markers types. Furthermore, although our results suggested that the ratio of the number of SSRs and SNPs required to obtain MRD or D estimates with similar precision is not constant across the various precision levels, we propose that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity.

Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L.

PubMed Central

Gong, L.; Stift, G.; Kofler, R.; Pachner, M.

2008-01-01

Until recently, only a few microsatellites have been available for Cucurbita, thus their development is highly desirable. The Austrian oil-pumpkin variety Gleisdorfer Ölkürbis (C. pepo subsp. pepo) and the C. moschata cultivar Soler (Puerto Rico) were used for SSR development. SSR-enriched partial genomic libraries were established and 2,400 clones were sequenced. Of these 1,058 (44%) contained an SSR at least four repeats long. Primers were designed for 532 SSRs; 500 primer pairs produced fragments of expected size. Of these, 405 (81%) amplified polymorphic fragments in a set of 12 genotypes: three C. moschata, one C. ecuadorensis, and eight C. pepo representing all eight cultivar groups. On an average, C. pepo and C. moschata produced 3.3 alleles per primer pair, showing high inter-species transferability. There were 187 SSR markers detecting polymorphism between the USA oil-pumpkin variety “Lady Godiva” (O5) and the Italian crookneck variety “Bianco Friulano” (CN), which are the parents of our previous F2 mapping population. It has been used to construct the first published C. pepo map, containing mainly RAPD and AFLP markers. Now the updated map comprises 178 SSRs, 244 AFLPs, 230 RAPDs, five SCARs, and two morphological traits (h and B). It contains 20 linkage groups with a map density of 2.9 cM. The observed genome coverage (Co) is 86.8%. Electronic supplementary material The online version of this article (doi:10.1007/s00122-008-0750-2) contains supplementary material, which is available to authorized users. PMID:18379753

Organelle Simple Sequence Repeat Markers Help to Distinguish Carpelloid Stamen and Normal Cytoplasmic Male Sterile Sources in Broccoli

PubMed Central

Shu, Jinshuai; Liu, Yumei; Li, Zhansheng; Zhang, Lili; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao

2015-01-01

We previously discovered carpelloid stamens when breeding cytoplasmic male sterile lines in broccoli (Brassica oleracea var. italica). In this study, hybrids and multiple backcrosses were produced from different cytoplasmic male sterile carpelloid stamen sources and maintainer lines. Carpelloid stamens caused dysplasia of the flower structure and led to hooked or coiled siliques with poor seed setting, which were inherited in a maternal fashion. Using four distinct carpelloid stamens and twelve distinct normal stamens from cytoplasmic male sterile sources and one maintainer, we used 21 mitochondrial simple sequence repeat (mtSSR) primers and 32 chloroplast SSR primers to identify a mitochondrial marker, mtSSR2, that can differentiate between the cytoplasm of carpelloid and normal stamens. Thereafter, mtSSR2 was used to identify another 34 broccoli accessions, with an accuracy rate of 100%. Analysis of the polymorphic sequences revealed that the mtSSR2 open reading frame of carpelloid stamen sterile sources had a deletion of 51 bases (encoding 18 amino acids) compared with normal stamen materials. The open reading frame is located in the coding region of orf125 and orf108 of the mitochondrial genomes in Brassica crops and had the highest similarity with Raphanus sativus and Brassica carinata. The current study has not only identified a useful molecular marker to detect the cytoplasm of carpelloid stamens during broccoli breeding, but it also provides evidence that the mitochondrial genome is maternally inherited and provides a basis for studying the effect of the cytoplasm on flower organ development in plants. PMID:26407159

Outcomes of patients with abdominoperineal resection (APR) and low anterior resection (LAR) who had very low rectal cancer.

PubMed

Yeom, Seung-Seop; Park, In Ja; Jung, Sung Woo; Oh, Se Heon; Lee, Jong Lyul; Yoon, Yong Sik; Kim, Chan Wook; Lim, Seok-Byung; Kim, Nayoung; Yu, Chang Sik; Kim, Jin Cheon

2017-10-01

We compared the oncological outcomes of sphincter-saving resection (SSR) and abdominoperineal resection (APR) in 409 consecutive patients with very low rectal cancer (i.e., tumors within 3 cm from the anal verge); 335 (81.9%) patients underwent APR and 74 (18.1%) underwent SSR. The APR group comprised higher proportions of men (67.5% vs 55.4%, P = .049) and advanced-stage patients (P < .001). Preoperative chemoradiotherapy (PCRT) was more frequently administered in the SSR group (83.8% vs 52.8%, P < .001). Overall, the systemic and local recurrence rates were 29.1% and 6.1%, respectively. On stratification according to PCRT and pathologic stage, the mode of surgery did not affect the recurrence type. Moreover, recurrence-free survival (RFS) did not differ according to the mode of surgery in different cancer stages. RFS was associated with ypT and ypN stages in patients who received PCRT, while pN stage, lymphovascular invasion (LVI), and circumferential resection margin (CRM) involvement were risk factors for RFS in those who did not receive PCRT. Notably, SSR was not found to be a risk factor for RFS in either subgroup. Patients who were stratified according to cancer stage and PCRT also showed no differences in RFS according to the mode of surgery. Our results demonstrate that, regardless of PCRT administration, SSR is an effective treatment for very low rectal cancer, while CRM is an important prognostic factor for patients who did not receive PCRT.

Developing new microsatellite markers in walnut (Juglans regia L.) from Juglans nigra genomic GA enriched library

Treesearch

Hayat Topcu; Nergiz Coban; Keith Woeste; Mehmet Sutyemez; Salih Kafkas

2015-01-01

We attempted to develop new polymorphic SSR primer pairs in walnut using sequences derived from Juglans nigra L. genomic enriched library with GA repeat. The designed 94 SSR primer pairs were subjected to gradient PCR in 12 walnut cultivars to determine their optimum annealing temperatures and to determine whether they produce bands. Then, the...

Sustained Silent Reading in Middle School and Its Impact on Students' Attitudes and Achievement

ERIC Educational Resources Information Center

Morgan, Margaret Peggy S.

2013-01-01

Sustained Silent Reading (SSR) is a period of time given to students to read self-selected materials during their school day. This study examines the effect of participation in a SSR program on reading attitudes and reading achievement of students as measured by the Adolescent Motivation to Read Profile (AMRP) and the Northwest Evaluation…

PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

PubMed

Kumar, Pankaj; Chaitanya, Pasumarthy S; Nagarajaram, Hampapathalu A

2011-01-01

PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in some bacteria. Although SSR-mediated phase variation and antigenic variations have been well-studied in some bacteria there seems a lot of other species of prokaryotes yet to be investigated for SSR mediated adaptive and other evolutionary advantages. As a part of our on-going studies on SSR polymorphism in prokaryotes we compared the genome sequences of various strains and isolates available for 85 different species of prokaryotes and extracted a number of SSRs showing length variations and created a relational database called PSSRdb. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc. The information provided in this database is very useful for further research and analysis of SSRs in prokaryotes.

Suprathreshold stochastic resonance in neural processing tuned by correlation.

PubMed

Durrant, Simon; Kang, Yanmei; Stocks, Nigel; Feng, Jianfeng

2011-07-01

Suprathreshold stochastic resonance (SSR) is examined in the context of integrate-and-fire neurons, with an emphasis on the role of correlation in the neuronal firing. We employed a model based on a network of spiking neurons which received synaptic inputs modeled by Poisson processes stimulated by a stepped input signal. The smoothed ensemble firing rate provided an output signal, and the mutual information between this signal and the input was calculated for networks with different noise levels and different numbers of neurons. It was found that an SSR effect was present in this context. We then examined a more biophysically plausible scenario where the noise was not controlled directly, but instead was tuned by the correlation between the inputs. The SSR effect remained present in this scenario with nonzero noise providing improved information transmission, and it was found that negative correlation between the inputs was optimal. Finally, an examination of SSR in the context of this model revealed its connection with more traditional stochastic resonance and showed a trade-off between supratheshold and subthreshold components. We discuss these results in the context of existing empirical evidence concerning correlations in neuronal firing.

Genetic characterization of rainfed upland New Rice for Africa (NERICA) varieties

PubMed Central

Fukuta, Yoshimichi; Konisho, Kunihiko; Senoo-Namai, Sachiko; Yanagihara, Seiji; Tsunematsu, Hiroshi; Fukuo, Ayumi; Kumashiro, Takashi

2012-01-01

A total of 18 rainfed upland New Rice for Africa (NERICA) varieties were categorized as the heavy panicle and low tillering types and early heading, in compared with 32 different varieties. These chromosome components were clarified using 243 SSR markers which showed polymorphism among NERICA varieties and their parents, CG 14 (O. glaberrima Steud.) and one of the recurrent parents, WAB-56-104 (O. sativa L.). NERICA varieties were classified into three groups, which corresponded with these parents’ continuation including two exceptions, NERICAs 14 and 17, by a cluster analysis using polymorphism data of SSR markers and 14 differential markers among them were selected to classify NERICA varieties. However, three groups: NERICAs, 3 and 4, NERICAs, 8, 9 and 11 and NERICAs, 15 and 16 were not distinguishable. Association analysis was carried out for characterization of NERICA varieties by using SSR markers genotype and phenotype of agronomic traits. A total of 131 quantitative trait loci between SSR markers and 11 agronomic traits were detected. The characteristics of early maturity and heavy panicle of upland NERICA varieties were succeeded from Asian rice varieties and the characteristics of high dry matter production and late heading were introduced from CG 14 and the other varieties. PMID:23136511

Suprathreshold stochastic resonance in neural processing tuned by correlation

NASA Astrophysics Data System (ADS)

Durrant, Simon; Kang, Yanmei; Stocks, Nigel; Feng, Jianfeng

2011-07-01

Suprathreshold stochastic resonance (SSR) is examined in the context of integrate-and-fire neurons, with an emphasis on the role of correlation in the neuronal firing. We employed a model based on a network of spiking neurons which received synaptic inputs modeled by Poisson processes stimulated by a stepped input signal. The smoothed ensemble firing rate provided an output signal, and the mutual information between this signal and the input was calculated for networks with different noise levels and different numbers of neurons. It was found that an SSR effect was present in this context. We then examined a more biophysically plausible scenario where the noise was not controlled directly, but instead was tuned by the correlation between the inputs. The SSR effect remained present in this scenario with nonzero noise providing improved information transmission, and it was found that negative correlation between the inputs was optimal. Finally, an examination of SSR in the context of this model revealed its connection with more traditional stochastic resonance and showed a trade-off between supratheshold and subthreshold components. We discuss these results in the context of existing empirical evidence concerning correlations in neuronal firing.

Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

PubMed

Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

2015-12-08

Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

Genetic Characterization of Turkish Snake Melon (Cucumis melo L. subsp. melo flexuosus Group) Accessions Revealed by SSR Markers.

PubMed

Solmaz, Ilknur; Kacar, Yildiz Aka; Simsek, Ozhan; Sari, Nebahat

2016-08-01

Snake melon is an important cucurbit crop especially in the Southeastern and the Mediterranean region of Turkey. It is consumed as fresh or pickled. The production is mainly done with the local landraces in the country. Turkey is one of the secondary diversification centers of melon and possesses valuable genetic resources which have different morphological characteristics in case of snake melon. Genetic diversity of snake melon genotypes collected from different regions of Turkey and reference genotypes obtained from World Melon Gene Bank in Avignon-France was examined using 13 simple sequence repeat (SSR) markers. A total of 69 alleles were detected, with an average of 5.31 alleles per locus. The polymorphism information content of SSR markers ranged from 0.19 to 0.57 (average 0.38). Based on cluster analysis, two major groups were defined. The first major group included only one accession (61), while the rest of all accessions grouped in the second major group and separated into different sub-clusters. Based on SSR markers, cluster analysis indicated that considerably high genetic variability exists among the examined accessions; however, Turkish snake melon accessions were grouped together with the reference snake melon accessions.

Sludge reduction and microbial community structure in an anaerobic/anoxic/oxic process coupled with potassium ferrate disintegration.

PubMed

An, Ying; Zhou, Zhen; Yao, Jie; Niu, Tianhao; Qiu, Zhan; Ruan, Danian; Wei, Haijuan

2017-12-01

An anaerobic/anoxic/oxic (AAO) wastewater treatment system combining with a potassium ferrate (K 2 FeO 4 ) oxidation side-stream reactor (SSR) was proposed for sludge reduction. Batch experiments showed that optimal K 2 FeO 4 dosage and reaction time for sludge disintegration was 100mg/g suspended solids (SS) and 24h, respectively. Subsequently, an AAO-SSR and a conventional AAO were operated in parallel to investigate effects of K 2 FeO 4 oxidation on process performance, sludge characteristics and microbial community structures. The AAO-SSR process operated under the optimized condition achieved efficient COD and NH 4 + -N removal, and reduced sludge by 47.5% with observed yield coefficient of 0.21gSS/g COD. K 2 FeO 4 addition broke sludge particles, increased dissolved organic matters in the mixed liquor, and improved sludge dewaterability. Illumina-MiSeq sequencing results showed that K 2 FeO 4 oxidation in the AAO-SSR decreased microbial richness and diversity, enriched slow growers (Dechloromonas), anaerobic fermentative bacteria (Azospira) and Fe(III)-reducing bacteria (Ferribacterium), but limited the growth of phosphate-accumulating organisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

EPHA2 Polymorphisms in Estonian Patients with Age-Related Cataract.

PubMed

Celojevic, Dragana; Abramsson, Alexandra; Seibt Palmér, Mona; Tasa, Gunnar; Juronen, Erkki; Zetterberg, Henrik; Zetterberg, Madeleine

2016-01-01

Ephrin receptors (Ephs) are tyrosine kinases that together with their ligands, ephrins, are considered important in cell-cell communication, especially during embryogenesis but also for epithelium homeostasis. Studies have demonstrated the involvement of mutations or common variants of the gene encoding Eph receptor A2 (EPHA2), in congenital cataract and in age-related cataract. This study investigated a number of disease-associated single nucleotide polymorphisms (SNPs) in EPHA2 in patients with age-related cataract. The study included 491 Estonian patients who had surgery for age-related cataract, classified as nuclear, cortical, posterior subcapsular and mixed lens opacities, and 185 controls of the same ethnical origin. Seven SNPs in EPHA2 (rs7543472, rs11260867, rs7548209, rs3768293, rs6603867, rs6678616, rs477558) were genotyped using TaqMan Allelic Discrimination. Statistical analyses for single factor associations used χ(2)-test and logistic regression was performed including relevant covariates (age, sex and smoking). In single-SNP allele analysis, only the rs7543472 showed a borderline significant association with risk of cataract (p = 0.048). Regression analysis with known risk factors for cataract showed no significant associations of the studied SNPs with cataract. Stratification by cataract subtype did not alter the results. Adjusted odds ratios were between 0.82 and 1.16 (95% confidence interval 0.61-1.60). The present study does not support a major role of EphA2 in cataractogenesis in an Estonian population.

Five-class height-weight mean and SD system applying Estonian reference values of height-weight mean and SD for systematization of seventeen-year-old conscripts' anthropometric data.

PubMed

Lintsi, Mart; Kaarma, Helje; Aunapuu, Marina; Arend, Andres

2007-03-01

A study of 739 conscripts aged 17 years from the town of Tartu and from the Tartu county was performed. Height, weight, 33 anthropometric measurements and 12 skinfolds were measured. The data were classified into five height-weight mean and SD-classes applying the Estonian reference values for this age and sex (Grünberg et al. 1998). There were 3 classes with conformity between height and weight class: 1--small (small height and small weight), 2--medium (medium height and medium weight), 3--large (large height and large weight), 4--weight class dominating (pyknomorphic) and 5--height class dominating (leptomorphic). It was found, that in classes 1, 2 and 3 the height and weight increase was in accordance with the increase in all heights, breadths and depths, circumferences, skinfolds, body fat, muscle and bone mass. In class 4 circumferences, skinfolds, body fat and muscle mass were bigger. In class 5 all heights and the relative bone mass were bigger. The present investigation confirms the assumption that the five height-weight mean and SD five-class system applying the Estonian reference values for classifying the anthropometric variables is suitable for seventeen-year-old conscripts. As well the border values of 5%, 50% and 95% for every anthropometrical variable in the five-classes were calculated, which may be helpful for practical classifying.

The chemical structure of Gloeocapsomorpha prisca microfossils: implications for their origin

NASA Astrophysics Data System (ADS)

Blokker, Peter; van Bergen, Pim; Pancost, Rich; Collinson, Margaret E.; de Leeuw, Jan W.; Sinninghe Damste, Jaap S.

2001-03-01

Two Estonian Kukersites (Ordovician) and two samples from the Guttenberg Member (Ordovician) of the Decorah formation (North America) containing botryoidal aggregates of Gloeocapsomorpha prisca were investigated by RuO 4 chemical degradation, FTIR, and flash pyrolysis-GC/MS to obtain information about the polymeric structure of these microfossils. The products formed upon oxidation by RuO 4 were analysed by GC/MS and revealed the presence of a wide range of carboxyl and/or carbonyl moiety containing compounds with carbon skeletons ranging from C 5 to C 20. The Estonian Kukersites reveal the presence of a characteristic set of mono-, di-, and tricarboxylic acids. These compounds suggest that the Estonian Kukersites are composed of a polymer consisting of mainly C 21 and C 23n-alkenyl resorcinol building blocks. Similarly, although the tricarboxylic acids are not present, the RuO 4 degradation product mixtures of the Guttenberg Member samples, suggest a poly( n-alkyl resorcinol) structure. The higher thermal maturity is most likely responsible for the different chemistry and morphology of the G. prisca microfossils in these samples. Because compounds like n-alkenyl resorcinols are known to polymerise under oxygenated conditions even in an aqueous environment, it is not per se necessary that these microfossils are composed of a selectively preserved biopolymeric cell wall. It is also possible that G. prisca microfossils are composed of a cell wall or sheath component that polymerised during senescence or diagenesis of the organism.

Retrospective Analysis of Clinical Performance of an Estonian Speech Recognition System for Radiology: Effects of Different Acoustic and Language Models.

PubMed

Paats, A; Alumäe, T; Meister, E; Fridolin, I

2018-04-30

The aim of this study was to analyze retrospectively the influence of different acoustic and language models in order to determine the most important effects to the clinical performance of an Estonian language-based non-commercial radiology-oriented automatic speech recognition (ASR) system. An ASR system was developed for Estonian language in radiology domain by utilizing open-source software components (Kaldi toolkit, Thrax). The ASR system was trained with the real radiology text reports and dictations collected during development phases. The final version of the ASR system was tested by 11 radiologists who dictated 219 reports in total, in spontaneous manner in a real clinical environment. The audio files collected in the final phase were used to measure the performance of different versions of the ASR system retrospectively. ASR system versions were evaluated by word error rate (WER) for each speaker and modality and by WER difference for the first and the last version of the ASR system. Total average WER for the final version throughout all material was improved from 18.4% of the first version (v1) to 5.8% of the last (v8) version which corresponds to relative improvement of 68.5%. WER improvement was strongly related to modality and radiologist. In summary, the performance of the final ASR system version was close to optimal, delivering similar results to all modalities and being independent on user, the complexity of the radiology reports, user experience, and speech characteristics.

Aesthetic Literacy: Observable Phenomena and Pedagogical Applications for Mobile Lifelong Learning (mLLL)

ERIC Educational Resources Information Center

Sean, Michael; Ihanainen, Pekka

2015-01-01

This paper proposed a method for developing capacity for lifelong learning in open spaces, defined here as places without predefined learning structures or objectives, through the cultivation of aesthetic literacy. This discussion will be situated within fieldwork performed by the authors in Helsinki, Finland, and Tallinn, Estonia, in 2013. Based…

Numerical study of Tallinn storm-water system flooding conditions using CFD simulations of multi-phase flow in a large-scale inverted siphon

NASA Astrophysics Data System (ADS)

Kaur, K.; Laanearu, J.; Annus, I.

2017-10-01

The numerical experiments are carried out for qualitative and quantitative interpretation of a multi-phase flow processes associated with malfunctioning of the Tallinn storm-water system during rain storms. The investigations are focused on the single-line inverted siphon, which is used as under-road connection of pipes of the storm-water system under interest. A multi-phase flow solver of Computational Fluid Dynamics software OpenFOAM is used for simulating the three-phase flow dynamics in the hydraulic system. The CFD simulations are performed with different inflow rates under same initial conditions. The computational results are compared essentially in two cases 1) design flow rate and 2) larger flow rate, for emptying the initially filled inverted siphon from a slurry-fluid. The larger flow-rate situations are under particular interest to detected possible flooding. In this regard, it is anticipated that the CFD solutions provide an important insight to functioning of inverted siphon under a restricted water-flow conditions at simultaneous presence of air and slurry-fluid.

Differentiation of “Candidatus Liberibacter asiaticus” Isolates by Variable-Number Tandem-Repeat Analysis ▿

PubMed Central

Katoh, Hiroshi; Subandiyah, Siti; Tomimura, Kenta; Okuda, Mitsuru; Su, Hong-Ji; Iwanami, Toru

2011-01-01

Four highly polymorphic simple sequence repeat (SSR) loci were selected and used to differentiate 84 Japanese isolates of “Candidatus Liberibacter asiaticus.” The Nei's measure of genetic diversity values for these four SSRs ranged from 0.60 to 0.86. The four SSR loci were also highly polymorphic in four isolates from Taiwan and 12 isolates from Indonesia. PMID:21239554

A genetic linkage map for hazelnut (Corylus avellana L.) based on RAPD and SSR markerswac

Treesearch

Shawn A. Mehlenbacher; Rebecca N. Brown; Eduardo R. Nouhra; Tufan Gokirmak; Nahla V. Bassil; Thomas L. Kubisiak

2006-01-01

A linkage map for European hazelnut (Corylus avellana L.) was constructed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers and the 2-way pseudotestcross approach. A full-sib population of 144 seedlings from the cross OSU 252.146 x OSU 414.062 was used. RAPD markers in testcross configuration,segregating 1:I, were...

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

PubMed Central

Daware, Anurag; Das, Sweta; Srivastava, Rishi; Badoni, Saurabh; Singh, Ashok K.; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

2016-01-01

Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16–74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7–8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice. PMID:27833617

Toxicity of a PAH photooxidation product to the bacteria Photobacterium phosphoreum and the duckweed Lemna gibba: Effects of phenanthrene and its primary photoproduct, phenanthrenequinone

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

McConkey, B.J.; Duxbury, C.L.; Dixon, D.G.

1997-05-01

Phenanthrene (PHE) undergoes a significant increase in toxicity after exposure to simulated or natural sunlight in aqueous media, coincident with the appearance of PHE photoproducts. To investigate whether the primary photoproduct of PHE, 9,10-phenanthrenequinone (PHEQ), contributes to the increased hazards of solutions containing photomodified PHE, toxicity assays were conducted using the marine bacteria Photobacterium phosphoreum and the aquatic plant Lemna gibba (duckweed). Photobacterium phosphoreum was exposed to PHE, PHEQ, a photomodified PHE mixture containing known amounts of PHE and PHEQ (pmPHE), and a mixture mimicking the amounts of PHE and PHEQ in the pmPHE mixture. The bacteria were found tomore » be equally sensitive to PHE in simulated solar radiation or darkness, with an EC50 of 0.53 mg/L. In both darkness or SSR, solutions containing PHEQ (with or without PHE) all exhibited an EC50 of 0.06 to 0.10 mg/L based on PHEQ concentrations, indicating that PHEQ was the primary active component of the pmPHE mixture. Lemna gibba was tested in SSR and visible light with PHE, PHEQ, and the pmPHE mixture. The calculated EC50 for PHE was 3.5 mg/L in SSR and 10.8 mg/L in visible light, showing that the presence of UV radiation in the SSR source increased the phytotoxicity of PHE. Strikingly, PHEQ was much more toxic to L. gibba than PHE in a light-independent manner. Thus, for both P. phosphoreum and L. gibba the major photooxidation product of PHE in SSR, PHEQ, is the more toxic of the two chemicals.« less

Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers

PubMed Central

Van Inghelandt, Delphine; Melchinger, Albrecht E.; Lebreton, Claude

2010-01-01

Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (c) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. Our study was based on 1,537 elite maize inbred lines genotyped with 359 SSR and 8,244 SNP markers. The average number of alleles per locus, of group specific alleles, and the gene diversity (D) were higher for SSRs than for SNPs. Modified Roger’s distance (MRD) estimates and membership probabilities of the STRUCTURE matrices were higher for SSR than for SNP markers but the germplasm organization in four heterotic pools was consistent with STRUCTURE results based on SSRs and SNPs. MRD estimates calculated for the two marker systems were highly correlated (0.87). Our results suggested that the same conclusions regarding the structure and the diversity of heterotic pools could be drawn from both markers types. Furthermore, although our results suggested that the ratio of the number of SSRs and SNPs required to obtain MRD or D estimates with similar precision is not constant across the various precision levels, we propose that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity. Electronic supplementary material The online version of this article (doi:10.1007/s00122-009-1256-2) contains supplementary material, which is available to authorized users. PMID:20063144

Transferability of microsatellite markers of Capsicum annuum L. to C. frutescens L. and C. chinense Jacq.

PubMed

Carvalho, S I C; Ragassi, C F; Oliveira, I B; Amaral, Z P S; Reifschneider, F J B; Faleiro, F G; Buso, G S C

2015-07-17

In order to support further genetic, diversity, and phylogeny studies of Capsicum species, the transferability of a Capsicum annuum L. simple sequence repeat (SSR) microsatellite set was analyzed for C. frutescens L. ("malagueta" and "tabasco" peppers) and C. chinense Jacq. (smell peppers, among other types). A total of 185 SSR primers were evaluated in 12 accessions from 115 C. frutescens L. and 480 C. chinense Jacq, representing different types within each species. Transferability to C. frutescens L. and C. chinense Jacq. occurred for 116 primers (62.7%). Nineteen (16.37%) were polymorphic in C. frutescens L. and 36 (31.03%) in C. chinense Jacq., 17 of which were coincident and could be used to analyze samples obtained for the 2 species. Among these primers, CA49 showed a different amplitude range of alleles between the 2 species (130-132 base pairs for C. frutescens L. and 120-128 base pairs for C. chinense Jacq.), and could differentiate the species. A total of 55 alleles were identified among the 19 polymorphic SSR loci among accessions of C. frutescens L., with the number of alleles per locus ranging from 2 to 5, a mean of 2.89, and the polymorphic information content ranging from 0.30 to 0.65. The number of alleles identified in C. chinense Jacq. was 119, ranging from 2 to 5 alleles per locus, an average of 3.30, and polymorphic information content from 0.19 to 0.68. The C. annuum L. SSR primers were most often transfer-able and polymorphic for C. frutescens L. and C. chinense Jacq., and we present a set of SSR for each species.

Spatio-temporal representativeness of ground-based downward solar radiation measurements

NASA Astrophysics Data System (ADS)

Schwarz, Matthias; Wild, Martin; Folini, Doris

2017-04-01

Surface solar radiation (SSR) is most directly observed with ground based pyranometer measurements. Besides measurement uncertainties, which arise from the pyranometer instrument itself, also errors attributed to the limited spatial representativeness of observations from single sites for their large-scale surrounding have to be taken into account when using such measurements for energy balance studies. In this study the spatial representativeness of 157 homogeneous European downward surface solar radiation time series from the Global Energy Balance Archive (GEBA) and the Baseline Surface Radiation Network (BSRN) were examined for the period 1983-2015 by using the high resolution (0.05°) surface solar radiation data set from the Satellite Application Facility on Climate Monitoring (CM-SAF SARAH) as a proxy for the spatiotemporal variability of SSR. By correlating deseasonalized monthly SSR time series form surface observations against single collocated satellite derived SSR time series, a mean spatial correlation pattern was calculated and validated against purely observational based patterns. Generally decreasing correlations with increasing distance from station, with high correlations (R2 = 0.7) in proximity to the observational sites (±0.5°), was found. When correlating surface observations against time series from spatially averaged satellite derived SSR data (and thereby simulating coarser and coarser grids), very high correspondence between sites and the collocated pixels has been found for pixel sizes up to several degrees. Moreover, special focus was put on the quantification of errors which arise in conjunction to spatial sampling when estimating the temporal variability and trends for a larger region from a single surface observation site. For 15-year trends on a 1° grid, errors due to spatial sampling in the order of half of the measurement uncertainty for monthly mean values were found.

Solar-simulating irradiation of the skin of human subjects in vivo produces Langerhans cell responses distinct from irradiation ex vivo and in vitro.

PubMed

Laihia, J K; Jansen, C T

2000-08-01

It has been postulated that Langerhans cells (LC) provide tolerogenic signals in the local impairment of cutaneous immune functions and antigen-specific tolerance induced by UV radiation. Studies in vitro and ex vivo have indicated that UV radiation may down-regulate the expression of costimulatory molecules on LC, leading to reduced antigen-presenting function. In contrast, we recently observed an up-regulatory stage in the number of human epidermal LC with induced expression of B7 costimulatory molecules 12-24 h after solar-simulating UV radiation (SSR) in vivo. To examine the apparent discrepancy between the observed human LC responses in vitro, ex vivo and in vivo, we compared the three protocols in a parallel fashion. The intact skin as well as skin explants and epidermal cell suspensions from the same individuals were irradiated with a single erythematogenic dose of SSR. The expression of cell surface markers in the epidermal cells was analysed with flow cytometry 24 h later. The number of CD1a+/HLA-DR+ LC increased post-SSR in vivo by a factor of 2.8+/-0.4, whereas in irradiated skin explants ex vivo or in cell suspensions in vitro, reduced numbers were seen. HLA-DR expression intensities were found to have increased on DR+ and CD1a+/DR+ cells in vivo. Similarly, SSR induced B7-2 (CD86) expression in CD1a+ cells significantly in vivo (P=0.031) but reduced the expression ex vivo or in vitro. We conclude that the early up-regulatory stage of human LC number and membrane markers, recorded at 24 h after a single exposure to SSR, is exclusively an in vivo phenomenon.

Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato.

PubMed

Ohyama, Akio; Shirasawa, Kenta; Matsunaga, Hiroshi; Negoro, Satomi; Miyatake, Koji; Yamaguchi, Hirotaka; Nunome, Tsukasa; Iwata, Hiroyoshi; Fukuoka, Hiroyuki; Hayashi, Takeshi

2017-08-01

Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F 2 population derived from a cross between two commercial F 1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F 1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F 2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

Exploiting rice-sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map.

PubMed

Ramu, P; Kassahun, B; Senthilvel, S; Ashok Kumar, C; Jayashree, B; Folkertsma, R T; Reddy, L Ananda; Kuruvinashetti, M S; Haussmann, B I G; Hash, C T

2009-11-01

The sequencing and detailed comparative functional analysis of genomes of a number of select botanical models open new doors into comparative genomics among the angiosperms, with potential benefits for improvement of many orphan crops that feed large populations. In this study, a set of simple sequence repeat (SSR) markers was developed by mining the expressed sequence tag (EST) database of sorghum. Among the SSR-containing sequences, only those sharing considerable homology with rice genomic sequences across the lengths of the 12 rice chromosomes were selected. Thus, 600 SSR-containing sorghum EST sequences (50 homologous sequences on each of the 12 rice chromosomes) were selected, with the intention of providing coverage for corresponding homologous regions of the sorghum genome. Primer pairs were designed and polymorphism detection ability was assessed using parental pairs of two existing sorghum mapping populations. About 28% of these new markers detected polymorphism in this 4-entry panel. A subset of 55 polymorphic EST-derived SSR markers were mapped onto the existing skeleton map of a recombinant inbred population derived from cross N13 x E 36-1, which is segregating for Striga resistance and the stay-green component of terminal drought tolerance. These new EST-derived SSR markers mapped across all 10 sorghum linkage groups, mostly to regions expected based on prior knowledge of rice-sorghum synteny. The ESTs from which these markers were derived were then mapped in silico onto the aligned sorghum genome sequence, and 88% of the best hits corresponded to linkage-based positions. This study demonstrates the utility of comparative genomic information in targeted development of markers to fill gaps in linkage maps of related crop species for which sufficient genomic tools are not available.

Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

PubMed

Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

2014-01-01

Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.

Association mapping to discover significant marker-trait associations for resistance against fusarium wilt variant 2 in pigeonpea [Cajanus cajan (L.) Millspaugh] using SSR markers.

PubMed

Patil, Prakash G; Dubey, Jyotirmay; Bohra, Abhishek; Mishra, R K; Saabale, P R; Das, Alok; Rathore, Meenal; Singh, N P

2017-08-01

Pigeonpea production is severely constrained by wilt disease caused by Fusarium udum. In the current study, we discover the putative genomic regions that control resistance response to variant 2 of fusarium wilt using association mapping approach. The association panel comprised of 89 diverse pigeonpea genotypes including seven varieties, three landraces and 79 germplasm lines. The panel was screened rigorously for 3 consecutive years (2013-14, 2014-15 and 2015-2016) against variant 2 in a wilt-sick field. A total of 65 pigeonpea specific hypervariable SSR markers (HASSRs) were screened representing seven linkage groups and 29 scaffolds of the pigeonpea genome. A total of 181 alleles were detected, with average values of gene diversity and polymorphism information content (PIC) of 0.55 and 0.47, respectively. Further analysis using model based (STRUCTURE) and distance based (clustering) approaches separated the entire pigeonpea collection into two distinct subgroups (K = 2). The marker trait associations (MTAs) were established based on three-year wilt incidence data and SSR dataset using a unified mixed linear model. Consequently, six SSR markers were identified, which were significantly associated with wilt resistance and explained up to 6% phenotypic variance (PV) across the years. Among these SSRs, HASSR18 was found to be the most stable and significant, accounting for 5-6% PV across the years. To the best of our knowledge, this is the first report of identification of favourable alleles for resistance to variant 2 of Fusarium udum in pigeonpea using association mapping. The SSR markers identified here will greatly facilitate marker assisted resistance breeding against fusarium wilt in pigeonpea.

Simplified sleep restriction for insomnia in general practice: a randomised controlled trial.

PubMed

Falloon, Karen; Elley, C Raina; Fernando, Antonio; Lee, Arier C; Arroll, Bruce

2015-08-01

Insomnia is common in primary care. Cognitive behavioural therapy for insomnia (CBT-I) is effective but requires more time than is available in the general practice consultation. Sleep restriction is one behavioural component of CBT-I. To assess whether simplified sleep restriction (SSR) can be effective in improving sleep in primary insomnia. Randomised controlled trial of patients in urban general practice settings in Auckland, New Zealand. Adults with persistent primary insomnia and no mental health or significant comorbidity were eligible. Intervention patients received SSR instructions and sleep hygiene advice. Control patients received sleep hygiene advice alone. Primary outcomes included change in sleep quality at 6 months measured by the Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI), and sleep efficiency (SE%). The proportion of participants reaching a predefined 'insomnia remission' treatment response was calculated. Ninety-seven patients were randomised and 94 (97%) completed the study. At 6-month follow-up, SSR participants had improved PSQI scores (6.2 versus 8.4, P<0.001), ISI scores (8.6 versus 11.1, P = 0.001), actigraphy-assessed SE% (difference 2.2%, P = 0.006), and reduced fatigue (difference -2.3 units, P = 0.04), compared with controls. SSR produced higher rates of treatment response (67% [28 out of 42] versus 41% [20 out of 49]); number needed to treat = 4 (95% CI = 2.0 to 19.0). Controlling for age, sex, and severity of insomnia, the adjusted odds ratio for insomnia remission was 2.7 (95% CI = 1.1 to 6.5). There were no significant differences in other outcomes or adverse effects. SSR is an effective brief intervention in adults with primary insomnia and no comorbidities, suitable for use in general practice. © British Journal of General Practice 2015.

Fatty Acid Profile and Unigene-Derived Simple Sequence Repeat Markers in Tung Tree (Vernicia fordii)

PubMed Central

Zhang, Lin; Jia, Baoguang; Tan, Xiaofeng; Thammina, Chandra S.; Long, Hongxu; Liu, Min; Wen, Shanna; Song, Xianliang; Cao, Heping

2014-01-01

Tung tree (Vernicia fordii) provides the sole source of tung oil widely used in industry. Lack of fatty acid composition and molecular markers hinders biochemical, genetic and breeding research. The objectives of this study were to determine fatty acid profiles and develop unigene-derived simple sequence repeat (SSR) markers in tung tree. Fatty acid profiles of 41 accessions showed that the ratio of α-eleostearic acid was increasing continuously with a parallel trend to the amount of tung oil accumulation while the ratios of other fatty acids were decreasing in different stages of the seeds and that α-eleostearic acid (18∶3) consisted of 77% of the total fatty acids in tung oil. Transcriptome sequencing identified 81,805 unigenes from tung cDNA library constructed using seed mRNA and discovered 6,366 SSRs in 5,404 unigenes. The di- and tri-nucleotide microsatellites accounted for 92% of the SSRs with AG/CT and AAG/CTT being the most abundant SSR motifs. Fifteen polymorphic genic-SSR markers were developed from 98 unigene loci tested in 41 cultivated tung accessions by agarose gel and capillary electrophoresis. Genbank database search identified 10 of them putatively coding for functional proteins. Quantitative PCR demonstrated that all 15 polymorphic SSR-associated unigenes were expressed in tung seeds and some of them were highly correlated with oil composition in the seeds. Dendrogram revealed that most of the 41 accessions were clustered according to the geographic region. These new polymorphic genic-SSR markers will facilitate future studies on genetic diversity, molecular fingerprinting, comparative genomics and genetic mapping in tung tree. The lipid profiles in the seeds of 41 tung accessions will be valuable for biochemical and breeding studies. PMID:25167054

On the ability of RegCM4 regional climate model to simulate surface solar radiation patterns over Europe: an assessment using satellite-based observations

NASA Astrophysics Data System (ADS)

Alexandri, G.; Georgoulias, A. K.; Zanis, P.; Katragkou, E.; Tsikerdekis, A.; Kourtidis, K.; Meleti, C.

2015-07-01

In this work, we assess the ability of RegCM4 regional climate model to simulate surface solar radiation (SSR) patterns over Europe. A decadal RegCM4 run (2000-2009) was implemented and evaluated against satellite-based observations from the Satellite Application Facility on Climate Monitoring (CM SAF) showing that the model simulates adequately the SSR patterns over the region. The bias between RegCM4 and CM SAF is +1.54 % for MFG (Meteosat First Generation) and +3.34 % for MSG (Meteosat Second Generation) observations. The relative contribution of parameters that determine the transmission of solar radiation within the atmosphere to the deviation appearing between RegCM4 and CM SAF SSR is also examined. Cloud macrophysical and microphysical properties such as cloud fractional cover (CFC), cloud optical thickness (COT) and cloud effective radius (Re) from RegCM4 are evaluated against data from CM SAF. The same procedure is repeated for aerosol optical properties such as aerosol optical depth (AOD), asymmetry factor (ASY) and single scattering albedo (SSA), as well as other parameters including surface broadband albedo (ALB) and water vapor amount (WV) using data from MACv1 aerosol climatology, from CERES satellite sensors and from ERA-Interim reanalysis. It is shown here that the good agreement between RegCM4 and satellite-based SSR observations can be partially attributed to counteracting effects among the above mentioned parameters. The contribution of each parameter to the RegCM4-CM SAF SSR deviations is estimated with the combined use of the aforementioned data and a radiative transfer model (SBDART). CFC, COT and AOD are the major determinants of these deviations; however, the other parameters also play an important role for specific regions and seasons.

Genetic Diversity and Association of EST-SSR and SCoT Markers with Rust Traits in Orchardgrass (Dactylis glomerata L.).

PubMed

Yan, Haidong; Zhang, Yu; Zeng, Bing; Yin, Guohua; Zhang, Xinquan; Ji, Yang; Huang, Linkai; Jiang, Xiaomei; Liu, Xinchun; Peng, Yan; Ma, Xiao; Yan, Yanhong

2016-01-08

Orchardgrass (Dactylis glomerata L.), is a well-known perennial forage species; however, rust diseases have caused a noticeable reduction in the quality and production of orchardgrass. In this study, genetic diversity was assessed and the marker-trait associations for rust were examined using 18 EST-SSR and 21 SCoT markers in 75 orchardgrass accessions. A high level of genetic diversity was detected in orchardgrass with an average genetic diversity index of 0.369. For the EST-SSR and SCoT markers, 164 and 289 total bands were obtained, of which 148 (90.24%) and 272 (94.12%) were polymorphic, respectively. Results from an AMOVA analysis showed that more genetic variance existed within populations (87.57%) than among populations (12.43%). Using a parameter marker index, the efficiencies of the EST-SSR and SCoT markers were compared to show that SCoTs have higher marker efficiency (8.07) than EST-SSRs (4.82). The results of a UPGMA cluster analysis and a STRUCTURE analysis were both correlated with the geographic distribution of the orchardgrass accessions. Linkage disequilibrium analysis revealed an average r² of 0.1627 across all band pairs, indicating a high extent of linkage disequilibrium in the material. An association analysis between the rust trait and 410 bands from the EST-SSR and SCoT markers using TASSEL software revealed 20 band panels were associated with the rust trait in both 2011 and 2012. The 20 bands obtained from association analysis could be used in breeding programs for lineage selection to prevent great losses of orchardgrass caused by rust, and provide valuable information for further association mapping using this collection of orchardgrass.

Diversity Analysis in Cannabis sativa Based on Large-Scale Development of Expressed Sequence Tag-Derived Simple Sequence Repeat Markers

PubMed Central

Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

2014-01-01

Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis. PMID:25329551

SSR and morphological trait based population structure analysis of 130 diverse flax (Linum usitatissimum L.) accessions.

PubMed

Choudhary, Shashi Bhushan; Sharma, Hariom Kumar; Kumar, Arroju Anil; Maruthi, Rangappa Thimmaiah; Mitra, Jiban; Chowdhury, Isholeena; Singh, Binay Kumar; Karmakar, Pran Gobinda

2017-02-01

A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST-SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous. The study assessed different diversity indices, AMOVA, population structure and included a principal coordinate analysis based on different marker systems. The highest diversity was exhibited by gSSR markers (SI=0.46; He=0.31; P=85.11). AMOVA based on all markers explained significant difference among fibre type, intermediate type and linseed type populations of flax. In terms of variation explained by different markers, EST-SSR markers (12%) better differentiated flax populations compared to morphological (9%) and gSSR (6%) markers at P=0.01. The maximum Nei's unbiased genetic distance (D=0.11) was observed between fibre type and linseed type exotic sub-populations based on EST-SSR markers. The combined structure analysis by using all markers grouped Indian fibre type accessions (63.4%) in a separate cluster along with the Indian intermediate type (48.7%), whereas Indian accessions (82.16%) of linseed type constituted an independent cluster. These findings were supported by the results of the principal coordinate analysis. Morphological markers employed in the study found complementary with microsatellite based markers in deciphering genetic diversity and population structure of the flax germplasm. Copyright © 2016 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.

PubMed

Taheri, Sima; Lee Abdullah, Thohirah; Yusop, Mohd Rafii; Hanafi, Mohamed Musa; Sahebi, Mahbod; Azizi, Parisa; Shamshiri, Redmond Ramin

2018-02-13

Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.

A computer analysis of the RF performance of a ground-mounted, air-supported radome

NASA Astrophysics Data System (ADS)

Punnett, M. B.; Joy, E. B.

Several reports and actual operating experience have highlighted the degradation of RF Performance which can occur when SSR or IFF antenna are mounted above primary search antenna within metal space frame or dielectric space frame radomes. These effects are usually attributed to both the high incidence angles and sensitivity of the low gain antennae to sidelobe changes due to scattered energy. Although it has been widely accepted that thin membrane radomes would provide superior performance for this application, there has been little supporting documentation. A plane-wave-spectrum (PWS) computer-based radome analysis was conducted to assess the performance of a specific air-supported radome for the SSR application. In conducting the analysis a mathematical model of a modern SSR antenna was combined with a model of an existing Birdair radome design.

An improved genetic map for Castanea mollissima/Castanea dentata and its relationship to the genetic map of Castanea sativa

Treesearch

P.H. Sisco; T.L. Kubisiak; M. Casasoli; T. Barreneche; A. Kremer; C. Clark; R.R. Sederoff; F.V. Hebard; F. Villani

2005-01-01

We have added 275 AFLP and 24 SSR markers and the 5SrDNA locus to a previously published genetic map based on a hybrid cross between Castanea mollissima and C. denata. The SSR markers, 5SrDNA locus, and one isozyme locus also permitted us to correlate the linkage groups in the published genetic map of C. sativa...

Polarization-controlled optimal scatter suppression in transient absorption spectroscopy

PubMed Central

Malý, Pavel; Ravensbergen, Janneke; Kennis, John T. M.; van Grondelle, Rienk; Croce, Roberta; Mančal, Tomáš; van Oort, Bart

2017-01-01

Ultrafast transient absorption spectroscopy is a powerful technique to study fast photo-induced processes, such as electron, proton and energy transfer, isomerization and molecular dynamics, in a diverse range of samples, including solid state materials and proteins. Many such experiments suffer from signal distortion by scattered excitation light, in particular close to the excitation (pump) frequency. Scattered light can be effectively suppressed by a polarizer oriented perpendicular to the excitation polarization and positioned behind the sample in the optical path of the probe beam. However, this introduces anisotropic polarization contributions into the recorded signal. We present an approach based on setting specific polarizations of the pump and probe pulses, combined with a polarizer behind the sample. Together, this controls the signal-to-scatter ratio (SSR), while maintaining isotropic signal. We present SSR for the full range of polarizations and analytically derive the optimal configuration at angles of 40.5° between probe and pump and of 66.9° between polarizer and pump polarizations. This improves SSR by (or compared to polarizer parallel to probe). The calculations are validated by transient absorption experiments on the common fluorescent dye Rhodamine B. This approach provides a simple method to considerably improve the SSR in transient absorption spectroscopy. PMID:28262765

Effects of nasal septum perforation repair on nasal airflow: An analysis using computational fluid dynamics on preoperative and postoperative three-dimensional models.

PubMed

Nomura, Tsutomu; Ushio, Munetaka; Kondo, Kenji; Kikuchi, Shigeru

2018-10-01

The purpose of this research is to examine the changes in nasal airflow dynamics before and after the nasal perforation repair. Three dimensional (3D) models of the nasal cavity before and after septal perforation repair was reconstructed using preoperative and postoperative computed tomography (CT) images of a patient. The numerical simulation was carried out using ANSYS CFX V15.0. Pre- and post-operative models were compared by their velocity, pressure (P), pressure gradient (PG), wall shear (WS), shear strain rate (SSR) and turbulence kinetic energy (TKE) in three plains. In the post-operative state, the cross flows disappeared. In preoperative state, there were areas showing high PG, WS, SSR at the posterior border of the perforation, which exactly correspond to the area showing erosive mucosa on endoscopic inspection of the patient. In postoperative state, such high PG, WS and SSR areas disappeared. High TKEs also disappeared after surgery. The effects of septal perforation repair on airflow dynamics were evaluated using computer fluid dynamics (CFD). High WS, PG and SSR observed at the edge of the septal perforation may be related to the clinical symptom such as nasal bleeding and pain. TKE was considered to cause nasal symptom. Copyright © 2018 Elsevier B.V. All rights reserved.

A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)1

PubMed Central

Wofford, Austin M.; Finch, Kristen; Bigott, Adam; Willyard, Ann

2014-01-01

• Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid simple sequence repeat (cpSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. • Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compared interspecific variation between cpSSRs and nucleotide sequences of ycf1 and tested intraspecific variation for cpSSRs using 911 samples in the P. ponderosa species complex. • Results: The cpSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions, and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. • Discussion: The protocol allows efficient genotyping of many samples. The cpSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for cpSSR loci in a plastome alignment for the target group. PMID:25202625

Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis

PubMed Central

Zheng, Jin-shuang; Sun, Cheng-zhen; Zhang, Shu-ning; Hou, Xi-lin; Bonnema, Guusje

2016-01-01

A significant fraction of the nuclear DNA of all eukaryotes is comprised of simple sequence repeats (SSRs). Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. In this paper, we report the distribution characterization of mono-, di-, and tri-nucleotide SSRs in Brassica rapa ssp. chinensis. Fluorescence in situ hybridization was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphotypes of B. rapa ssp. chinensis, with tri-nucleotide SSRs being more prevalent in the genome of B. rapa ssp. chinensis. We determined the chromosomal locations of mono-, di-, and tri-nucleotide repeat loci. The results showed that the chromosomal distribution of SSRs in the different morphotypes is non-random and motif-dependent, and allowed us to characterize the relative variability in terms of SSR numbers and similar chromosomal distributions in centromeric/peri-centromeric heterochromatin. The differences between SSR repeats with respect to abundance and distribution indicate that SSRs are a driving force in the genomic evolution of B. rapa species. Our results provide a comprehensive view of the SSR sequence distribution and evolution for comparison among morphotypes B. rapa ssp. chinensis. PMID:27507974

Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis.

PubMed

Zheng, Jin-Shuang; Sun, Cheng-Zhen; Zhang, Shu-Ning; Hou, Xi-Lin; Bonnema, Guusje

2016-01-01

A significant fraction of the nuclear DNA of all eukaryotes is comprised of simple sequence repeats (SSRs). Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. In this paper, we report the distribution characterization of mono-, di-, and tri-nucleotide SSRs in Brassica rapa ssp. chinensis. Fluorescence in situ hybridization was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphotypes of B. rapa ssp. chinensis, with tri-nucleotide SSRs being more prevalent in the genome of B. rapa ssp. chinensis. We determined the chromosomal locations of mono-, di-, and tri-nucleotide repeat loci. The results showed that the chromosomal distribution of SSRs in the different morphotypes is non-random and motif-dependent, and allowed us to characterize the relative variability in terms of SSR numbers and similar chromosomal distributions in centromeric/peri-centromeric heterochromatin. The differences between SSR repeats with respect to abundance and distribution indicate that SSRs are a driving force in the genomic evolution of B. rapa species. Our results provide a comprehensive view of the SSR sequence distribution and evolution for comparison among morphotypes B. rapa ssp. chinensis.

Development of SSR Markers Linked to Low Hydrocyanic Acid Content in Sorghum-Sudan Grass Hybrid Based on BSA Method.

PubMed

Xiao-Xia, Yu; Zhi-Hua, Liu; Zhuo, Yu; Yue, Shi; Xiao-Yu, Li

2016-01-01

Sorghum-Sudan grass hybrid containing high hydrocyanic acid content can cause hydrocyanic acid poisoning to the livestock and limit the popularization of this forage crop. Molecular markers associated with low hydrocyanic acid content can speed up the process of identification of genotypes with low hydrocyanic acid content. In the present study, 11 polymorphic SSR primers were screened and used for bulked segregant analysis and single marker analysis. Three SSR markers Xtxp7230, Xtxp7375 and Bnlg667960 associated with low hydrocyanic acid content were rapidly identified by BSA. In single marker analysis, six markers Xtxp7230, Xtxp7375, Bnlg667960, Xtxp67-11, Xtxp295-7 and Xtxp12-9 were linked to low hydrocyanic acid content, which explained the proportion of phenotypic variation from 7.6 % to 41.2 %. The markers identified by BSA were also verified by single marker analysis. The three SSR marker bands were then cloned and sequenced for sequence homology analysis in NCBI. It is the first report on the development of molecular markers associated with low hydrocyanic acid content in sorghum- Sudan grass hybrid. These markers will be useful for genetic improvement of low hydrocyanic acid sorghum-Sudan grass hybrid by marker-assisted breeding.

Genetic Diversity of Namibian Pennisetum glaucum (L.) R. BR. (Pearl Millet) Landraces Analyzed by SSR and Morphological Markers.

PubMed

McBenedict, Billy; Chimwamurombe, Percy; Kwembeya, Ezekeil; Maggs-Kölling, Gillian

2016-01-01

Current Pennisetum glaucum (L.) R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation's food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs) and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia.

Genetic Diversity of Namibian Pennisetum glaucum (L.) R. BR. (Pearl Millet) Landraces Analyzed by SSR and Morphological Markers

PubMed Central

McBenedict, Billy; Chimwamurombe, Percy; Kwembeya, Ezekeil; Maggs-Kölling, Gillian

2016-01-01

Current Pennisetum glaucum (L.) R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation's food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs) and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia. PMID:27433479

Developing new scenarios for water allocation negotiations: a case study of the Euphrates River Basin

NASA Astrophysics Data System (ADS)

Jarkeh, Mohammad Reza; Mianabadi, Ameneh; Mianabadi, Hojjat

2016-10-01

Mismanagement and uneven distribution of water may lead to or increase conflict among countries. Allocation of water among trans-boundary river neighbours is a key issue in utilization of shared water resources. The bankruptcy theory is a cooperative Game Theory method which is used when the amount of demand of riparian states is larger than total available water. In this study, we survey the application of seven methods of Classical Bankruptcy Rules (CBRs) including Proportional (CBR-PRO), Adjusted Proportional (CBR-AP), Constrained Equal Awards (CBR-CEA), Constrained Equal Losses (CBR-CEL), Piniles (CBR-Piniles), Minimal Overlap (CBR-MO), Talmud (CBR-Talmud) and four Sequential Sharing Rules (SSRs) including Proportional (SSR-PRO), Constrained Equal Awards (SSR-CEA), Constrained Equal Losses (SSR-CEL) and Talmud (SSR-Talmud) methods in allocation of the Euphrates River among three riparian countries: Turkey, Syria and Iraq. However, there is not a certain documented method to find more equitable allocation rule. Therefore, in this paper, a new method is established for choosing the most appropriate allocating rule which seems to be more equitable than other allocation rules to satisfy the stakeholders. The results reveal that, based on the new propose model, the CBR-AP seems to be more equitable to allocate the Euphrates River water among Turkey, Syria and Iraq.

Toxicity of Water Accommodated Fractions of Estonian Shale Fuel Oils to Aquatic Organisms.

PubMed

Blinova, Irina; Kanarbik, Liina; Sihtmäe, Mariliis; Kahru, Anne

2016-02-01

Estonia is the worldwide leading producer of the fuel oils from the oil shale. We evaluated the ecotoxicity of water accommodated fraction (WAF) of two Estonian shale fuel oils ("VKG D" and "VKG sweet") to aquatic species belonging to different trophic levels (marine bacteria, freshwater crustaceans and aquatic plants). Artificial fresh water and natural lake water were used to prepare WAFs. "VKG sweet" (lower density) proved more toxic to aquatic species than "VKG D" (higher density). Our data indicate that though shale oils were very toxic to crustaceans, the short-term exposure of Daphnia magna to sub-lethal concentrations of shale fuel oils WAFs may increase the reproductive potential of survived organisms. The weak correlation between measured chemical parameters (C10-C40 hydrocarbons and sum of 16 PAHs) and WAF's toxicity to studied species indicates that such integrated chemical parameters are not very informative for prediction of shale fuel oils ecotoxicity.

Skill-related differences between athletes and nonathletes in speed discrimination.

PubMed

Thomson, Kaivo; Watt, Anthony; Liukkonen, Jarmo

2008-12-01

This study examined differences in decision-making time and accurscy as attributes of speed discrimination between participants skilled and less skilled in ball games. A total of 130 men, ages 18 to 28 years (M=21.2, SD=2.6), participated. The athlete sample (skilled group) comprised Estonian National League volleyball (n=26) and basketball players (n=27). The nonathlete sample (less skilled group) included 77 soldiers of the Estonian Defence Force with no reported top level experience in ball games. Speed-discrimination stimuli were images of red square shapes presented moving along the sagittal axis at four different virtual velocities on a computer (PC) screen which represented the frontal plane. Analysis indicated that only decision-making time was significantly different between the elite athlete and nonathlete groups. This finding suggests a possible effect of ball-game skills for decision-making time in speed discrimination.

When Public Acts Like Private: The Failure of Estonia's School Choice Mechanism

ERIC Educational Resources Information Center

Poder, Kaire; Lauri, Triin

2014-01-01

This article aims to show the segregating effect of the market-like matching of students and schools at the basic school level. The natural experiment case is Tallinn, the capital of Estonia. The current school choice mechanism applied in this case is based on entrance tests. There are increasingly over-subscribed intra-catchment area public…

Active Learning Methods in Programming for Non-IT Students

ERIC Educational Resources Information Center

Mironova, Olga; Amitan, Irina; Vilipõld, Jüri; Saar, Merike

2016-01-01

The purpose of this study is to demonstrate a teaching approach and some teaching strategies in an Informatics course for the first-year non-IT students at the Department of Informatics of Tallinn University of Technology, Estonia. The authors suggest some solutions for making the course, which is usually complicated, more dynamic and attractive,…

Rapid Urbanization of Red Foxes in Estonia: Distribution, Behaviour, Attacks on Domestic Animals, and Health-Risks Related to Zoonotic Diseases

PubMed Central

Plumer, Liivi; Davison, John; Saarma, Urmas

2014-01-01

Urban areas are becoming increasingly important for wildlife as diminishing natural habitats no longer represent a suitable environment for many species. Red foxes (Vulpes vulpes) are nowadays common in many cities worldwide, and in recent years they have colonized urban areas in Estonia. We used a public web-based questionnaire approach to evaluate the distribution and behaviour of Estonian urban foxes, to detect related problems and to assess health risks to humans and domestic animals. In total, 1205 responses were collected throughout the country. Foxes have colonized the majority of Estonian towns (33 out of 47) in a relatively short period of time, and have already established breeding dens in several towns. Despite their recent arrival, the behaviour of Estonian urban foxes is similar to that reported in longer-established urban fox populations: they are mostly active during night-time, often visit city centres and some also have dens in such locations. Certain characteristics of urban foxes serve as a basis for conflict with humans: foxes have entered houses and attacked domestic animals, killing cats and poultry. About 8% of reported foxes exhibited symptoms of sarcoptic mange, a disease that also infects domestic animals, especially dogs. The proportion of mange-infected foxes was higher in large urban areas. In addition to mange, a substantial fraction of red foxes in Estonia are known to be infected with the life-threatening tapeworm Echinococcus multilocularis, the causative agent of alveolar echinococcosis. Therefore, urban foxes may represent a source of serious infectious disease for pets and humans. PMID:25531399

An epidemiological perspective of personalized medicine: the Estonian experience

PubMed Central

Milani, L; Leitsalu, L; Metspalu, A

2015-01-01

Milani L, Leitsalu L, Metspalu A (University of Tartu). An epidemiological perspective of personalized medicine: the Estonian experience (Review). J Intern Med 2015; 277: 188–200. The Estonian Biobank and several other biobanks established over a decade ago are now starting to yield valuable longitudinal follow-up data for large numbers of individuals. These samples have been used in hundreds of different genome-wide association studies, resulting in the identification of reliable disease-associated variants. The focus of genomic research has started to shift from identifying genetic and nongenetic risk factors associated with common complex diseases to understanding the underlying mechanisms of the diseases and suggesting novel targets for therapy. However, translation of findings from genomic research into medical practice is still lagging, mainly due to insufficient evidence of clinical validity and utility. In this review, we examine the different elements required for the implementation of personalized medicine based on genomic information. First, biobanks and genome centres are required and have been established for the high-throughput genomic screening of large numbers of samples. Secondly, the combination of susceptibility alleles into polygenic risk scores has improved risk prediction of cardiovascular disease, breast cancer and several other diseases. Finally, national health information systems are being developed internationally, to combine data from electronic medical records from different sources, and also to gradually incorporate genomic information. We focus on the experience in Estonia, one of several countries with national goals towards more personalized health care based on genomic information, where the unique combination of elements required to accomplish this goal are already in place. PMID:25339628

Rapid urbanization of red foxes in Estonia: distribution, behaviour, attacks on domestic animals, and health-risks related to zoonotic diseases.

PubMed

Plumer, Liivi; Davison, John; Saarma, Urmas

2014-01-01

Urban areas are becoming increasingly important for wildlife as diminishing natural habitats no longer represent a suitable environment for many species. Red foxes (Vulpes vulpes) are nowadays common in many cities worldwide, and in recent years they have colonized urban areas in Estonia. We used a public web-based questionnaire approach to evaluate the distribution and behaviour of Estonian urban foxes, to detect related problems and to assess health risks to humans and domestic animals. In total, 1205 responses were collected throughout the country. Foxes have colonized the majority of Estonian towns (33 out of 47) in a relatively short period of time, and have already established breeding dens in several towns. Despite their recent arrival, the behaviour of Estonian urban foxes is similar to that reported in longer-established urban fox populations: they are mostly active during night-time, often visit city centres and some also have dens in such locations. Certain characteristics of urban foxes serve as a basis for conflict with humans: foxes have entered houses and attacked domestic animals, killing cats and poultry. About 8% of reported foxes exhibited symptoms of sarcoptic mange, a disease that also infects domestic animals, especially dogs. The proportion of mange-infected foxes was higher in large urban areas. In addition to mange, a substantial fraction of red foxes in Estonia are known to be infected with the life-threatening tapeworm Echinococcus multilocularis, the causative agent of alveolar echinococcosis. Therefore, urban foxes may represent a source of serious infectious disease for pets and humans.

Chromosomal microarray analysis as a first-tier clinical diagnostic test: Estonian experience.

PubMed

Zilina, Olga; Teek, Rita; Tammur, Pille; Kuuse, Kati; Yakoreva, Maria; Vaidla, Eve; Mölter-Väär, Triin; Reimand, Tiia; Kurg, Ants; Ounap, Katrin

2014-03-01

Chromosomal microarray analysis (CMA) is now established as the first-tier cytogenetic diagnostic test for fast and accurate detection of chromosomal abnormalities in patients with developmental delay/intellectual disability (DD/ID), multiple congenital anomalies (MCA), and autism spectrum disorders (ASD). We present our experience with using CMA for postnatal and prenatal diagnosis in Estonian patients during 2009-2012. Since 2011, CMA is on the official service list of the Estonian Health Insurance Fund and is performed as the first-tier cytogenetic test for patients with DD/ID, MCA or ASD. A total of 1191 patients were analyzed, including postnatal (1072 [90%] patients and 59 [5%] family members) and prenatal referrals (60 [5%] fetuses). Abnormal results were reported in 298 (25%) patients, with a total of 351 findings (1-3 per individual): 147 (42%) deletions, 106 (30%) duplications, 89 (25%) long contiguous stretches of homozygosity (LCSH) events (>5 Mb), and nine (3%) aneuploidies. Of all findings, 143 (41%) were defined as pathogenic or likely pathogenic; for another 143 findings (41%), most of which were LCSH, the clinical significance remained unknown, while 61 (18%) reported findings can now be reclassified as benign or likely benign. Clinically relevant findings were detected in 126 (11%) patients. However, the proportion of variants of unknown clinical significance was quite high (41% of all findings). It seems that our ability to detect chromosomal abnormalities has far outpaced our ability to understand their role in disease. Thus, the interpretation of CMA findings remains a rather difficult task requiring a close collaboration between clinicians and cytogeneticists.

Variation in sequences containing microsatellite motifs in the perennial biomass and forage grass, Phalaris arundinacea (Poaceae).

PubMed

Barth, Susanne; Jankowska, Marta Jolanta; Hodkinson, Trevor Roland; Vellani, Tia; Klaas, Manfred

2016-03-22

Forty three microsatellite markers were developed for further genetic characterisation of a forage and biomass grass crop, for which genomic resources are currently scarce. The microsatellite markers were developed from a normalized EST-SSR library. All of the 43 markers gave a clear banding pattern on 3% Metaphor agarose gels. Eight selected SSR markers were tested in detail for polymorphism across eleven DNA samples of large geographic distribution across Europe. The new set of 43 SSR markers will help future research to characterise the genetic structure and diversity of Phalaris arundinacea, with a potential to further understand its invasive character in North American wetlands, as well as aid in breeding work for desired biomass and forage traits. P. arundinacea is particularly valued in the northern latitude as a crop with high biomass potential, even more so on marginal lands.

A case study on stratified settlement and rebound characteristics due to dewatering in Shanghai subway station.

PubMed

Wang, Jianxiu; Huang, Tianrong; Sui, Dongchang

2013-01-01

Based on the Yishan Metro Station Project of Shanghai Metro Line number 9, a centrifugal model test was conducted to investigate the behavior of stratified settlement and rebound (SSR) of Shanghai soft clay caused by dewatering in deep subway station pit. The soil model was composed of three layers, and the dewatering process was simulated by self-invention of decompressing devise. The results indicate that SSR occurs when the decompression was carried out, and only negative rebound was found in sandy clay, but both positive and negative rebound occurred in the silty clay, and the absolute value of rebound in sandy clay was larger than in silty clay, and the mechanism of SSR was discussed with mechanical sandwich model, and it was found that the load and cohesive force of different soils was the main source of different responses when decompressed.

Generation of Unbiased Ionospheric Corrections in Brazilian Region for GNSS positioning based on SSR concept

NASA Astrophysics Data System (ADS)

Monico, J. F. G.; De Oliveira, P. S., Jr.; Morel, L.; Fund, F.; Durand, S.; Durand, F.

2017-12-01

Mitigation of ionospheric effects on GNSS (Global Navigation Satellite System) signals is very challenging, especially for GNSS positioning applications based on SSR (State Space Representation) concept, which requires the knowledge of spatial correlated errors with considerable accuracy level (centimeter). The presence of satellite and receiver hardware biases on GNSS measurements difficult the proper estimation of ionospheric corrections, reducing their physical meaning. This problematic can lead to ionospheric corrections biased of several meters and often presenting negative values, which is physically not possible. In this contribution, we discuss a strategy to obtain SSR ionospheric corrections based on GNSS measurements from CORS (Continuous Operation Reference Stations) Networks with minimal presence of hardware biases and consequently physical meaning. Preliminary results are presented on generation and application of such corrections for simulated users located in Brazilian region under high level of ionospheric activity.

Polymorphic chloroplast microsatellite markers in the octoploid Lepidium meyenii (Brassicaceae) and cross-species amplification in Lepidium.

PubMed

Hasan, Nabeeh A; Mummenhoff, Klaus; Quiros, Carlos F; Tay, C David; Bailey, C Donovan

2010-10-01

As a crop and medicinal plant, the octoploid Andean endemic Lepidium meyenii suffers from taxonomic uncertainty. Few molecular markers are available to genotype individuals or track gene flow in wild and cultivated material. • Using available sequence data, eight cpSSR primer pairs were developed for L. meyenii. Levels of polymorphism checked in 56 individual L. meyenii, including cultivated and wild material, revealed that the number of alleles per locus ranged from three to five, and intrapopulation allele frequencies ranged from 0.071 to 1.0. Polymerase-chain-reaction screens using our cpSSR primers in 27 other Lepidium species and three Coronopus species suggested a high degree of interspecific amplification. • These polymorphic cpSSR markers should prove useful in characterizing genetic variation among cultivated and wild L. meyenii. Additionally, interspecific amplifications suggest that these markers will be useful for the study of related taxa.

A Case Study on Stratified Settlement and Rebound Characteristics due to Dewatering in Shanghai Subway Station

PubMed Central

Wang, Jianxiu; Huang, Tianrong; Sui, Dongchang

2013-01-01

Based on the Yishan Metro Station Project of Shanghai Metro Line number 9, a centrifugal model test was conducted to investigate the behavior of stratified settlement and rebound (SSR) of Shanghai soft clay caused by dewatering in deep subway station pit. The soil model was composed of three layers, and the dewatering process was simulated by self-invention of decompressing devise. The results indicate that SSR occurs when the decompression was carried out, and only negative rebound was found in sandy clay, but both positive and negative rebound occurred in the silty clay, and the absolute value of rebound in sandy clay was larger than in silty clay, and the mechanism of SSR was discussed with mechanical sandwich model, and it was found that the load and cohesive force of different soils was the main source of different responses when decompressed. PMID:23878521

Phylogenetic relationships of chrysanthemums in Korea based on novel SSR markers.

PubMed

Khaing, A A; Moe, K T; Hong, W J; Park, C S; Yeon, K H; Park, H S; Kim, D C; Choi, B J; Jung, J Y; Chae, S C; Lee, K M; Park, Y J

2013-11-07

Chrysanthemums are well known for their esthetic and medicinal values. Characterization of chrysanthemums is vital for their conservation and management as well as for understanding their genetic relationships. We found 12 simple sequence repeat markers (SSRs) of 100 designed primers to be polymorphic. These novel SSR markers were used to evaluate 95 accessions of chrysanthemums (3 indigenous and 92 cultivated accessions). Two hundred alleles were identified, with an average of 16.7 alleles per locus. KNUCRY-77 gave the highest polymorphic information content value (0.879), while KNUCRY-10 gave the lowest (0.218). Similar patterns of grouping were observed with a distance-based dendrogram developed using PowerMarker and model-based clustering with Structure. Three clusters with some admixtures were identified by model-based clustering. These newly developed SSR markers will be useful for further studies of chrysanthemums, such as taxonomy and marker-assisted selection breeding.

Development of Simple Sequence Repeats (SSR) markers in Setaria italica (Poaceae) and cross-amplification in related species.

PubMed

Lin, Heng-Sheng; Chiang, Chih-Yun; Chang, Song-Bin; Kuoh, Chang-Sheng

2011-01-01

Foxtail millet is one of the world's oldest cultivated crops. It has been adopted as a model organism for providing a deeper understanding of plant biology. In this study, 45 simple sequence repeats (SSR) markers of Setaria italica were developed. These markers showing polymorphism were screened in 223 samples from 12 foxtail millet populations around Taiwan. The most common dinucleotide and trinucleotide repeat motifs are AC/TG (84.21%) and CAT (46.15%). The average number of alleles (N(a)), the average heterozygosities observed (H(o)) and expected (H(e)) are 3.73, 0.714, 0.587, respectively. In addition, 24 SSR markers had shown transferability to six related Poaceae species. These new markers provide tools for examining genetic relatedness among foxtail millet populations and other related species. It is suitable for germplasm management and protection in Poaceae.

Development of Simple Sequence Repeats (SSR) Markers in Setaria italica (Poaceae) and Cross-Amplification in Related Species

PubMed Central

Lin, Heng-Sheng; Chiang, Chih-Yun; Chang, Song-Bin; Kuoh, Chang-Sheng

2011-01-01

Foxtail millet is one of the world’s oldest cultivated crops. It has been adopted as a model organism for providing a deeper understanding of plant biology. In this study, 45 simple sequence repeats (SSR) markers of Setaria italica were developed. These markers showing polymorphism were screened in 223 samples from 12 foxtail millet populations around Taiwan. The most common dinucleotide and trinucleotide repeat motifs are AC/TG (84.21%) and CAT (46.15%). The average number of alleles (Na), the average heterozygosities observed (Ho) and expected (He) are 3.73, 0.714, 0.587, respectively. In addition, 24 SSR markers had shown transferability to six related Poaceae species. These new markers provide tools for examining genetic relatedness among foxtail millet populations and other related species. It is suitable for germplasm management and protection in Poaceae. PMID:22174636

E-microsatellite markers for Centella asiatica (Gotu Kola) genome: validation and cross-transferability in Apiaceae family for plant omics research and development.

PubMed

Sahu, Jagajjit; Das Talukdar, Anupam; Devi, Kamalakshi; Choudhury, Manabendra Dutta; Barooah, Madhumita; Modi, Mahendra Kumar; Sen, Priyabrata

2015-01-01

Abstract Centella asiatica (Gotu Kola) is a plant that grows in tropical swampy regions of the world and has important medicinal and culinary use. It is often considered as part of Ayurvedic medicine, traditional African medicine, and traditional Chinese medicine. The unavailability of genomics resources is significantly impeding its genetic improvement. To date, no attempt has been made to develop Expressed Sequence Tags (ESTs) derived Simple Sequence Repeat (SSR) markers (eSSRs) from the Centella genome. Hence, the present study aimed to develop eSSRs and their further experimental validation and cross-transferability of these markers in different genera of the Apiaceae family to which Centella belongs. An in-house pipeline was developed for the entire analyses by combining bioinformatics tools and perl scripts. A total of 4443 C. asiatica EST sequences from dbEST were processed, which generated 2617 nonredundant high quality EST sequences consisting 441 contigs and 2176 singletons. Out of 1776.5 kb of examined sequences, 417 (15.9%) ESTs containing 686 SSRs were detected with a density of one SSR per 2.59 kb. The gene ontology study revealed 282 functional domains involved in various processes, components, and functions, out of which 64 ESTs were found to have both SSRs and functional domains. Out of 603 designed EST-SSR primers, 18 pairs of primers were selected for validation based on the optimum parameter value. Reproducible amplification was obtained for six primer pairs in C. asiatica that were further tested for cross-transferability in nine other important genera/species of the Apiaceae family. Cross-transferability of the EST-SSR markers among the species were examined and Centella javanica showed highest transferability (83.3%). The study revealed six highly polymorphic EST-SSR primers with an average PIC value of 0.95. In conclusion, these EST-SSR markers hold a big promise for the genomics analysis of Centella asiatica, to facilitate comparative map-based analyses across other related species within the Apiaceae family, and future marker-assisted breeding programs. To the best of our knowledge, this is the first report of development of EST-SSRs in Centella asiatica by in silico approaches, which offers a veritable potential in further use in plant omics research and development.

Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies

PubMed Central

2012-01-01

Background Yellow lupin (Lupinus luteus L.) is a minor legume crop characterized by its high seed protein content. Although grown in several temperate countries, its orphan condition has limited the generation of genomic tools to aid breeding efforts to improve yield and nutritional quality. In this study, we report the construction of 454-expresed sequence tag (EST) libraries, carried out comparative studies between L. luteus and model legume species, developed a comprehensive set of EST-simple sequence repeat (SSR) markers, and validated their utility on diversity studies and transferability to related species. Results Two runs of 454 pyrosequencing yielded 205 Mb and 530 Mb of sequence data for L1 (young leaves, buds and flowers) and L2 (immature seeds) EST- libraries. A combined assembly (L1L2) yielded 71,655 contigs with an average contig length of 632 nucleotides. L1L2 contigs were clustered into 55,309 isotigs. 38,200 isotigs translated into proteins and 8,741 of them were full length. Around 57% of L. luteus sequences had significant similarity with at least one sequence of Medicago, Lotus, Arabidopsis, or Glycine, and 40.17% showed positive matches with all of these species. L. luteus isotigs were also screened for the presence of SSR sequences. A total of 2,572 isotigs contained at least one EST-SSR, with a frequency of one SSR per 17.75 kbp. Empirical evaluation of the EST-SSR candidate markers resulted in 222 polymorphic EST-SSRs. Two hundred and fifty four (65.7%) and 113 (30%) SSR primer pairs were able to amplify fragments from L. hispanicus and L. mutabilis DNA, respectively. Fifty polymorphic EST-SSRs were used to genotype a sample of 64 L. luteus accessions. Neighbor-joining distance analysis detected the existence of several clusters among L. luteus accessions, strongly suggesting the existence of population subdivisions. However, no clear clustering patterns followed the accession’s origin. Conclusion L. luteus deep transcriptome sequencing will facilitate the further development of genomic tools and lupin germplasm. Massive sequencing of cDNA libraries will continue to produce raw materials for gene discovery, identification of polymorphisms (SNPs, EST-SSRs, INDELs, etc.) for marker development, anchoring sequences for genome comparisons and putative gene candidates for QTL detection. PMID:22920992

Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies.

PubMed

Parra-González, Lorena B; Aravena-Abarzúa, Gabriela A; Navarro-Navarro, Cristell S; Udall, Joshua; Maughan, Jeff; Peterson, Louis M; Salvo-Garrido, Haroldo E; Maureira-Butler, Iván J

2012-08-24

Yellow lupin (Lupinus luteus L.) is a minor legume crop characterized by its high seed protein content. Although grown in several temperate countries, its orphan condition has limited the generation of genomic tools to aid breeding efforts to improve yield and nutritional quality. In this study, we report the construction of 454-expresed sequence tag (EST) libraries, carried out comparative studies between L. luteus and model legume species, developed a comprehensive set of EST-simple sequence repeat (SSR) markers, and validated their utility on diversity studies and transferability to related species. Two runs of 454 pyrosequencing yielded 205 Mb and 530 Mb of sequence data for L1 (young leaves, buds and flowers) and L2 (immature seeds) EST- libraries. A combined assembly (L1L2) yielded 71,655 contigs with an average contig length of 632 nucleotides. L1L2 contigs were clustered into 55,309 isotigs. 38,200 isotigs translated into proteins and 8,741 of them were full length. Around 57% of L. luteus sequences had significant similarity with at least one sequence of Medicago, Lotus, Arabidopsis, or Glycine, and 40.17% showed positive matches with all of these species. L. luteus isotigs were also screened for the presence of SSR sequences. A total of 2,572 isotigs contained at least one EST-SSR, with a frequency of one SSR per 17.75 kbp. Empirical evaluation of the EST-SSR candidate markers resulted in 222 polymorphic EST-SSRs. Two hundred and fifty four (65.7%) and 113 (30%) SSR primer pairs were able to amplify fragments from L. hispanicus and L. mutabilis DNA, respectively. Fifty polymorphic EST-SSRs were used to genotype a sample of 64 L. luteus accessions. Neighbor-joining distance analysis detected the existence of several clusters among L. luteus accessions, strongly suggesting the existence of population subdivisions. However, no clear clustering patterns followed the accession's origin. L. luteus deep transcriptome sequencing will facilitate the further development of genomic tools and lupin germplasm. Massive sequencing of cDNA libraries will continue to produce raw materials for gene discovery, identification of polymorphisms (SNPs, EST-SSRs, INDELs, etc.) for marker development, anchoring sequences for genome comparisons and putative gene candidates for QTL detection.

Introgression Threatens the Genetic Diversity of Quercus austrocochinchinensis (Fagaceae), an Endangered Oak: A Case Inferred by Molecular Markers

PubMed Central

An, Miao; Deng, Min; Zheng, Si-Si; Jiang, Xiao-Long; Song, Yi-Gang

2017-01-01

Natural introgression can cause negative effects where rare species experience genetic assimilation and invade by their abundant congeners. Quercus austrocochinchinensis and Q. kerrii (subgenus Cyclobalanopsis) are a pair of closely related species in the Indo-China area. Morphological intermediates of the two species have been reported in this region. In this study, we used AFLP, SSR and two key leaf morphological diagnostic traits to study the two Q. austrocochinchinensis populations, two pure Q. kerrii and two putative hybrid populations in China. Rates of individual admixture were examined using the Bayesian clustering programs STRUCTURE and NewHybrids, with no a priori species assignment. In total, we obtained 151 SSR alleles and 781 polymorphic loci of AFLP markers. Population differentiation inferred by SSR and AFLP was incoherent with recognized species boundaries. Bayesian admixture analyses and principal coordinate analysis identified more hybrids and backcrossed individuals than morphological intermediates in the populations. SSR inferred a wide genetic assimilation in Q. austrocochinchinensis, except for subpopulation D2 in the core area of Xi-Shuang-Ban-Na Nature Reserve (XSBN). However, AFLP recognized more Q. austrocochinchinensis purebreds than SSR. Analysis using NewHybrids on AFLP data indicated that these hybridized individuals were few F2 and predominantly backcrosses with both parental species. All these evidences indicate the formation of a hybrid swarm at XSBN where the two species co-exist. Both AFLP and SSR recognized that the core protected area of XSBN (D2) has a high percentage of Q. austrocochinchinensis purebreds and a unique germplasm. The Hainan population and the other subpopulations of XSBN of the species might have lost their genetic integrity. Our results revealed a clear genetic differentiation in the populations and subpopulations of Q. austrocochinchinensis and ongoing introgression between Q. austrocochinchinensis and Q. kerrii at the disturbed contact areas. Combining the results from genetic and morphological analyses, the conservation of subpopulation D2 should be prioritized. Conservation and restoration of the integrity of tropical ravine rainforest is an important long-term goal for the successful conservation of Q. austrocochinchinensis. The fine-scale landscape might play an essential role in shaping the spatial patterns of hybridization. Further studies are needed to evaluate these patterns and dynamics. PMID:28270827

[An evaluation of the economic loss from intestinal helminthiases in the Uzbek SSR].

PubMed

Abdiev, T A; Zubitskaia, M A; Kovalenko, A F; Fuzaĭlov, Iu M; Baratov, R D; Ziganshina, N Kh; Isaeva, Kh B; Borukhov, S M; Priezzhaeva, N G; Musaeva, G A

1990-01-01

Calculations of economic loss costs due to procedures for helminth detection and the out-patient treatment of recognized cases of enterobiasis, hymenolepiasis, taeniasis, ascariasis, trichocephaliasis in the Uzbek SSR in 1985 were made as were the costs of inpatient treatment in the specialized clinics in 1986 with account for the loss due to the related decrease in the national output and payments for disability. Their total turned to be about 1.8 million rubles.

Attitudes of Major Soviet Nationalities. Volume IV. Central Asia. Kazakhstan, Kirgizistan, Turkmenistan, Uzbekistan, Tadzhikistan.

DTIC Science & Technology

1973-06-01

attitudes. IV. Demography Although Uzbekistan is somewhat smaller in area than neighboring Turkmenistan, it has nearly six times the population--close...Uzbekistan - Demography - 2 Table A.2. National Composition of Uzbek SSR 19 26a 19 39b 1959 c 1 970c T number % number % number % number % Total . Uzbek...Mullyadzbanov, Narodo naseleniye Ilzbekskoi SSR (Tashkent, 1967): 177. c Pravda Vostoka (April 28), 1971: 2. 4 Uzbekistan - Demography - 3 the extraordinary

CMD: a Cotton Microsatellite Database resource for Gossypium genomics

PubMed Central

Blenda, Anna; Scheffler, Jodi; Scheffler, Brian; Palmer, Michael; Lacape, Jean-Marc; Yu, John Z; Jesudurai, Christopher; Jung, Sook; Muthukumar, Sriram; Yellambalase, Preetham; Ficklin, Stephen; Staton, Margaret; Eshelman, Robert; Ulloa, Mauricio; Saha, Sukumar; Burr, Ben; Liu, Shaolin; Zhang, Tianzhen; Fang, Deqiu; Pepper, Alan; Kumpatla, Siva; Jacobs, John; Tomkins, Jeff; Cantrell, Roy; Main, Dorrie

2006-01-01

Background The Cotton Microsatellite Database (CMD) is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. Description At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. Conclusion The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp. PMID:16737546

Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

PubMed

Edwards, J D; Baldo, A M; Mueller, L A

2016-01-01

Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

Analytical analyses of startup measurements associated with the first use of LEU fuel in Romania`s 14-MW TRIGA reactor

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

Bretscher, M.M.; Snelgrove, J.L.; Ciocanescu, M.

1992-12-01

The 14-MW TRIGA steady state reactor (SSR) is located in Pitesti, Romania. Beginning with an HEU core (10 wt% U), the reactor first went critical in November 1979 but was shut down ten years later because of insufficient excess reactivity. Last November the Institute for Nuclear Research (INR), which operates the SSR, received from the ANL RERTR program a shipment of 125 LEU pins fabricated by General Atomics and of the same geometry as the original fuel but with an enrichment of 19.7% 235U and a loading of 45 wt% U. Using 100 of these pins, four LEU clusters, eachmore » containing a 5 x 5 square array of fuel rods, were assembled. These four LEU clusters replaced the four most highly burned HEU elements in the SSR. The reactor resumed operations last February with a 35-element mixed HEU/LEU core configuration. In preparation for full power operation of the SSR with this mixed HEU/LEU core, a number of measurements were made. These included control rod calibrations, excess reactivity determinations, worths of experiment facilities, reaction rate distributions, and themocouple measurements of fuel temperatures as a function of reactor power. This paper deals with a comparison of some of these measured reactor parameters with corresponding analytical calculations.« less

Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies.

PubMed

Vidal, Newton Medeiros; Grazziotin, Ana Laura; Ramos, Helaine Christine Cancela; Pereira, Messias Gonzaga; Venancio, Thiago Motta

2014-01-01

Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

Reconstruction of an SSR-based Magnaporthe oryzae physical map to locate avirulence gene AvrPi12.

PubMed

Li, Tonghui; Wen, Jianqiang; Zhang, Yaling; Correll, James; Wang, Ling; Pan, Qinghua

2018-05-31

Pathogen avirulence (Avr) genes can evolve rapidly when challenged by the widespread deployment of host genes for resistance. They can be effectively isolated by positional cloning provided a robust and well-populated genetic map is available. An updated, SSR-based physical map of the rice blast pathogen Magnaporthe oryzae (Mo) has been constructed based on 116 of the 120 SSRs used to assemble the last map, along with 18 newly developed ones. A comparison between the two versions of the map has revealed an altered marker content and order within most of the Mo chromosomes. The avirulence gene AvrPi12 was mapped in a population of 219 progeny derived from a cross between the two Mo isolates CHL42 and CHL357. A bulked segregant analysis indicated that the gene was located on chromosome 6, a conclusion borne out by an analysis of the pattern of segregation shown by individual isolates. Six additional PCR-based markers were developed to improve the map resolution in the key region. AvrPi12 was finally located within the sub-telomeric region of chromosome 6, distal to the SSR locus LSM6-5. The improved SSR-based linkage map should be useful as a platform for gene mapping and isolation in Mo. It was used to establish the location of AvrPi12, thereby providing a starting point for its positional cloning.

Transthoracic ultrasonic tissue indices identify patients with severe left anterior descending artery stenosis. Correlation with fractional flow reserve. Pilot study.

PubMed

Dobrowolski, Piotr; Kowalski, Mirosław; Rybicka, Justyna; Lech, Agnieszka; Tyczyński, Paweł; Witkowski, Adam; Hoffman, Piotr

2016-01-01

The aim of this study was to evaluate the potential clinical application of ultrasonic tissue indices, with a focus on systolic strain (SS) and systolic strain rate (SSR) parameters derived from transthoracic echocardiography, in the assessment of left anterior descending artery (LAD) stenosis. The data of 30 patients with significant LAD stenosis were analysed. All patients underwent transthoracic echocardiography to obtain systolic myocardial velocity (Sm), longitudinal SS, and SSR from basal, mid, and apical segments of anterior and inferior walls in two-chamber apical view. Severity of LAD obstruction was measured by means of fractional flow reserve (FFR) during coronary catheterisation. Systolic velocities, strain, and strain rate measured in basal, middle, and apical segments of the anterior left ventricular (LV) wall were lower when compared to those obtained from the corresponding, i.e. unaffected, inferior LV wall. There was a significant correlation between FFR and the value of SS, SSR characterising the apical LV segment of the anterior wall (r = -0.583, p = 0.01; r = -0.598, p = 0.01, respectively). Moreover, we found significant correlation between FFR and Sm in the mid-segment of the LV anterior wall (r = 0.611, p = 0.009). We conclude that SS and SSR obtained from the apical segment of the anterior LV wall may be related to the severity of LAD stenosis.

Development of Genomic Simple Sequence Repeats (SSR) by Enrichment Libraries in Date Palm.

PubMed

Al-Faifi, Sulieman A; Migdadi, Hussein M; Algamdi, Salem S; Khan, Mohammad Altaf; Al-Obeed, Rashid S; Ammar, Megahed H; Jakse, Jerenj

2017-01-01

Development of highly informative markers such as simple sequence repeats (SSR) for cultivar identification and germplasm characterization and management is essential for date palms genetic studies. The present study documents the development of SSR markers and assesses genetic relationships of commonly grown date palm (Phoenix dactylifera L.) cultivars in different geographical regions of Saudi Arabia. A total of 93 novel simple sequence repeat (SSR) markers were screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs are dinucleotide, 25% trinucleotide, 3% tetranucleotide, and 1% pentanucleotide motives and show 100% polymorphism. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis illustrates that cultivars trend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) reveals genetic variation among and within cultivars of 27% and 73%, respectively, according to the geographical distribution of the cultivars. Developed microsatellite markers are of additional value to date palm characterization, tools which can be used by researchers in population genetics, cultivar identification, as well as genetic resource exploration and management. The cultivars tested exhibited a significant amount of genetic diversity and could be suitable for successful breeding programs. Genomic sequences generated from this study are available at the National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).

Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.)

PubMed Central

Urasaki, Naoya; Goeku, Satoko; Kaneshima, Risa; Takamine, Tomonori; Tarora, Kazuhiko; Takeuchi, Makoto; Moromizato, Chie; Yonamine, Kaname; Hosaka, Fumiko; Terakami, Shingo; Matsumura, Hideo; Yamamoto, Toshiya; Shoda, Moriyuki

2015-01-01

To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a ‘piping-leaf-type’ cultivar, ‘Yugafu’, and a ‘spiny-tip-leaf-type’ variety, ‘Yonekura’. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the ‘spiny-leaf type’ as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding. PMID:26175625

Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.).

PubMed

Urasaki, Naoya; Goeku, Satoko; Kaneshima, Risa; Takamine, Tomonori; Tarora, Kazuhiko; Takeuchi, Makoto; Moromizato, Chie; Yonamine, Kaname; Hosaka, Fumiko; Terakami, Shingo; Matsumura, Hideo; Yamamoto, Toshiya; Shoda, Moriyuki

2015-06-01

To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the 'spiny-leaf type' as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding.

Directional reflectance factors for monitoring spatial changes in soil surface structure and soil organic matter erosion in agricultural systems

NASA Astrophysics Data System (ADS)

Croft, H.; Anderson, K.

2012-04-01

Soils can experience rapid structural degradation in response to land cover changes, resulting in reduced soil productivity, increased erodibility and a loss of soil organic matter (SOM). The breakdown of soil aggregates through slaking and raindrop impact is linked to organic matter turnover, with subsequently eroded material often displaying proportionally more SOM. A reduction in aggregate stability is reflected in a decline in soil surface roughness (SSR), indicating that a soil structural change can be used to highlight soil vulnerability to SOM loss through mineralisation or erosion. Accurate, spatially-continuous measurements of SSR are therefore needed at a variety of spatial and temporal scales to understand the spatial nature of SOM erosion and deposition. Remotely-sensed data can provide a cost-effective means of monitoring changes in soil surface condition over broad spatial extents. Previous work has demonstrated the ability of directional reflectance factors to monitor soil crusting within a controlled laboratory experiment, due to changes in the levels of self-shadowing effects by soil aggregates. However, further research is needed to test this approach in situ, where other soil variables may affect measured reflectance factors and to investigate the use of directional reflectance factors for monitoring soil erosion processes. This experiment assesses the potential of using directional reflectance factors to monitor changes in SSR, aggregate stability and soil organic carbon (SOC) content for two agricultural conditions. Five soil plots representing tilled and seedbed soils were subjected to different durations of natural rainfall, producing a range of different levels of SSR. Directional reflectance factors were measured concomitantly with sampling for soil structural and biochemical tests at each soil plot. Soil samples were taken to measure aggregate stability (wet sieving), SOC (loss on ignition) and soil moisture (gravimetric method). SSM values varied from 8.70 to 20.05% and SOC from 1.33 to 1.05%, across all soil plots. Each plot was characterised using a close-range laser scanning device with a 2 mm sampling interval. The point laser data were geostatistically analysed to provide a spatially-distributed measure of SSR, giving sill variance values from 3.15 to 22.99. Reflectance factors from the soil states were measured using a ground-based hyperspectral spectroradiometer (400-2500 nm) attached to an A-frame device. This method allowed measurement at a range of viewing zenith angles from extreme forwardscatter (-60°) to extreme backscatter (+60°) at a 10° sampling resolution in the solar principal plane. Reflectance measurements were compared to geostatistically-derived indicators of SSR from the laser profile data. Forward-scattered reflectance factors exhibited a very strong relationship to SSR (R2 = 0.84 at -60°; p< 0.05), demonstrating the operational potential of directional reflectance for providing SSR measurements, despite conflicting variation in SSM. SSM also presented an interesting directional signal (R2 = 0.99 at +20°; p< 0.01). Furthermore, the results showed an important link between SRR decline as measured using directional reflectance, with a decline in aggregate stability and SOC content. These findings provide an empirical and theoretical basis for the future retrieval of spatially-continuous assessments of soil surface structure and carbon turnover within a landscape context.

EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

PubMed Central

2010-01-01

Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2. Conclusions The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species. PMID:20712870

Novel SSR Markers from BAC-End Sequences, DArT Arrays and a Comprehensive Genetic Map with 1,291 Marker Loci for Chickpea (Cicer arietinum L.)

PubMed Central

Nayak, Spurthi N.; Varghese, Nicy; Shah, Trushar M.; Penmetsa, R. Varma; Thirunavukkarasu, Nepolean; Gudipati, Srivani; Gaur, Pooran M.; Kulwal, Pawan L.; Upadhyaya, Hari D.; KaviKishor, Polavarapu B.; Winter, Peter; Kahl, Günter; Town, Christopher D.; Kilian, Andrzej; Cook, Douglas R.; Varshney, Rajeev K.

2011-01-01

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes. PMID:22102885

IL-11, IL-1α, IL-6, and TNF-α are induced by solar radiation in vitro and may be involved in facial subcutaneous fat loss in vivo.

PubMed

Li, Wen-Hwa; Pappas, Apostolos; Zhang, Li; Ruvolo, Eduardo; Cavender, Druie

2013-07-01

The loss of subcutaneous (sc) fat is associated with aging. Inflammatory cytokines, such as interleukin-1 α (IL-1α), interleukin-11 (IL-11) and tumor necrosis factor-α (TNF-α), are known to inhibit the differentiation of preadipocytes. This study investigated the potential role of inflammatory cytokines in solar-radiation-induced facial fat loss. Cultured fibroblasts, keratinocytes, and skin equivalents were exposed to various doses of radiation from a solar simulator. Inflammatory cytokines' mRNA production and protein secretion were examined by qRT-PCR and ELISA, respectively. In some experiments, epidermal-dermal equivalents were pretreated topically with a broad-spectrum sunscreen prior to solar simulated radiation (SSR). Human facial preadipocytes treated with recombinant IL-11 or with conditioned media from solar-irradiated equivalents were evaluated for the level of adipocyte differentiation by image analyses, Oil red O staining, and the expression of adipocyte differentiation markers. IL-11, IL-1α, IL-6, and TNF-α protein secretion were induced from epidermal-dermal equivalents by exposure to SSR. A sunscreen prevented SSR-induced inflammatory cytokines production from such equivalents. Exposure of facial preadipocytes to conditioned medium from solar-irradiated epidermal-dermal equivalents inhibited their differentiation into mature adipocytes. Consequently, conditioned medium from sunscreen-pretreated, solar-irradiated equivalents did not inhibit differentiation of preadipocytes. A cocktail of neutralizing antibodies to IL-11, IL-1α, IL-6 and TNF-α significantly reduced the SSR-induced inhibition of preadipocyte differentiation. These results support the hypothesis that SSR-induced inflammatory cytokine may be involved in the photoaging-induced loss of facial subcutaneous fat. Inhibition of this process, e.g. by sunscreens, might slow or prevent photoaging-induced changes in facial contouring. Copyright © 2013 Japanese Society for Investigative Dermatology. Published by Elsevier Ireland Ltd. All rights reserved.

Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)

PubMed Central

Biswas, Manosh Kumar; Xu, Qiang; Mayer, Christoph; Deng, Xiuxin

2014-01-01

Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community. PMID:25148383

Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis).

PubMed

Biswas, Manosh Kumar; Xu, Qiang; Mayer, Christoph; Deng, Xiuxin

2014-01-01

Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.

Generation of human auditory steady-state responses (SSRs). II: Addition of responses to individual stimuli.

PubMed

Santarelli, R; Maurizi, M; Conti, G; Ottaviani, F; Paludetti, G; Pettorossi, V E

1995-03-01

In order to investigate the generation of the 40 Hz steady-state response (SSR), auditory potentials evoked by clicks were recorded in 16 healthy subjects in two stimulating conditions. Firstly, repetition rates of 7.9 and 40 Hz were used to obtain individual middle latency responses (MLRs) and 40 Hz-SSRs, respectively. In the second condition, eight click trains were presented at a 40 Hz repetition rate and an inter-train interval of 126 ms. We extracted from the whole train response: (1) the response-segment taking place after the last click of the train (last click response, LCR), (2) a modified LCR (mLCR) obtained by clearing the LCR from the amplitude enhancement due to the overlapping of the responses to the clicks preceding the last within the stimulus train. In comparison to MLRs, the most relevant feature of the evoked activity following the last click of the train (LCRs, mLCRs) was the appearance in the 50-110 ms latency range of one (in 11 subjects) or two (in 2 subjects) additional positive-negative deflections having the same periodicity as that of MLR waves. The grand average (GA) of the 40 Hz-SSRs was compared with three predictions synthesized by superimposing: (1) the GA of MLRs, (2) the GA of LCRs, (3) the GA of mLCRs. Both the MLR and mLCR predictions reproduced the recorded signal in amplitude while the LCR prediction amplitude resulted almost twice that of the 40 Hz-SSR. With regard to the phase, the MLR, LCR and mLCR closely predicted the recorded signal. Our findings confirm the effectiveness of the linear addition mechanism in the generation of the 40 Hz-SSR. However the responses to individual stimuli within the 40 Hz-SSR differ from MLRs because of additional periodic activity. These results suggest that phenomena related to the resonant frequency of the activated system may play a role in the mechanisms which interact to generate the 40 Hz-SSR.

Evaluating the Influence of the Microsatellite Marker Set on the Genetic Structure Inferred in Pyrus communis L.

PubMed Central

Urrestarazu, Jorge; Royo, José B.; Santesteban, Luis G.; Miranda, Carlos

2015-01-01

Fingerprinting information can be used to elucidate in a robust manner the genetic structure of germplasm collections, allowing a more rational and fine assessment of genetic resources. Bayesian model-based approaches are nowadays majorly preferred to infer genetic structure, but it is still largely unresolved how marker sets should be built in order to obtain a robust inference. The objective was to evaluate, in Pyrus germplasm collections, the influence of the SSR marker set size on the genetic structure inferred, also evaluating the influence of the criterion used to select those markers. Inferences were performed considering an increasing number of SSR markers that ranged from just two up to 25, incorporated one at a time into the analysis. The influence of the number of SSR markers used was evaluated comparing the number of populations and the strength of the signal detected, and also the similarity of the genotype assignments to populations between analyses. In order to test if those results were influenced by the criterion used to select the SSRs, several choosing scenarios based on the discrimination power or the fixation index values of the SSRs were tested. Our results indicate that population structure could be inferred accurately once a certain SSR number threshold was reached, which depended on the underlying structure within the genotypes, but the method used to select the markers included on each set appeared not to be very relevant. The minimum number of SSRs required to provide robust structure inferences and adequate measurements of the differentiation, even when low differentiation levels exist within populations, was proved similar to that of the complete list of recommended markers for fingerprinting. When a SSR set size similar to the minimum marker sets recommended for fingerprinting it is used, only major divisions or moderate (F ST>0.05) differentiation of the germplasm are detected. PMID:26382618

A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts

PubMed Central

Shirasawa, Kenta; Hand, Melanie L.; Henderson, Steven T.; Okada, Takashi; Johnson, Susan D.; Taylor, Jennifer M.; Spriggs, Andrew; Siddons, Hayley; Hirakawa, Hideki; Isobe, Sachiko; Tabata, Satoshi; Koltunow, Anna M. G.

2015-01-01

Background and Aims Apomixis in plants generates clonal progeny with a maternal genotype through asexual seed formation. Hieracium subgenus Pilosella (Asteraceae) contains polyploid, highly heterozygous apomictic and sexual species. Within apomictic Hieracium, dominant genetic loci independently regulate the qualitative developmental components of apomixis. In H. praealtum, LOSS OF APOMEIOSIS (LOA) enables formation of embryo sacs without meiosis and LOSS OF PARTHENOGENESIS (LOP) enables fertilization-independent seed formation. A locus required for fertilization-independent endosperm formation (AutE) has been identified in H. piloselloides. Additional quantitative loci appear to influence the penetrance of the qualitative loci, although the controlling genes remain unknown. This study aimed to develop the first genetic linkage maps for sexual and apomictic Hieracium species using simple sequence repeat (SSR) markers derived from expressed transcripts within the developing ovaries. Methods RNA from microdissected Hieracium ovule cell types and ovaries was sequenced and SSRs were identified. Two different F1 mapping populations were created to overcome difficulties associated with genome complexity and asexual reproduction. SSR markers were analysed within each mapping population to generate draft linkage maps for apomictic and sexual Hieracium species. Key Results A collection of 14 684 Hieracium expressed SSR markers were developed and linkage maps were constructed for Hieracium species using a subset of the SSR markers. Both the LOA and LOP loci were successfully assigned to linkage groups; however, AutE could not be mapped using the current populations. Comparisons with lettuce (Lactuca sativa) revealed partial macrosynteny between the two Asteraceae species. Conclusions A collection of SSR markers and draft linkage maps were developed for two apomictic and one sexual Hieracium species. These maps will support cloning of controlling genes at LOA and LOP loci in Hieracium and should also assist with identification of quantitative loci that affect the expressivity of apomixis. Future work will focus on mapping AutE using alternative populations. PMID:25538115

A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera.

PubMed

Cheng, Yunjiang; de Vicente, M Carmen; Meng, Haijun; Guo, Wenwu; Tao, Nengguo; Deng, Xiuxin

2005-06-01

Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and used to analyze chloroplast diversity of Citrus and closely related genera. Fourteen cpSSR primer pairs from the chloroplast genomes of tobacco (Nicotiana tabacum L.) and Arabidopsis were found useful for analyzing the Citrus chloroplast genome (cpDNA) and recoded with the prefix SPCC (SSR Primers for Citrus Chloroplast). Eleven of the 14 primer pairs revealed some degree of polymorphism among 34 genotypes of Citrus, Fortunella, Poncirus and some of their hybrids, with polymorphism information content (PIC) values ranging from 0.057 to 0.732, and 18 haplotypes were identified. The cpSSR data were analyzed with NTSYS-pc software, and the genetic relationships suggested by the unweighted pair group method based on arithmetic means (UPGMA) dendrogram were congruent with previous taxonomic investigations: the results showed that all samples fell into seven major clusters, i.e., Citrus medica L., Poncirus, Fortunella, C. ichangensis Blanco, C. reticulata Swingle, C. aurantifolia (Christm.) Swingle and C. grandis (L.) Osbeck. The results of previous studies combined with our cpSSR analyses revealed that: (1) Calamondin (C. madurensis Swingle) is the result of hybridization between kumquat (Fortunella) and mandarin (C. reticulata), where kumquat acted as the female parent; (2) Ichang papeda (C. ichangensis) has a unique taxonomic status; and (3) although Bendiguangju mandarin (C. reticulata) and Satsuma mandarin (C. reticulata) are similar in fruit shape and leaf morphology, they have different maternal parents. Bendiguangju mandarin has the same cytoplasm as sweet orange (C. sinensis), whereas Satsuma mandarin has the cytoplasm of C. reticulata. Seventeen PCR products from SPCC1 and 21 from SPCC11 were cloned and sequenced. The results revealed that mononucleotide repeats as well as insertions and deletions of small segments of DNA were associated with SPCC1 polymorphism, whereas polymorphism generated by SPCC11 was essentially due to the variation in length of the mononucleotide repeats.

Spontaneous splenic rupture in infectious mononucleosis: conservative management with gradual percutaneous drainage of a subcapsular hematoma.

PubMed

Schwarz, M; Zaidenstein, L; Freud, E; Neuman, M; Ziv, N; Kornreich, L; Zer, M

1999-01-01

Spontaneous splenic rupture (SSR) is a rare but potentially lethal complication of infectious mononucleosis (IM). Because the inflamed spleen is usually enlarged, congested, and friable, emergency splenectomy is recommended. We describe the conservative management of a SSR in a 16-year-old boy with IM. A pigtail catheter was inserted under ultrasonographic guidance and left in place for 36 h. This allowed the successful evacuation of the hematoma without compromising the splenic parenchyma.

Highly-dispersive electromagnetic induced transparency in planar symmetric metamaterials.

PubMed

Lu, Xiqun; Shi, Jinhui; Liu, Ran; Guan, Chunying

2012-07-30

We propose, design and experimentally demonstrate highly-dispersive electromagnetically induced transparency (EIT) in planar symmetric metamaterials actively switched and controlled by angles of incidence. Full-wave simulation and measurement results show EIT phenomena, trapped-mode excitations and the associated local field enhancement of two symmetric metamaterials consisting of symmetrically split rings (SSR) and a fishscale (FS) metamaterial pattern, respectively, strongly depend on angles of incidence. The FS metamaterial shows much broader spectral splitting than the SSR metamaterial due to the surface current distribution variation.

Two viral strains and a possible novel recombinant are responsible for the explosive injecting drug use-associated HIV type 1 epidemic in Estonia.

PubMed

Zetterberg, Veera; Ustina, Valentina; Liitsola, Kirsi; Zilmer, Kai; Kalikova, Nelli; Sevastianova, Ksenia; Brummer-Korvenkontio, Henrikki; Leinikki, Pauli; Salminen, Mika O

2004-11-01

HIV-1 infection has been rare in Estonia. In 2000, an explosive epidemic among injecting drug users was detected in the Eastern border region, resulting in 3603 newly reported cases by the end of 2003. The molecular epidemiology of the outbreak was studied to establish whether the Estonian epidemic is linked to the epidemics in Eastern Europe. Over 200 newly infected individuals were prospectively sampled from June 2000 to March 2002 in a geographically representative way, with known dates of diagnosis and information of probable route of transmission. Viral regions coding for two viral gene regions were directly sequenced from plasma viral RNA and phylogenetically analyzed. In addition, a larger region coding for the entire env gene was sequenced from one sample and studied for indications of possible recombinant structure. The Estonian HIV outbreak was found to be caused by simultaneous introduction of two strains: a minor subtype A strain very similar to the Eastern European subtype A strain (approximately 8% of cases), and a second major strain (77%) found to be most closely related to the CRF06-cpx strain, previously described only from African countries. The variability in the two clusters was very low, suggesting point source introductions. Ten percent of cases seemed to be newly generated recombinants of the A and CRF06-cpx strains. Analysis of viral diversification over time revealed a rate of change within the V3 region of 0.83%/year for the CRF06-cpx strain, consistent with findings from other subtypes. Due to the relatively frequently found novel recombinant forms, the Estonian HIV-1 epidemic may allow studies of coinfection and intersubtype recombination in detail.

Problematic Smartphone Use, Deep and Surface Approaches to Learning, and Social Media Use in Lectures.

PubMed

Rozgonjuk, Dmitri; Saal, Kristiina; Täht, Karin

2018-01-08

Several studies have shown that problematic smartphone use (PSU) is related to detrimental outcomes, such as worse psychological well-being, higher cognitive distraction, and poorer academic outcomes. In addition, many studies have shown that PSU is strongly related to social media use. Despite this, the relationships between PSU, as well as the frequency of social media use in lectures, and different approaches to learning have not been previously studied. In our study, we hypothesized that both PSU and the frequency of social media use in lectures are negatively correlated with a deep approach to learning (defined as learning for understanding) and positively correlated with a surface approach to learning (defined as superficial learning). The study participants were 415 Estonian university students aged 19-46 years (78.8% females; age M = 23.37, SD = 4.19); the effective sample comprised 405 participants aged 19-46 years (79.0% females; age M = 23.33, SD = 4.21). In addition to basic socio-demographics, participants were asked about the frequency of their social media use in lectures, and they filled out the Estonian Smartphone Addiction Proneness Scale and the Estonian Revised Study Process Questionnaire. Bivariate correlation analysis showed that PSU and the frequency of social media use in lectures were negatively correlated with a deep approach to learning and positively correlated with a surface approach to learning. Mediation analysis showed that social media use in lectures completely mediates the relationship between PSU and approaches to learning. These results indicate that the frequency of social media use in lectures might explain the relationships between poorer academic outcomes and PSU.

Mortality and causes of death after traumatic spinal cord injury in Estonia

PubMed Central

Sabre, Liis; Rekand, Tiina; Asser, Toomas; Kõrv, Janika

2013-01-01

Study design Retrospective population-based study with mortality follow-up. Objective To study mortality, causes and risk factors for death in Estonian patients with traumatic spinal cord injury (TSCI). Setting All Estonian hospitals. Methods Medical records of patients with TSCI from all regional, central, general, and rehabilitation hospitals in Estonia from 1997 to 2007, were retrospectively reviewed. Mortality status was ascertained as of 31 December 2011. Causes of death were collected from the Estonian Causes of Death Registry. Standardized mortality ratios (SMRs) were calculated for the entire sample and for causes of death. A Cox proportional hazards modeling was used to identify the risk indicators for death. Results During the observation period (1997–2011) 162 patients of 595 died. Nearly half of the patients (n = 76) died during the first year after TSCI. The main causes of death were external causes (30%), cardiovascular disease (29%). and suicide (8%). The overall SMR was 2.81 (95% confidence interval 2.40–3.28) and SMR was higher for women than for men (3.80 vs. 2.70). Cause-specific SMRs were markedly elevated for sepsis and suicide. Mortality was significantly affected by the age at the time of injury, neurological level, and extent of the injury as well as the year of TSCI and complications. Conclusion Life expectancy is significantly decreased in patients with TSCI in Estonia compared with the general population. Deaths during the first year after the injury have an important impact on statistics. Treatment of cardiovascular diseases, infections, and prevention of suicide are useful for reducing mortality in patients with TSCI. PMID:24090049

Diversity in mental fatigue and social profile of patients with myasthenia gravis in two different Northern European countries.

PubMed

Sabre, Liis; Westerberg, Elisabet; Liik, Maarika; Punga, Anna R

2017-04-01

Self-estimated health can be used for comparison of different diseases between countries. It is important to elaborate on whether disparities in self-estimated health are due to disease-specific parameters or socioeconomic differences. In this study, we aimed at evaluating clinical and social similarities and differences in myasthenia gravis (MG) patients between comparable regions in two Baltic Sea countries, Estonia and Sweden. This cross-sectional study included southern counties in Sweden and Estonia of comparable size. All patients with a confirmed MG diagnosis were asked to answer two questionnaires including demographic and disease-specific data, lifestyle issues, and mental fatigue (Fatigue Severity Scale [FSS]). Clinical fatigue was assessed objectively through the Quantitative Myasthenia Gravis Score (QMG). Thirty-six of 92 identified patients in Estonia and 40 of 70 identified MG patients in Sweden chose to participate in the study. The demographic characteristics and symptoms reported by the patients were similar. QMG score did not differ; however, the Estonian patients scored their current subjective disease severity significantly higher (5.6 ± 2.8) compared to the Swedish patients (3.4 ± 2.3, p  = .0005). Estonian patients also had significantly higher FSS scores (5.0 ± 1.7) than Swedish patients (3.5 ± 1.6; p  = .001). Swedish patients were more active and performed physical activity more regularly (29.1% in Estonia and 74.2% in Sweden, p  = .004). Although, the patients had comparable clinical fatigue, Estonian patients evaluated their health state as being more severe and reported more mental fatigue than Swedish patients. These data indicate large regional differences in disease perception of MG, which is important to consider in international studies.

Problematic Smartphone Use, Deep and Surface Approaches to Learning, and Social Media Use in Lectures †

PubMed Central

Rozgonjuk, Dmitri; Saal, Kristiina

2018-01-01

Several studies have shown that problematic smartphone use (PSU) is related to detrimental outcomes, such as worse psychological well-being, higher cognitive distraction, and poorer academic outcomes. In addition, many studies have shown that PSU is strongly related to social media use. Despite this, the relationships between PSU, as well as the frequency of social media use in lectures, and different approaches to learning have not been previously studied. In our study, we hypothesized that both PSU and the frequency of social media use in lectures are negatively correlated with a deep approach to learning (defined as learning for understanding) and positively correlated with a surface approach to learning (defined as superficial learning). The study participants were 415 Estonian university students aged 19–46 years (78.8% females; age M = 23.37, SD = 4.19); the effective sample comprised 405 participants aged 19–46 years (79.0% females; age M = 23.33, SD = 4.21). In addition to basic socio-demographics, participants were asked about the frequency of their social media use in lectures, and they filled out the Estonian Smartphone Addiction Proneness Scale and the Estonian Revised Study Process Questionnaire. Bivariate correlation analysis showed that PSU and the frequency of social media use in lectures were negatively correlated with a deep approach to learning and positively correlated with a surface approach to learning. Mediation analysis showed that social media use in lectures completely mediates the relationship between PSU and approaches to learning. These results indicate that the frequency of social media use in lectures might explain the relationships between poorer academic outcomes and PSU. PMID:29316697

A survey of parentally reported sleep health disorders in Estonian 8-9 year old children.

PubMed

Vaher, Heisl; Kasenõmm, Priit; Vasar, Veiko; Veldi, Marlit

2013-12-04

Pediatric sleep research is rather new in Estonia. There has not been a comprehensive study of age specific sleep disorders in Estonian children. The aim of this study was to investigate sleep disorders in a sample of Estonian second grade children.We hypothesized that:: Children with low BMI are as susceptible to SDB as are children with high BMI. Under weight children are susceptible to residual SDB after adenotonsillectomy. Parasomnias present with SDB in children.• Excessive day time sleepiness is a significant symptom which leads parents to suspect sleep disorders in their child. A retrospective questionnaire based survey was used to analyze factors influencing sleep, parasomnias, daytime sleepiness, and sleep disordered breathing (SDB). 1065 Pediatric Sleep Questionnaire (PSQ) packets were distributed by post to randomly selected parents of second grade students; 703 (66%) subjects were included in the study group; each parent/guardian participant had one second grade child. Descriptive statistics were used to compare characteristics of SDB symptomatic and healthy children. We used logistic regression to analyze factors influencing sleep and parasomnias in relation to SDB severity. Odds ratios (OR) and 95% CI were used to estimate relative risk. Parents of children with SDB complaints seem to pay attention to sleep disorders especially when a child is suffering from excessive day time sleepiness. Parasomnias are present simultaneously with SDB and tend to worsen in relation to more severe SDB complaints. Many underweight children have SDB symptoms after adenotonsillectomy. SDB symptoms are found in both overweight and underweight children. Both groups should be observed, especially in terms of the current focus on overweight children. Careful follow up after SDB treatment is necessary in case of under and overweight children. Parental suspicions regarding SDB are noticeably higher in cases of excessive daytime sleepiness in their children.

Individual and work-related risk factors for musculoskeletal pain: a cross-sectional study among Estonian computer users.

PubMed

Oha, Kristel; Animägi, Liina; Pääsuke, Mati; Coggon, David; Merisalu, Eda

2014-05-28

Occupational use of computers has increased rapidly over recent decades, and has been linked with various musculoskeletal disorders, which are now the most commonly diagnosed occupational diseases in Estonia. The aim of this study was to assess the prevalence of musculoskeletal pain (MSP) by anatomical region during the past 12 months and to investigate its association with personal characteristics and work-related risk factors among Estonian office workers using computers. In a cross-sectional survey, the questionnaires were sent to the 415 computer users. Data were collected by self-administered questionnaire from 202 computer users at two universities in Estonia. The questionnaire asked about MSP at different anatomical sites, and potential individual and work related risk factors. Associations with risk factors were assessed by logistic regression. Most respondents (77%) reported MSP in at least one anatomical region during the past 12 months. Most prevalent was pain in the neck (51%), followed by low back pain (42%), wrist/hand pain (35%) and shoulder pain (30%). Older age, right-handedness, not currently smoking, emotional exhaustion, belief that musculoskeletal problems are commonly caused by work, and low job security were the statistically significant risk factors for MSP in different anatomical sites. A high prevalence of MSP in the neck, low back, wrist/arm and shoulder was observed among Estonian computer users. Psychosocial risk factors were broadly consistent with those reported from elsewhere. While computer users should be aware of ergonomic techniques that can make their work easier and more comfortable, presenting computer use as a serious health hazard may modify health beliefs in a way that is unhelpful.

Occlusal traits and orthodontic treatment need in 7‐ to 10‐year‐olds in Estonia

PubMed Central

Saag, Mare; Svedström‐Oristo, Anna‐Liisa; Peltomäki, Timo; Vinkka‐Puhakka, Heli

2017-01-01

Abstract The aim of this study was to evaluate the distribution of occlusal traits and orthodontic treatment need and complexity in Estonian 7‐ to 10‐year‐old children. This data provides solid information for planning of orthodontic care. Data of 392 Estonian children (198 girls and 194 boys, mean age 9.0 years, range 7.1–10.4 years) was analysed in this cross‐sectional study. Assessed traits included first molar and canine sagittal relationship, overjet, overbite, crowding, midline diastema, crossbite, and scissor bite. Orthodontic treatment need and complexity were assessed using the Index of Complexity, Outcome, and Need. Parents' opinion regarding their child's teeth was determined using a questionnaire. The most prevalent occlusal traits were canine class I sagittal relationship (73.7%), midline diastema (73.0%), molar class I sagittal relationship (57.4%), and overbite ≥3.5 mm (51.8%). According to the Index of Complexity, Outcome, and Need, 64.3% of Estonian elementary school children were in need of orthodontic treatment. Treatment complexity was simple in 12.5%, mild in 38.8%, moderate in 22.7%, difficult in 14.0%, and very difficult in 12.0% of the children. Approximately 66.4% of the parents felt that their child needed orthodontic treatment. This study confirms earlier findings indicating that the most frequent sagittal relationship is class I in the first molars and class I in the canines. However, the sagittal relationship was asymmetric in more than half of the children. Correlation between objectively defined treatment need and parents' desire for treatment was high in Estonia. PMID:29744185

Effect of magnetic coupling on non-radiative relaxation time of Fe3+ sites on LaAl1-xFexO3 pigments

NASA Astrophysics Data System (ADS)

Novatski, A.; Somer, A.; Maranha, F. G.; de Souza, E. C. F.; Andrade, A. V. C.; Antunes, S. R. M.; Borges, C. P. F.; Dias, D. T.; Medina, A. N.; Astrath, N. G. C.

2018-02-01

Inorganic pigments of the system LaAl1-xFexO3 were prepared by the Pechini and the Solid State Reaction (SSR) methods. Magnetic interactions and non-radiative relaxation time were analyzed by means of phase-resolved photoacoustic spectroscopy and electron paramagnetic resonance (EPR) techniques. EPR results show a change in the magnetic behavior from paramagnetic (x = 0.2 and 0.4) to antiferromagnetic (x = 1.0), which is believed to be a result of the SSR preparation method. Trends in the optical absorption bands of the Fe3+ are attributed to their electronic transitions, and the increase in the band's intensity at 480 and 550 nm was assigned to the increase in the magnetic coupling between Fe-Fe. The phase-resolved method is capable of distinguishing between the two preparation methods, and it is possible to infer that SSR modifies the magnetic coupling of Fe-Fe with x.

Genetic Confirmation of Mungbean (Vigna radiata) and Mashbean (Vigna mungo) Interspecific Recombinants using Molecular Markers.

PubMed

Abbas, Ghulam; Hameed, Amjad; Rizwan, Muhammad; Ahsan, Muhammad; Asghar, Muhammad J; Iqbal, Nayyer

2015-01-01

Molecular confirmation of interspecific recombinants is essential to overcome the issues like self-pollination, environmental influence, and inadequacy of morphological characteristics during interspecific hybridization. The present study was conducted for genetic confirmation of mungbean (female) and mashbean (male) interspecific crosses using molecular markers. Initially, polymorphic random amplified polymorphic DNA (RAPD), universal rice primers (URP), and simple sequence repeats (SSR) markers differentiating parent genotypes were identified. Recombination in hybrids was confirmed using these polymorphic DNA markers. The NM 2006 × Mash 88 was most successful interspecific cross. Most of true recombinants confirmed by molecular markers were from this cross combination. SSR markers were efficient in detecting genetic variability and recombination with reference to specific chromosomes and particular loci. SSR (RIS) and RAPD identified variability dispersed throughout the genome. In conclusion, DNA based marker assisted selection (MAS) efficiently confirmed the interspecific recombinants. The results provided evidence that MAS can enhance the authenticity of selection in mungbean improvement program.

Microstructure and tuber properties of potato varieties with different genetic profiles.

PubMed

Romano, Annalisa; Masi, Paolo; Aversano, Riccardo; Carucci, Francesca; Palomba, Sara; Carputo, Domenico

2018-01-15

The objectives of this research were to study tuber starch characteristics and chemical - thermal properties of 21 potato varieties, and to determine their genetic diversity through SSR markers. Starch granular size varied among samples, with a wide diameter distribution (5-85μm), while granule shapes were similar. Differential Scanning Calorimeter analysis showed that the transition temperatures (69°C-74°C) and enthalpies of gelatinization (0.9J/g-3.8J/g) of tubers were also variety dependent. SSR analysis allowed the detection of 157 alleles across all varieties, with an average value of 6.8 alleles per locus. Variety-specific alleles were also identified. SSR-based cluster analysis revealed that varieties with interesting quality attributes were distributed among all clusters and sub-clusters, suggesting that the genetic basis of traits analyzed may differ among our varieties. The information obtained in this study may be useful to identify and develop varieties with slowly digestible starch. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sequential Service Restoration for Unbalanced Distribution Systems and Microgrids

DOE PAGES

Chen, Bo; Chen, Chen; Wang, Jianhui; ...

2017-07-07

The resilience and reliability of modern power systems are threatened by increasingly severe weather events and cyber-physical security events. An effective restoration methodology is desired to optimally integrate emerging smart grid technologies and pave the way for developing self-healing smart grids. In this paper, a sequential service restoration (SSR) framework is proposed to generate restoration solutions for distribution systems and microgrids in the event of large-scale power outages. The restoration solution contains a sequence of control actions that properly coordinate switches, distributed generators, and switchable loads to form multiple isolated microgrids. The SSR can be applied for three-phase unbalanced distributionmore » systems and microgrids and can adapt to various operation conditions. Mathematical models are introduced for three-phase unbalanced power flow, voltage regulators, transformers, and loads. Furthermore, the SSR problem is formulated as a mixed-integer linear programming model, and its effectiveness is evaluated via the modified IEEE 123 node test feeder.« less

Sequential Service Restoration for Unbalanced Distribution Systems and Microgrids

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

Chen, Bo; Chen, Chen; Wang, Jianhui

The resilience and reliability of modern power systems are threatened by increasingly severe weather events and cyber-physical security events. An effective restoration methodology is desired to optimally integrate emerging smart grid technologies and pave the way for developing self-healing smart grids. In this paper, a sequential service restoration (SSR) framework is proposed to generate restoration solutions for distribution systems and microgrids in the event of large-scale power outages. The restoration solution contains a sequence of control actions that properly coordinate switches, distributed generators, and switchable loads to form multiple isolated microgrids. The SSR can be applied for three-phase unbalanced distributionmore » systems and microgrids and can adapt to various operation conditions. Mathematical models are introduced for three-phase unbalanced power flow, voltage regulators, transformers, and loads. Furthermore, the SSR problem is formulated as a mixed-integer linear programming model, and its effectiveness is evaluated via the modified IEEE 123 node test feeder.« less

Neurophysiological and clinical effects of dry needling in patients with upper trapezius myofascial trigger points.

PubMed

Abbaszadeh-Amirdehi, Maryam; Ansari, Noureddin Nakhostin; Naghdi, Soofia; Olyaei, Gholamreza; Nourbakhsh, Mohammad Reza

2017-01-01

Dry needling (DN) is a widely used in treatment of myofascial trigger points (MTrPs). The purpose of this pretest-posttest clinical trial was to investigate the neurophysiological and clinical effects of DN in patients with MTrPs. A sample of 20 patients (3 man, 17 women; mean age 31.7 ± 10.8) with upper trapezius MTrPs received one session of deep DN. The outcomes of neuromuscular junction response (NMJR), sympathetic skin response (SSR), pain intensity (PI) and pressure pain threshold (PPT) were measured at baseline and immediately after DN. There were significant improvements in SSR latency and amplitude, pain, and PPT after DN. The NMJR decreased and returned to normal after DN. A single session of DN to the active upper trapezius MTrP was effective in improving pain, PPT, NMJR, and SSR in patients with myofascial trigger points. Further studies are needed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development and Characterization of Microsatellite Markers for the Cape Gooseberry Physalis peruviana

PubMed Central

Simbaqueba, Jaime; Sánchez, Pilar; Sanchez, Erika; Núñez Zarantes, Victor Manuel; Chacon, Maria Isabel; Barrero, Luz Stella; Mariño-Ramírez, Leonardo

2011-01-01

Physalis peruviana, commonly known as Cape gooseberry, is an Andean Solanaceae fruit with high nutritional value and interesting medicinal properties. In the present study we report the development and characterization of microsatellite loci from a P. peruviana commercial Colombian genotype. We identified 932 imperfect and 201 perfect Simple Sequence Repeats (SSR) loci in untranslated regions (UTRs) and 304 imperfect and 83 perfect SSR loci in coding regions from the assembled Physalis peruviana leaf transcriptome. The UTR SSR loci were used for the development of 162 primers for amplification. The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana. We obtained an amplification rate of 83% and a polymorphic rate of 22%. Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species. PMID:22039540

POLYMORPHIC CHLOROPLAST MICROSATELLITE MARKERS IN THE OCTOPLOID LEPIDIUM MEYENII (BRASSICACEAE) AND CROSS-SPECIES AMPLIFICATION IN LEPIDIUM

PubMed Central

Hasan, Nabeeh A.; Mummenhoff, Klaus; Quiros, Carlos F.; Tay, C. David; Bailey, C. Donovan

2013-01-01

Premise of the study As a crop and medicinal plant, the octoploid Andean endemic Lepidium meyenii suffers from taxonomic uncertainty. Few molecular markers are available to genotype individuals or track gene flow in wild and cultivated material. Methods and Results Using available sequence data, eight cpSSR primer pairs were developed for L. meyenii. Levels of polymorphism checked in 56 individual L. meyenii, including cultivated and wild material, revealed that the number of alleles per locus ranged from three to five, and intrapopulation allele frequencies ranged from 0.071 to 1.0. Polymerase-chain-reaction screens using our cpSSR primers in 27 other Lepidium species and three Coronopus species suggested a high degree of interspecific amplification. Conclusions These polymorphic cpSSR markers should prove useful in characterizing genetic variation among cultivated and wild L. meyenii. Additionally, interspecific amplifications suggest that these markers will be useful for the study of related taxa. PMID:21616787

Characterization and Amplification of Gene-Based Simple Sequence Repeat (SSR) Markers in Date Palm.

PubMed

Zhao, Yongli; Keremane, Manjunath; Prakash, Channapatna S; He, Guohao

2017-01-01

The paucity of molecular markers limits the application of genetic and genomic research in date palm (Phoenix dactylifera L.). Availability of expressed sequence tag (EST) sequences in date palm may provide a good resource for developing gene-based markers. This study characterizes a substantial fraction of transcriptome sequences containing simple sequence repeats (SSRs) from the EST sequences in date palm. The EST sequences studied are mainly homologous to those of Elaeis guineensis and Musa acuminata. A total of 911 gene-based SSR markers, characterized with functional annotations, have provided a useful basis not only for discovering candidate genes and understanding genetic basis of traits of interest but also for developing genetic and genomic tools for molecular research in date palm, such as diversity study, quantitative trait locus (QTL) mapping, and molecular breeding. The procedures of DNA extraction, polymerase chain reaction (PCR) amplification of these gene-based SSR markers, and gel electrophoresis of PCR products are described in this chapter.

Development and characterization of microsatellite markers for the Cape gooseberry Physalis peruviana.

PubMed

Simbaqueba, Jaime; Sánchez, Pilar; Sanchez, Erika; Núñez Zarantes, Victor Manuel; Chacon, Maria Isabel; Barrero, Luz Stella; Mariño-Ramírez, Leonardo

2011-01-01

Physalis peruviana, commonly known as Cape gooseberry, is an Andean Solanaceae fruit with high nutritional value and interesting medicinal properties. In the present study we report the development and characterization of microsatellite loci from a P. peruviana commercial Colombian genotype. We identified 932 imperfect and 201 perfect Simple Sequence Repeats (SSR) loci in untranslated regions (UTRs) and 304 imperfect and 83 perfect SSR loci in coding regions from the assembled Physalis peruviana leaf transcriptome. The UTR SSR loci were used for the development of 162 primers for amplification. The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana. We obtained an amplification rate of 83% and a polymorphic rate of 22%. Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species.

Gender differences in factors associated with sexual intercourse among Estonian adolescents.

PubMed

Part, Kai; Rahu, Kaja; Rahu, Mati; Karro, Helle

2011-06-01

To examine factors associated with early sexual intercourse among 15 to 16-year-old adolescents by gender. The data were collected from a random sample of Estonian basic schools' ninth grade pupils in 1999 using self-completed questionnaires. A multivariate logistic regression analysis for boys and girls was used to test for associations between sexual intercourse, and personal gender role-related attitudes, attitudes towards sexual intercourse, pubertal timing, smoking status and experience of drunkenness. Of the respondents, 14.6% of boys and 13.1% of girls had experienced sexual intercourse. Traditional gender role-related attitudes were associated with sexual intercourse among girls, but not among boys. Smoking and experience of drunkenness was strongly associated with sexual intercourse for both genders. Gender differences in the association between gender role-related attitudes and early sexual intercourse were observed among 15 to 16-year-olds in Estonia. Smoking and experience of drunkenness were strongly related to sexual intercourse for both genders.

MixFit: Methodology for Computing Ancestry-Related Genetic Scores at the Individual Level and Its Application to the Estonian and Finnish Population Studies.

PubMed

Haller, Toomas; Leitsalu, Liis; Fischer, Krista; Nuotio, Marja-Liisa; Esko, Tõnu; Boomsma, Dorothea Irene; Kyvik, Kirsten Ohm; Spector, Tim D; Perola, Markus; Metspalu, Andres

2017-01-01

Ancestry information at the individual level can be a valuable resource for personalized medicine, medical, demographical and history research, as well as for tracing back personal history. We report a new method for quantitatively determining personal genetic ancestry based on genome-wide data. Numerical ancestry component scores are assigned to individuals based on comparisons with reference populations. These comparisons are conducted with an existing analytical pipeline making use of genotype phasing, similarity matrix computation and our addition-multidimensional best fitting by MixFit. The method is demonstrated by studying Estonian and Finnish populations in geographical context. We show the main differences in the genetic composition of these otherwise close European populations and how they have influenced each other. The components of our analytical pipeline are freely available computer programs and scripts one of which was developed in house (available at: www.geenivaramu.ee/en/tools/mixfit).

Probing the perceptual and cognitive underpinnings of braille reading. An Estonian population study.

PubMed

Veispak, Anneli; Boets, Bart; Männamaa, Mairi; Ghesquière, Pol

2012-01-01

Similar to many sighted children who struggle with learning to read, a proportion of blind children have specific difficulties related to reading braille which cannot be easily explained. A lot of research has been conducted to investigate the perceptual and cognitive processes behind (impairments in) print reading. Very few studies, however, have aimed for a deeper insight into the relevant perceptual and cognitive processes involved in braille reading. In the present study we investigate the relations between reading achievement and auditory, speech, phonological and tactile processing in a population of Estonian braille reading children and youngsters and matched sighted print readers. Findings revealed that the sequential nature of braille imposes constant decoding and effective recruitment of phonological skills throughout the reading process. Sighted print readers, on the other hand, seem to switch between the use of phonological and lexical processing modes depending on the familiarity, length and structure of the word. Copyright © 2012 Elsevier Ltd. All rights reserved.

Application of strengths, weaknesses, opportunities and threats analysis in the development of a health technology assessment program.

PubMed

Gibis, B; Artiles, J; Corabian, P; Meiesaar, K; Koppel, A; Jacobs, P; Serrano, P; Menon, D

2001-10-01

There has been recent interest in developing a health technology assessment (HTA) function in Estonia. A group of individuals knowledgeable about HTA in Canada, Germany, Romania and Spain, along with representatives of the University of Tartu, Estonia, was convened by the Institute of Health Economics in Edmonton, Canada, to consider options for such a function. In a one-day workshop strengths, weaknesses, opportunities and threats (SWOT) analyses of HTA were conducted, first at a 'global' level, and then of the Estonian situation. The 'global' SWOT analysis yielded a large number of items that pertain to institutionalized HTA in a generic sense, i.e. not based on any individual HTA agency. The 'Estonian' SWOT yielded a subset of items, which pertain to development of HTA in that country. Ten actionable steps were then developed on the basis of this subset, which could be used to initiate the creation of an HTA body in Estonia.

Preschool Achievement in Finland and Estonia: Cross-Cultural Comparison between the Cities of Helsinki and Tallinn

ERIC Educational Resources Information Center

Ojala, Mikko; Talts, Leida

2007-01-01

Each child In Finland and in Estonia receives preschool training for a year before going to school, based on a new national framework curriculum of preschool education. The aim of the present study was to compare children's learning achievements in nine target areas, based on the teacher's evaluations at the end of the preschool year, in both…

Transverse Kick Analysis of SSR1 Due to Possible Geometrical Variations in Fabrication

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

Yakovlev, V.P.; /Fermilab; Awida, M.H.

2012-05-01

Due to fabrication tolerance, it is expected that some geometrical variations could happen to the SSR1 cavities of Project X, like small shifts in the transverse direction of the beam pipe or the spoke. It is necessary to evaluate the resultant transverse kick due to these geometrical variations, in order to make sure that they are within the limits of the correctors in the solenoids. In this paper, we report the transverse kick values for various fabrications errors and the sensitivity of the beam to these errors. Transverse kick that could happen in SSR1 cavities due to geometrical variations ofmore » the fabricated cavities from the designed geometry has been analysed and evaluated. From fabrication experience, three kinds of variations were under investigation concerning the alignment of both the beam pipe and spoke with respect to the beam axis. Simulation study has been carried out implementing these variations in the simulation model. CMM measurements of five fabricated SSR1 cavities were carried out to investigate the amount of physical misalignments of the beam pipe and spoke. Bead-pull measurements were also conducted to evaluate the transverse kick values in the fabricated cavities. Simulation and measurements are relatively in good agreement. Maximum kick in the fabricated cavities is within 154 keV that would induce about 1.12 mrad beam deviation, which could be definitely corrected with the 10 mrad specified correctors of Project X.« less

The ESASSI-08 cruise in the South Scotia Ridge region: preliminary analysis of hydrodynamic and biogeochemical data

NASA Astrophysics Data System (ADS)

Gomis, D.; Flexas, M. M.; Palmer, M.; Jordà, G.; Orsi, A. H.; Yvon-Lewis, S. A.

2009-04-01

The ESASSI-08 oceanographic cruise carried out in January 2008 was the major milestone of ESASSI, the Spanish component of SASSI (a core project of the International Polar Year devoted to study the shelf-slope exchanges in different locations of Antarctica). The sampling strategy of the cruise consisted of 11 full-depth CTD/ADCP sections across the northern and southern slope of the South Scotia Ridge (SSR), between Elephant and Orkney Islands. The sections extend from shelf waters to open sea and the profiles were gathered at an unprecedented spatial resolution over the slope (about 2 nm). Water samples for chemical and biological analysis were also collected at each station; the analyzed parameters include trace gases (CFCs), oxygen isotopes, carbon-related parameters, and nutrients. In this presentation we show the overall distribution of the main variables across the different sections. Namely, we present: a water mass analysis (in terms of potential temperature, salinity and neutral density), estimates of velocities and fluxes across different transects and distributions of biogeochemical parameters. The ultimate aims of the ESASSI project are: 1) to elucidate the fate of the ASF when it enters the SSR from the Weddell Sea; 2) to estimate the shelf-slope exchanges for different parameters; and 3) to quantify the importance of the ventilation associated with intermediate waters flowing over the SSR with respect to the ventilation associated with bottom waters that are blocked by the SSR and flow around the Orkney Plateau.

Development of a Gene-Centered SSR Atlas as a Resource for Papaya (Carica papaya) Marker-Assisted Selection and Population Genetic Studies

PubMed Central

Vidal, Newton Medeiros; Grazziotin, Ana Laura; Ramos, Helaine Christine Cancela; Pereira, Messias Gonzaga; Venancio, Thiago Motta

2014-01-01

Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community. PMID:25393538

Population structure of wild bananas, Musa balbisiana, in China determined by SSR fingerprinting and cpDNA PCR-RFLP.

PubMed

Ge, X J; Liu, M H; Wang, W K; Schaal, B A; Chiang, T Y

2005-04-01

Both demographic history and dispersal mechanisms influence the apportionment of genetic diversity among plant populations across geographical regions. In this study, phylogeography and population structure of wild banana, Musa balbisiana, one of the progenitors of cultivated bananas and plantains in China were investigated by an analysis of genetic diversity of simple sequence repeat (SSR) fingerprint markers and cpDNA PCR-RFLP. A chloroplast DNA (cpDNA) genealogy of 21 haplotypes identified two major clades, which correspond to two geographical regions separated by the Beijiang and Xijiang rivers, suggesting a history of vicariance. Significant genetic differentiation was detected among populations with cpDNA markers, a result consistent with limited seed dispersal in wild banana mediated by foraging of rodents. Nuclear SSR data also revealed significant geographical structuring in banana populations. In western China, however, there was no detected phylogeograpahical pattern, possibly due to frequent pollen flow via fruit bats. In contrast, populations east of the Beijiang River and the population of Hainan Island, where long-range soaring pollinators are absent, are genetically distinct. Colonization-extinction processes may have influenced the evolution of Musa populations, which have a metapopulation structure and are connected by migrating individuals. Effective gene flow via pollen, estimated from the nuclear SSR data, is 3.65 times greater than gene flow via seed, estimated from cpDNA data. Chloroplast and nuclear DNAs provide different insights into phylogeographical patterns of wild banana populations and, taken together, can inform conservation practices.

Antipathy of Trichoderma against Sclerotium rolfsii Sacc.: Evaluation of Cell Wall-Degrading Enzymatic Activities and Molecular Diversity Analysis of Antagonists.

PubMed

Hirpara, Darshna G; Gajera, Harsukh P; Hirpara, Hitesh Z; Golakiya, Balubhai A

2017-01-01

The fungus Trichoderma is a teleomorph of the Hypocrea genus and associated with biological control of plant diseases. The microscopic, biochemical, and molecular characterization of Trichoderma was carried out and evaluated for in vitro antagonistic activity against the fungal pathogen Sclerotium rolfsii causing stem rot disease in groundnut. In total, 11 isolates of Trichoderma were examined for antagonism at 6 and 12 days after inoculation (DAI). Out of 11, T. virens NBAII Tvs12 evidenced the highest (87.91%) growth inhibition of the test pathogen followed by T. koningii MTCC 796 (67.03%), T. viride NBAII Tv23 (63.74%), and T. harzianum NBAII Th1 (60.44%). Strong mycoparasitism was observed in the best antagonist Tvs12 strain during 6-12 DAI. The specific activity of cell wall-degrading enzymes - chitinase and β-1,3-glucanase - was positively correlated with growth inhibition of the test pathogen. In total, 18 simple sequence repeat (SSR) polymorphisms were reported to amplify 202 alleles across 11 Trichoderma isolates. The average polymorphism information content for SSR markers was found to be 0.80. The best antagonist Tvs 12 was identified with 7 unique SSR alleles amplified by 5 SSR markers. Clustering patterns of 11 Trichoderma strains showed the best antagonist T. virens NBAII Tvs 12 outgrouped with a minimum 3% similarity from the rest of Trichoderma. © 2017 S. Karger AG, Basel.

Wide-cross whole-genome radiation hybrid mapping of cotton (Gossypium hirsutum L.).

PubMed Central

Gao, Wenxiang; Chen, Z Jeffrey; Yu, John Z; Raska, Dwaine; Kohel, Russell J; Womack, James E; Stelly, David M

2004-01-01

We report the development and characterization of a "wide-cross whole-genome radiation hybrid" (WWRH) panel from cotton (Gossypium hirsutum L.). Chromosomes were segmented by gamma-irradiation of G. hirsutum (n = 26) pollen, and segmented chromosomes were rescued after in vivo fertilization of G. barbadense egg cells (n = 26). A 5-krad gamma-ray WWRH mapping panel (N = 93) was constructed and genotyped at 102 SSR loci. SSR marker retention frequencies were higher than those for animal systems and marker retention patterns were informative. Using the program RHMAP, 52 of 102 SSR markers were mapped into 16 syntenic groups. Linkage group 9 (LG 9) SSR markers BNL0625 and BNL2805 had been colocalized by linkage analysis, but their order was resolved by differential retention among WWRH plants. Two linkage groups, LG 13 and LG 9, were combined into one syntenic group, and the chromosome 1 linkage group marker BNL4053 was reassigned to chromosome 9. Analyses of cytogenetic stocks supported synteny of LG 9 and LG 13 and localized them to the short arm of chromosome 17. They also supported reassignment of marker BNL4053 to the long arm of chromosome 9. A WWRH map of the syntenic group composed of linkage groups 9 and 13 was constructed by maximum-likelihood analysis under the general retention model. The results demonstrate not only the feasibility of WWRH panel construction and mapping, but also complementarity to traditional linkage mapping and cytogenetic methods. PMID:15280245

Sedentary behaviours among Australian adolescents.

PubMed

Hardy, Louise L; Dobbins, Timothy; Booth, Michael L; Denney-Wilson, Elizabeth; Okely, Anthony D

2006-12-01

To describe the prevalence and distribution (by demographic characteristics and body mass index [BMI] category) of sedentary behaviour among Australian adolescents aged 11-15 years. Cross-sectional representative population survey of school students (n = 2,750) in New South Wales, conducted in 2004. Students' self-reported time spent during a usual week in five categories of sedentary behaviour (small screen recreation [SSR], education, cultural, social and non-active travel). Height and weight were measured. Grade 6, 8 and 10 students spent approximately 34 hours, 41 hours and 45 hours/week of their discretionary time, respectively, engaged in sedentary behaviour. Urban students and students from Asian-speaking backgrounds spent significantly more time sedentary than students from rural areas or other cultural backgrounds. SSR accounted for 60% and 54% of sedentary behaviour among primary and high school students, respectively. Overweight and obese students spent more time in SSR than healthy weight students. Out-of-school hours educational activities accounted for approximately 20% of sedentary behaviour and increased with age. Girls spent twice the time in social activities compared with boys. Time spent in cultural activities declined with age. Sedentary behaviours among young people differ according to sex, age and cultural background. At least half of all time spent in sedentary behaviours was spent engaged in SSR. BMI was significantly associated with sedentary behaviour among some children, but not consistently across age groups. A clear understanding of young people's patterns of sedentary behaviour is required to develop effective and sustainable intervention programs to promote healthy living.

The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci.

PubMed

Georgi, Laura; Johnson-Cicalese, Jennifer; Honig, Josh; Das, Sushma Parankush; Rajah, Veeran D; Bhattacharya, Debashish; Bassil, Nahla; Rowland, Lisa J; Polashock, James; Vorsa, Nicholi

2013-03-01

The first genetic map of cranberry (Vaccinium macrocarpon) has been constructed, comprising 14 linkage groups totaling 879.9 cM with an estimated coverage of 82.2 %. This map, based on four mapping populations segregating for field fruit-rot resistance, contains 136 distinct loci. Mapped markers include blueberry-derived simple sequence repeat (SSR) and cranberry-derived sequence-characterized amplified region markers previously used for fingerprinting cranberry cultivars. In addition, SSR markers were developed near cranberry sequences resembling genes involved in flavonoid biosynthesis or defense against necrotrophic pathogens, or conserved orthologous set (COS) sequences. The cranberry SSRs were developed from next-generation cranberry genomic sequence assemblies; thus, the positions of these SSRs on the genomic map provide information about the genomic location of the sequence scaffold from which they were derived. The use of SSR markers near COS and other functional sequences, plus 33 SSR markers from blueberry, facilitates comparisons of this map with maps of other plant species. Regions of the cranberry map were identified that showed conservation of synteny with Vitis vinifera and Arabidopsis thaliana. Positioned on this map are quantitative trait loci (QTL) for field fruit-rot resistance (FFRR), fruit weight, titratable acidity, and sound fruit yield (SFY). The SFY QTL is adjacent to one of the fruit weight QTL and may reflect pleiotropy. Two of the FFRR QTL are in regions of conserved synteny with grape and span defense gene markers, and the third FFRR QTL spans a flavonoid biosynthetic gene.

Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa).

PubMed

Mondal, Tapan Kumar; Ganie, Showkat Ahmad

2014-02-10

Salinity is an important abiotic stress that affects agricultural production and productivity. It is a complex trait that is regulated by different molecular mechanisms. miRNAs are non-coding RNAs which are highly conserved and regulate gene expression. Simple sequence repeats (SSRs) are robust molecular markers for studying genetic diversity. Although several SSR markers are available now, challenge remains to identify the trait-specific SSRs which can be used for marker assisted breeding. In order to understand the genetic diversity of salt responsive-miRNA genes in rice, SSR markers were mined from 130 members of salt-responsive miRNA genes of rice and validated among the contrasting panels of tolerant as well as susceptible rice genotypes, each with 12 genotypes. Although 12 miR-SSRs were found to be polymorphic, only miR172b-SSR was able to differentiate the tolerant and susceptible genotypes in 2 different groups. It had also been found that miRNA genes were more diverse in susceptible genotypes than the tolerant one (as indicated by polymorphic index content) which might interfere to form the stem-loop structure of premature miRNA and their subsequent synthesis in susceptible genotypes. Thus, we concluded that length variations of the repeats in salt responsive miRNA genes may be responsible for a possible sensitivity to salinity adaptation. This is the first report of characterization of trait specific miRNA derived SSRs in plants. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterization of some bread wheat genotypes using molecular markers for drought tolerance.

PubMed

Ateş Sönmezoğlu, Özlem; Terzi, Begüm

2018-02-01

Because of its wide geographical adaptation and importance in human nutrition, wheat is one of the most important crops in the world. However, wheat yield has reduced due to drought stress posing threat to sustainability and world food security in agricultural production. The first stage of drought tolerant variety breeding occurs on the molecular and biochemical characterization and classification of wheat genotypes. The aim of the present study is characterization of widely grown bread wheat cultivars and breeding lines for drought tolerance so as to be adapted to different regions in Turkey. The genotypes were screened with molecular markers for the presence of QTLs mapped to different chromosomes. Results of the molecular studies identified and detected 15 polymorphic SSR markers which gave the clearest PCR bands among the control genotypes. At the end of the research, bread wheat genotypes which were classified for tolerance or sensitivity to drought and the genetic similarity within control varieties were determined by molecular markers. According to SSR based dendrogram, two main groups were obtained for drought tolerance. At end of the molecular screening with SSR primers, genetic similarity coefficients were obtained that ranged from 0.14 to 0.71. The ones numbered 8 and 11 were the closest genotypes to drought tolerant cultivar Gerek 79 and the furthest genotypes from this cultivar were number 16 and to drought sensitive cultivar Sultan 95. The genotypes as drought tolerance due to their SSR markers scores are expected to provide useful information for drought related molecular breeding studies.

Transcriptome characterization and SSR discovery in large-scale loach Paramisgurnus dabryanus (Cobitidae, Cypriniformes).

PubMed

Li, Caijuan; Ling, Qufei; Ge, Chen; Ye, Zhuqing; Han, Xiaofei

2015-02-25

The large-scale loach (Paramisgurnus dabryanus, Cypriniformes) is a bottom-dwelling freshwater species of fish found mainly in eastern Asia. The natural germplasm resources of this important aquaculture species has been recently threatened due to overfishing and artificial propagation. The objective of this study is to obtain the first functional genomic resource and candidate molecular markers for future conservation and breeding research. Illumina paired-end sequencing generated over one hundred million reads that resulted in 71,887 assembled transcripts, with an average length of 1465bp. 42,093 (58.56%) protein-coding sequences were predicted; and 43,837 transcripts had significant matches to NCBI nonredundant protein (Nr) database. 29,389 and 14,419 transcripts were assigned into gene ontology (GO) categories and Eukaryotic Orthologous Groups (KOG), respectively. 22,102 (31.14%) transcripts were mapped to 302 KEGG pathways. In addition, 15,106 candidate SSR markers were identified, with 11,037 pairs of PCR primers designed. 400 primers pairs of SSR selected randomly were validated, of which 364 (91%) pairs of primers were able to produce PCR products. Further test with 41 loci and 20 large-scale loach specimens collected from the four largest lakes in China showed that 36 (87.8%) loci were polymorphic. The transcriptomic profile and SSR repertoire obtained in this study will facilitate population genetic studies and selective breeding of large-scale loach in the future. Copyright © 2015. Published by Elsevier B.V.

Genetic analysis and association of simple sequence repeat markers with storage root yield, dry matter, starch and β-carotene content in sweetpotato.

PubMed

Yada, Benard; Brown-Guedira, Gina; Alajo, Agnes; Ssemakula, Gorrettie N; Owusu-Mensah, Eric; Carey, Edward E; Mwanga, Robert O M; Yencho, G Craig

2017-03-01

Molecular markers are needed for enhancing the development of elite sweetpotato ( Ipomoea batatas (L.) Lam) cultivars with a wide range of commercially important traits in sub-Saharan Africa. This study was conducted to estimate the heritability and determine trait correlations of storage root yield, dry matter, starch and β-carotene content in a cross between 'New Kawogo' × 'Beauregard'. The study was also conducted to identify simple sequence repeat (SSR) markers associated with these traits. A total of 287 progeny and the parents were evaluated for two seasons at three sites in Uganda and genotyped with 250 SSR markers. Broad sense heritability (H 2 ) for storage root yield, dry matter, starch and β-carotene content were 0.24, 0.68, 0.70 and 0.90, respectively. Storage root β-carotene content was negatively correlated with dry matter (r = -0.59, P < 0.001) and starch (r = -0.93, P < 0.001) content, while storage root yield was positively correlated with dry matter (r = 0.57, P = 0.029) and starch (r = 0.41, P = 0.008) content. Through logistic regression, a total of 12, 4, 6 and 8 SSR markers were associated with storage root yield, dry matter, starch and β-carotene content, respectively. The SSR markers used in this study may be useful for quantitative trait loci analysis and selection for these traits in future.

Genetic analysis and association of simple sequence repeat markers with storage root yield, dry matter, starch and β-carotene content in sweetpotato

PubMed Central

Yada, Benard; Brown-Guedira, Gina; Alajo, Agnes; Ssemakula, Gorrettie N.; Owusu-Mensah, Eric; Carey, Edward E.; Mwanga, Robert O.M.; Yencho, G. Craig

2017-01-01

Molecular markers are needed for enhancing the development of elite sweetpotato (Ipomoea batatas (L.) Lam) cultivars with a wide range of commercially important traits in sub-Saharan Africa. This study was conducted to estimate the heritability and determine trait correlations of storage root yield, dry matter, starch and β-carotene content in a cross between ‘New Kawogo’ × ‘Beauregard’. The study was also conducted to identify simple sequence repeat (SSR) markers associated with these traits. A total of 287 progeny and the parents were evaluated for two seasons at three sites in Uganda and genotyped with 250 SSR markers. Broad sense heritability (H2) for storage root yield, dry matter, starch and β-carotene content were 0.24, 0.68, 0.70 and 0.90, respectively. Storage root β-carotene content was negatively correlated with dry matter (r = −0.59, P < 0.001) and starch (r = −0.93, P < 0.001) content, while storage root yield was positively correlated with dry matter (r = 0.57, P = 0.029) and starch (r = 0.41, P = 0.008) content. Through logistic regression, a total of 12, 4, 6 and 8 SSR markers were associated with storage root yield, dry matter, starch and β-carotene content, respectively. The SSR markers used in this study may be useful for quantitative trait loci analysis and selection for these traits in future. PMID:28588391

High polymorphism in Est-SSR loci for cellulose synthase and β-amylase of sugarcane varieties (Saccharum spp.) used by the industrial sector for ethanol production.

PubMed

Augusto, Raphael; Maranho, Rone Charles; Mangolin, Claudete Aparecida; Pires da Silva Machado, Maria de Fátima

2015-01-01

High and low polymorphisms in simple sequence repeats of expressed sequence tag (EST-SSR) for specific proteins and enzymes, such as β-amylase, cellulose synthase, xyloglucan endotransglucosylase, fructose 1,6-bisphosphate aldolase, and fructose 1,6-bisphosphatase, were used to illustrate the genetic divergence within and between varieties of sugarcane (Saccharum spp.) and to guide the technological paths to optimize ethanol production from lignocellulose biomass. The varieties RB72454, RB867515, RB92579, and SP813250 on the second stage of cutting, all grown in the state of Paraná (PR), and the varieties RB92579 and SP813250 cultured in the PR state and in Northeastern Brazil, state of Pernambuco (PE), were analyzed using five EST-SSR primers for EstC66, EstC67, EstC68, EstC69, and EstC91 loci. Genetic divergence was evident in the EstC67 and EstC69 loci for β-amylase and cellulose synthase, respectively, among the four sugarcane varieties. An extremely high level of genetic differentiation was also detected in the EstC67 locus from the RB82579 and SP813250 varieties cultured in the PR and PE states. High polymorphism in SSR of the cellulose synthase locus may explain the high variability of substrates used in pretreatment and enzymatic hydrolysis processes, which has been an obstacle to effective industrial adaptations.

Solid-State Recorders Enhance Scientific Data Collection

NASA Technical Reports Server (NTRS)

2010-01-01

Under Small Business Innovation Research (SBIR) contracts with Goddard Space Flight Center, SEAKR Engineering Inc., of Centennial, Colorado, crafted a solid-state recorder (SSR) to replace the tape recorder onboard a Spartan satellite carrying NASA's Inflatable Antenna Experiment. Work for that mission and others has helped SEAKR become the world leader in SSR technology for spacecraft. The company has delivered more than 100 systems, more than 85 of which have launched onboard NASA, military, and commercial spacecraft including imaging satellites that provide much of the high-resolution imagery for online mapping services like Google Earth.

From a Guerrilla Force to a State Military: An Assessment of the Transformation of the Sudan People’s Liberation Army (SPLA) from 2006-2010

DTIC Science & Technology

2011-12-01

was caught up between academics and the final struggles for the independence of my country. Special thanks go to my command at the SPLA GHQs for...about the effect of “local ownership ” on SSR effectiveness. International donors and recipient governments agree that local ownership is important to...about both the level of local ownership and the success of SSR.24 Based on the limited capacity of the Sierra Leonean government to generate

Cultural Resources Survey, Harry S. Truman Dam and Reservoir Project, Missouri. Volume 2. Historical Resources: Historical Gazetteer and Mitigation Recommendations.

DTIC Science & Technology

1983-02-01

Arnica -- herb with yellow flowers made into tincture and used as stimulant and curative for bruises and sprains) Now extinct. GH Arthur (Vernon) Village...Bedford • lost influence, renamed Handley. WHA, NHl Bee Branch (Henry) A tributary of Big Creek in the NW Big Creek T. S named for the wild bees so...T. named for its location amid many wild cherry trees. SSR Cherry Grove School (Bates) For flora. SSR S S 0 S 43 0 Cherry Valley School (Cedar) For

Lifelong Learning and Teacher Development. Estonian Studies in Education. Volume 4

ERIC Educational Resources Information Center

Mikk, Jaan, Ed.; Veisson, Marika, Ed.; Luik, Piret, Ed.

2012-01-01

The papers in this collection contribute to the understanding of several aspects of lifelong learning. Two papers highlight the characteristics of reflection among teachers including self-evaluation and blogging. Two other papers study cooperation in lifelong learning--one, the impact of communities on professional learning among university…

Hot and Cold Ethnicities in the Baltic States

ERIC Educational Resources Information Center

Ehala, Martin; Zabrodskaja, Anastassia

2014-01-01

The article discusses the temperatures of the main ethnic groups in the Baltic states: Estonians, Latvians, Lithuanians, and their three Russian-speaking communities, and the Latgalian and Polish minority groups in Latvia and Lithuania, respectively. The study uses a triangulated methodology that includes a survey questionnaire for quantitative…

Combining Cognitive and Interactive Approaches to Lingua Receptiva

ERIC Educational Resources Information Center

Bahtina, Daria; ten Thije, Jan D.; Wijnen, Frank

2013-01-01

This study takes an experimental approach to "lingua receptiva" (LaRa), a communication mode in which interlocutors each use their own--different--native language. In contrast to previous work on LaRa, this study investigates the phenomenon in genetically unrelated languages. Native speakers of Estonian and Russian were engaged in a…

Stakeholder Perspectives: CLIL Programme Management in Estonia

ERIC Educational Resources Information Center

Mehisto, Peeter; Asser, Hiie

2007-01-01

In 2000, Estonia launched a voluntary Estonian language CLIL programme for seven year-olds in four Russian-medium schools. The programme has expanded rapidly to a total of 48 kindergartens and schools. This paper reports on research into stakeholder perspectives on programme management. In addition to surveying parents, teachers, vice-principals…

The Information Culture of Higher Education Institutions: The Estonian Case

ERIC Educational Resources Information Center

Lauri, Liia; Heidmets, Mati; Virkus, Sirje

2016-01-01

Introduction: This paper focuses on the information culture of higher education institutions in Estonia. The aim of the study is to explore the relationship between information culture, information management and job satisfaction, leadership style, and self-reported individual performance. Method: A total of 160 faculty members from twelve…

Constructing Model of Teachers' Innovative Behaviour in School Environment

ERIC Educational Resources Information Center

Nemeržitski, S.; Loogma, K.; Heinla, E.; Eisenschmidt, E.

2013-01-01

Teachers' innovative behaviour influences not only their teaching practices and professional habits, but also has an impact on students' creation of novel and original ideas. In spite of the increasing demand for innovative behaviour, and also relatively high academic achievements of Estonian students in international comparison, teachers in…

Teachers' Views of Curriculum Policy: The Case of Estonia

ERIC Educational Resources Information Center

Erss, Maria; Mikser, Rain; Löfström, Erika; Ugaste, Aino; Rõuk, Vadim; Jaani, Juta

2014-01-01

Unlike in England, since the late 1980s the rhetoric of curriculum reforms has been overwhelmingly decentralist in many countries. However, decentralisation has often involved the delegation of centrally appointed tasks, rather than a real shift in power. The Estonian case demonstrates how a decentralised curriculum policy with centralised control…

Professionalism of Preschool Teachers in Estonia, Finland, Sweden and Hungary

ERIC Educational Resources Information Center

Peterson, Tiina; Veisson, Marika; Hujala, Eeva; Härkönen, Ulla; Sandberg, Anette; Johansson, Inge; Bakosi, Eva Kovacsne

2016-01-01

The current study investigated the ratings of Estonian, Finnish, Swedish and Hungarian preschool teachers and principals regarding the professionalism of preschool teachers within a cross-cultural context. According to reports commissioned by the European Commission and OECD, the professionalism of preschool teachers is a key factor in ensuring…

A Study in Content Language Acquisition

ERIC Educational Resources Information Center

Broer, Kathleen

2003-01-01

This study examines how young second language learners acquire academic language. Among the main language groups represented were Punjabi, Hindi, Tamil, Estonian, Serbian, Arabic as well as 23 other language groups. I monitored over 75 students, in grades 1, 2 and 4. I was interested in exploring what strategies best promoted coherence in…

Technological Knowledge and Reasoning in Finnish and Estonian Technology Education

ERIC Educational Resources Information Center

Autio, Ossi; Soobik, Mart

2017-01-01

The main idea of this research was to find out if there is a relationship between students' undertakings within Craft and Technology education and their ability to understand technological concepts. Study participants' technological knowledge and reasoning was measured with a questionnaire regarding mechanical systems connected with simple…

A Large-Scale Cross-Linguistic Investigation of the Acquisition of Passive

ERIC Educational Resources Information Center

Armon-Lotem, Sharon; Haman, Ewa; de López, Kristine Jensen; Smoczynska, Magdalena; Yatsushiro, Kazuko; Szczerbinski, Marcin; van Hout, Angeliek; Dabašinskiene, Ineta; Gavarró, Anna; Hobbs, Erin; Kamandulyte-Merfeldiene, Laura; Katsos, Napoleon; Kunnari, Sari; Nitsiou, Chrisa; Olsen, Lone Sundahl; Parramon, Xavier; Sauerland, Uli; Torn-Leesik, Reeli; van der Lely, Heather

2016-01-01

This cross-linguistic study evaluates children's understanding of passives in 11 typologically different languages: Catalan, Cypriot Greek, Danish, Dutch, English, Estonian, Finnish, German, Hebrew, Lithuanian, and Polish. The study intends to determine whether the reported gaps between the comprehension of active and passive and between short and…

Hybrid Warfare in the Baltics: Threats and Potential Responses

DTIC Science & Technology

2017-02-23

9 Martin Hurt, Lessons Identified in Crimea: Does Estonia’s National Defence Model Meet Our Needs? Tallinn, Estonia: International...Monuments’ in Estonia,” Nationalities Papers, Vol. 36, No. 3, July 2008, p. 436; Martin Ehala, “The Bronze Soldier: Identity Threat and Maintenance in...Ukraine Petro Poroshenko,” July 1, 2014. As of June 20, 2016: http://www.president.gov.ua/en/news/zvernennya-prezidenta-ukrayini- petra -poroshenka

Combined Application of Shallow Seismic Reflection and High-resolution Refraction Exploration Approach to Active Fault Survey, Central Orogenic Belt, China

NASA Astrophysics Data System (ADS)

Lin, S.; Luo, D.; Yanlin, F.; Li, Y.

2016-12-01

Shallow Seismic Reflection (SSR) is a major geophysical exploration method with its exploration depth range, high-resolution in urban active fault exploration. In this paper, we carried out (SSR) and High-resolution refraction (HRR) test in the Liangyun Basin to explore a buried fault. We used NZ distributed 64 channel seismic instrument, 60HZ high sensitivity detector, Geode multi-channel portable acquisition system and hammer source. We selected single side hammer hit multiple overlay, 48 channels received and 12 times of coverage. As there are some coincidence measuring lines of SSR and HRR, we chose multi chase and encounter observation system. Based on the satellite positioning, we arranged 11 survey lines in our study area with total length for 8132 meters. GEOGIGA seismic reflection data processing software was used to deal with the SSR data. After repeated tests from the aspects of single shot record compilation, interference wave pressing, static correction, velocity parameter extraction, dynamic correction, eventually got the shallow seismic reflection profile images. Meanwhile, we used Canadian technology company good refraction and tomographic imaging software to deal with HRR seismic data, which is based on nonlinear first arrival wave travel time tomography. Combined with drilling geological profiles, we explained 11 measured seismic profiles. Results show 18 obvious fault feature breakpoints, including 4 normal faults of south-west, 7 reverse faults of south-west, one normal fault of north-east and 6 reverse faults of north-east. Breakpoints buried depth is 15-18 meters, and the inferred fault distance is 3-12 meters. Comprehensive analysis shows that the fault property is reverse fault with northeast incline section, and fewer branch normal faults presenting southwest incline section. Since good corresponding relationship between the seismic interpretation results, drilling data and SEM results on the property, occurrence, broken length of the fault, we considered the Liangyun fault to be an active fault which has strong activity during the Neogene Pliocene and early Pleistocene, Middle Pleistocene period. The combined application of SSR and HRR can provide more parameters to explain the seismic results, and improve the accuracy of the interpretation.

A Conceptual Analysis of Perspective Taking in Support of Socioscientific Reasoning

NASA Astrophysics Data System (ADS)

Kahn, Sami

Scientific literacy is concerned with the informed citizens' ability to negotiate scientifically-related societal issues. The suite of skills necessary to negotiate these complex issues is referred to as Socioscientific Reasoning (SSR). SSR requires, among other things, perspective-taking abilities in order to consider the multi-faceted nature of these open-ended, debatable socioscientific issues (SSI). Developing interventions and instruments to foster and measure perspective taking in support of SSR is therefore critical to the promotion of functional scientific literacy through both research and practice. Although widely studied in many disciplines, perspective taking is a particularly tangled construct that has been used to describe a range of activities representing different psychological domains and applied interchangeably with related constructs such as role taking, empathy, and theory of mind. This ambiguity makes it difficult to ensure construct validity and prevents science education researchers from honing in on the precise skills they wish to study and promote. To clarify the construct of perspective taking, this study undertook a conceptual analysis to operationalize perspective taking, drawing comparisons and distinctions between it and related constructs. Further, by applying a method known as conception development, perspective taking was positioned in the context of SSR, particularly as it relates to moral development, in order to devise a more precise construct relating perspective taking to SSR called socioscientific perspective taking (SSPT). It is asserted that SSPT requires engagement with others or their circumstances, an etic/emic shift, and a moral context comprised of reflective and reflexive judgment. Finally, in order to identify promising interventions for promoting SSPT in the science classroom, the newly-developed SSPT construct was applied to a series of extensively researched curricular frameworks that promote perspective taking in three non-science disciplines including historical empathy (social studies education), method acting (theater education), and autism intervention (special education). The aim of this theoretical inquiry was to translate successful perspective-taking interventions into SSI contexts, yielding an array of promising approaches for fostering SSPT while assessing the feasibility of each of these fields as potential sources for novel and expansive work in SSI to promote scientific literacy. Implications for science education research and practice are discussed.

Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species.

PubMed

Ziya Motalebipour, Elmira; Kafkas, Salih; Khodaeiaminjan, Mortaza; Çoban, Nergiz; Gözel, Hatice

2016-12-07

Pistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species. To explore the genome structure of pistachio, a genome survey was performed using the Illumina platform at approximately 40× coverage depth in the P. vera cv. Siirt. The K-mer analysis indicated that pistachio has a genome that is about 600 Mb in size and is highly heterozygous. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds at N50 = 3.4 kb with a total of 513.5 Mb. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 P. vera cultivars and 20 wild Pistacia genotypes (four genotypes from each five wild Pistacia species) belonging to P. atlantica, P. integerrima, P. chinenesis, P. terebinthus, and P. lentiscus genotypes. Overall 135 SSR loci amplified in all 44 cultivars and genotypes, 41 were polymorphic in six Pistacia species. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species. The results from a genome survey of pistachio suggest that the genome size of pistachio is about 600 Mb with a high heterozygosity rate. This information will help to design whole genome sequencing strategies for pistachio. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia.

Genetic relationships among seven sections of genus Arachis studied by using SSR markers

PubMed Central

2010-01-01

Background The genus Arachis, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the Arachis species are diploids (2n = 2x = 20) and the tetraploid species (2n = 2x = 40) are found in sections Arachis, Extranervosae and Rhizomatosae. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of Arachis by using simple sequence repeat (SSR) markers developed from Arachis hypogaea genomic library and gene sequences from related genera of Arachis. Results The average transferability rate of 101 SSR markers tested to section Arachis and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, Arachis pusilla exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (A. duranensis) and the B-genome accession ICG 8206 (A. ipaënsis) were found most closely related to A. hypogaea. Conclusion A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of Arachis, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of A. monticola and A. hypogaea as well as on the most probable donor of A and B-genomes of cultivated groundnut. PMID:20089171

Tagging and mapping of SSR marker for rust resistance gene in lentil (Lens culinaris Medikus subsp. culinaris).

PubMed

Dikshit, H K; Singh, Akanksha; Singh, D; Aski, M; Jain, Neelu; Hegde, V S; Basandrai, A K; Basandrai, D; Sharma, T R

2016-06-01

Lentil, as an economical source of protein, minerals and vitamins, plays important role in nutritional security of the common man. Grown mainly in West Asia, North Africa (WANA) region and South Asia, it suffers from several biotic stresses such as wilt, rust, blight and broomrape. Lentil rust caused by autoecious fungus Uromyces viciae fabae (Pers.) Schroet is a serious lentil disease in Algeria, Bangladesh, Ethiopia, India, Italy, Morocco, Pakistan and Nepal. The disease symptoms are observed during flowering and early podding stages. Rust causes severe yield losses in lentil. It can only be effectively controlled by identifying the resistant source, understanding its inheritance and breeding for host resistance. The obligate parasitic nature of pathogen makes it difficult to maintain the pathogen in culture and to apply it to screen segregating progenies under controlled growth conditions. Hence, the use of molecular markers will compliment in identification of resistant types in different breeding programs. Here, we studied the inheritance of resistance to rust in lentil using F₁, F₂ and F₂:₃ from cross PL 8 (susceptible) x L 4149 (resistant) varieties. The phenotyping of lentil population was carried out at Sirmour, India. The result of genetic analysis revealed that a single dominant gene controls rust resistance in lentil genotype L 4149. The F2 population from this cross was used to tag and map the rust resistance gene using SSR and SRAP markers. Markers such as 270 SRAP and 162 SSR were studied for polymorphism and 101 SRAP and 33 SSRs were found to be polymorphic between the parents. Two SRAP and two SSR markers differentiated the resistant and susceptible bulks. SSR marker Gllc 527 was estimated to be linked to rust resistant locus at a distance of 5.9 cM. The Gllc 527 marker can be used for marker assisted selection for rust resistance; however, additional markers closer to rust resistant locus are required. The markers linked to the rust resistance gene can serve as starting points for map-based cloning of the rust resistance gene.

A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts.

PubMed

Shirasawa, Kenta; Hand, Melanie L; Henderson, Steven T; Okada, Takashi; Johnson, Susan D; Taylor, Jennifer M; Spriggs, Andrew; Siddons, Hayley; Hirakawa, Hideki; Isobe, Sachiko; Tabata, Satoshi; Koltunow, Anna M G

2015-03-01

Apomixis in plants generates clonal progeny with a maternal genotype through asexual seed formation. Hieracium subgenus Pilosella (Asteraceae) contains polyploid, highly heterozygous apomictic and sexual species. Within apomictic Hieracium, dominant genetic loci independently regulate the qualitative developmental components of apomixis. In H. praealtum, LOSS OF APOMEIOSIS (LOA) enables formation of embryo sacs without meiosis and LOSS OF PARTHENOGENESIS (LOP) enables fertilization-independent seed formation. A locus required for fertilization-independent endosperm formation (AutE) has been identified in H. piloselloides. Additional quantitative loci appear to influence the penetrance of the qualitative loci, although the controlling genes remain unknown. This study aimed to develop the first genetic linkage maps for sexual and apomictic Hieracium species using simple sequence repeat (SSR) markers derived from expressed transcripts within the developing ovaries. RNA from microdissected Hieracium ovule cell types and ovaries was sequenced and SSRs were identified. Two different F1 mapping populations were created to overcome difficulties associated with genome complexity and asexual reproduction. SSR markers were analysed within each mapping population to generate draft linkage maps for apomictic and sexual Hieracium species. A collection of 14 684 Hieracium expressed SSR markers were developed and linkage maps were constructed for Hieracium species using a subset of the SSR markers. Both the LOA and LOP loci were successfully assigned to linkage groups; however, AutE could not be mapped using the current populations. Comparisons with lettuce (Lactuca sativa) revealed partial macrosynteny between the two Asteraceae species. A collection of SSR markers and draft linkage maps were developed for two apomictic and one sexual Hieracium species. These maps will support cloning of controlling genes at LOA and LOP loci in Hieracium and should also assist with identification of quantitative loci that affect the expressivity of apomixis. Future work will focus on mapping AutE using alternative populations. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Development of Microsatellite Markers for Buffalograss ( Buchloë dactyloides ; Poaceae), a Drought-Tolerant Turfgrass Alternative

DOE PAGES

Hadle, Jacob J.; Konrade, Lauren A.; Beasley, Rochelle R.; ...

2016-08-03

Buchloë dactyloides (Nutt.) Engelm. (buffalograss; Poaceae) is a low-growing, perennial C4 grass that is a dominant component of shortgrass prairies of the North American Great Plains (Shearman et al., 2004). Beyond this significant ecosystem role, buffalograss has been widely adopted as a drought-tolerant turfgrass alternative, particularly notable as a native-species option in North America. Like many dominant Great Plains grasses, B. dactyloides comprises an autopolypoid series, including diploids (2n = 20), tetraploids, pentaploids, and hexaploids (Johnson et al., 2001). Preserving the full range of buffalograss phenotypic and genotypic diversity and utilizing this diversity for crop improvement will require an understandingmore » of the distribution of genetic variation among cytotypes and across its large geographic range. Beyond numerous methodological advantages (Guichoux et al., 2011), microsatellites, or simple sequence repeat (SSR) markers,are an attractive genetic tool for studies of wide-ranging polyploid series given their codominant nature and applicability to museum-derived DNAs. Because SSR data are routinely obtainable from DNA extracted from museum tissue (Wandeler et al., 2007), these samples can be used to quickly and economically obtain comparative genotypic data from all portions of a large geographic range. Currently no buffalograss-specific SSR loci are available, as previous studies have relied on a mixture of dominant and codominant loci that were designed for other taxa (Budak et al., 2004). In this study, a set of SSR loci are designed from B. dactyloides genomic sequence data. The variability of these loci are then evaluated in six populations from numerous portions of the buffalograss range.« less

The 1998-2001 submarine lava balloon eruption at the Serreta ridge (Azores archipelago): Constraints from volcanic facies architecture, isotope geochemistry and magnetic data

NASA Astrophysics Data System (ADS)

Madureira, Pedro; Rosa, Carlos; Marques, Ana Filipa; Silva, Pedro; Moreira, Manuel; Hamelin, Cédric; Relvas, Jorge; Lourenço, Nuno; Conceição, Patrícia; Pinto de Abreu, Manuel; Barriga, Fernando J. A. S.

2017-01-01

The most recent submarine eruption observed offshore the Azores archipelago occurred between 1998 and 2001 along the submarine Serreta ridge (SSR), 4-5 nautical miles WNW of Terceira Island. This submarine eruption delivered abundant basaltic lava balloons floating at the sea surface and significantly changed the bathymetry around the eruption area. Our work combines bathymetry, volcanic facies cartography, petrography, rock magnetism and geochemistry in order to (1) track the possible vent source at seabed, (2) better constrain the Azores magma source(s) sampled through the Serreta submarine volcanic event, and (3) interpret the data within the small-scale mantle source heterogeneity framework that has been demonstrated for the Azores archipelago. Lava balloons sampled at sea surface display a radiogenic signature, which is also correlated with relatively primitive (low) 4He/3He isotopic ratios. Conversely, SSR lavas are characterized by significantly lower radiogenic 87Sr/86Sr, 206Pb/204Pb and 208Pb/204Pb ratios than the lava balloons and the onshore lavas from the Terceira Island. SSR lavas are primitive, but incompatible trace-enriched. Apparent decoupling between the enriched incompatible trace element abundances and depleted radiogenic isotope ratios is best explained by binary mixing of a depleted MORB source and a HIMU­type component into magma batches that evolved by similar shallower processes in their travel to the surface. The collected data suggest that the freshest samples collected in the SSR may correspond to volcanic products of an unnoticed and more recent eruption than the 1998-2001 episode.

Expanding the repertoire of microsatellite markers for polymorphism studies in Indian accessions of mung bean (Vigna radiata L. Wilczek).

PubMed

Shrivastava, Divya; Verma, Priyanka; Bhatia, Sabhyata

2014-09-01

Limited availability of validated, polymorphic microsatellite markers in mung bean (Vigna radiata), an important food legume of India, has been a major hurdle towards its improvement and higher yield. The present study was undertaken in order to develop a new set of microsatellite markers and utilize them for the analysis of genetic diversity within mung bean accessions from India. A GA/CT enriched library was constructed from V. radiata which resulted in 1,250 putative recombinant clones of which 850 were sequenced. SSR motifs were identified and their flanking sequences were utilized to design 328 SSR primer pairs. Of these, 48 SSR markers were employed for assessing genetic diversity among 76 mung bean accessions from various geographical locations in India. Two hundred and thirty four alleles with an average of 4.85 alleles per locus were detected at 48 loci. The polymorphic information content (PIC) per locus varied from 0.1 to 0.88 (average: 0.49 per locus). The observed and expected heterozygosities ranged from 0.40 to 0.95 and 0.40 to 0.81 respectively. Based on Jaccard's similarity matrix, a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA) analysis which revealed that one accession from Bundi, Rajasthan was clustered out separately while remaining accessions were grouped into two major clusters. The markers generated in this study will help in expanding the repertoire of the available SSR markers thereby facilitating analysis of genetic diversity, molecular mapping and ultimately broadening the scope for genetic improvement of this legume.

Development of Microsatellite Markers for Buffalograss ( Buchloë dactyloides ; Poaceae), a Drought-Tolerant Turfgrass Alternative

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

Hadle, Jacob J.; Konrade, Lauren A.; Beasley, Rochelle R.

Buchloë dactyloides (Nutt.) Engelm. (buffalograss; Poaceae) is a low-growing, perennial C4 grass that is a dominant component of shortgrass prairies of the North American Great Plains (Shearman et al., 2004). Beyond this significant ecosystem role, buffalograss has been widely adopted as a drought-tolerant turfgrass alternative, particularly notable as a native-species option in North America. Like many dominant Great Plains grasses, B. dactyloides comprises an autopolypoid series, including diploids (2n = 20), tetraploids, pentaploids, and hexaploids (Johnson et al., 2001). Preserving the full range of buffalograss phenotypic and genotypic diversity and utilizing this diversity for crop improvement will require an understandingmore » of the distribution of genetic variation among cytotypes and across its large geographic range. Beyond numerous methodological advantages (Guichoux et al., 2011), microsatellites, or simple sequence repeat (SSR) markers,are an attractive genetic tool for studies of wide-ranging polyploid series given their codominant nature and applicability to museum-derived DNAs. Because SSR data are routinely obtainable from DNA extracted from museum tissue (Wandeler et al., 2007), these samples can be used to quickly and economically obtain comparative genotypic data from all portions of a large geographic range. Currently no buffalograss-specific SSR loci are available, as previous studies have relied on a mixture of dominant and codominant loci that were designed for other taxa (Budak et al., 2004). In this study, a set of SSR loci are designed from B. dactyloides genomic sequence data. The variability of these loci are then evaluated in six populations from numerous portions of the buffalograss range.« less

Assessment of genetic diversity of Tunisian orange, Citrus sinensis (L.) Osbeck using microsatellite (SSR) markers.

PubMed

Mahjbi, A; Oueslati, A; Baraket, G; Salhi-Hannachi, A; Zehdi Azouzi, S

2016-05-20

Citrus are one of the most cultivated crops in the world. Economically, they are very important fruit trees in Tunisia. Little is known about the genetic diversity of the Tunisian Citrus germplasm. Exploring this diversity is a prerequisite for the identification and characterization of the local germplasm to circumvent and controlling genetic erosion caused by biotic and abiotic stress to aid its conservation and use. In the present study, we explored the genetic diversity of 20 Tunisian orange cultivars [Citrus sinensis (L.) Osbeck] and established their relationships by using seven simple sequence repeat (SSR) loci. In total, 37 alleles and 44 genotypes were scored. The sizes of alleles ranged from 90 to 280 bp. The number of alleles per locus was from 4 to 7, with an average of 5.28. Polymorphic information content value changed from 0.599 to 0.769 with an average of 0.675. Analysis of the genotypes revealed a heterozygote deficiency across all the genotypes. The observed heterozygosity varied from 0 to 1 (average of 0.671). Cluster analysis showed that three groups could be distinguished and the polymorphism occurred independently of the geographical origin of the studied orange cultivars. The detected SSR genotypes allowed the establishment of an identification key with a discriminating power of 100%. Multivariate analysis and the neighbor-joining phylogenetic tree indicated a narrow genetic base for the orange cultivars. The usefulness of SSR markers for orange fingerprinting and evaluation of the genetic diversity in the Tunisian germplasm are discussed in this paper.

Phylogenetic inference and SSR characterization of tropical woody bamboos tribe Bambuseae (Poaceae: Bambusoideae) based on complete plastid genome sequences.

PubMed

Vieira, Leila do Nascimento; Dos Anjos, Karina Goulart; Faoro, Helisson; Fraga, Hugo Pacheco de Freitas; Greco, Thiago Machado; Pedrosa, Fábio de Oliveira; de Souza, Emanuel Maltempi; Rogalski, Marcelo; de Souza, Robson Francisco; Guerra, Miguel Pedro

2016-05-01

The complete plastome sequencing is an efficient option for increasing phylogenetic resolution and evolutionary studies, as well as may greatly facilitate the use of plastid DNA markers in plant population genetic studies. Merostachys and Guadua stand out as the most common and the highest potential utilization bamboos indigenous of Brazil. Here, we sequenced the complete plastome sequences of the Brazilian Guadua chacoensis and Merostachys sp. to perform full plastome phylogeny and characterize the occurrence, type, and distribution of SRRs using 20 Bambuseae species. The determined plastome sequence of Merostachys sp. and G. chacoensis is 136,334 and 135,403 bp in size, respectively, with an identical gene content and typical quadripartite structure consisting of a pair of IRs separated by the LSC and SSC regions. The Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of Paleotropical and Neotropical Bamboos clades. The Neotropical bamboos segregated into three well-supported lineages, Chusqueinae, Guaduinae, and Arthrostylidiinae, with the last two forming a well-supported sister relationship. Paleotropical bamboos segregated into two well-supported lineages, Hickeliinae and Bambusinae + Melocanninae. We identified 141.8 cpSSR in Bambuseae plastomes and an inferior value (38.15) for plastome coding sequences. Among them, we identified 16 polymorphic SSR loci, with number of alleles varying from 3 to 10. These 16 polymorphic cpSSR loci in Bambuseae plastome can be assessed for the intraspecific level of polymorphism, leading to innovative highly sensitive phylogeographic and population genetics studies for this tribe.

Increasing Susceptibility of the Global Network of Food Trade to Climate Disturbances

NASA Astrophysics Data System (ADS)

Puma, M. J.; Bose, S.; Chon, S.; Cook, B.

2013-12-01

Globalization of agriculture through trade liberalization has led to a dramatic transformation of the global network of food trade. The many benefits of this globalization include greater and more efficient global agricultural production, reduced variability of regional and global food supplies, and savings in global water resources. However, a potential hidden cost is an increasingly fragile network that is more susceptible to shocks or disruptions. Recent studies suggest that complex systems, like the global food trade network, may have architectural features typically associated with the existence of tipping points and susceptibility to collapse. Here we present evidence that this global agricultural network is increasingly connected, homogeneous, and in a state where network nodes (here countries) can flip between alternate states. We use production and trade data from 1986 to 2009 to identify shifts in national self sufficiency and to quantify changes in connectivity and homogeneity of the wheat, maize and rice trade. We then simulate the possible impacts of climate and crop-disease disruptions, which could potentially trigger a global food crisis through an export-restriction-induced domino effect. Changes in self-sufficiency ratio (SSR) over time for various country groups. The SSR is computed based on production and trade of cereals and starchy roots. (Top row) Time series of SSR for the Group of Eight + Five (G8+5) countries. The '+ Five' refers to the five leading emerging economies in the world. (Bottom row) Boxplots of average SSR over two periods (1986-1990 and 2005-2009) for countries designated as 'Annex I' and 'Least Developed Countries' (LDC) by the United Nations.

Time- and frequency-domain parameters of heart rate variability and sympathetic skin response in Parkinson's disease.

PubMed

Maetzler, Walter; Karam, Marie; Berger, Monika Fruhmann; Heger, Tanja; Maetzler, Corina; Ruediger, Heinz; Bronzova, Juliana; Lobo, Patricia Pita; Ferreira, Joaquim J; Ziemssen, Tjalf; Berg, Daniela

2015-03-01

The autonomic nervous system (ANS) is regularly affected in Parkinson's disease (PD). Information on autonomic dysfunction can be derived from e.g. altered heart rate variability (HRV) and sympathetic skin response (SSR). Such parameters can be quantified easily and measured repeatedly which might be helpful for evaluating disease progression and therapeutic outcome. In this 2-center study, HRV and SSR of 45 PD patients and 26 controls were recorded. HRV was measured during supine metronomic breathing and analyzed in time- and frequency-domains. SSR was evoked by repetitive auditory stimulation. Various ANS parameters were compared (1) between patients and healthy controls, (2) to clinical scales (Unified Parkinson's disease rating scale, Mini-Mental State Examination, Becks Depression Inventory), and (3) to disease duration. Root mean square of successive differences (RMSSD) and low frequency/high frequency (LF/HF) ratio differed significantly between PD and controls. Both, HRV and SSR parameters showed low or no association with clinical scores. Time-domain parameters tended to be affected already at early PD stages but did not consistently change with longer disease duration. In contrast, frequency-domain parameters were not altered in early PD phases but tended to be lower (LF, LF/HF ratio), respectively higher (HF) with increasing disease duration. This report confirms previous results of altered ANS parameters in PD. In addition, it suggests that (1) these ANS parameters are not relevantly associated with motor, behavioral, and cognitive changes in PD, (2) time-domain parameters are useful for the assessment of early PD, and (3) frequency-domain parameters are more closely associated with disease duration.

Towards High Spa-Temporal Resolution Estimates of Surface Radiative Fluxes from Geostationary Satellite Observations for the Tibetan Plateau

NASA Astrophysics Data System (ADS)

Niu, X.; Yang, K.; Tang, W.; Qin, J.

2014-12-01

Surface Solar Radiation (SSR) plays an important role of the hydrological and land process modeling, which particularly contributes more than 90% to the total melt energy for the Tibetan Plateau (TP) ice melting. Neither surface measurement nor existing remote sensing products can meet that requirement in TP. The well-known satellite products (i.e. ISCCP-FD and GEWEX-SRB) are in relatively low spatial resolution (0.5º-2.5º) and temporal resolution (3-hourly, daily, or monthly). The objective of this study is to develop capabilities to improved estimates of SSR in TP based on geostationary satellite observations from the Multi-functional Transport Satellite (MTSAT) with high spatial (0.05º) and temporal (hourly) resolution. An existing physical model, the UMD-SRB (University of Maryland Surface Radiation Budget) which is the basis of the GEWEX-SRB model, is re-visited to improve SSR estimates in TP. The UMD-SRB algorithm transforms TOA radiances into broadband albedos in order to infer atmospheric transmissivity which finally determines the SSR. Specifically, main updates introduced in this study are: implementation at 0.05º spatial resolution at hourly intervals integrated to daily and monthly time scales; and improvement of surface albedo model by introducing the most recently developed Global Land Surface Broadband Albedo Product (GLASS) based on MODIS data. This updated inference scheme will be evaluated against ground observations from China Meteorological Administration (CMA) radiation stations and three TP radiation stations contributed from the Institute of Tibetan Plateau Research.

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

Ranieri, M.G.A., E-mail: gabi.ranieri@ig.com.br; Aguiar, E.C.; Cilense, M.

Highlights: • Bi{sub 4}Ti{sub 3}O{sub 12} thick films were obtained by SSR and PPM methods. • Both systems crystallize in an orthorhombic structure. • Textured characteristics were evidenced. • Grain morphology affects the P–E loops. - Abstract: Bismuth titanate powders (Bi{sub 4}Ti{sub 3}O{sub 12}-BIT) were fabricated by solid state reaction (SSR) and polymeric precursor method (PPM). From these powders, Bi{sub 4}Ti{sub 3}O{sub 12} pellets were obtained by tape-casting using plate-like templates particles prepared by a molten salt method. The BIT phase crystallizes in an orthorhombic structure type with space group Fmmm. Agglomeration of the particles, which affects the densification ofmore » the ceramic, electrical conduction and leakage current at high electric fields, was monitored by transmission electronic microscopy (TEM) analyses. FEG-SEM indicated that different shape of grains of BIT ceramics was influenced by the processing route. Both SSR and PPM methods lead to unsaturated P–E loops of BIT ceramics originating from the highly c-axis orientation and high conductivity which was affected by charge carriers flowing normally to the grain boundary of the crystal lattice.« less

Effects of nasal septum perforation repair surgery on three-dimensional airflow: an evaluation using computational fluid dynamics.

PubMed

Nomura, Tsutomu; Ushio, Munetaka; Kondo, Kenji; Yamasoba, Tatsuya

2015-11-01

The purpose of this research is to determine the cause of nasal perforation symptoms and to predict post-operative function after nasal perforation repair surgery. A realistic three-dimensional (3D) model of the nose with a septal perforation was reconstructed using a computed tomography (CT) scan from a patient with nasal septal defect. The numerical simulation was carried out using ANSYS CFX V13.0. Pre- and post-operative models were compared by their velocity, pressure gradient (PG), wall shear (WS), shear strain rate (SSR) and turbulence kinetic energy in three plains. In the post-operative state, the crossflows had disappeared, and stream lines bound to the olfactory cleft area had appeared. After surgery, almost all of high-shear stress areas were disappeared comparing pre-operative model. In conclusion, the effects of surgery to correct nasal septal perforation were evaluated using a three-dimensional airflow evaluation. Following the surgery, crossflows disappeared, and WS, PG and SSR rate were decreased. A high WS.PG and SSR were suspected as causes of nasal perforation symptoms.

Genomic validation of PB 260 clone of rubber (Hevea brasiliensis) at Cikumpay Plantation by SSR marker

NASA Astrophysics Data System (ADS)

Royani, J. I.; Safarrida, A.; Rachmawati, I.; Khairiyah, H.; Mustika, I. P.; Suyono, A.; Rudiyana, Y.; Kubil; Nurjaya; Arianto, A.

2017-05-01

Rubber from Hevea brasiliensis is the only commercial natural rubber in the world. Propagation of rubber trees usually done by grafting and seed germination. BPPT had been producing rubber tree by in vitro technique with embryo somatic methods. Validation of mother plant for in vitro propagation is important to compare between mother plant and propagated plants. The aim for this research was to validation of PB 260 clone that planted at Cikumpay Plantation by SSR marker. Sampling of 10 rubber leaves were done at Cikumpay Plantation based on GPS position from the area of PB 260 clone. Rubber leaves were isolated with CTAB modification method to obtained DNA. Four of SSR primers from rubber, i.e.: hmac 4, hmac 5, hmct 1, and hmct 5, were used as primers to amplification of rubber DNA. The result showed that no band that different from 10 rubber of PB 260 clone at Cikumpay Plantation. This research will continue to compare genomic validation between mother plant and propagated plants that had been produced from BPPT.

Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica

PubMed Central

Vásquez-Mayorga, Marcela; Fuchs, Eric J.; Hernández, Eduardo J.; Herrera, Franklin; Hernández, Jesús; Moreira, Ileana; Arnáez, Elizabeth

2017-01-01

We estimated the genetic diversity of 50 Jatropha curcas samples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values for J. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f =  − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of the Jatropha curcas germplasm bank in Costa Rica. PMID:28289556

Genome-Wide Association of Rice Blast Disease Resistance and Yield-Related Components of Rice.

PubMed

Wang, Xueyan; Jia, Melissa H; Ghai, Pooja; Lee, Fleet N; Jia, Yulin

2015-12-01

Robust disease resistance may require an expenditure of energy that may limit crop yield potential. In the present study, a subset of a United States Department of Agriculture rice core collection consisting of 151 accessions was selected using a major blast resistance (R) gene, Pi-ta, marker and was genotyped with 156 simple sequence repeat (SSR) markers. Disease reactions to Magnaporthe oryzae, the causal agent of rice blast disease, were evaluated under greenhouse and field conditions, and heading date, plant height, paddy and brown seed weight in two field environments were analyzed, using an association mapping approach. A total of 21 SSR markers distributed among rice chromosomes 2 to 12 were associated with blast resistance, and 16 SSR markers were associated with seed weight, heading date, and plant height. Most noticeably, shorter plants were significantly correlated with resistance to blast, rice genomes with Pi-ta were associated with lighter seed weights, and the susceptible alleles of RM171 and RM6544 were associated with heavier seed weight. These findings unraveled a complex relationship between disease resistance and yield-related components.

Comparison of simple sequence repeats in 19 Archaea.

PubMed

Trivedi, S

2006-12-05

All organisms that have been studied until now have been found to have differential distribution of simple sequence repeats (SSRs), with more SSRs in intergenic than in coding sequences. SSR distribution was investigated in Archaea genomes where complete chromosome sequences of 19 Archaea were analyzed with the program SPUTNIK to find di- to penta-nucleotide repeats. The number of repeats was determined for the complete chromosome sequences and for the coding and non-coding sequences. Different from what has been found for other groups of organisms, there is an abundance of SSRs in coding regions of the genome of some Archaea. Dinucleotide repeats were rare and CG repeats were found in only two Archaea. In general, trinucleotide repeats are the most abundant SSR motifs; however, pentanucleotide repeats are abundant in some Archaea. Some of the tetranucleotide and pentanucleotide repeat motifs are organism specific. In general, repeats are short and CG-rich repeats are present in Archaea having a CG-rich genome. Among the 19 Archaea, SSR density was not correlated with genome size or with optimum growth temperature. Pentanucleotide density had an inverse correlation with the CG content of the genome.