ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors.

High throughput sequencing of adaptive immune receptor repertoire (AIRR-seq) has provided numerous human immunoglobulin (IG) sequences allowing specific B cell receptor (BCR) studies such as the antigen-driven evolution of antibodies (soluble forms of the membrane-bound IG part of the BCR). AIRR-seq data allows researchers to examine intraclonal differences caused primarily by somatic hypermutations in IG genes and affinity maturation. Exploring this essential adaptive immunity process could help elucidate the generation of antibodies with high affinity or broadly neutralizing activities. Retracing their evolutionary history could also clarify how vaccines or pathogen exposition drive the humoral immune response, and unravel the clonal architecture of B cell tumors. Computational methods are necessary for large-scale analysis of AIRR-seq properties. However, there is no efficient and interactive tool for analyzing intraclonal diversity, permitting users to explore adaptive immune receptor repertoires in biological and clinical applications. Here we present ViCloD, a web server for large-scale visual analysis of repertoire clonality and intraclonal diversity. ViCloD uses preprocessed data in the format defined by the Adaptive Immune Receptor Repertoire (AIRR) Community. Then, it performs clonal grouping and evolutionary analyses, producing a collection of useful plots for clonal lineage inspection. The web server presents diverse functionalities, including repertoire navigation, clonal abundance analysis, and intraclonal evolutionary tree reconstruction. Users can download the analyzed data in different table formats and save the generated plots as images. ViCloD is a simple, versatile, and user-friendly tool that can help researchers and clinicians to analyze B cell intraclonal diversity. Moreover, its pipeline is optimized to process hundreds of thousands of sequences within a few minutes, allowing an efficient investigation of large and complex repertoires.

Reconstructing B cell lineage trees with minimum spanning tree and genotype abundances.

B cell receptor (BCR) genes exposed to an antigen undergo somatic hypermutations and Darwinian antigen selection, generating a large BCR-antibody diversity. This process, known as B cell affinity maturation, increases antibody affinity, forming a specific B cell lineage that includes the unmutated ancestor and mutated variants. In a B cell lineage, cells with a higher antigen affinity will undergo clonal expansion, while those with a lower affinity will not proliferate and probably be eliminated. Therefore, cellular (genotype) abundance provides a valuable perspective on the ongoing evolutionary process. Phylogenetic tree inference is often used to reconstruct B cell lineage trees and represents the evolutionary dynamic of BCR affinity maturation. However, such methods should process B-cell population data derived from experimental sampling that might contain different cellular abundances. There are a few phylogenetic methods for tracing the evolutionary events occurring in B cell lineages; best-performing solutions are time-demanding and restricted to analysing a reduced number of sequences, while time-efficient methods do not consider cellular abundances. We propose ClonalTree, a low-complexity and accurate approach to construct B-cell lineage trees that incorporates genotype abundances into minimum spanning tree (MST) algorithms. Using both simulated and experimental data, we demonstrate that ClonalTree outperforms MST-based algorithms and achieves a comparable performance to a method that explores tree-generating space exhaustively. Furthermore, ClonalTree has a lower running time, being more convenient for building B-cell lineage trees from high-throughput BCR sequencing data, mainly in biomedical applications, where a lower computational time is appreciable. It is hundreds to thousands of times faster than exhaustive approaches, enabling the analysis of a large set of sequences within minutes or seconds and without loss of accuracy. The source code is freely available at github.com/julibinho/ClonalTree.

A multi-objective based clustering for inferring BCR clonal lineages from high-throughput B cell repertoire data.

The adaptive B cell response is driven by the expansion, somatic hypermutation, and selection of B cell clonal lineages. A high number of clonal lineages in a B cell population indicates a highly diverse repertoire, while clonal size distribution and sequence diversity reflect antigen selective pressure. Identifying clonal lineages is fundamental to many repertoire studies, including repertoire comparisons, clonal tracking, and statistical analysis. Several methods have been developed to group sequences from high-throughput B cell repertoire data. Current methods use clustering algorithms to group clonally-related sequences based on their similarities or distances. Such approaches create groups by optimizing a single objective that typically minimizes intra-clonal distances. However, optimizing several objective functions can be advantageous and boost the algorithm convergence rate. Here we propose MobiLLe, a new method based on multi-objective clustering. Our approach requires V(D)J annotations to obtain the initial groups and iteratively applies two objective functions that optimize cohesion and separation within clonal lineages simultaneously. We show that our method greatly improves clonal lineage grouping on simulated benchmarks with varied mutation rates compared to other tools. When applied to experimental repertoires generated from high-throughput sequencing, its clustering results are comparable to the most performing tools and can reproduce the results of previous publications. The method based on multi-objective clustering can accurately identify clonally-related antibody sequences and presents the lowest running time among state-of-art tools. All these features constitute an attractive option for repertoire analysis, particularly in the clinical context. MobiLLe can potentially help unravel the mechanisms involved in developing and evolving B cell malignancies.

Effect of depletion forces on the morphological structure of carboxymethyl cellulose and micro/nano cellulose fiber suspensions.

Cellulose nanofibers (CNF) can present a high viscosity and thixotropic behavior when dispersed in water. In this work, CNF isolated from sugarcane bagasse and modified by N-oxyl-2,2,6,6-tetramethylpiperidine (TEMPO) oxidation was added to a solution of carboxymethyl cellulose (CMC). This process produced an unexpected viscosity due to a synergistic effect that was observed macroscopically through rheology analysis. The phenomenon known as depletion flocculation was observed, which was caused by the reduction of the excluded volume. The interactions of the system were studied by ultraviolet-visible spectroscopy (UV-Vis), optical microscopy, and cryogenic transmission electron microscopy (cryo-TEM), which demonstrated the presence of the particle/polymer repulsion and subsequent formation of domains composed of aligned micro and nanocellulose particles clusters and nanofibers distributed throughout the sample, forming a percolated 3D structure responsible for a strong gelling and colloidal stability.

Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean.

The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths but show little or no response to the more attenuated red/far-red wavelengths. Here, we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared with other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum, and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs.

Self-assembly of polyion-surfactant ion complex salts in mixtures with water and n-alcohols.

Phase behavior and structural features were investigated for "complex salts", consisting of the cationic hexadecyltrimethylammonium (CTA) surfactant with polyacrylate (PA(n), n = 30 or 6000) counterions, mixed with water and different n-alcohols (ethanol, butanol, hexanol, octanol, and decanol). The liquid crystalline structures formed were identified by small-angle X-ray scattering measurements, which provided information about the changes in the geometry of the aggregates as functions of the concentration and chain length of the added n-alcohol. The obtained results were compared with a previous work on similar ternary mixtures of the same cationic surfactant but with the monomeric bromide counterion, CTABr (Fontell, K.; Khan, A.; Lindström, B.; Maciejewska, D.; Puang-Ngern, S. Colloid Polym. Sci., 1991, 269, 727). In general, the same phases were detected in systems with the complex salts CTAPA(n) as in systems with CTABr, but the swelling of the various liquid crystalline phases by water was much more limited in the complex salt systems. An isotropic alcoholic phase was observed with all alcohols and the size of this region of the phase diagram increased for the shorter alcohols, except for ethanol. For mixtures with octanol and ethanol, in particular, the extensions of the disordered isotropic phases were larger for the complex salt with the shorter polyacrylate ions.

Structure and phase equilibria of mixtures of the complex salt hexadecyltrimethylammonium polymethacrylate, water and different oils.

This work reports on phase diagrams for mixtures of a complex salt formed by a cationic surfactant and an oppositely charged polyelectrolyte, hexadecyltrimethylammonium polymethacrylate, in binary mixtures with water and in ternary mixtures containing water and organic solvents of different polarity ('oils'): decanol, octanol, p-xylene and cyclohexane. The liquid crystalline structures formed were identified by small angle X-ray scattering measurements, which also provided information about changes in the size of the aggregates as a function of the system composition. These results are analysed in comparison with others previously reported [Bernardes et al., J. Phys. Chem. B 110 (2006) 10332-10340] for the analog complex formed with polyacrylate and, in general, reveal that the presence of an extra methylene group in the polymer chain does not produce significant changes in the complex phase diagrams nor in the structure of the liquid crystalline phases formed. Additionally, the obtained results confirm once more the approach used to analyze these kinds of systems formed by polymer and oppositely charged surfactant.