Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins

Milk production is an economically important sector of global agriculture. Much attention has been paid to the identification of quantitative trait loci (QTL) associated with milk, fat, and protein yield and the genetic and molecular mechanisms underlying them. Copy number variation (CNV) is an emerging class of variants which may be associated with complex traits. In this study, we performed a genome-wide association between CNVs and milk production traits in 26,362 Holstein bulls and cows. A total of 99 candidate CNVs were identified using Illumina BovineSNP50 array data, and association tests for each production trait were performed using a linear regression analysis with PCA correlation. A total of 34 CNVs on 22 chromosomes were significantly associated with at least one milk production trait after false discovery rate (FDR) correction. Some of those CNVs were located within or near known QTL for milk production traits. We further investigated the relationship between associated CNVs with neighboring SNPs. For all 82 combinations of traits and CNVs (less than 400 kb in length), we found 17 cases where CNVs directly overlapped with tag SNPs and 40 cases where CNVs were adjacent to tag SNPs. In 5 cases, CNVs located were in strong linkage disequilibrium with tag SNPs, either within or adjacent to the same haplotype block. There were an additional 20 cases where CNVs did not have a significant association with SNPs, suggesting that the effects of those CNVs were probably not captured by tag SNPs. We conclude that combining CNV with SNP analyses reveals more genetic variations underlying milk production traits than those revealed by SNPs alone.https://doi.org/10.1186/1471-2164-15-68

Effect of the Hydrofluoroether Cosolvent Structure in Acetonitrile-Based Solvate Electrolytes on the Li^+ Solvation Structure and Li–S Battery Performance

We evaluate hydrofluoroether (HFE) cosolvents with varying degrees of fluorination in the acetonitrile-based solvate electrolyte to determine the effect of the HFE structure on the electrochemical performance of the Li–S battery. Solvates or sparingly solvating electrolytes are an interesting electrolyte choice for the Li–S battery due to their low polysulfide solubility. The solvate electrolyte with a stoichiometric ratio of LiTFSI salt in acetonitrile, (MeCN)_2–LiTFSI, exhibits limited polysulfide solubility due to the high concentration of LiTFSI. We demonstrate that the addition of highly fluorinated HFEs to the solvate yields better capacity retention compared to that of less fluorinated HFE cosolvents. Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that HFEs exhibiting a higher degree of fluorination coordinate to Li+ at the expense of MeCN coordination, resulting in higher free MeCN content in solution. However, the polysulfide solubility remains low, and no crossover of polysulfides from the S cathode to the Li anode is observed

Effect of the Hydrofluoroether Cosolvent Structure in Acetonitrile-Based Solvate Electrolytes on the Li^+ Solvation Structure and Li–S Battery Performance

We evaluate hydrofluoroether (HFE) cosolvents with varying degrees of fluorination in the acetonitrile-based solvate electrolyte to determine the effect of the HFE structure on the electrochemical performance of the Li–S battery. Solvates or sparingly solvating electrolytes are an interesting electrolyte choice for the Li–S battery due to their low polysulfide solubility. The solvate electrolyte with a stoichiometric ratio of LiTFSI salt in acetonitrile, (MeCN)_2–LiTFSI, exhibits limited polysulfide solubility due to the high concentration of LiTFSI. We demonstrate that the addition of highly fluorinated HFEs to the solvate yields better capacity retention compared to that of less fluorinated HFE cosolvents. Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that HFEs exhibiting a higher degree of fluorination coordinate to Li+ at the expense of MeCN coordination, resulting in higher free MeCN content in solution. However, the polysulfide solubility remains low, and no crossover of polysulfides from the S cathode to the Li anode is observed

Histological and transcriptome-wide level characteristics of fetal myofiber hyperplasia during the second half of gestation in Texel and Ujumqin sheep

<p>Abstract</p> <p>Background</p> <p>Whether myofibers increase with a pulsed-wave mode at particular developmental stages or whether they augment evenly across developmental stages in large mammals is unclear. Additionally, the molecular mechanisms of myostatin in myofiber hyperplasia at the fetal stage in sheep remain unknown. Using the first specialized transcriptome-wide sheep oligo DNA microarray and histological methods, we investigated the gene expression profile and histological characteristics of developing fetal ovine longissimus muscle in Texel sheep (high muscle and low fat), as a myostatin model of natural mutation, and Ujumqin sheep (low muscle and high fat). Fetal skeletal muscles were sampled at 70, 85, 100, 120, and 135 d of gestation.</p> <p>Results</p> <p>Myofiber number increased sharply with a pulsed-wave mode at certain developmental stages but was not augmented evenly across developmental stages in fetal sheep. The surges in myofiber hyperplasia occurred at 85 and 120 d in Texel sheep, whereas a unique proliferative surge appeared at 100 d in Ujumqin sheep. Analysis of the microarray demonstrated that immune and hematological systems' development and function, lipid metabolism, and cell communication were the biological functions that were most differentially expressed between Texel and Ujumqin sheep during muscle development. Pathways associated with myogenesis and the proliferation of myoblasts, such as calcium signaling, chemokine (C-X-C motif) receptor 4 signaling, and vascular endothelial growth factor signaling, were affected significantly at specific fetal stages, which underpinned fetal myofiber hyperplasia and postnatal muscle hypertrophy. Moreover, we identified some differentially expressed genes between the two breeds that could be potential myostatin targets for further investigation.</p> <p>Conclusions</p> <p>Proliferation of myofibers proceeded in a pulsed-wave mode at particular fetal stages in the sheep. The myostatin mutation changed the gene expression pattern in skeletal muscle at a transcriptome-wide level, resulting in variation in myofiber phenotype between Texel and Ujumqin sheep during the second half of gestation. Our findings provide a novel and dynamic description of the effect of myostatin on skeletal muscle development, which contributes to understanding the biology of muscle development in large mammals.</p

METIS research advances towards the 5G mobile and wireless system definition

[EN] The Mobile and wireless communications Enablers for the Twenty-twenty Information Society (METIS) project is laying the foundations of Fifth Generation (5G) mobile and wireless communication system putting together the point of view of vendors, operators, vertical players, and academia. METIS envisions a 5G system concept that efficiently integrates new applications developed in the METIS horizontal topics and evolved versions of existing services and systems. This article provides a first view on the METIS system concept, highlights the main features including architecture, and addresses the challenges while discussing perspectives for the further research work.Part of this work has been performed in the framework of the FP7 project ICT-317669 METIS, which is partly funded by the European Commission. The authors would like to acknowledge the contributions of their colleagues in METIS with special thanks to Petar Popovski, Peter Fertl, David Gozalvez-Serrano, Andreas Hoglund, Zexian Li, and Krystian Pawlak. Also thanks to Josef Eichinger and Malte Schellmann for the fruitful discussions during the revision of this article.Monserrat Del Río, JF.; Mange, G.; Braun, V.; Tullberg, H.; Zimmermann, G.; Bulakci, O. (2015). METIS research advances towards the 5G mobile and wireless system definition. EURASIP Journal on Wireless Communications and Networking. 2015(53):1-16. https://doi.org/10.1186/s13638-015-0302-9S116201553Cisco, in Global Mobile Data Traffic Forecast Update, 2014–2019 White Paper, February 2015. http://www.cisco.com/c/en/us/solutions/collateral/service-provider/visual-networking-index-vni/white_paper_c11-520862.pdfMETIS, in Mobile and wireless communications Enablers for the Twenty-twenty Information Society, EU 7th Framework Programme project, http://www.metis2020.com .ICT-317669 METIS project, in Scenarios, requirements and KPIs for 5G mobile and wireless system, Deliverable D1.1, May 2013, https://www.metis2020.com/documents/deliverables/B Ahlgren, C Dannewitz, C Imbrenda, D Kutscher, B Ohlman, A survey of information-centric networking. IEEE Commun Mag 50(7), 26–36 (2012)A Osseiran, F Boccardi, V Braun, K Kusume, P Marsch, M Maternia, O Queseth, M Schellmann, H Schotten, H Taoka, H Tullberg, MA Uusitalo, B Timus, M Fallgren, Scenarios for the 5G mobile and wireless communications: the vision of the METIS project. IEEE Commun Mag 52(5), 26–35 (2014)D Gomez-Barquero, D Calabuig, JF Monserrat, N Garcia and J Perez-Romero, Hopfield neural network - based approach for joint dynamic resource allocation in heterogeneous wireless networks, in Proceedings 64th IEEE Vehicular Technology Conference (VTC), Montreal. 2006JF Monserrat, P Sroka, G Auer, J Cabrejas, D Martin-Sacristan, A Mihovska, R Rossi, A. Saul, R. Schoenen, Advanced Radio Resource Management for IMT-Advanced in WINNER+ (II), in Proc. Future Network and Mobile Summit, pp.1-9, June 2010.F Boccardi, RW Heath, A Lozano, TL Marzetta, P Popovski, Five disruptive technology directions for 5G. IEEE Commun Mag 52(2), 74–80 (2014)JG Andrews, S Buzzi, C Wan, SV Hanly, A Lozano, ACK Soong, JC Zhang, What will 5G be? IEEE J Sel Area Comm 32(6), 1065–1082 (2014)MN Tehrani, M Uysal, H Yanikomeroglu, Device-to-device communication in 5G cellular networks: challenges, solutions, and future directions. IEEE Commun Mag 52(5), 86–92 (2014)N Bhushan, L Junyi, D Malladi, R Gilmore, D Brenner, A Damnjanovic, R Sukhavasi, C Patel, S Geirhofer, Network densification: the dominant theme for wireless evolution into 5G. IEEE Commun Mag 52(2), 82–89 (2014)K Okino, T Nakayama, C Yamazaki, H Sato, Y Kusano, Pico Cell Range Expansion with Interference Mitigation toward LTE-Advanced Heterogeneous Networks, in Proc. of IEEE International Conference on Communications (ICC), 2011.P Mugen, L Dong, W Yao, L Jian Li, C Hsiao-Hwa, Self-configuration and self-optimization in LTE-advanced heterogeneous networks. IEEE Commun Mag 51(5), 36–45 (2013)I Siomina, D Yuan, Load Balancing in Heterogeneous LTE: Range Optimization via Offset and Load-coupling Characterization, in Proc. of IEEE Int. Conference on Communications (ICC). June 2012.KI Pedersen, Y Wang, B Soret, F Frederiksen, eICIC Functionality and Performance for LTE HetNet Co-Channel Deployments, in Proc. of IEEE Vehicular Technology Conf, Sep 2012X Gu, X Deng, Q Li, L Zhang, W Li, Capacity Analysis and Optimization in Heterogeneous Network with Adaptive Cell Range Control, Int. J. Antennas. Propag. 2014(215803), 10 (2014)K Smiljkovikj, P Popovski, L Gavrilovska, Analysis of the Decoupled Access for DL and UL in Wireless Heterogeneous Networks, in IEEE Wireless Communications Letters, in press, doi:10.1109/LWC.2015.2388676.P Agyapong, M. Iwamura, D. Staehle, W. Kiess, A. Benjebbour, Design considerations for a 5G network architecture. IEEE Commun Mag 52(11), 65–75 (2014)L Yan, X Fang, Reliability Evaluation of 5G C/U-plane Decoupled Architecture for High-speed Railway. EURASIP J Wirel Commun Netw 2014, 127 (2014)B Zafar, S Gherekhloo, M Haardt, Analysis of multihop relaying networks: communication between range-limited and cooperative nodes. IEEE Veh Technol Mag 7(3), 40–47 (2012)Study on Mobile Relay for Evolved Universal Terrestrial Radio Access (E-UTRA), 3GPP TR 36.836, V2.0.2, July 2013.A Krendzel, LTE-A Mobile Relay Handling: Architecture Aspects, in Proc. of the 19th European Wireless Conference (EW), Guildford, UK, pp. 1–6, 2013.M Khanfouci, Y Sui, A Papadogiannis, and M Färber, Moving Relays and Mobility aspects, ARTIST4G project deliverable D3.5c-v2.0, 2012.F Haider, M Dianati, and R Tafazolli, A Simulation Based Study of Mobile Femtocell Assisted LTE Networks, in Proc. Of the 7th International Wireless Communications and Mobile Computing Conference (IWCMC), Istanbul, Turkey, pp. 2198–2203, 2011F Haider, W Haiming, H Haas, Y Dongfeng, W Haiming, G Xiqi, Y Xiao-Hu, E Hepsaydir, Spectral efficiency enalysis of mobile Femtocell based cellular systems, in Proc. of the 13th International Conference on Communication Technology (ICCT), Jinan, pp. 347–351, September 2011.ICT-317669 METIS project, Initial report on horizontal topics, first results and 5G system concept, Deliverable D6.2, April 2014, https://www.metis2020.com/documents/deliverables/Study on LTE Device to Device Proximity Services, 3GPP TR 36.843, 2014.V Yazıcı, UC Kozat, M Oguz, Sunay, A new control plane for 5G network architecture with a case study on unified handoff, mobility, and routing management. IEEE Commun Mag 52(11), 76–85 (2014)F Malandrino, C Casetti, C-F Chiasserini, Toward D2D-enhanced heterogeneous networks. IEEE Commun Mag 52(11), 94–100 (2014)A Asadi, Q Wang, V Mancuso, A survey on device-to-Device communication in cellular networks. IEEE Commun Surv Tutor 16(4), 1801–1819 (2014)D Feng, L Lu, YY Wu, GY Li, G Feng, S Li, Device-to-device communications underlaying cellular networks. IEEE Trans Commun 61(8), 3541–3551 (2013)C Xu, L Song, Z Han, Q Zhao, X Wang, X Cheng, B Jiao, Efficiency resource allocation for device-to-device underlay communication systems: a reverse iterative combinatorial auction based approach. IEEE J Sel Area Comm 31(9), 348–358 (2013)S Lingyang, D Niyato, H Zhu, E Hossain, Game-theoretic resource allocation methods for device-to-device communication. IEEE Wireless Commun 21(3), 136–144 (2014)G Aloi, M Di Felice, V Loscrì, P Pace, G Ruggeri, Spontaneous smartphone networks as a user-centric solution for the future internet. IEEE Commun Mag 52(12), 26–33 (2014)PA Frangoudis, GC Polyzos, Security and performance challenges for user-centric wireless networking. IEEE Commun Mag 52(12), 48–55 (2014)ITU-R M.2079, in Technical and operational information for identifying Spectrum for the terrestrial component of future development of IMT-2000 and IMT-Advanced, 2006AB MacKenzie, LA DaSilva, Application of signal processing to addressing wireless data demand [in the spotlight]. IEEE Signal Process Mag 29(6), 168–166 (2012)X Cheng, Y Koucheryavy, Y Li, F Zhao, T Znati (ed.), Dynamic Spectrum Access for Throughput, Delay, and Fairness Enhancement In Cognitive Radio Networks, EURASIP J Wirel Commun Netw, November 2014MR Akdeniz, Y Liu, MK Samimi, S Sun, S Rangan, TS Rappaport, E Erkip, Millimeter wave channel modeling and cellular capacity evaluation. IEEE J Sel Area Comm 32(6), 1164–1179 (2014)A Adhikary, E Al Safadi, M Samimi, R Wang, G Caire, TS Rappaport, AF Molisch, Joint spatial division and multiplexing for mm-wave channels. IEEE J Sel Area Comm 32(6), 1239–1255 (2014)K Pentikousis, Y Wang, W Hu, Mobileflow: toward software-defined mobile networks. IEEE Commun Mag 51(7), 44–53 (2013)E3 D2.4. Cognitive Function mapping to Networks Architectures, Standard Engineering and Software Technologies for Cognitive Radios, E3 Project Deliverable 2.4, December 2009.R Wang, H Hu, X Yang, Potentials and challenges of C-RAN supporting Multi-RATs toward 5G mobile networks. IEEE. Access. 2(1187), 1195 (2014)V Jungnickel, K Manolakis, W Zirwas, B Panzner, V Braun, M Lossow, M Sternad, R Apelfrojd, T Svensson, The role of small cells, coordinated multipoint, and massive MIMO in 5G. IEEE Commun Mag 52(5), 44–51 (2014)E Larsson, O Edfors, F Tufvesson, T Marzetta, Massive MIMO for next generation wireless systems. IEEE Commun Mag 52(2), 186–195 (2014)W Roh, S Ji-Yun, P Jeongho, L Byunghwan, L Jaekon, K Yungsoo, C Jaeweon, C Kyungwhoon, F Aryanfar, Millimeter-wave Beamforming as an Enabling Technology for 5G Cellular Communications: Theoretical Feasibility and Prototype Results. IEEE Commun Mag 2(2), 106–113 (2014)AL Swindlehust, E Ayanoglu, P Heydari, F Capolino, Millimeter-wave massive MIMO: the next wireless revolution? IEEE Commun Mag 52(9), 56–62 (2014)L Lu, GY Li, AL Swindlehurst, A Ashikhmin, Z Rui, An overview of massive MIMO: benefits and challenges. IEEE J Sel Top Signal Process 8(5), 742–758 (2014)S Roger, D Calabuig, J Cabrejas, JF Monserrat, Multi-user non-coherent detection for downlink MIMO communication. IEEE Signal Process Lett 21(10), 1225–1229 (2014)X Wang, M Chen, T Taleb, A Ksentini, V Leung, Cache in the air: exploiting content caching and delivery techniques for 5G systems. IEEE Commun Mag 52(2), 131–139 (2014)ETSI ISG NFV (Operator Group), Network Functions Virtualisation – Network Operator Perspectives on Industry Progress, Updated White Paper, October 2013NGMN Alliance, in Suggestions on potential solutions for C-RAN, White Paper, January 2013ETSI ISG NFV, Network Functions Virtualisation (NFV); Virtual Network Functions Architecture, v1.1.1, Dec 2014.A Tzanakaki, MP Anastasopoulos, GS Zervas, BR Rofoee, R Nejabati, D Simeonidou, Virtualization of heterogeneous wireless-optical network and IT infrastructures in support of cloud and mobile cloud services. IEEE Commun Mag 51(8), 155–161 (2013)A Manzalini, R Saracco, C Buyukkoc, P Chemuouil, S Kukliński, A Gladisch, M Fukui, W Shen, M Fujiwara, K Shimano, E Dekel, D Soldani, M Ulema, W Cerroni, F Callegati, G Schembra, V Riccobene, C Mas Machuca, A Galis, J Mueller, Software-Defined Networks for Future Networks and Services: Main Technical Challenges and Business Implications, IEEE Workshop SDN4FNS, 1–16, 2013CEPT ECC, in Licensed Shared Access (LSA), ECC Report 205, February 2014IEEE 802.11, in IEEE 802.11-2012 Part11: Wireless LAN Medium Access Control (MAC) and Physical Layer (PHY) Specifications, IEEE Standard, March 2012D Martín-Sacristán, JF Monserrat, J Cabrejas-Peñuelas, D Calabuig, S Garrigas, N Cardona, On the way towards fourth-generation mobile: 3GPP LTE and LTE-Advanced. EURASIP J Wirel Commun Netw 2009, 10 (2009)ICT-317669 METIS, Final report on architecture, Deliverable D6.4, January 2015, https://www.metis2020.com/documents/deliverables/ICT-317669 METIS, Report on simulation results and evaluations, Deliverable D6.5, February 2015, https://www.metis2020.com/documents/deliverables/Ö Bulakci, Z Ren, C Zhou, J Eichinger, P Fertl, S Stanczak, Dynamic Nomadic Node Selection for Performance Enhancement in Composite Fading/Shadowing Environments, (IEEE VTC 2014-Spring, Seoul, South Korea)ICT-317669 METIS, Final report on network-level solutions, Deliverable D4.3 Version 1, February 201

Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1 Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future