PSI-B-20 A scan for signatures of selection in Russian Romanov sheep breed based on ROH hot spots analysis

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 225-226
Author(s):  
Tatiana E Deniskova ◽  
Alexandra S Abdelmanova ◽  
Arsen V Dotsev ◽  
Olga Koshkina ◽  
Andrey Rodionov ◽  
...  
Keyword(s):  
Production Systems ◽  
Embryo Implantation ◽  
Gonad Development ◽  
R Package ◽  
Lipid Binding ◽  
Prolactin Secretion ◽  
Analysis Tool ◽  
Sheep Population ◽  
Reproduction Traits ◽  
Signatures Of Selection

Abstract The world-famous Romanov breed of sheep fits easily into different production systems including private households, smallholders, and large farms. Such a resilience and extraordinary reproduction traits combining with good meat qualities have made the Romanov breed as a choice to produce mutton in the Central Russia regions. However, little is known on genetic mechanisms underlying the complex of specific traits of this breed. In this regard, we performed a scan of signatures of selection by identification of runs of homozygosity (ROH) islands in the Romanov sheep population. Forty-eight samples of the Romanov sheep from the Yaroslavl and Kaluga regions of Russia were genotyped using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). ROHs were estimated in the R package “detectRUNS” using window-free method for consecutive. The ROH shared in more than 50% of sheep were considered as ROH islands. The genes overlapped with the ROH islands were annotated using Ensembl genome browser 103. Enrichment for functional categories of the identified genes was performed using DAVID Functional Annotation Bioinformatics Microarray Analysis tool. More than 88 SNPs were found in ROH islands located on OAR1, OAR10, OAR11, OAR13, OAR14, OAR15, OAR16, OAR17 and OAR18. We detected a major group of genes related to reproduction traits. The identified candidates included UBE2Q1 (embryo implantation, fertilization, prolactin secretion), RNF17 (spermiogenesis), HSD11B2 (pregnancy, follicle function), FANCA (gonad development), and CUBN (embryonic development). In addition, several identified genes were involved in fatty acid metabolism (ACOX1, HAO2, and EIF6), lipid transport (OSBPL11), and biosynthesis of lipid-binding serum glycoproteins (BPIFB4) as well as in osteoblast differentiation (ADAR). The studies will be continued on a larger sample with further validation of the most promising candidate genes. Genotyping of twenty-four samples was performed within RFBR project No. 20-516-56002. Other twenty-four SNP-genotypes were generated within the theme No. 0445-2019-0024.

scholarly journals Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
E. F. Dzomba ◽  
M. Chimonyo ◽  
R. Pierneef ◽  
F. C. Muchadeyi
Keyword(s):  
South African ◽  
Production Systems ◽  
Smallholder Farmers ◽  
R Package ◽  
Population History ◽  
Chromosome 15 ◽  
Runs Of Homozygosity ◽  
The South ◽  
Selection Pressures ◽  
Sheep Population

Abstract Background Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1–6 Mb, 6–12 Mb, 12–24 Mb, 24–48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands. Results A total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1–6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns. Conclusions Overall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study.

A New Analysis Tool for Continuous Glucose Monitor Data

2021 ◽  
pp. 193229682110289
Author(s):  
Evan Olawsky ◽  
Yuan Zhang ◽  
Lynn E Eberly ◽  
Erika S Helgeson ◽  
Lisa S Chow
Keyword(s):  
Glucose Monitoring ◽  
Glycemic Variability ◽  
R Package ◽  
Analysis Tool ◽  
Continuous Glucose Monitor ◽  
Analysis Tools ◽  
R Shiny ◽  
Primary Driver ◽  
Rich Information ◽  
Web App

Background: With the development of continuous glucose monitoring systems (CGMS), detailed glycemic data are now available for analysis. Yet analysis of this data-rich information can be formidable. The power of CGMS-derived data lies in its characterization of glycemic variability. In contrast, many standard glycemic measures like hemoglobin A1c (HbA1c) and self-monitored blood glucose inadequately describe glycemic variability and run the risk of bias toward overreporting hyperglycemia. Methods that adjust for this bias are often overlooked in clinical research due to difficulty of computation and lack of accessible analysis tools. Methods: In response, we have developed a new R package rGV, which calculates a suite of 16 glycemic variability metrics when provided a single individual’s CGM data. rGV is versatile and robust; it is capable of handling data of many formats from many sensor types. We also created a companion R Shiny web app that provides these glycemic variability analysis tools without prior knowledge of R coding. We analyzed the statistical reliability of all the glycemic variability metrics included in rGV and illustrate the clinical utility of rGV by analyzing CGM data from three studies. Results: In subjects without diabetes, greater glycemic variability was associated with higher HbA1c values. In patients with type 2 diabetes mellitus (T2DM), we found that high glucose is the primary driver of glycemic variability. In patients with type 1 diabetes (T1DM), we found that naltrexone use may potentially reduce glycemic variability. Conclusions: We present a new R package and accompanying web app to facilitate quick and easy computation of a suite of glycemic variability metrics.

P–322 Addressing progesterone and cAMP signalling pathways for decidualization induction of endometrial stromal cells of patients with endometriosis

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
J Moyer ◽  
D Dunj. Baston-Buest ◽  
G Wennemuth ◽  
A Bielfeld ◽  
R Grümmer
Keyword(s):  
Stromal Cells ◽  
Day Treatment ◽  
Embryo Implantation ◽  
Flow Cytometric Analysis ◽  
Prolactin Secretion ◽  
In Vivo Model ◽  
Endometrial Stromal Cells ◽  
Simultaneous Application

Abstract Study question Which compounds/compound combinations are most effective in decidualization induction of endometrial stromal cells (ESCs) of patients with and without endometriosis? Summary answer Combination of compounds addressing different steps in the signalling cascade of decidualization induce decidualization more effectively than application of the individual compounds alone. What is known already Decidualization is the monthly recurring differentiation process of the ESCs in preparation for embryo implantation in human. Undifferentiated ESCs reveal an increased potential to proliferate and invade after retrograde menstruation. This may lead to the formation of ectopic lesions and the manifestation of the chronic gynaecological disease of endometriosis due to an impairment of the decidualization process. Study design, size, duration Compounds and compound combinations addressing the progesterone receptor- or the cAMP-mediated pathway were evaluated with regard to their own and their synergistic potential to induce decidualization of ESCs from women with (n = 10) and without (n = 10) endometriosis during a 6-day treatment. Participants/materials, setting, methods Human primary ESCs were isolated via enzymatic-mechanic digestion from eutopic endometrium from women with and without endometriosis and treated for 6 days in vitro with different progestins (progesterone, medoxyprogesterone acetate (MPA)), 8-Br-cAMP, forskolin, or phosphodiesterase (PDE)-inhibitor (Rolipram) alone or in combination. The degree of decidualization induction was quantified by morphological, biochemical (prolactin) and molecular (HAND2, FOXO1) parameters by means of ELISA, flow cytometric analysis, Realtime PCR and Western blot analysis. Main results and the role of chance After 6 days of treatment, decidualization was induced by forskolin as well as by 8-Br-cAMP whereas progestins or PDE alone hardly induced prolactin secretion by ESCs as a marker of decidualization. A change of morphology from undifferentiated fibroblast-like cells to rounded cells could be observed in parallel with the secretion of prolactin. Forskolin and 8-Br-cAMP-induced decidualization was significantly enhanced by MPA but not by progesterone. These effects were similar in ESCs from women with and without endometriosis. Moreover, forskolin-induced decidualization was significantly enhanced by simultaneous application of PDE. Interestingly, this effect was higher in cells of patients with endometriosis. An induction of decidualization in ESCs was associated with a parallel increase of the process-associated transcription factors HAND2 and FOXO1. This rise of transcription was markedly increased in combination with MPA but not with progesterone. Limitations, reasons for caution Endometrial tissue was obtained from women undergoing infertility treatment and thus may differ from the endometrium of fertile women. Results obtained from primary cells in vitro may not cover the in vivo situation in all respects. Wider implications of the findings: The results of this study provide baseline data for the development of a possible therapeutical approach to induce decidualization as a treatment option for endometriosis. Further research is required to determine the effectiveness of the in vitro tested compound combinations in an in vivo model. Trial registration number Not applicable

P-322 Addressing progesterone and cAMP signalling pathways for decidualization induction of endometrial stromal cells of patients with endometriosis

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
J Moyer ◽  
D Dunja Baston-Buest ◽  
G Wennemuth ◽  
A Bielfeld ◽  
R Grümmer
Keyword(s):  
Stromal Cells ◽  
Day Treatment ◽  
Embryo Implantation ◽  
Flow Cytometric Analysis ◽  
Prolactin Secretion ◽  
In Vivo Model ◽  
Endometrial Stromal Cells ◽  
Simultaneous Application

Abstract Study question Which compounds/compound combinations are most effective in decidualization induction of endometrial stromal cells (ESCs) of patients with and without endometriosis? Summary answer Combination of compounds addressing different steps in the signalling cascade of decidualization induce decidualization more effectively than application of the individual compounds alone. What is known already Decidualization is the monthly recurring differentiation process of the ESCs in preparation for embryo implantation in human. Undifferentiated ESCs reveal an increased potential to proliferate and invade after retrograde menstruation. This may lead to the formation of ectopic lesions and the manifestation of the chronic gynaecological disease of endometriosis due to an impairment of the decidualization process. Study design, size, duration Compounds and compound combinations addressing the progesterone receptor- or the cAMP-mediated pathway were evaluated with regard to their own and their synergistic potential to induce decidualization of ESCs from women with (n = 10) and without (n = 10) endometriosis during a 6-day treatment. Participants/materials, setting, methods Human primary ESCs were isolated via enzymatic-mechanic digestion from eutopic endometrium from women with and without endometriosis and treated for 6 days in vitro with different progestins (progesterone, medoxyprogesterone acetate (MPA)), 8-Br-cAMP, forskolin, or phosphodiesterase (PDE)-inhibitor (Rolipram) alone or in combination. The degree of decidualization induction was quantified by morphological, biochemical (prolactin) and molecular (HAND2, FOXO1) parameters by means of ELISA, flow cytometric analysis, Realtime PCR and Western blot analysis. Main results and the role of chance After 6 days of treatment, decidualization was induced by forskolin as well as by 8-Br-cAMP whereas progestins or PDE alone hardly induced prolactin secretion by ESCs as a marker of decidualization. A change of morphology from undifferentiated fibroblast-like cells to rounded cells could be observed in parallel with the secretion of prolactin. Forskolin and 8-Br-cAMP-induced decidualization was significantly enhanced by MPA but not by progesterone. These effects were similar in ESCs from women with and without endometriosis. Moreover, forskolin-induced decidualization was significantly enhanced by simultaneous application of PDE. Interestingly, this effect was higher in cells of patients with endometriosis. An induction of decidualization in ESCs was associated with a parallel increase of the process-associated transcription factors HAND2 and FOXO1. This rise of transcription was markedly increased in combination with MPA but not with progesterone. Limitations, reasons for caution Endometrial tissue was obtained from women undergoing infertility treatment and thus may differ from the endometrium of fertile women. Results obtained from primary cells in vitro may not cover the in vivo situation in all respects. Wider implications of the findings The results of this study provide baseline data for the development of a possible therapeutical approach to induce decidualization as a treatment option for endometriosis. Further research is required to determine the effectiveness of the in vitro tested compound combinations in an in vivo model. Trial registration number not applicable

An Analytical/Numerical Procedure for Structural Analysis of Hybrid Riser Systems

2005 ◽  
Author(s):  
G. J. O. Rodrigues ◽  
Daniel C. T. Cardoso ◽  
Beatriz S. L. P. de Lima ◽  
Breno P. Jacob ◽  
Antonio C. Fernandes
Keyword(s):  
Finite Element ◽  
Dynamic Simulation ◽  
Production Systems ◽  
Three Dimensional ◽  
Numerical Procedure ◽  
Solution Procedure ◽  
Analysis Tool ◽  
Full Time ◽  
Transient Effects ◽  
Dimensional Solution

In deep and ultra-deep water petroleum exploitation activities, floating production systems such as semi submersible platforms and FPSO (Floating Production, Storage and Offloading) units have been commonly employed. However, the utilization of flexible risers in ultra-deep waters has been hindered by technical and economical reasons. On the other hand, first order motions from the floating unit due to environmental loads are not favorable to the use of Steel Catenary Risers (SCR) in a free-hanging configuration. This fact has motivated several studies on hybrid riser systems, including the system studied in this work, which is based on a sub-surface buoy with large dimensions, moored to the seabed by tethers. This system employs flexible lines connecting the floating unit to the buoy, in the region where dynamic effects are more relevant due to the floating unit motions, and also SCRs that extend from the buoy to the seabed, in the region where dynamic motions are not so significant. The objective of this work is to describe a solution procedure for the analysis of such a hybrid riser system. This procedure is based on an analytical formulation that is solved numerically. One of the main features of this procedure is the fact that it takes into account the effects of current loads acting on the lines. Current profiles can be considered, with direction and velocities varying with depth, therefore configuring a full three-dimensional solution. This procedure can be employed either as a preliminary static analysis tool, to be used in parametric studies in order to assess the feasibility of candidate configurations of hybrid riser systems, or else for the generation of finite-element meshes for a full time-domain nonlinear dynamic simulation. It is important to start the dynamic simulation from a statically balanced configuration, since the transient effects can be dramatically shortened and the total simulation time can be reduced. The results obtained from this procedure are compared with a discrete solution obtained using a nonlinear finite-element based solver. The strategy considered here is intended to be an approach that will speed up the tasks involved in the design of hybrid risers systems based on the subsurface buoy concept.

Genetic parameters for tropical beef cattle in northern Australia: a review

1993 ◽  
Vol 44 (2) ◽  
pp. 179 ◽  
Author(s):  
GP Davis
Keyword(s):  
Genetic Parameters ◽  
Production Systems ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Genetic Correlations ◽  
Environmental Stresses ◽  
Northern Australia ◽  
Weighted Mean ◽  
Weaning Weight ◽  
Reproduction Traits

This paper reviews published estimates of genetic parameters for traits of growth, reproduction and resistance to environmental stresses for Bos indicus and Zebu derived breeds in northern Australia. Most published estimates of heritabilities for growth and reproduction traits were higher for tropically adapted breeds in northern Australia than for Bos taurus breeds in temperate Australia. Weighted mean estimates of heritabilities for the direct component of weaning weight were 39% for the Brahman breed and 30% for Zebu-derived breeds in northern Australia compared with 13% for Bos taurus breeds in temperate areas of Australia. Mean estimates for the maternal component of weaning weight were 5, 24 and 13% respectively. Mean heritabilities for yearling and 550 day weights for Zebu derived breeds in northern Australia (24 and 25%) were similar to those for Bos taurus breeds in temperate areas, though estimates for Brahmans were higher (39 and 39%). Published estimates of heritabilities of later weights (700 and 900 days), which are most relevant to northern Australian production systems, were rare but averaged between 32 and 45% for Zebu-derived breeds and Brahmans. Weighted mean heritability for female calving success was 14% and for realised bull fertility was 5%. Published estimates of heritabilities of scrota1 circumference averaged 31%, and testosterone response to GNRH stimulation was 52%. Heritabilities of resistance to various environmental stresses were all moderate with weighted means between 20 and 34%. Genetic correlations between growth, reproduction and resistance to environmental stresses are also reviewed. There appears to be predictable variation in estimates of parameters between breeds in different environments which is related to level of resistance to environmental stresses, and this is likely to affect the prediction of breeding values for cattle in northern Australia.

Computational Tool for the Dynamic Analysis of Flexible Risers Incorporating Bending Hysteresis

2007 ◽  
Author(s):  
Russell Smith ◽  
Tommie Carr ◽  
Michael Lane
Keyword(s):  
Production Systems ◽  
New Technology ◽  
Fatigue Loading ◽  
Bending Stiffness ◽  
Analysis Tool ◽  
Flexible Pipe ◽  
Recent Developments ◽  
Dynamic Bending ◽  
Increasing Demand ◽  
Bending Response

Non-bonded flexible-pipe risers provide a structurally compliant solution in offshore floating production systems for the recovery of oil & gas. The bending stiffness of the flexible pipe is an important property in designing the riser system to safely withstand extreme and fatigue loading conditions. These risers have two fundamentally different bending stiffness properties that depend on if the riser system is pressurized or depressurized. A depressurized riser has a comparatively small linear bending stiffness. Most riser designs apply this stiffness as its produces conservative (large) bending responses. In recent years, the bending response predicted from the depressurized bending stiffness has proven overly conservative and there has been an increasing demand to consider the larger hysteretic bending stiffness of the pressurized riser. The objective is to reduce the conservatism and achieve an approved safe design. Recent developments have advanced the modeling of flexible riser bending with hysteresis and this capability has now been incorporated into an industry standard finite-element riser analysis tool. This paper describes the background of hysteresis in relation to non-bonded flexible pipes and outlines the methodology of the riser motions software that incorporates bending stiffness with hysteresis. Riser systems where the dynamic bending response is critical to the success of the design are the main applications that will benefit from this new technology. Examples include: i.) The dynamic bending response at the seabed touchdown of a deepwater catenary riser. ii.) Bending at an interface with the riser hang-off or subsea tie-in.

Genetics of early and lifetime annual reproductive performance in cows of two tropical beef genotypes in northern Australia

2014 ◽  
Vol 54 (1) ◽  
pp. 1 ◽  
Author(s):  
D. J. Johnston ◽  
S. A. Barwick ◽  
G. Fordyce ◽  
R. G. Holroyd ◽  
P. J. Williams ◽  
...  
Keyword(s):  
Reproductive Performance ◽  
Reproductive Tract ◽  
Production Systems ◽  
Comprehensive Evaluation ◽  
Genetic Correlations ◽  
Reproductive Traits ◽  
Female Reproduction ◽  
Reproduction Traits ◽  
Beef Cattle Breeds ◽  
Calving Rate

Reproduction records from 2137 cows first mated at 2 years of age and recorded through to 8.5 years of age were used to study the genetics of early and lifetime reproductive performance from two genotypes (1020 Brahman and 1117 Tropical Composite) in tropical Australian production systems. Regular ultrasound scanning of the reproductive tract, coupled with full recording of mating, calving and weaning histories, allowed a comprehensive evaluation of a range of reproductive traits. Results showed components traits of early reproductive performance had moderate to high heritabilities, especially in Brahmans. The heritability of lactation anoestrous interval in 3-year-old cows was 0.51 ± 0.18 and 0.26 ± 0.11 for Brahman and Tropical Composite, respectively. Heritabilities of binary reproductive output traits (conception rate, pregnancy rate, calving rate and weaning rate) from first and second matings were generally moderate to high on the underlying scale. Estimates ranged from 0.15 to 0.69 in Brahman and 0.15 to 0.34 in Tropical Composite, but were considerably lower when expressed on the observed scale, particularly for those traits with high mean levels. Heritabilities of lifetime reproduction traits were low, with estimates of 0.11 ± 0.06 and 0.07 ± 0.06 for lifetime annual weaning rate in Brahman and Tropical Composite, respectively. Significant differences in mean reproductive performance were observed between the two genotypes, especially for traits associated with anoestrus in first-lactation cows. Genetic correlations between early-in-life reproductive measures and lifetime reproduction traits were moderate to high. Genetic correlations between lactation anoestrous interval and lifetime annual weaning rate were –0.62 ± 0.24 in Brahman and –0.87 ± 0.32 in Tropical Composite. The results emphasise the substantial opportunity that exists to genetically improve weaning rates in tropical beef cattle breeds by focusing recording and selection on early-in-life female reproduction traits, particularly in Brahman for traits associated with lactation anoestrus.

scholarly journals UCSCXenaShiny: An R Package for Exploring and Analyzing UCSC Xena Public Datasets in Web Browser

2020 ◽  
Author(s):  
Shixiang Wang ◽  
Yi Xiong ◽  
Kai Gu ◽  
Longfei Zhao ◽  
Yin Li ◽  
...  
Keyword(s):  
R Package ◽  
Data Availability ◽  
Analysis Tool ◽  
Omics Data ◽  
Analysis Framework ◽  
Web Browser ◽  
Research Opportunities ◽  
Public Projects ◽  
R Shiny ◽  
Public Datasets

Motivation: UCSC Xena platform provides huge amounts of processed cancer omics data from big public projects like TCGA or individual reserach groups for enabling unprecedented research opportunities. In 2019, we developed UCSCXenaTools, an R package for retrieval of UCSC Xena data. However, an easier dataset exploration and analysis tool is still lack, especially for researchers without programming experience. Results: We develop UCSCXenaShiny, an R Shiny package to quickly explore, download all datasets from UCSC Xena data hubs. In addiction, a module based analysis framework is constructed to analyze and visualize data. Availability: https://github.com/openbiox/UCSCXenaShiny or https://cran.r-project.org/package=UCSCXenaShiny.

Sign in / Sign up

Export Citation Format

Share Document