Many single-cell sequencing technologies are now available, but it is still difficult to apply multiple sequencing technologies to the same single cell. In this paper, we propose an unsupervised manifold alignment algorithm, MMD-MA, for integrating multiple measurements carried out on disjoint aliquots of a given population of cells. Effectively, MMD-MA performs an in silico co-assay by embedding cells measured in different ways into a learned latent space. In the MMD-MA algorithm, single-cell data points from multiple domains are aligned by optimizing an objective function with three components: (1) a maximum mean discrepancy (MMD) term to encourage the differently measured points to have similar distributions in the latent space, (2) a distortion term to preserve the structure of the data between the input space and the latent space, and (3) a penalty term to avoid collapse to a trivial solution. Notably, MMD-MA does not require any correspondence information across data modalities, either between the cells or between the features. Furthermore, MMD-MA's weak distributional requirements for the domains to be aligned allow the algorithm to integrate heterogeneous types of single cell measures, such as gene expression, DNA accessibility, chromatin organization, methylation, and imaging data. We demonstrate the utility of MMD-MA in simulation experiments and using a real data set involving single-cell gene expression and methylation data.

International audienceSurface Plasmon Resonance (SPR) has become a central tool for label-free characterization of biomolecular interactions. Based on monitoring of amplitude characteristics, conventional SPR sensors have been extensively explored, commercialized and applied for studies of many important interactions (antigen-antibody, protein-ligand etc), but this technology still lacks of sensitivity for the detection of relatively small and low copy number compounds. Phase-sensitive SPR has recently emerged as an upgrade of this technology to resolve the sensitivity issue. Profiting from a sharp phase jump under SPR and ultra-sensitive tools of its control, this technology offers up to 100-time improvement of the detection limit, giving access to the detection of trace amounts of small molecular weight analytes (drugs etc). This paper intends to provide a tutorial on basic concepts of phase detection in SPR sensing, compare the performance of phase- and amplitude-sensitive sensors, review recent progress in the development and applications of phase-sensitive SPR sensors, and outline future prospects and trends of this technology

Under certain conditions, a surface plasmon wave along a metal-dielectric interface can be excited by an optical beam. The reflected optical beam will then undergo changes in both intensity and phase. As the level of intensity or phase change is quite sensitive to the coupling conditions such as the molecule concentration on the metal surface, this phenomenon has been utilized for label-free detection of biological species and characterization of molecular interactions during the last two decades. Currently, most of the commercial surface plasmon resonance (SPR) sensors rely on the detection of absorption dip in angular or wavelength spectrum. However, recent researches have shown that phase detection has the potential to achieve lower limit of detection (LoD) and higher throughput. This paper, thus, intends to review various schemes and configurations for SPR phase detection. The performance advantages and disadvantages of various schemes will be emphasized. It is hoped that this paper will provide some insights to researchers interested in SPR sensing and help them to develop SPR sensors with better sensitivity and higher throughput.

The potential of 5-aminolevulenic acid (ALA) to enhance the salt tolerance of cucumber (Cucumis sativus L.) seedlings was investigated. ALA was applied at various concentrations (0, 1, 10, 25, 50, and 100 mg dm -3 ) as foliar spray or root watering. Then the seedlings were exposed to 0 or 75 mM NaCl for 5 d. NaCl stress reduced the root and leaf dry masses, leaf area, and the leaf net CO 2 assimilation rate. These reductions were counteracted by exogenous ALA, and the most efficient was 50 mg dm -3 concentration via foliar spray. ALA decreased the H 2 O 2 contents and increased the activities of ascorbate peroxidase (APX) and glutathione reductase (GR) in NaCl-treated cucumber roots and leaves and the activity of catalase (CAT) in leaves. The ALA application also up-regulated the expressions of CAT and cAPX genes in roots and leaves and the expression of GR gene in roots of the NaCl treated cucumber plants.

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The Phalaenopsis orchid is an important potted flower of high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802,’ a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal that the key role of PhAGL6b in the regulation of labellum organ development involves alternative splicing in the big lip mutant. Petal or sepal overexpressing PhAGL6b leads to the conversion into a lip-like structure. We also discovered that the gibberellin pathway that regulates the expression of flowering time genes during the reproductive phase change is induced by cool temperature. Our work thus depicted a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.