Biology subjects

Barbosa, R.

Publications and source records attributed to Barbosa, R..

6 recordsLinked to original sources

bioRxiv2025

AXIS: A Lab-in-the-Loop Machine Learning approach for generalized detection of macromolecular crystals.

Macromolecular crystallography provides mechanistic understanding of biological processes and can be applied in drug design. Nowadays, the use of robotic systems for crystal growth and diffraction analysis is widespread and high throughput protein-to-structure pipelines for ligand and fragment screening are revolutionizing the field. However, the identification of crystals is still largely carried out through manual inspection, sometimes involving tens of thousands of images, which represents a bottleneck in an otherwise highly automated process. Here we describe AXIS, an AI-based Crystal Identification System combining the DINOv2 computer vision model, state-of-the-art transfer learning and MARCO, the largest crystallization dataset available to date, for automated crystal detection. AXIS can operate both with visible and UV light images and integrates a Lab-In-The-Loop approach combining ML and expert inputs for continuous learning and specialization. AXIS enables automated annotation of large crystallization image datasets with performance and accuracy comparable to that of human experts and the Lab-In-The-Loop approach introduced here enables efficient adaptation to local conditions facilitating widespread application, which has been a major limitation to date. AXIS can help correct human errors in image annotation and removes critical bottlenecks, particularly in the context of extensive crystallization screens or high throughput applications like fragment and ligand screening unlocking the potential for higher levels of automation that are key both in fundamental and translational research. Appendix A. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=183 SRC="FIGDIR/small/685844v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@c47ab4org.highwire.dtl.DTLVardef@153ce2dorg.highwire.dtl.DTLVardef@1050086org.highwire.dtl.DTLVardef@165965b_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

Jchain-driven cre enables specific genetic manipulation and timestamping of plasma cell in their niche.

Plasma cells (PC)s are essential for protection from infection, and at the origin of incurable cancers. Current studies do not circumvent limitations of removing PCs from their microenvironment and confound formation and maintenance. This is in part due to the lack of tools to perform specific genetic manipulation in vivo. Also, studies of PC population dynamics have mostly relied on the use of nucleotide analog incorporation that does not label quiescent cells, a property of most PCs. Here we characterize in detail a genetic tool (JchaincreERT2) that permits first-ever specific genetic manipulation in PC in vivo, across immunoglobulin isotypes. Using this tool we found that PC numbers remained constant over-time and that PC decay was compensated by the emergence of new cells, supporting an homeostatic turnover of the population. The JchaincreERT2 genetic tool paves the way for in-depth mechanistic understanding of PC biology and pathology in vivo, in their microenvironment. HighlightsJchain expression occurs in most plasma cells across immunoglobulin isotypes JchaincreERT2 mediated genetic manipulation is effective only in plasma cells Genetic timestamping of plasma cells reveals homeostatic regulation

immunology↗

bioRxiv2020

Co-activation of NF-κB and MYC renders cancer cells addicted to IL6 for survival and phenotypic stability

NF-{kappa}B and MYC are found co-deregulated in human B and plasma-cell cancers. In physiology, NF-{kappa}B is necessary for terminal B-to-plasma cell differentiation, whereas MYC repression is required. It is thus unclear if NF-{kappa}B/MYC co-deregulation is developmentally compatible in carcinogenesis and/or impacts cancer cell differentiation state, possibly uncovering unique sensitivities. Using a mouse system to trace cell lineage and oncogene activation we found that NF-{kappa}B/MYC co-deregulation originated cancers with a plasmablast-like phenotype, alike human plasmablastic-lymphoma and was linked to t(8;14)[MYC-IGH] multiple myeloma. Notably, in contrast to NF-{kappa}B or MYC activation alone, co-deregulation rendered cells addicted to IL6 for survival and phenotypic stability. We propose that conflicting oncogene-driven differentiation pressures can be accommodated at a cost in poorly-differentiated cancers. SignificanceOur studies improve the understanding of cancer pathogenesis by demonstrating that co-deregulation of NF-{kappa}B and MYC synergize in forming a cancer with a poorly-differentiated state. The cancers in the mouse system share features with human Plasmablastic lymphoma that has a dismal prognosis and no standard of care, and with t(8;14)[MYC-IGH] Multiple myeloma, which is in overall resistant to standard therapy. Notably, we found that NF-{kappa}B and MYC co-deregulation uniquely render cells sensitive to IL6 deprivation, providing a road-map for patient selection. Because of the similarity of the cancers arising in the compound mutant mouse model with that of human Plasmablastic lymphoma and t(8;14)[MYC-IGH] Multiple myeloma, this model could serve in preclinical testing to investigate novel therapies for these hard-to-treat diseases. HighlightsO_LINF-{kappa}B and MYC co-activation originates (pre)plasmablast-like cancer C_LIO_LINF-{kappa}B/MYC+ renders cancer cells addicted to IL6 for survival and phenotypic stability C_LIO_LINF-{kappa}B/MYC+ cancers are alike a fraction of human plasmablastic lymphoma C_LIO_LIt(8;14)[MYC-IGH] multiple myeloma is linked to a NF-{kappa}B/MYC co-activation signature C_LI

cancer biology↗

bioRxiv2019

A popular Indian clove-based mosquito repellent is a false economy

Insect repellents are important prophylactic tools for travelers to and populations living in endemic areas of malaria, dengue, encephalitis, and other vector-borne diseases, and the first line of defense against emerging arboviruses. However, the cost of daily applications of even the most affordable and the gold standard of insect repellents, DEET, is still high for low-income populations where repellents are needed the most. An Indian clove-based homemade recipe has been presented as a panacea. We analyzed this homemade repellent and confirmed by behavioral measurements and odorant receptor responses that eugenol is the active ingredient in this formulation. Prepared as advertised, this homemade repellent is ineffective, whereas 5X more concentrated extracts from the brand most enriched in eugenol showed moderate repellency activity against Culex quinquefasciatus and Aedes aegypti. DEET showed higher performance when compared to the 5X concentrated formulation and is available in the same market at a lower price than the cost of the ingredients to prepare the homemade formulation.

ecology↗

bioRxiv2019

Conspecific larval extracts along with biotoxin to attract-and-kill mosquitoes

One of the strategies of integrated vector management is to lure gravid mosquitoes for surveillance purposes or to entice them to lay eggs in water containing toxins that kill the offspring (attract-and-kill or trap-and-kill). Typically, the major challenge of this approach is the development of a lure that stimulates oviposition plus a toxin with no deterrent effect. Bacillus thuringiensis var. israelensis (Bti) satisfies the latter criterion, but lures for these autocidal gravid traps are sorely needed. We observed that gravid Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus laid significantly more eggs in cups with extracts from 4th-stage larvae (4L) of the same or different species. No activity was found when 4L were extracted with hexane, diethyl ether, methanol, or butanol, but activity was observed with dimethyl sulfoxide extracts. Larval extracts contained both oviposition stimulant(s)/attractant(s) and deterrent(s), which partitioned in the water and hexane phases, respectively. Lyophilized larval extracts were active after a month, but activity was reduced by keeping the sample at 4{degrees}C. In the tested range of 0.1 to 1 larvae-equivalent per milliliter, oviposition activity increased in a dose-dependent manner. In field experiments, Ae. aegpti laid significantly more eggs in traps loaded with larval extracts plus Bti than in control traps with water plus Bti.

ecology↗

bioRxiv2019

Anthropogenic Soils Promote Biodiversity in Amazonian Rainforests

Amazonian Dark Earths (ADEs) are fertile anthropic soils found throughout Amazonia, resulting from long-term occupation by pre-Columbian societies. Although the chemistry of these soils is well known, their biodiversity, particularly soil invertebrate communities have been neglected. To address this, we characterised soil macroinvertebrate communities and their activities in ADEs, comparing them with adjacent reference soils under forests and agriculture, at nine archaeological sites. We found 667 morphospecies and a tenacious pre-Columbian biodiversity footprint, with 40% of species found exclusively in ADEs. Soil biological activity was higher in ADEs than in adjacent soils, and associated with higher biomass and richness of organisms known to engineer the ecosystem. We show that these habitats have unique species pools, but that contemporary land-use causes nutrient loss and threatens their diversity. Both past and present human activities alter biodiversity and its distribution in Amazonia, and further efforts are needed to recognize and preserve these ADEs and their biodiversity.

zoology↗