scholarly journals Shed skin as a source of DNA for genotyping-by-sequencing (GBS) in reptiles

2019 ◽  
Author(s):  
Thomas D Brekke ◽  
Liam Shier ◽  
Matthew J Hegarty ◽  
John F Mulley
Keyword(s):  
Genotyping By Sequencing ◽  
Direct Result ◽  
Good Source ◽  
Genetic Studies ◽  
Reduced Representation ◽  
The Public ◽  
Large Numbers ◽  
Corn Snake ◽  
Skin Samples ◽  
Transitions And Transversions

AbstractAssociation and genetic mapping studies aimed at linking genotype to phenotype are powerful tools that require large numbers of samples, complicating their use in long-lived species with low fecundity. Shed skins of snakes and other reptiles contain DNA; are a safe and ethical way of non-invasively sampling large numbers of individuals; and provide a simple mechanism by which to involve the public in scientific research. Here we test whether the DNA in dried shed skins mailed to us from citizen scientists is suitable for reduced representation sequencing approaches, specifically genotyping-by-sequencing (GBS). We find that shed skin samples provide DNA of sufficient quality and quantity for GBS, although libraries from shed skin resulted in fewer sequenced reads than libraries from snap-frozen muscle, and contained slightly fewer variants (70,685 SNPs versus 97,724). This issue is a direct result of lower read counts of the shed skin samples, and can be rectified quite simply with deeper sequencing. Skin-derived libraries also have a very slight (but significantly different) profile of transitions and transversions, suggesting that DNA damage occurs but is minimal. We conclude that shed skin-derived DNA is a good source of genomic DNA for a variety of genetic studies, and use it to identify sex-linked scaffolds in the corn snake genome.

scholarly journals Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 222
Author(s):  
Bartosz Ulaszewski ◽  
Joanna Meger ◽  
Jaroslaw Burczyk
Keyword(s):  
Population Genomics ◽  
De Novo ◽  
Genetic Studies ◽  
Genomic Libraries ◽  
Reduced Representation ◽  
Large Numbers ◽  
Broadleaved Tree Species ◽  
Fagus Sylvatica L ◽  
Reference Genomes ◽  
Future Population

Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.

scholarly journals Humane Slaughter of Edible Decapod Crustaceans

Animals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1089
Author(s):  
Francesca Conte ◽  
Eva Voslarova ◽  
Vladimir Vecerek ◽  
Robert William Elwood ◽  
Paolo Coluccio ◽  
...  
Keyword(s):  
Cognitive Capacity ◽  
Decapod Crustaceans ◽  
The Public ◽  
Large Numbers ◽  
Increasing Demand

Vast numbers of crustaceans are produced by aquaculture and caught in fisheries to meet the increasing demand for seafood and freshwater crustaceans. Simultaneously, the public is increasingly concerned about current methods employed in their handling and killing. Recent evidence has shown that decapod crustaceans probably have the capacity to suffer because they show responses consistent with pain and have a relatively complex cognitive capacity. For these reasons, they should receive protection. Despite the large numbers of crustaceans transported and slaughtered, legislation protecting their welfare, by using agreed, standardized methods, is lacking. We review various stunning and killing systems proposed for crustaceans, and assess welfare concerns. We suggest the use of methods least likely to cause suffering and call for the implementation of welfare guidelines covering the slaughter of these economically important animals.

RELIGIOUS CHANGE AND THE TIMING OF BAPTISM IN ENGLAND, 1538–1750

2009 ◽  
Vol 52 (2) ◽  
pp. 269-294 ◽  
Author(s):  
P. M. KITSON
Keyword(s):  
Sixteenth Century ◽  
Early Modern ◽  
Early Modern Period ◽  
Religious Change ◽  
Public Performance ◽  
The Public ◽  
Modern Period ◽  
Medieval Church ◽  
Large Numbers ◽  
Common Prayer

ABSTRACTThe religious reforms of the sixteenth century exerted a profound impact upon the liturgy of baptism in England. While historians' attention has been drawn to the theological debates concerning the making of the sign of the cross, the new baptism liturgy contained within the Book of common prayer also placed an innovative importance on the public performance of the rite in the presence of the whole congregation on Sundays and other holy days. Both religious radicals and conservatives contested this stress on ceremony and publicity throughout the early modern period. Through the collection of large numbers of baptism dates from parish registers, it is possible to measure adherence to these new requirements across both space and time. Before the introduction of the first prayer book in 1549, there was considerable uniformity among communities in terms of the timing of baptism, and the observed patterns are suggestive of conformity to the requirements of the late medieval church. After the mid-sixteenth century, parishes exhibited a range of responses, ranging from enthusiastic adoption by many communities to complete disregard in religiously conservative parts of Lancashire and Cheshire. Additionally, the popularity of saints' festivals as popular days for baptism fell markedly after 1660, suggesting a decline in the observance of these feasts.

Preemption in Public Health: The Dynamics of Clean Indoor Air Laws

2003 ◽  
Vol 31 (S4) ◽  
pp. 84-85 ◽  
Author(s):  
Elva Yañez ◽  
Gary Cox ◽  
Mike Cooney ◽  
Robert Eadie
Keyword(s):  
Public Health ◽  
Indoor Air ◽  
Tobacco Industry ◽  
Political Influence ◽  
Direct Result ◽  
Special Interest Groups ◽  
Policy Action ◽  
Local Public Health ◽  
The Public ◽  
City Councils

Preemption is a powerful strategy used by special interest groups to undermine strong, local public health standards. Currently, 20 states in the U.S. have preemption ordinances in place related to clean indoor air initiatives. These preemption laws are the direct result of an ongoing and aggressive campaign of tobacco companies to thwart clean indoor air initiatives, which ultimately, according to tobacco industry internal documents, cause significant reductions in their annual revenues. Clean indoor air policies have arisen from a greater understanding of the documented health risks associated with exposure to secondhand smoke and action by local government (city councils, county commissions, and boards of health) to protect the public from these hazards. The efforts of the tobacco industry undermine local authority and seek to shift policy action to the state and federal levels, where the industry has greater political influence.

scholarly journals DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing

2018 ◽  
Vol 19 (11) ◽  
pp. 3542 ◽  
Author(s):  
Ángela Prudencio ◽  
Olaf Werner ◽  
Pedro Martínez-García ◽  
Federico Dicenta ◽  
Rosa Ros ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Prunus Persica ◽  
Prolonged Exposure ◽  
Genotyping By Sequencing ◽  
Fruit Trees ◽  
Prunus Dulcis ◽  
Dormancy Release ◽  
Release Process ◽  
Cold Temperatures ◽  
Reduced Representation

DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.

scholarly journals Clinical signs of trachoma are prevalent among Solomon Islanders who have no persistent markers of prior infection with Chlamydia trachomatis

2018 ◽  
Vol 3 ◽  
pp. 14
Author(s):  
Robert Butcher ◽  
Oliver Sokana ◽  
Kelvin Jack ◽  
Leslie Sui ◽  
Charles Russell ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
Sexual Debut ◽  
Solomon Islands ◽  
Clinical Signs ◽  
World Health ◽  
Direct Result ◽  
Policy Makers ◽  
The Public ◽  
High Prevalence ◽  
Health Organization

Background: The low population-prevalence of trachomatous trichiasis and high prevalence of trachomatous inflammation–follicular (TF) provide contradictory estimates of the magnitude of the public health threat from trachoma in the Solomon Islands. Improved characterisation of the biology of trachoma in the region may support policy makers as they decide what interventions are required. Here, age-specific profiles of anti-Pgp3 antibodies and conjunctival scarring were examined to determine whether there is evidence of ongoing transmission and pathology from ocular Chlamydia trachomatis (Ct) infection. Methods: A total of 1511 individuals aged ≥1 year were enrolled from randomly selected households in 13 villages in which >10% of children aged 1–9 years had TF prior to a single round of azithromycin mass drug administration undertaken six months previously. Blood was collected to be screened for antibodies to the Ct antigen Pgp3. Tarsal conjunctival photographs were collected for analysis of scarring severity. Results: Anti-Pgp3 seropositivity was 18% in 1–9 year olds, sharply increasing around the age of sexual debut to reach 69% in those over 25 years. Anti-Pgp3 seropositivity did not increase significantly between the ages of 1–9 years and was not associated with TF (p=0.581) or scarring in children (p=0.472). Conjunctival scars were visible in 13.1% of photographs. Mild (p<0.0001) but not severe (p=0.149) scars increased in prevalence with age. Conclusions: Neither conjunctival scars nor lymphoid follicles were associated with antibodies to Ct, suggesting that they are unlikely to be a direct result of ocular Ct infection. Clinical signs of trachoma were prevalent in this population but were not indicative of the underlying rates of Ct infection. The current World Health Organization guidelines for trachoma elimination indicated that this population should receive intervention with mass distribution of antibiotics, but the data presented here suggest that this may not have been appropriate.

scholarly journals The representation and tenure of female principals in public enterprises in emerging markets: A protracted dearth?

2021 ◽  
Vol 10 (1) ◽  
pp. 58-73
Author(s):  
Ralph Marenga
Keyword(s):  
Emerging Market ◽  
Gender Diversity ◽  
Public Enterprise ◽  
Public Enterprises ◽  
Contributing Factors ◽  
Reduced Representation ◽  
Female Principals ◽  
The Public ◽  
Robust Implementation ◽  
Implementation Gaps

The reduced representation and tenure of women as public enterprise (PE) principals in Namibia as an emerging market and developing country are concerning (Mboti, 2014; Menges, 2020). The contributing factors are an element literature fails to address explicitly in the Namibian case. This paper, therefore, aims to consolidate evidence on whether the underrepresentation and limited tenures of female principals in Namibian PEs signal a protracted dearth of women in such positions. Methodically, a desk review is used to analyse the literature. Key findings of this paper identify the absence of top-down hands-on leadership; legal and policy implementation gaps; failure to declare gender diversity as imperative in the public sector; failure to focus on helping women gain broad line experience early on, among others, as contributing factors that have disadvantaged female principals in Namibian PEs. The challenges women face in being appointed or completing their tenure as PE principals over the years signal a protracted dearth of women in positions of PE principals in Namibia. Understanding these dynamics is relevant for enhancing Namibia’s policy efforts to curb the further proliferation of patriarchy as nuanced in the glass ceiling. This paper recommends the robust implementation of existing anti-patriarchy legislation.

Financial Access to Care Does Not Guarantee Better Care for Children

PEDIATRICS ◽  
1994 ◽  
Vol 93 (3) ◽  
pp. 506-508
Author(s):  
Arthur F. Kohrman
Keyword(s):  
Health Care ◽  
Access To Care ◽  
Health Care Reform ◽  
Vulnerable Children ◽  
Financial Access ◽  
Public And Private ◽  
The Public ◽  
Large Numbers ◽  
Care System

The thoughtful and cautionary pieces by Newacheck et al1 and Perrin et al2 remind us of how much we have achieved in piecing together care for vulnerable children, how far there is yet to go, and how the transition to the long-overdue health care reform might worsen, rather than improve our present arrangements. In the absence of a rational, planned care system for children, especially for those who are poor or who require extensive services, pediatricians and child advocates in both the public and private sectors have managed to cobble together at least the possibility of decent services for large numbers of children, with some payment to those who provide those services.

scholarly journals Religious Community Responses to the Public Policy of the Indonesian Government Related to the covid-19 Pandemic

2020 ◽  
Vol 8 (2-3) ◽  
pp. 273-283
Author(s):  
Amos Sukamto ◽  
S. Panca Parulian
Keyword(s):  
Catholic Church ◽  
Government Regulation ◽  
Religious Community ◽  
Religious Activities ◽  
Government Regulations ◽  
Holy Communion ◽  
The Public ◽  
Indonesian Government ◽  
Large Numbers ◽  
Pentecostal Churches

Abstract The purpose of this article is to analyze religious responses to the policy of Indonesian government in dealing with the covid-19 pandemic. Article 4 of Government Regulation (PP) No. 21/2020 mentions restrictions on religious activities. The response of the religious community to this government policy was varied. The Council of Indonesian Ulama, Majelis Ulama Indonesia (mui), issued several fatwas containing a ban on worship involving large numbers of people. A small group of fanatic Muslims initially opposed the policy, but eventually followed it. Among Protestants, the mainstream and Pentecostal churches under the Communion of Churches in Indonesia (pgi) are highly coordinated with government regulations. Some Pentecostal churches attempted to continue holding worship together for reasons of holy communion, but eventually they followed government regulations. The Catholic church followed government regulations consistently.

Crowdsourcing Investigations

2014 ◽  
Vol 6 (4) ◽  
pp. 60-75 ◽  
Author(s):  
Andrea H. Tapia ◽  
Nicolas J. LaLone
Keyword(s):  
Public Opinion ◽  
Sentiment Analysis ◽  
Ethical Dilemmas ◽  
The Internet ◽  
Social Approval ◽  
Online Groups ◽  
The Public ◽  
Large Numbers ◽  
Boston Marathon Bombing ◽  
Boston Marathon

In this paper the authors illustrate the ethical dilemmas that arise when large public investigations in a crisis are crowdsourced. The authors focus the variations in public opinion concerning the actions of two online groups during the immediate aftermath of the Boston Marathon Bombing. These groups collected and organized relief for victims, collected photos and videos taken of the bombing scene and created online mechanisms for the sharing and analysis of images collected online. They also used their large numbers and the affordances of the Internet to produce an answer to the question, “who was the perpetrator, and what kind of bomb was used?” The authors view their actions through public opinion, through sampling Twitter and applying a sentiment analysis to this data. They use this tool to pinpoint moments during the crisis investigation when the public became either more positively or negatively inclined toward the actions of the online publics. The authors use this as a surrogate, or proxy, for social approval or disapproval of their actions, which exposes large swings in public emotion as ethical lines are crossed by online publics.

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