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Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multiomics datasets into a resource comprising >2.8 million nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550,000 cell type-specific regulatory elements and >1.4 million single-cell expression quantitative trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.

Genomic profiling in postmortem brain from autistic individuals has consistently revealed convergent molecular changes. What drives these changes and how they relate to genetic susceptibility in this complex condition are not well understood. We performed deep single-nucleus RNA sequencing (snRNA-seq) to examine cell composition and transcriptomics, identifying dysregulation of cell type-specific gene regulatory networks (GRNs) in autism spectrum disorder (ASD), which we corroborated using single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) and spatial transcriptomics. Transcriptomic changes were primarily cell type specific, involving multiple cell types, most prominently interhemispheric and callosal-projecting neurons, interneurons within superficial laminae, and distinct glial reactive states involving oligodendrocytes, microglia, and astrocytes. Autism-associated GRN drivers and their targets were enriched in rare and common genetic risk variants, connecting autism genetic susceptibility and cellular and circuit alterations in the human brain.

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types., Competing Interests: Competing interests Z. Weng (UMass Chan Medical School) co-founded and serves as a scientific advisor for Rgenta Inc. From April 11, 2022, N.L. Jorstad (Allen Institute for Brain Science) has been an employee of Genentech. K.P.W. (National University of Singapore) is a shareholder in Tempus AI and Provaxus Inc. The other authors declare no competing interests.

Understanding how genetic variation exerts its effects on the human brain in health and disease has been greatly informed by functional genomic characterization. Studies over the last decade have demonstrated robust evidence of convergent transcriptional and epigenetic profiles in post-mortem cerebral cortex from individuals with Autism Spectrum Disorder (ASD). Here, we perform deep single nuclear (sn) RNAseq to elucidate changes in cell composition, cellular transcriptomes and putative candidate drivers associated with ASD, which we corroborate using snATAC-seq and spatial profiling. We find changes in cell state composition representing transitions from homeostatic to reactive profiles in microglia and astrocytes, a pattern extending to oligodendrocytes and blood brain barrier cells. We identify profound changes in differential expression involving thousands of genes across neuronal and glial subtypes, of which a substantial portion can be accounted for by specific transcription factor networks that are significantly enriched in common and rare genetic risk for ASD. These data, which are available as part of the PsychENCODE consortium, provide robust causal anchors and resultant molecular phenotypes for understanding ASD changes in human brain.

The underdevelopment of the higher education system in Guatemala and the fragility of its science and technology (S&T) contexts have compelled a significant number of talented Guatemalan scientists to be trained, educated, and employed abroad. The relocation of such skilled human power to different countries and regions has resulted in a growing Guatemalan Scientific Diaspora (GSD). Until recently, the emigration of scientists from the Global South to scientifically advanced countries in the North was studied as it negatively impacted the countries of origin. However, technological upgrades and globalization have progressively shifted the paradigm in which such scientific diasporas interact and connect, thus enabling them to influence their home countries positively. Due to the lack of knowledge-based evidence and functioning connecting platforms, the value and potential of the GSD in their involvement in proposing solutions to complex socio-economic, environmental, and other challenges faced by Guatemalan society remain unknown. Moreover, the lack of interaction of relevant stakeholders (S&T policy agents, international partners, higher education institutions and research centers, industry, and relevant not governmental organizations) represents a pervasive obstacle to the untapped impact of the GSD in the country. This study outlines the Guatemalan scientific diasporas' networking as a mechanism for building research excellence and intellectual capital. This force could respond to the need to strengthen the national science capacities and meet the demands for knowledge production and access to broader sectors of society. This research applied qualitative methodology that, through the conduction of focus group discussions and semi-structured interviews with members of the Guatemalan scientific community and relevant key stakeholders, delved into the existence and articulation of the GSD and potential stages for their engagement with their country of origin. Findings highlight the importance of digital and technological pathways that might leverage the GSD's knowledge and experience, channeling skills, and international connections for better interaction with the Guatemalan society. Furthermore, the discussion addresses how technology might turn brain drain into brain circulation, enabling the articulation of the GSD as a viable opportunity to generate collaboration between scientists abroad and local actors, ultimately impacting the building and development of Guatemalan science and national research capacities., Competing Interests: SA was employed by New Sun Road. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Bonilla, Romero-Oliva, Arrechea, Ortiz Osejo, Mazariegos, Alonzo, Orellana-Corrales, del Valle and Montenegro-Bethancourt.)

Kinetic stability of proteins determines their susceptibility to irreversibly unfold in a time-dependent process, and therefore its half-life. A residue displacement analysis of temperature-induced unfolding molecular dynamics simulations was recently employed to define the thermal flexibility of proteins. This property was found to be correlated with the activation energy barrier (E act ) separating the native from the transition state in the denaturation process. The E act was determined from the application of a two-state irreversible model to temperature unfolding experiments using differential scanning calorimetry (DSC). The contribution of each residue to the thermal flexibility of proteins is used here to propose multiple mutations in triosephosphate isomerase (TIM) from Trypanosoma brucei (TbTIM) and Trypanosoma cruzi (TcTIM), two parasites closely related by evolution. These two enzymes, taken as model systems, have practically identical structure but large differences in their kinetic stability. We constructed two functional TIM variants with more than twice and less than half the activation energy of their respective wild-type reference structures. The results show that the proposed strategy is able to identify the crucial residues for the kinetic stability in these enzymes. As it occurs with other protein properties reflecting their complex behavior, kinetic stability appears to be the consequence of an extensive network of inter-residue interactions, acting in a concerted manner. The proposed strategy to design variants can be used with other proteins, to increase or decrease their functional half-life., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Proteins with great sequence similarity usually have similar structure, function and other physicochemical properties. But in many cases, one or more of the physicochemical or functional characteristics differ, sometimes very considerably, among these homologous proteins. To better understand how critical amino acids determine quantitative properties of function in proteins, the responsible residues must be located and identified. This can be difficult to achieve, particularly in cases where multiple amino acids are involved. In this work, two triosephosphate isomerases with very high similarity from two related human parasites were used to address one such problem. We demonstrate that a seventy-fold difference in the reactivity of an interface cysteine to the sulfhydryl reagent methylmethane sulfonate in these two enzymes depends on three amino acids located far away from this critical residue and which could not have been predicted using other current methods. Starting from previous observations with chimeric proteins involving these two triosephosphate isomerases, we developed a strategy involving additive mutant enzymes and selected site directed mutants to locate and identify the three amino acids. These three residues seem to induce changes in the interface cysteine in reactivity by increasing (or decreasing) its apparent pKa. Some enzymes with four to seven mutations also exhibited altered reactivity. This study completes a strategy for identifying key residues in the sequences of proteins that can have applications in future protein structure-function studies.

Background: Overweight and obesity prevalence in children is now on the rise in low/middle-income countries, including Guatemala. Fast food consumption is a recognized contributing factor to this rise. Fast food restaurants use health claims, toy giveaways, price incentives and fast service to promote children's combo meals. This study sought to assess the use of toy giveaways, time to delivery and price incentives as marketing strategies in fast food chain restaurants in Guatemala. In addition, we sought to compare nutritional quality of combo meals with and without health claims., Methods: We visited one restaurant from each of the 8 major fast food chains in Guatemala and purchased all children's combo meals to assess the prevalence of toy giveaways, health claims, and difference in delivery time and price between the combo meal and each meal item purchased separately. Each item was then classified as "healthy" or "less healthy" using the UK Nutrition Profile Model. Nutrition information was collected on-site, from the restaurant website, or by calling the customer service phone number., Results: We found 114 combo meals, 21 (18.4%) of which were children's combo meals. Five (24%) had nutrition information, all were classified by our analysis as "less healthy", and three had a health claim. On average, combo meals were US$1.93 less expensive than purchasing children's meal items individually ( p  = 0.01). Time to delivery was 1.44 min faster for combo meals compared to purchasing meal items individually ( p  = 0.19)., Conclusions: Children's fast food combo meals in Guatemala were promoted using several marketing strategies that encourage consumption, including offering toy giveaways and price incentives. In addition, nutrition information is lacking in fast food chain restaurants. Public health advocates in Guatemala should consider a comprehensive approach to encourage healthier choices within fast food restaurants including policies that require fruit and vegetable options for meal side dishes, accessible and easy to read nutrition information, and restrict the use of toy giveaways.

Triosephosphate isomerase (TIM) is an essential Trypanosoma cruzi enzyme and one of the few validated drug targets for Chagas disease. The known inhibitors of this enzyme behave poorly or have low activity in the parasite. In this work, we used symmetrical diarylideneketones derived from structures with trypanosomicidal activity. We obtained an enzymatic inhibitor with an IC50 value of 86 nm without inhibition effects on the mammalian enzyme. These molecules also affected cruzipain, another essential proteolytic enzyme of the parasite. This dual activity is important to avoid resistance problems. The compounds were studied in vitro against the epimastigote form of the parasite, and nonspecific toxicity to mammalian cells was also evaluated. As a proof of concept, three of the best derivatives were also assayed in vivo. Some of these derivatives showed higher in vitro trypanosomicidal activity than the reference drugs and were effective in protecting infected mice. In addition, these molecules could be obtained by a simple and economic green synthetic route, which is an important feature in the research and development of future drugs for neglected diseases., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Recent studies revealed that a significant fraction of any given proteome is presented by proteins that do not have unique 3D structures as a whole or in significant parts. These intrinsically disordered proteins possess dramatic structural and functional variability, being especially enriched in signaling and regulatory functions since their lack of fixed structure defines their ability to be involved in interaction with several proteins and allows them to be re-used in multiple pathways. Among recognized disorder-based protein functions are interactions with nucleic acids and multi-target binding; i.e., the functions ascribed to many spliceosomal proteins. Therefore, the spliceosome, a multimegadalton ribonucleoprotein machine catalyzing the excision of introns from eukaryotic pre-mRNAs, represents an attractive target for the focused analysis of the abundance and functionality of intrinsic disorder in its proteinaceous components. In yeast cells, spliceosome consists of five small nuclear RNAs (U1, U2, U4, U5, and U6) and a range of associated proteins. Some of these proteins constitute cores of the corresponding snRNA-protein complexes known as small nuclear ribonucleoproteins (snRNPs). Other spliceosomal proteins have various auxiliary functions. To gain better understanding of the functional roles of intrinsic disorder, we have studied the prevalence of intrinsically disordered proteins in the yeast spliceosome using a wide array of bioinformatics methods. Our study revealed that similar to the proteins associated with human spliceosomes (Korneta & Bujnicki, 2012), proteins found in the yeast spliceosome are enriched in intrinsic disorder.

For a better comprehension of the structure-function relationship in proteins it is necessary to identify the amino acids that are relevant for measurable protein functions. Because of the numerous contacts that amino acids establish within proteins and the cooperative nature of their interactions, it is difficult to achieve this goal. Thus, the study of protein-ligand interactions is usually focused on local environmental structural differences. Here, using a pair of triosephosphate isomerase enzymes with extremely high homology from two different organisms, we demonstrate that the control of a seventy-fold difference in reactivity of the interface cysteine is located in several amino acids from two structurally unrelated regions that do not contact the cysteine sensitive to the sulfhydryl reagent methylmethane sulfonate, nor the residues in its immediate vicinity. The change in reactivity is due to an increase in the apparent pKa of the interface cysteine produced by the mutated residues. Our work, which involved grafting systematically portions of one protein into the other protein, revealed unsuspected and multisite long-range interactions that modulate the properties of the interface cysteines and has general implications for future studies on protein structure-function relationships.