Developing a platform of environmental omics for the green-lipped mussel Perna viridis

Session Track: Aquatic and terrestrial ecotoxicologyOral presentationConference Theme: Science across bridges, borders and boundariesThe green-lipped mussel Perna viridis is an important marine biomonitor species in pollution monitoring and ecotoxicological studies in Asia-Pacific region, and considered as a subtropical equivalent biomonitor of the temperate Mytilus species. However, the genomic information of P. viridis is still largely unexplored when compared with Mytilus species. This study aimed to establish a transcriptomic profile of P. viridis using the next generation sequencing technology and provide a good representative set of genomic information for elucidation of toxic mechanisms upon pollution stresses and identification of a suite of suitable biomarkers for monitoring marine pollution and environmental stresses. To obtain a wide spectrum of environmental-associated transcripts, adult mussels (4-5 cm shell length) were collected from different locations in Hong Kong and from those after 24-hour exposures to various challenges of physical stresses and chemical pollutants, so as to cover a wide range of stress-associated transcription patterns for future environmental studies. Two males and females from each location and from each treatment were chosen for obtaining the three target tissues (i.e., hepatopancreas, gill and adductor muscle). For each sex and each tissue type, a total RNA sample was extracted from pooled tissues from the field and laboratory treated mussels. The RNA sample was subjected to cDNA library construction, followed by the RNA-sequencing using a Solexa GAIIx (Illumina). Including the splicing variants, a de novo assembly of a total length of 295,064,579 base-pair (bp) contig was obtained, with 233,257 contigs assembled of an average size of 1264 bp. The 192,879 non-redundant assembled transcripts were blasted against the NCBI nr database and three molluscan EST databases, and resulted in 44,713 transcripts with at least a blast hit, and having a top match with the sequences from the Pacific oyster, Crassostrea gigas (27,651 transcripts). A total of 5,131 transcripts were assigned with KEGG annotation involving in 329 pathways. Based on multivariate statistical analysis, expression patterns of genes from stress associated responses and detoxification were strongly tissue-specific but the differences between genders were little. The anticipated genomic database generated from this study will further strengthen the role of P. viridis as a universal marine biomonitor in the Asia-Pacific region.published_or_final_versio

De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies

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Linguistic Structure Guided Context Modeling for Referring Image Segmentation

Referring image segmentation aims to predict the foreground mask of the object referred by a natural language sentence. Multimodal context of the sentence is crucial to distinguish the referent from the background. Existing methods either insufficiently or redundantly model the multimodal context. To tackle this problem, we propose a "gather-propagate-distribute" scheme to model multimodal context by cross-modal interaction and implement this scheme as a novel Linguistic Structure guided Context Modeling (LSCM) module. Our LSCM module builds a Dependency Parsing Tree suppressed Word Graph (DPT-WG) which guides all the words to include valid multimodal context of the sentence while excluding disturbing ones through three steps over the multimodal feature, i.e., gathering, constrained propagation and distributing. Extensive experiments on four benchmarks demonstrate that our method outperforms all the previous state-of-the-arts.Comment: Accepted by ECCV 2020. Code is available at https://github.com/spyflying/LSCM-Refse

De novo transcriptome analysis for mechanistic study of organotin-mediated endocrine disruption in Reishia Clavigera

Poster presentation: P-63Human ImpactsMany endocrine disrupting compounds are bioaccumulative and toxic to a wide range of marine organisms, leading to reproductive impairment, development of cancer and abnormal metabolism. For instance, organotin compounds (OTs) such as tributyltin and triphenyltin can induce the development of imposex (i.e., superimposition of male sexual organs) in females of over 200 gastropod species. OTs have been widely used as biocides in antifouling paints and industrial applications. Thus they have been released into the marine environment, posing risks to non-target marine organisms and human health. Although many studies have been conducted to ...postprin

Modelling of content-aware indicators for effective determination of shot boundaries in compressed MPEG videos

In this paper, a content-aware approach is proposed to design multiple test conditions for shot cut detection, which are organized into a multiple phase decision tree for abrupt cut detection and a finite state machine for dissolve detection. In comparison with existing approaches, our algorithm is characterized with two categories of content difference indicators and testing. While the first category indicates the content changes that are directly used for shot cut detection, the second category indicates the contexts under which the content change occurs. As a result, indications of frame differences are tested with context awareness to make the detection of shot cuts adaptive to both content and context changes. Evaluations announced by TRECVID 2007 indicate that our proposed algorithm achieved comparable performance to those using machine learning approaches, yet using a simpler feature set and straightforward design strategies. This has validated the effectiveness of modelling of content-aware indicators for decision making, which also provides a good alternative to conventional approaches in this topic

Magnetic Resonance Imaging of Bone Marrow Cell-Mediated Interleukin-10 Gene Therapy of Atherosclerosis

A characteristic feature of atherosclerosis is its diffuse involvement of arteries across the entire human body. Bone marrow cells (BMC) can be simultaneously transferred with therapeutic genes and magnetic resonance (MR) contrast agents prior to their transplantation. Via systemic transplantation, these dual-transferred BMCs can circulate through the entire body and thus function as vehicles to carry genes/contrast agents to multiple atherosclerosis. This study was to evaluate the feasibility of using in vivo MR imaging (MRI) to monitor BMC-mediated interleukin-10 (IL-10) gene therapy of atherosclerosis.For in vitro confirmation, donor mouse BMCs were transduced by IL-10/lentivirus, and then labeled with a T2-MR contrast agent (Feridex). For in vivo validation, atherosclerotic apoE(-/-) mice were intravenously transplanted with IL-10/Feridex-BMCs (Group I, n = 5) and Feridex-BMCs (Group II, n = 5), compared to controls without BMC transplantation (Group III, n = 5). The cell migration to aortic atherosclerotic lesions was monitored in vivo using 3.0T MRI with subsequent histology correlation. To evaluate the therapeutic effect of BMC-mediated IL-10 gene therapy, we statistically compared the normalized wall indexes (NWI) of ascending aortas amongst different mouse groups with various treatments.Of in vitro experiments, simultaneous IL-10 transduction and Feridex labeling of BMCs were successfully achieved, with high cell viability and cell labeling efficiency, as well as IL-10 expression efficiency (≥90%). Of in vivo experiments, MRI of animal groups I and II showed signal voids within the aortic walls due to Feridex-created artifacts from the migrated BMCs in the atherosclerotic plaques, which were confirmed by histology. Histological quantification showed that the mean NWI of group I was significantly lower than those of group II and group III (P<0.05).This study has confirmed the possibility of using MRI to track, in vivo, IL-10/Feridex-BMCs recruited to atherosclerotic lesions, where IL-10 genes function to prevent the progression of atherosclerosis

Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation

Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates

Coherent ac spin current transmission across an antiferromagnetic CoO insulator

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: Data are available from the corresponding author upon reasonable request.The recent discovery of spin current transmission through antiferromagnetic insulating materials opens up vast opportunities for fundamental physics and spintronics applications. The question currently surrounding this topic is: whether and how could THz antiferromagnetic magnons mediate a GHz spin current? This mismatch of frequencies becomes particularly critical for the case of coherent ac spin current, raising the fundamental question of whether a GHz ac spin current can ever keep its coherence inside an antiferromagnetic insulator and so drive the spin precession of another ferromagnet layer coherently? Utilizing element- and time-resolved x-ray pump-probe measurements on Py/Ag/CoO/Ag/Fe75Co25/MgO(001) heterostructures, here we demonstrate that a coherent GHz ac spin current pumped by the Py ferromagnetic resonance can transmit coherently across an antiferromagnetic CoO insulating layer to drive a coherent spin precession of the Fe75Co25 layer. Further measurement results favor thermal magnons rather than evanescent spin waves as the mediator of the coherent ac spin current in CoO.US Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering DivisionNational Science Foundation (NSF)National Research Foundation of KoreaEngineering and Physical Sciences Research Council (EPSRC)National Key Research and Development Program of CHIN

Movement Protein Pns6 of Rice dwarf phytoreovirus Has Both ATPase and RNA Binding Activities

Cell-to-cell movement is essential for plant viruses to systemically infect host plants. Plant viruses encode movement proteins (MP) to facilitate such movement. Unlike the well-characterized MPs of DNA viruses and single-stranded RNA (ssRNA) viruses, knowledge of the functional mechanisms of MPs encoded by double-stranded RNA (dsRNA) viruses is very limited. In particular, many studied MPs of DNA and ssRNA viruses bind non-specifically ssRNAs, leading to models in which ribonucleoprotein complexes (RNPs) move from cell to cell. Thus, it will be of special interest to determine whether MPs of dsRNA viruses interact with genomic dsRNAs or their derivative sRNAs. To this end, we studied the biochemical functions of MP Pns6 of Rice dwarf phytoreovirus (RDV), a member of Phytoreovirus that contains a 12-segmented dsRNA genome. We report here that Pns6 binds both dsRNAs and ssRNAs. Intriguingly, Pns6 exhibits non-sequence specificity for dsRNA but shows preference for ssRNA sequences derived from the conserved genomic 5′- and 3′- terminal consensus sequences of RDV. Furthermore, Pns6 exhibits magnesium-dependent ATPase activities. Mutagenesis identified the RNA binding and ATPase activity sites of Pns6 at the N- and C-termini, respectively. Our results uncovered the novel property of a viral MP in differentially recognizing dsRNA and ssRNA and establish a biochemical basis to enable further studies on the mechanisms of dsRNA viral MP functions