4D TeleCast: Towards Large Scale Multi-site and Multi-view Dissemination of 3DTI Contents

3D Tele-immersive systems create real-time multi-stream and multi-view 3D collaborative contents from multiple sites to allow interactive shared activities in virtual environments. Applications of 3DTI include online sports, tele-health, remote learning and collaborative arts. In addition to interactive participants in 3DTI environments, we envision a large number of passive non-interactive viewers that (a) watch the interactive activities in 3DTI shared environments, and (b) select views of the activities at run time. To achieve this vision, we present 4D TeleCast, a novel multi-stream 3D content distribution framework for non-interactive viewers providing the functionality of multi-view selection. It addresses the following challenges: (1) supporting a large number of concurrent multi-stream viewers as well as multi-views, (2) preserving the unique nature of 3DTI multi-stream and multi-view dependencies at the viewers, and (3) allowing dynamic viewer behavior such as view changes and large-scale simultaneous viewer arrivals or departures. We divide the problem space into two: (1) multi-stream overlay construction problem that aims to minimize the cost of distribution of multi-stream contents, and maximize the number of concurrent viewers with sufficient viewer dynamism in terms of their resources and availabilities, and (2) effective resource utilization problem that aims to preserve the multi-stream dependencies in a view considering the heterogeneous resource constraints at the viewers. We evaluate 4D TeleCast using extensive simulations with 3DTI activity data and PlanetLab traces.published or submitted for publicationis peer reviewe

"I'm the Jedi!" - A Case Study of User Experience in 3D Tele-immersive Gaming

Abstract—In this paper, we present the results from a quantitative and qualitative study of distributed gaming in 3D tele-immersive (3DTI) environments. We explore the Qual-ity of Experience (QoE) of users in the new cyber-physical gaming environment. Guided by a theoretical QoE model, we conducted a case study and evaluated the impact of various Quality of Service (QoS) metrics (e.g., end-to-end delay, visual quality, etc.) on 3DTI gaming experience. We also identified a number of non-technical factors that are not captured by the original theoretical model, such as age, social interaction, and physical setup. Our analysis highlights new implications for the next-generation gaming system design, as well as a more comprehensive conceptual framework that captures non-technical influences for user experience in such environments

Sequencing and de novo Analysis of Crassostrea angulata (Fujian Oyster) from 8 Different Developing Phases Using 454 GSFlx

Research on the mechanism for early development of shellfish, such as body plan, shell formation, settlement and metamorphosis is currently an active research field. However, studies were still limited and not deep enough because of the lack of genomic resources such as genome or transcriptome sequences. In the present research, de novo transcriptome sequencing was performed for Crassostrea angulata, the most economically important cultured oyster species in China, at eight early developmental stages using the 454 sequencing technology. A total of 555,215 reads were produced with an average length of 309 nucleotides that were then assembled into 10,462 contigs. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Six unique sequences related to settlement, metamorphosis and growth were subsequently analyzed by real-time PCR. Given the lack of whole genome information for oysters, transcriptome and de novo analysis of C. angulata from the eight different developing phases will provide important and useful information on early development mechanism and help genetic breeding of shellfish.National Basic Research Program of China [2010CB1264000]; Hi-Tech Research and Development (863) Program of China [2010AA10A110]; Shellfish Modern Agro-industry Technology Research System [nycytx-47

Comparative genome microsynteny illuminates the fast evolution of nuclear mitochondrial segments (NUMTs) in mammals

The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-And-Absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference

Six reference-quality genomes reveal evolution of bat adaptations

Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our �Tool to infer Orthologs from Genome Alignments� (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease.s E.W.M. and M.P. were supported by the Max Planck Society and were partially funded by the Federal Ministry of Education and Research (grant 01IS18026C). All data produced in Dresden were funded directly by the Max Planck Society. S.C.V., P.D. and K.L. were funded by a Max Planck Research Group awarded to S.C.V. from the Max Planck Society, and a Human Frontiers Science Program (HFSP) Research grant awarded to S.C.V. (RGP0058/2016). M.H. was funded by the German Research Foundation (HI 1423/3-1) and the Max Planck Society. E.C.T. was funded by a European Research Council Research Grant (ERC2012-StG311000), UCD Wellcome Institutional Strategic Support Fund, financed jointly by University College Dublin and SFI-HRB-Wellcome Biomedical Research Partnership (ref 204844/Z/16/Z) and Irish Research Council Consolidator Laureate Award. G.M.H. was funded by a UCD Ad Astra Fellowship. G.J. and E.C.T. were funded from the Royal Society/Royal Irish Academy cost share programme. L.M.D. was supported by NSF-DEB 1442142 and 1838273, and NSF-DGE 1633299. D.A.R. was supported by NSF-DEB 1838283. E.D.J. and O.F. were funded by the Rockefeller University and the Howard Hughes Medical Institute. We thank Stony Brook Research Computing and Cyberinfrastructure, and the Institute for Advanced Computational Science at Stony Brook University for access to the high-performance SeaWulf computing system (which was made possible by a National Science Foundation grant (no. 1531492)); the Long Read Team of the DRESDEN-concept Genome Center, DFG NGS Competence Center, part of the Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden; S. Kuenzel and his team of the Max Planck Institute of Evolutionary Biology; members of the Vertebrate Genomes Laboratory at The Rockefeller University for their support; L. Wiegrebe, U. Firzlaff and M. Yartsev, who gave us access to captive colonies of Phyllostomus and Rousettus bats and aided with tissue sample collection; and M. Springer, for completing the SVDquartet analyses, and providing phylogenetic input and expertise

Large-scale genome sampling reveals unique immunity and metabolic adaptations in bats

SCV was supported by a Max Planck Research Group awarded by the Max Planck Gesellschaft, a Human Frontiers Science Program Grant (RGP0058/2016) and a UKRI Future Leaders Fellowship (MR/T021985/1).Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defence receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defence response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance antiviral immune response while dampening inflammatory signalling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.PostprintPeer reviewe

Transcriptome Analysis of the Octopus vulgaris Central Nervous System

Background: Cephalopoda are a class of Mollusca species found in all the world's oceans. They are an important model organism in neurobiology. Unfortunately, the lack of neuronal molecular sequences, such as ESTs, transcriptomic or genomic information, has limited the development of molecular neurobiology research in this unique model organism. Results: With high-throughput Illumina Solexa sequencing technology, we have generated 59,859 high quality sequences from 12,918,391 paired-end reads. Using BLASTx/BLASTn, 12,227 contigs have blast hits in the Swissprot, NR protein database and NT nucleotide database with E-value cutoff 1e(-5). The comparison between the Octopus vulgaris central nervous system (CNS) library and the Aplysia californica/Lymnaea stagnalis CNS ESTs library yielded 5.93%/13.45% of O. vulgaris sequences with significant matches (1e(-5)) using BLASTn/tBLASTx. Meanwhile the hit percentage of the recently published Schistocerca gregaria, Tilapia or Hirudo medicinalis CNS library to the O. vulgaris CNS library is 21.03%-46.19%. We constructed the Phylogenetic tree using two genes related to CNS function, Synaptotagmin-7 and Synaptophysin. Lastly, we demonstrated that O. vulgaris may have a vertebrate-like Blood-Brain Barrier based on bioinformatic analysis. Conclusion: This study provides a mass of molecular information that will contribute to further molecular biology research on O. vulgaris. In our presentation of the first CNS transcriptome analysis of O. vulgaris, we hope to accelerate the study of functional molecular neurobiology and comparative evolutionary biology.National fund for oceanography research in Public Interest [201005013]; National Key Technology RD Program [2011BAD13

Quantitative evaluation of the immunodeficiency of a mouse strain by tumor engraftments

© 2015 Ye et al. Background: The mouse is an organism that is widely used as a mammalian model for studying human physiology or disease, and the development of immunodeficient mice has provided a valuable tool for basic and applied human disease research. Following the development of large-scale mouse knockout programs and genome-editing tools, it has become increasingly efficient to generate genetically modified mouse strains with immunodeficiency. However, due to the lack of a standardized system for evaluating the immuno-capacity that prevents tumor progression in mice, an objective choice of the appropriate immunodeficient mouse strains to be used for tumor engrafting experiments is difficult. Methods: In this study, we developed a tumor engraftment index (TEI) to quantify the immunodeficiency response to hematologic malignant cells and solid tumor cells of six immunodeficient mouse strains and C57BL/6 wild-type mouse (WT). Results: Mice with a more severely impaired immune system attained a higher TEI score. We then validated that the NOD-scid-IL2Rg-/- (NSI) mice, which had the highest TEI score, were more suitable for xenograft and allograft experiments using multiple functional assays. Conclusions: The TEI score was effectively able to reflect the immunodeficiency of a mouse strain.Link_to_subscribed_fulltex