Towards Conservation of Omani Local Chicken: Phenotypic Characteristics, Management Practices and Performance Traits

Characterizing local chicken types and their mostly rural production systems is prerequisite for designing and implementing development and conservation programs. This study evaluated the management practices of small-scale chicken keepers and the phenotypic and production traits of their chickens in Oman, where conservation programs for local livestock breeds have currently started. Free-range scavenging was the dominant production system, and logistic regression analysis showed that socio-economic factors such as training in poultry keeping, household income, income from farming and gender of chicken owners influenced feeding, housing, and health care practices (p<0.05). A large variation in plumage and shank colors, comb types and other phenotypic traits within and between Omani chicken populations were observed. Male and female body weight differed (p<0.05), being 1.3±0.65 kg and 1.1±0.86 kg respectively. Flock size averaged 22±7.7 birds per household with 4.8 hens per cock. Clutch size was 12.3±2.85 and annual production 64.5±2.85 eggs per hen. Egg hatchability averaged 88±6.0% and annual chicken mortality across all age and sex categories was 16±1.4%. The strong involvement of women in chicken keeping makes them key stakeholders in future development and conservation programs, but the latter should be preceded by a comprehensive study of the genetic diversity of the Omani chicken populations

Opening the black box of energy modelling: Strategies and lessons learned

The global energy system is undergoing a major transition, and in energy planning and decision-making across governments, industry and academia, models play a crucial role. Because of their policy relevance and contested nature, the transparency and open availability of energy models and data are of particular importance. Here we provide a practical how-to guide based on the collective experience of members of the Open Energy Modelling Initiative (Openmod). We discuss key steps to consider when opening code and data, including determining intellectual property ownership, choosing a licence and appropriate modelling languages, distributing code and data, and providing support and building communities. After illustrating these decisions with examples and lessons learned from the community, we conclude that even though individual researchers' choices are important, institutional changes are still also necessary for more openness and transparency in energy research

Development of 200-GHz to 2.7-THz multiplier chains for submillimeter-wave heterodyne receivers

Several astrophysics and Earth observation space missions planned for the near future will require submillimeter-wave heterodyne radiometers for spectral line observations. One of these, the Far InfraRed and Submillimeter Telescope will perform high-sensitivity, high-resolution spectroscopy in the 400 to 2700 GHz range with a seven channel super- conducting heterodyne receiver complement. The local oscillators for all these channels will be constructed around state-of-the-art GaAs power amplifiers in the 71 to 115 GHz range, followed by planar Schottky diode multiplier chains. The Jet Propulsion Laboratory is responsible for developing the multiplier chains for the 1.2, 1.7, and 2.7 THz bands. This paper will focus on the designs and technologies being developed to enhance the current state- of-the-art, which is based on discrete planar or whisker contacted GaAs Schottky diode chips mounted in waveguide blocks. We are proposing a number of new planar integrated circuit and device topologies to implement multipliers at these high frequencies. Approaches include substrateless, framed and frameless GaAs membrane circuitry with single, and multiple planar integrated Schottky diodes. Circuits discussed include 200 and 400 GHz doublers, a 1.2 THz tripler and a 2.4 THz doubler. Progress to date, with the implications of this technology development for future Earth and space science instruments, is presented

Cattle transhumance and agropastoral nomadic herding practices in central Cameroon

Abstract Background In sub-Saharan Africa, livestock transhumance represents a key adaptation strategy to environmental variability. In this context, seasonal livestock transhumance also plays an important role in driving the dynamics of multiple livestock infectious diseases. In Cameroon, cattle transhumance is a common practice during the dry season across all the main livestock production zones. Currently, the little recorded information of the migratory routes, grazing locations and nomadic herding practices adopted by pastoralists, limits our understanding of pastoral cattle movements in the country. GPS-tracking technology in combination with a questionnaire based-survey were used to study a limited pool of 10 cattle herds from the Adamawa Region of Cameroon during their seasonal migration, between October 2014 and May 2015. The data were used to analyse the trajectories and movement patterns, and to characterize the key animal health aspects related to this seasonal migration in Cameroon. Results Several administrative Regions of the country were visited by the transhumant herds over more than 6 months. Herds travelled between 53 and 170 km to their transhumance grazing areas adopting different strategies, some travelling directly to their destination areas while others having multiple resting periods and grazing areas. Despite their limitations, these are among the first detailed data available on transhumance in Cameroon. These reports highlight key livestock health issues and the potential for multiple types of interactions between transhumant herds and other domestic and wild animals, as well as with the formal livestock trading system. Conclusion Overall, these findings provide useful insights into transhumance patterns and into the related animal health implications recorded in Cameroon. This knowledge could better inform evidence-based approaches for designing infectious diseases surveillance and control measures and help driving further studies to improve the understanding of risks associated with livestock movements in the region

Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit

Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies

Interaction between polymorphisms of the Human Leukocyte Antigen and HPV-16 Variants on the risk of invasive cervical cancer

<p>Abstract</p> <p>Background</p> <p>Persistent infection with oncogenic types of human papillomavirus (HPV) is the major risk factor for invasive cervical cancer (ICC), and non-European variants of HPV-16 are associated with an increased risk of persistence and ICC. HLA class II polymorphisms are also associated with genetic susceptibility to ICC. Our aim is to verify if these associations are influenced by HPV-16 variability.</p> <p>Methods</p> <p>We characterized HPV-16 variants by PCR in 107 ICC cases, which were typed for <it>HLA-DQA1</it>, <it>DRB1 </it>and <it>DQB1 </it>genes and compared to 257 controls. We measured the magnitude of associations by logistic regression analysis.</p> <p>Results</p> <p>European (E), Asian-American (AA) and African (Af) variants were identified. Here we show that inverse association between <it>DQB1*05 </it>(adjusted odds ratio [OR] = 0.66; 95% confidence interval [CI]: 0.39–1.12]) and HPV-16 positive ICC in our previous report was mostly attributable to AA variant carriers (OR = 0.27; 95%CI: 0.10–0.75). We observed similar proportions of <it>HLA DRB1*1302 </it>carriers in E-P positive cases and controls, but interestingly, this allele was not found in AA cases (p = 0.03, Fisher exact test). A positive association with <it>DRB1*15 </it>was observed in both groups of women harboring either E (OR = 2.99; 95% CI: 1.13–7.86) or AA variants (OR = 2.34; 95% CI: 1.00–5.46). There was an inverse association between <it>DRB1*04 </it>and ICC among women with HPV-16 carrying the 350T [83L] single nucleotide polymorphism in the <it>E6 </it>gene (OR = 0.27; 95% CI: 0.08–0.96). An inverse association between <it>DQB1*05 </it>and cases carrying 350G (83V) variants was also found (OR = 0.37; 95% CI: 0.15–0.89).</p> <p>Conclusion</p> <p>Our results suggest that the association between HLA polymorphism and risk of ICC might be influenced by the distribution of HPV-16 variants.</p

3640 Unique EST Clusters from the Medaka Testis and Their Potential Use for Identifying Conserved Testicular Gene Expression in Fish and Mammals

BACKGROUND: The fish medaka is the first vertebrate capable of full spermatogenesis in vitro from self-renewing spermatogonial stem cells to motile test-tube sperm. Precise staging and molecular dissection of this process has been hampered by the lack of suitable molecular markers. METHODOLOGY AND PRINCIPAL FINDINGS: We have generated a normalized medaka testis cDNA library and obtained 7040 high quality sequences representing 3641 unique gene clusters. Among these, 1197 unique clusters are homologous to known genes, and 2444 appear to be novel genes. Ontology analysis shows that the 1197 gene products are implicated in diverse molecular and cellular processes. These genes include markers for all major types of testicular somatic and germ cells. Furthermore, markers were identified for major spermatogenic stages ranging from spermatogonial stem cell self-renewal to meiosis entry, progression and completion. Intriguingly, the medaka testis expresses at least 13 homologs of the 33 mouse X-chromosomal genes that are enriched in the testis. More importantly, we show that key components of several signaling pathways known to be important for testicular function in mammals are well represented in the medaka testicular EST collection. CONCLUSIONS/SIGNIFICANCE: Medaka exhibits a considerable similarity in testicular gene expression to mammals. The medaka testicular EST collection we obtained has wide range coverage and will not only consolidate our knowledge on the comparative analysis of known genes' functions in the testis but also provide a rich resource to dissect molecular events and mechanism of spermatogenesis in vivo and in vitro in medaka as an excellent vertebrate model

Opening the black box of energy modelling: Strategies and lessons learned

The global energy system is undergoing a major transition, and in energy planning and decision-making across governments, industry and academia, models play a crucial role. Because of their policy relevance and contested nature, the transparency and open availability of energy models and data are of particular importance. Here we provide a practical how-to guide based on the collective experience of members of the Open Energy Modelling Initiative (Openmod). We discuss key steps to consider when opening code and data, including determining intellectual property ownership, choosing a licence and appropriate modelling languages, distributing code and data, and providing support and building communities. After illustrating these decisions with examples and lessons learned from the community, we conclude that even though individual researchers' choices are important, institutional changes are still also necessary for more openness and transparency in energy research