Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells.

Capturing the full complexity of the diverse hierarchical interactions in the protein interactome is challenging. Here we report a DNA-barcoding method for the multiplexed mapping of pairwise and higher-order protein interactions and their dynamics within cells. The method leverages antibodies conjugated with barcoded DNA strands that can bidirectionally hybridize and covalently link to linearize closely spaced interactions within individual 3D protein complexes, encoding and decoding the protein constituents and the interactions among them. By mapping protein interactions in cancer cells and normal cells, we found that tumour cells exhibit a larger diversity and abundance of protein complexes with higher-order interactions. In biopsies of human breast-cancer tissue, the method accurately identified the cancer subtype and revealed that higher-order protein interactions are associated with cancer aggressiveness.

IF-City: Intelligible Fair City Planning to Measure, Explain and Mitigate Inequality.

With the increasing pervasiveness of Artificial Intelligence (AI), many visual analytics tools have been proposed to examine fairness, but they mostly focus on data scientist users. Instead, tackling fairness must be inclusive and involve domain experts with specialized tools and workflows. Thus, domain-specific visualizations are needed for algorithmic fairness. Furthermore, while much work on AI fairness has focused on predictive decisions, less has been done for fair allocation and planning, which require human expertise and iterative design to integrate myriad constraints. We propose the Intelligible Fair Allocation (IF-Alloc) Framework that leverages explanations of causal attribution (Why), contrastive (Why Not) and counterfactual reasoning (What If, How To) to aid domain experts to assess and alleviate unfairness in allocation problems. We apply the framework to fair urban planning for designing cities that provide equal access to amenities and benefits for diverse resident types. Specifically, we propose an interactive visual tool, Intelligible Fair City Planner (IF-City), to help urban planners to perceive inequality across groups, identify and attribute sources of inequality, and mitigate inequality with automatic allocation simulations and constraint-satisfying recommendations (IF-Plan). We demonstrate and evaluate the usage and usefulness of IF-City on a real neighborhood in New York City, US, with practicing urban planners from multiple countries, and discuss generalizing our findings, application, and framework to other use cases and applications of fair allocation.

Imma Sort by Two or More Attributes With Interpretable Monotonic Multi-Attribute Sorting.

Many choice problems often involve multiple attributes which are mentally challenging, because only one attribute is neatly sorted while others could be randomly arranged. We hypothesize that perceiving approximately monotonic trends across multiple attributes is key to the overall interpretability of sorted results, because users can easily predict the attribute values of the next items. We extend a ranking principal curve model to tune monotonic trends in attributes and present Imma Sort to sort items by multiple attributes simultaneously by trading-off the monotonicity in the primary sorted attribute to increase the human predictability for other attributes. We characterize how it performs for varying attribute correlations, attribute preferences, list lengths and number of attributes. We further extend Imma Sort with ImmaAnchor and ImmaCenter to improve the learnability and efficiency to search sorted items with conflicting attributes. We demonstrate usage scenarios for two applications and evaluate its learnability, usability, interpretability, and user performance in prediction and search tasks. We find that Imma Sort improves the interpretability and satisfaction of sorting by ≥ 2 attributes. We discuss why, when, where, and how to deploy Imma Sort for real-world applications.

Epigenetic silencing of Plasmodium falciparum genes linked to erythrocyte invasion.

The process of erythrocyte invasion by merozoites of Plasmodium falciparum involves multiple steps, including the formation of a moving junction between parasite and host cell, and it is characterised by the redundancy of many of the receptor-ligand interactions involved. Several parasite proteins that interact with erythrocyte receptors or participate in other steps of invasion are encoded by small subtelomerically located gene families of four to seven members. We report here that members of the eba, rhoph1/clag, acbp, and pfRh multigene families exist in either an active or a silenced state. In the case of two members of the rhoph1/clag family, clag3.1 and clag3.2, expression was mutually exclusive. Silencing was clonally transmitted and occurred in the absence of detectable DNA alterations, suggesting that it is epigenetic. This was demonstrated for eba-140. Our data demonstrate that variant or mutually exclusive expression and epigenetic silencing in Plasmodium are not unique to genes such as var, which encode proteins that are exported to the surface of the erythrocyte, but also occur for genes involved in host cell invasion. Clonal variant expression of invasion-related ligands increases the flexibility of the parasite to adapt to its human host.

The MTIP-myosin A complex in blood stage malaria parasites.

Parasites of the Apicomplexa phylum use an actomyosin motor to drive invasion of host cells. The motor complex is located at the parasite's periphery between the plasma membrane and an inner membrane complex. A crucial component of this complex is myosin tail domain interacting protein (MTIP) identified in the murine malaria parasite Plasmodium yoelii. Here, we show that MTIP is expressed in Plasmodium falciparum merozoites, localises to the periphery of the cell and is present in a complex with myosin A. The MTIP-myosin A tail interaction has a Kd of 235 nM and calcium ions do not play a role in modulating the binding affinity of the two molecules, despite reports of a predicted EF-hand in MTIP. Antibodies to MTIP were used to immobilise the MTIP-myosin A complex, allowing actin binding and motility to be examined. Measurement of actin filament velocities powered by myosin A revealed a velocity of 3.51 microm s(-1), a speed comparable to fast muscle myosins. A short peptide derived from the tail of myosin A (C-MyoA) bound to MTIP and was able to disrupt the association of MTIP and myosin A in parasite lysates. C-MyoA peptidomimetic compounds that disrupt the MTIP-myosin A interaction are predicted to inhibit parasite motility and host cell invasion, which may be targets for new therapeutic approaches.

Apical expression of three RhopH1/Clag proteins as components of the Plasmodium falciparum RhopH complex.

The Plasmodium falciparum high molecular mass rhoptry protein ('PfRhopH') complex is important for parasite growth and comprises three distinct gene products: RhopH1, RhopH2 and RhopH3. We have previously shown that P. falciparum RhopH1 is encoded by either PFC0110w (clag3.2) or PFC0120w (clag3.1), members of the previously-named clag (cytoadherence-linked asexual gene) multigene family. In this report, we have further characterized rhoph1/clag members in terms of gene structure, transcription and protein expression. The cDNA sequences for all five rhoph1/clag members were determined, confirming previous in silico predictions of intron-exon boundaries. All member genes were transcribed in HB3 and 3D7 parasite lines, but clag3.2 was not transcribed in Dd2 parasites. The peak abundance of transcripts for all genes was observed during the late schizont stage. Antisera specific to Clag2 and Clag3.1 localized these proteins to the apical end of merozoites in segmented schizonts, and both proteins are found to be components of the PfRhopH complex. PfRhopH complex that was immunoprecipitated with anti-Clag9 antibody contained neither Clag2 nor Clag3.1, thereby suggesting that PfRhopH complexes contain only individual rhoph1/clag gene products. Since the PfRhopH complex binds the erythrocyte surface, and RhopH2 and RhopH3 are encoded by single copy genes, the RhopH1/Clag proteins may serve to confer some degree of specificity to the roles of the individual complexes.

The Plasmodium falciparum clag9 gene encodes a rhoptry protein that is transferred to the host erythrocyte upon invasion.

The first gene characterizing the clag (cytoadherence linked asexual gene) family of Plasmodium falciparum was identified on chromosome 9. The protein product (Clag9) was implicated in cytoadhesion, the binding of infected erythrocytes to host endothelial cells, but little information on the biochemical characteristics of this protein is available. Other genes related to clag9 have been identified on different chromosomes. These genes encode similar amino acid sequences, but clag9 shows least conservation. Clag9 was detected in schizonts, merozoites and ring-stage parasites after protease digestion and peptide analysis by mass spectrometry. Using antisera raised against unique regions of Clag9 and against RhopH2, a component of the RhopH high-molecular-mass protein complex of merozoites, immunofluorescence co-localized the two proteins to the apical region of merozoites. Immunoelectron microscopy co-localized Clag9 and RhopH2 exclusively to the basal bulb region of rhoptries rather than to their apical ducts. The same Clag9-specific antibodies bound the RhopH complex, and the protein was detected in the complex purified by antibodies to RhopH2. Clag9 protein was also shown to be present in ring-stage parasites, carried through from the previous cycle with the RhopH complex, in a location identical to that of RhopH2. Transcription of the clag9 gene was shown to occur at the same time as the genes for other members of the RhopH complex, rhoph2 and 3. The results indicate that Clag9 is part of the RhopH complex and suggest that, within this complex, the protein previously designated RhopH1 is composed of more than one protein product of the clag gene family. The results cast doubt on a direct role for Clag9 in cytoadhesion; we suggest that the primary role of the RhopH complex is in remodelling the infected red blood cell after invasion by the merozoite. The complex may have multiple functions dependent on its exact composition, which may include, with respect to Clag9, a contribution to the mechanism of cytoadhesion.