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Despite established efficacy for oral pre-exposure prophylaxis (PrEP) in reducing HIV incidence, multi-level barriers within the health system, clinics, and the processes that shape practice have hindered service delivery and subsequent population-level effects. We applied the Consolidated Framework for Implementation Research (CFIR) to assess the context of PrEP delivery for adolescent girls and young women (AGYW) in rural South Africa and identify the factors supporting and impeding PrEP implementation to develop strategies to improve PrEP delivery. Between 2021 and 2022, we conducted in-depth interviews with five young women with PrEP use experience and 11 healthcare providers as well as four key informant stakeholder interviews. Tailored interviews organized around the CFIR domains provided multiple perspectives on the inter-connected processes, gaps, and opportunities between health systems, clinics, communities, and PrEP services. Shifts in PrEP policies, funding pressures, and inconsistent communications from the National Department of Health spurred fragmented planning, engagement, execution, and monitoring of PrEP delivery processes within clinics already struggling to address multiple population health needs. Resulting challenges included: conflicting priorities within clinics and across NGO partners, unclear goals and targets, staffing and space constraints, and insufficient community engagement. Individual clinics' implementation climate and readiness to deliver PrEP varied in terms of operational plans and delivery models. Interviewees reported complexity of initiation procedures and support for PrEP maintenance, with opportunities to improve systems communications and processes to facilitate integrated services and more user-friendly experiences. Applying CFIR identified opportunities to strengthen PrEP delivery across levels within this complex service delivery setting.

Community engagement is a key pathway for incorporating social considerations into the development of utility-scale renewable energy facilities. Prior literature recommends meaningful, early community engagement to both improve siting outcomes and empower the public to participate in decision-making, but there is no recent nor comprehensive understanding of industry experiences with engagement. This study provides a critical contribution by revealing the practices and perspectives of project developers. We draw upon a survey of 123 professionals employed at 62 unique companies across the United States. We demonstrate that developers are highly concerned about the impact of community opposition on project deployment, and that they already use a variety of engagement strategies and adjust project designs in response to community feedback. However, the public is generally not made aware of project proposals until after land for the project is secured, and industry expenditures on engagement activities pale in comparison to other project development costs. We draw upon Arnstein's ladder of citizen participation to operationalize the engagement preferences of developers, and find that the majority of developers prefer that members of the public provide input but not recommend or make decisions. We characterize this preference as ‘halfway up the ladder’, compared to the idealized vision of full citizen empowerment envisioned in narratives of just transition. These findings contribute to discussion of the role and potential for community engagement to attend to justice in the energy transition.

Recognizing that centuries of mistreatment of low-income and minority communities by governments and corporations have resulted in widespread exposure to environmental harms, academics and policymakers are seeking ways to improve environmental justice. While it is commonly assumed that improved procedural justice (meaningful participation in decision making) should improve distributive justice (equitable distribution of environmental harms and benefits), empirical evidence of this link is nascent. This paper evaluates whether differing approaches to procedural justice shape recognition of distributive injustices by policymakers, focusing on implementation of the National Environmental Policy Act (NEPA) in Puerto Rico. NEPA requires federal agencies to evaluate the potential environmental impacts of projects they implement, fund, or permit; this review commonly includes an assessment of the project's impacts on distributive justice. Drawing on document analysis and interviews with project developers, regulators, and community organizations, we explore how and why four NEPA reviews consider distributional impacts. In all four cases, the community mobilized to voice concerns about the proposed projects' impacts, but the lead agencies and project developers did not always create the space for those voices to collaboratively shape the review. This demonstrates the role of the project developer in how distributive justice considerations are treated, as project leads have discretion on whether and when to provide space for community groups to participate in the process. This research makes two primary contributions. First, by linking features of the decision-making process with environmental justice-related outputs, this research provides practical understanding of ways to support distributive justice and expands knowledge about how participatory governance works within the context of US environmental policy. Second, by studying NEPA's implementation in Puerto Rico, we assess challenges associated with implementing Environmental Impact Assessment in a territorial setting, where the demographics and intensity of environmental problems are distinct from the 'traditional' American context the policies were designed to protect.

Drosophila prolongata is a member of the melanogaster species group and rhopaloa subgroup native to the subtropical highlands of Southeast Asia. This species exhibits an array of recently evolved male-specific morphological, physiological, and behavioral traits that distinguish it from its closest relatives, making it an attractive model for studying the evolution of sexual dimorphism and testing theories of sexual selection. The lack of genomic resources has impeded the dissection of the molecular basis of sex-specific development and behavior in this species. To address this, we assembled the genome of D. prolongata using long-read sequencing and Hi-C scaffolding, resulting in a highly complete and contiguous (scaffold N50 2.2 Mb) genome assembly of 220 Mb. The repetitive content of the genome is 24.6%, the plurality of which are long terminal repeats retrotransposons (33.2%). Annotations based on RNA-seq data and homology to related species revealed a total of 19,330 genes, of which 16,170 are protein-coding. The assembly includes 98.5% of Diptera BUSCO genes, including 93.8% present as a single copy. Despite some likely regional duplications, the completeness of this genome suggests that it can be readily used for gene expression, genome-wide association studies (GWAS), and other genomic analyses.

Alterations in the nuclear envelope are linked to a variety of rare diseases termed laminopathies. A single amino acid substitution at position 12 (A12T) of the human nuclear envelope protein BAF (Barrier to Autointegration Factor) causes Néstor-Guillermo Progeria Syndrome (NGPS). This premature ageing condition leads to growth retardation and severe skeletal defects, but the underlying mechanisms are unknown. Here, we have generated a novel in vivo model for NGPS by modifying the baf-1 locus in C. elegans to mimic the human NGPS mutation. These baf-1(G12T) mutant worms displayed multiple phenotypes related to fertility, lifespan, and stress resistance. Importantly, nuclear morphology deteriorated faster during aging in baf-1(G12T) compared to wild-type animals, recapitulating an important hallmark of cells from progeria patients. Although localization of BAF-1(G12T) was similar to wild-type BAF-1, lamin accumulation at the nuclear envelope was reduced in mutant worms. Tissue-specific chromatin binding and transcriptome analyses showed reduced BAF-1 association in most genes deregulated by the baf-1(G12T) mutation, suggesting that altered BAF chromatin association induces NGPS phenotypes via altered gene expression.

Make-on-demand chemical libraries have drastically increased the reach of molecular docking, with the enumerated ready-to-dock ZINC-22 library approaching 6.4 billion molecules (July 2024). While ever-growing libraries result in better-scoring molecules, the computational resources required to dock all of ZINC-22 make this endeavor infeasible for most. Here, we organize and traverse chemical space with hierarchical navigable small-world graphs, a method we term retrieval augmented docking (RAD). RAD recovers most virtual actives, despite docking only a fraction of the library. Furthermore, RAD is protein-agnostic, supporting additional docking campaigns without additional computational overhead. In depth, we assess RAD on published large-scale docking campaigns against D4 and AmpC spanning 99.5 million and 138 million molecules, respectively. RAD recovers 95% of DOCK virtual actives for both targets after evaluating only 10% of the libraries. In breadth, RAD shows widespread applicability against 43 DUDE-Z proteins, evaluating 50.3 million associations. On average, RAD recovers 87% of virtual actives while docking 10% of the library without sacrificing chemical diversity.

Despite some progress, universal access to safe water, sanitation and hygiene (WASH) by 2030-a remit of Sustainable Development Goal 6-remains a distant prospect in many countries. Policy-makers and implementers of the WASH sector are challenged to track a new path. This research aimed to identify core orienting themes of the sector, as legacies of past processes, which can provide insights for its future. We reviewed global policy, science and programmatic documents and carried out 19 expert interviews to track the evolution of the global WASH sector over seven decades. We situated this evolution in relation to wider trends in global health and development over the same time period.With transnational flows of concern, expertise and resources from high-income to lower-income countries, the WASH sector evolved over decades of international institutionalisation of health and development with (1) a focus on technologies (technicalisation), (2) a search for generalised solutions (universalisation), (3) attempts to make recipients responsible for environmental health (responsibilisation) and (4) the shaping of programmes around quantifiable outcomes (metricisation). The emergent commitment of the WASH sector to these core themes reflects a pragmatic response in health and development to depoliticise poverty and social inequalities in order to enable action. This leads to questions about what potential solutions have been obscured, a recognition which might be understood as 'uncomfortable knowledge'-the knowns that have had to be unknown, which resonate with concerns about deep inequalities, shrinking budgets and the gap between what could and has been achieved.

This systematic review examines the landscape of extracellular vesicle (EV)-related clinical trials to elucidate the field's trends in clinical applications and EV-related methodologies, with an additional focus on the acknowledgement of EV subpopulations. By analysing data from public reporting repositories, we catalogued 471 EV-related clinical trials to date, with indications for over 200 diseases. Diagnostics and companion diagnostics represented the bulk of EV-related clinical trials with cancer being the most frequent application. EV-related therapeutics trials mainly utilized mesenchymal stromal cell (MSC) EVs and were most frequently used for treatment of respiratory illnesses. Ultracentrifugation and RNA-sequencing were the most common isolation and characterization techniques; however, methodology for each was not frequently reported in study records. Most of the reported characterization relied on bulk characterization of EV isolates, with only 11% utilizing EV subpopulations in their experimental design. While this may be connected to a lack of available techniques suitable for clinical implementation, it also highlights the opportunity for use of EV subpopulations to improve translational efforts. As academic research identifies more chemically distinct subpopulations and technologies for their enrichment, we forecast to more refined EV trials in the near future. This review emphasizes the need for meticulous methodological reporting and consideration of EV subpopulations to enhance the translational success of EV-based interventions, pointing towards a paradigm shift in personalized medicine.

Synthetic biology primarily uses genetic engineering to control living cells. In contrast, recent work has ushered in the architectural engineering of living cells through intracellular materials. Specifically, Cyborg Bacteria are created by incorporating synthetic PEG-based hydrogel inside cells. Cyborg Bacteria do not replicate but maintain essential cellular functions, including metabolism and protein synthesis. Thus far, Cyborg Bacteria have been engineered using one primary composition of intracellular hydrogel components. Here, we demonstrate the versatility of controlling the physical and biochemical aspects of Cyborg Bacteria using different structures of hydrogels. The intracellular cell-gel architecture is modulated using a different photoinitiator, PEG-diacrylate (PEG-DA) of different molecular weights, 4arm PEG-DA, and dsDNA-PEG. We show that the molecular weight of the PEG-DA affects the generation and metabolism of Cyborg Bacteria. In addition, we show that the hybrid dsDNA-PEG intracellular hydrogel controls protein expression levels of the Cyborg Bacteria through post-transcriptional regulation and polymerase sequestration. Our work creates a new frontier of modulating intracellular gel components to control Cyborg Bacteria function and architecture.

mRNAs interact with RNA-binding proteins (RBPs) throughout their processing and maturation. While efforts have assigned RBPs to RNA substrates, less exploration has leveraged protein-protein interactions (PPIs) to study proteins in mRNA life-cycle stages. We generated an RNA-aware, RBP-centric PPI map across the mRNA life cycle in human cells by immunopurification-mass spectrometry (IP-MS) of ∼100 endogenous RBPs with and without RNase, augmented by size exclusion chromatography-mass spectrometry (SEC-MS). We identify 8,742 known and 20,802 unreported interactions between 1,125 proteins and determine that 73% of the IP-MS-identified interactions are RNA regulated. Our interactome links many proteins, some with unknown functions, to specific mRNA life-cycle stages, with nearly half associated with multiple stages. We demonstrate the value of this resource by characterizing the splicing and export functions of enhancer of rudimentary homolog (ERH), and by showing that small nuclear ribonucleoprotein U5 subunit 200 (SNRNP200) interacts with stress granule proteins and binds cytoplasmic RNA differently during stress.

The health of incarcerated populations is intertwined with the health of security staff, but the social mechanisms, and especially the specific interventions, that might mitigate these health harms are underexplored. We examine one possible mechanism of interrelated health harms: whether and how jail security staff are willing and able to care for mentally ill detainees. We hypothesize that the attitudes of security staff towards care affect the well-being of everyone in a jail setting-staff, as well as detainees. Analyzing 539 anonymous respondent surveys administered to a stratified cluster sample of security staff working in a large U.S. county jail system, we (1) describe the prevalence of a perceived duty to care and availability of caring resources among security staff and (2) analyze whether variations in a duty to care and caring resources predict outcomes associated with staff and detainee well-being. Across five maximum likelihood models estimated, both perceived duty to care and availability of caring resources are significantly associated with collaborative relationships with medical staff, increased perceptions of personal safety, decreased frequency of hostile encounters, and better self-reported health outcomes. Our models explain 20 percent of the variation in self-reported health outcomes (R2 = .20), a meaningful effect of care on security personnel's well-being. Our findings suggest security staff have an often-overlooked duty to care akin to that experienced by healthcare staff. Among healthcare staff, dual loyalty trainings have successfully amplified caring duties relative to security duties; similar trainings for security staff might better leverage their caring duties to improve both staff and detainee well-being.

There have been impressive advances in the physical and mathematical modelling of complex physiological systems in the last few decades, with the potential to revolutionise personalised healthcare with patient-specific evidence-based diagnosis, risk assessment and treatment decision support using digital twins. However, practical progress and genuine clinical impact hinge on successful model calibration, parameter estimation and uncertainty quantification, which calls for novel innovative adaptions and methodological extensions of contemporary state-of-the-art inference techniques from Statistics and Machine Learning. In the present study, we focus on two computational fluid-dynamics (CFD) models of the blood systemic and pulmonary circulation. We discuss state-of-the-art emulation techniques based on deep learning and Gaussian processes, which are coupled with established inference techniques based on greedy optimisation, simulated annealing, Markov Chain Monte Carlo, History Matching and rejection sampling for computationally fast inference of unknown parameters of the CFD models from blood flow and pressure data. The inference task was set as a competitive challenge which the participants had to conduct within a limited time frame representative of clinical requirements. The performance of the methods was assessed independently and objectively by the challenge organisers, based on a ground truth that was unknown to the method developers. Our results indicate that for the systemic challenge, in which an idealised case of noise-free data was considered, the relative deviation from the ground-truth in parameter space ranges from 10−5% (highest-performing method) to 3% (lowest-performing method). For the pulmonary challenge, for which noisy data was generated, the performance ranges from 0.9% to 7% deviation for the parameter posterior mean, and from 35% to 570% deviation for the parameter posterior variance.

Understanding the mechanisms of the cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short cell cycle, and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. By analyzing experimental data, this study shows that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional multiscale chemical-mechanical model was developed and used to suggest and test hypothesized impacts of aging on bud morphogenesis. Experimentally calibrated model simulations showed that during the early stage of budding, tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip, a process guided by the polarized Cdc42 signal. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage as observed in experiments in this work. The model simulation results suggest that the localization of new cell surface material insertion, regulated by chemical signal polarization, could be weakened due to cellular aging in yeast and other cell types, leading to the change and stabilization of the bud aspect ratio.

Despite the substantial number of studies on the relationships between crime patterns and built environments, the impacts of street-level built environments on crime patterns have not been definitively determined due to the limitations of obtaining detailed streetscape data and conventional analysis models. To fill these gaps, this study focuses on the non-linear relationships and threshold effects between built environments and local crime patterns at the level of a street segment in the City of Santa Ana, California. Using Google Street View (GSV) and semantic segmentation techniques, we quantify the features of the built environment in GSV images. Then, we examine the non-linear relationships and threshold effects between built environment factors and crime by applying interpretable machine learning (IML) methods. While the machine learning models, especially Deep Neural Network (DNN), outperformed negative binomial regression in predicting future crime events, particularly advantageous was that they allowed us to obtain a deeper understanding of the complex relationship between crime patterns and environmental factors. The results of interpreting the DNN model through IML indicate that most streetscape elements showed non-linear relationships and threshold effects with crime patterns that cannot be easily captured by conventional regression model specifications. The non-linearities and threshold effects revealed in this study can shed light on the factors associated with crime patterns and contribute to policy development for public safety from crime.

Maleimide and amidine functionalities often appear in medicinal and natural product targets. We describe a catalyst-free, three-component coupling reaction for the synthesis of amidinomaleimides. This one-pot reaction fuses a broad range of secondary amines and aldehydes with azidomaleimides. The conditions are mild, simple, modular, high yielding, and amenable to aqueous solvents. Most reaction products can be sufficiently purified without column chromatography. The synthesis creates complex, multifunctional molecules with four different molecules, including a tripeptide, arrayed around an amidinomaleimide core.

The rapid evolution of viruses generates proteins that are essential for infectivity and replication but with unknown functions, due to extreme sequence divergence1. Here, using a database of 67,715 newly predicted protein structures from 4,463 eukaryotic viral species, we found that 62% of viral proteins are structurally distinct and lack homologues in the AlphaFold database2,3. Among the remaining 38% of viral proteins, many have non-viral structural analogues that revealed surprising similarities between human pathogens and their eukaryotic hosts. Structural comparisons suggested putative functions for up to 25% of unannotated viral proteins, including those with roles in the evasion of innate immunity. In particular, RNA ligase T-like phosphodiesterases were found to resemble phage-encoded proteins that hydrolyse the host immune-activating cyclic dinucleotides 3',3'- and 2',3'-cyclic GMP-AMP (cGAMP). Experimental analysis showed that RNA ligase T homologues encoded by avian poxviruses similarly hydrolyse cGAMP, showing that RNA ligase T-mediated targeting of cGAMP is an evolutionarily conserved mechanism of immune evasion that is present in both bacteriophage and eukaryotic viruses. Together, the viral protein structural database and analyses presented here afford new opportunities to identify mechanisms of virus-host interactions that are common across the virome.

Human cell line models, including the neuronal precursor line LUHMES, are important for investigating developmental transcriptional dynamics within imprinted regions, particularly the 15q11-q13 Angelman (AS) and Prader-Willi (PWS) syndrome locus. AS results from loss of maternal UBE3A in neurons, where the paternal allele is silenced by a convergent antisense transcript UBE3A-ATS, a lncRNA that terminates at PWAR1 in non-neurons. qRT-PCR analysis confirmed the exclusive and progressive increase in UBE3A-ATS in differentiating LUHMES neurons, validating their use for studying UBE3A silencing. Genome-wide transcriptome analyses revealed changes to 11 834 genes during neuronal differentiation, including the upregulation of most genes within the 15q11-q13 locus. To identify dynamic changes in chromatin loops linked to transcriptional activity, we performed a HiChIP validated by 4C, which identified two neuron-specific CTCF loops between MAGEL2-SNRPN and PWAR1-UBE3A. To determine if allele-specific differentially methylated regions (DMR) may be associated with CTCF loop anchors, whole genome long-read nanopore sequencing was performed. We identified a paternally hypomethylated DMR near the SNRPN upstream loop anchor exclusive to neurons and a paternally hypermethylated DMR near the PWAR1 CTCF anchor exclusive to undifferentiated cells, consistent with increases in neuronal transcription. Additionally, DMRs near CTCF loop anchors were observed in both cell types, indicative of allele-specific differences in chromatin loops regulating imprinted transcription. These results provide an integrated view of the 15q11-q13 epigenetic landscape during LUHMES neuronal differentiation, underscoring the complex interplay of transcription, chromatin looping, and DNA methylation. They also provide insights for future therapeutic approaches for AS and PWS.

Human papillomavirus (HPV) is the most common sexually transmitted infection on U.S. college campuses. Although HPV vaccination is recommended through age 26, current efforts to improve vaccination rates have predominantly focused on adolescents. Consequently, vaccine uptake remains suboptimal among young adults. This represents a significant missed opportunity, as young adults face the highest risk for new HPV infections. To contextualize the factors impacting decision-making process for this vulnerable population, this study reports key themes that emerged from in-depth interviews with participants (N = 30) who had completed an online intervention study for HPV vaccination among college students. Twelve (40%) of the interviewees vaccinated after exposure to the intervention. Findings centered around empowerment among young adults as the facilitator to get the HPV vaccine: key themes emerged were (1) convenience is critical and empowering; (2) adulthood identity, marked by a heightened sense of autonomy, accountability, and responsibility for self/future self and others, is empowering; (3) equal access to health care and preventive resources is empowering, especially for participants with low socioeconomic status; and (4) accurate knowledge provided in the intervention destigmatized HPV vaccination to empower young adults to make informed decisions. Digital interventions with messages highlighting a newly gained autonomy, future-oriented self and social responsibility, inclusive and accurate knowledge, and providing navigation to improve access may enhance HPV vaccination among young adults.

Automated annotations of protein functions are error-prone because of our lack of knowledge of protein functions. For example, it is often impossible to predict the correct substrate for an enzyme or a transporter. Furthermore, much of the knowledge that we do have about the functions of proteins is missing from the underlying databases. We discuss how to use interactive tools to quickly find different kinds of information relevant to a protein's function. Many of these tools are available via PaperBLAST (http://papers.genomics.lbl.gov). Combining these tools often allows us to infer a protein's function. Ideally, accurate annotations would allow us to predict a bacterium's capabilities from its genome sequence, but in practice, this remains challenging. We describe interactive tools that infer potential capabilities from a genome sequence or that search a genome to find proteins that might perform a specific function of interest. Database URL: http://papers.genomics.lbl.gov.

Glycosylation is a predominant strategy plants use to fine-tune the properties of small molecule metabolites to affect their bioactivity, transport, and storage. It is also important in biotechnology and medicine as many glycosides are utilized in human health. Small molecule glycosylation is largely carried out by family 1 glycosyltransferases. Here, we report a structural and biochemical investigation of UGT95A1, a family 1 GT enzyme from Pilosella officinarum that exhibits a strong, unusual regiospecificity for the 3'-O position of flavonoid acceptor substrate luteolin. We obtained an apo crystal structure to help drive the analyses of a series of binding site mutants, revealing that while most residues are tolerant to mutations, key residues M145 and D464 are important for overall glycosylation activity. Interestingly, E347 is crucial for maintaining the strong preference for 3'-O glycosylation, while R462 can be mutated to increase regioselectivity. The structural determinants of regioselectivity were further confirmed in homologous enzymes. Our study also suggests that the enzyme contains large, highly dynamic, disordered regions. We showed that while most disordered regions of the protein have little to no implication in catalysis, the disordered regions conserved among investigated homologs are important to both the overall efficiency and regiospecificity of the enzyme. This report represents a comprehensive in-depth analysis of a family 1 GT enzyme with a unique substrate regiospecificity and may provide a basis for enzyme functional prediction and engineering.

Abstract: Beginning in 2007, the Chinese state used liberalising policy and funding to encourage the expansion of large‐scale grain farming. Despite this support, many of the new farms have struggled financially and folded. Drawing on Foucauldian biopolitics and resource security literature, I argue that, with modernised agriculture, the state primarily sought to create not commercial farms, but the redundant farming infrastructure needed to buffer its growing reliance on food imports, abide by global trade regulations, and sustain its urban export manufacturing economy. These balancing efforts harmed commercial farmers: land commodification and policy funding incentivised urban government officials to intervene in rural land‐use planning, but low global market aligned grain prices disincentivised them from considering the place‐particular viability of their plans for producers. This article contributes to critical agrarian change literature by highlighting how modernist states become beholden to rational scientific techniques and sacrifice rural areas for increasingly vulnerable urban areas.

CRISPR-based high-throughput genome-wide loss-of-function screens are a valuable approach to functional genetics and strain engineering. The yeast Komagataella phaffii is a host of particular interest in the biopharmaceutical industry and as a metabolic engineering host for proteins and metabolites. Here, we design and validate a highly active 6-fold coverage genome-wide sgRNA library for this biotechnologically important yeast containing 30,848 active sgRNAs targeting over 99% of its coding sequences. Conducting fitness screens in the absence of functional non-homologous end joining (NHEJ), the dominant DNA repair mechanism in K. phaffii, provides a quantitative means to assess the activity of each sgRNA in the library. This approach allows for the experimental validation of each guide's targeting activity, leading to more precise screening outcomes. We used this approach to conduct growth screens with glucose as the sole carbon source and identify essential genes. Comparative analysis of the called gene sets identified a core set of K. phaffii essential genes, many of which relate to metabolic engineering targets, including protein production, secretion, and glycosylation. The high activity, genome-wide CRISPR library developed here enables functional genomic screening in K. phaffii, applied here to gene essentiality classification, and promises to enable other genetic screens.

Adenosine deaminases acting on RNA (ADARs) are enzymes that catalyze the hydrolytic deamination of adenosine to inosine. The editing feature of ADARs has garnered much attention as a therapeutic tool to repurpose ADARs to correct disease-causing mutations at the mRNA level in a technique called site-directed RNA editing (SDRE). Administering a short guide RNA oligonucleotide that hybridizes to a mutant sequence forms the requisite dsRNA substrate, directing ADARs to edit the desired adenosine. However, much is still unknown about ADARs' selectivity and sequence-specific effects on editing. Atomic-resolution structures can help provide additional insight to ADARs' selectivity and lead to novel guide RNA designs. Indeed, recent structures of ADAR domains have expanded our understanding on RNA binding and the base-flipping catalytic mechanism. These efforts have enabled the rational design of improved ADAR guide strands and advanced the therapeutic potential of the SDRE approach. While no full-length structure of any ADAR is known, this review presents an exposition of the structural basis for function of the different ADAR domains, focusing on human ADAR2. Key insights are extrapolated to human ADAR1, which is of substantial interest because of its widespread expression in most human tissues.

BackgroundIndividuals with intellectual disabilities experience barriers to quality healthcare. To reduce this disparity, equipping medical trainees with the knowledge and skills required for treating this patient population is critical. Our aim is to describe the breadth of instructional interventions and identify gaps in intellectual disability medical education curricula.MethodUsing scoping review methods, the intellectual disability programmes described in 27 articles were evaluated and their coverage of the six core competencies on disability for health care education was examined.ResultsThe most frequently represented core competencies were disability conceptual frameworks, professionalism and communication, and clinical assessment, which were, in most programmes, fulfilled by activities involving individuals with intellectual disabilities. Uneven competency coverage warrants consideration.ConclusionsConsiderable variabilities exist in medical school curricula on intellectual disabilities. Using core competencies on disability for health care education for curricular design and evaluation would provide a coherent training experience in this important area.

Electroporation is a technique to introduce DNA constructs into cells using electric current. Here, we present a protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage. We describe steps for setting up and conducting electroporation. We then detail procedures for collecting, fixing, and mounting embryos and counting expression. This protocol can be used to study the expression of enhancers via reporter assays, manipulating cells using genes or modified genes such as dominant negatives, and genome editing. For complete details on the use and execution of this protocol, please refer to Song, et al.1.

It remains a challenge to produce soft robots that can mimic the responsive adaptability of living organisms. Rather than fabricating soft robots from bulk hydrogels,hydrogels are integrated into the interfacial assembly of aqueous two-phase systems to generate ultra-soft and elastic all-aqueous aquabots that exhibit responsive adaptability, that can shrink on demand and have electrically conductive functions. The adaptive functions of the aquabots provide a new platform to develop minimally invasive surgical devices, targeted drug delivery systems, and flexible electronic sensors and actuators.

In many animal species, the oocyte meiotic spindle, which is required for chromosome segregation, forms without centrosomes. In some systems, Ran-GEF on chromatin initiates spindle assembly. We found that in Caenorhabditis elegans oocytes, endogenously-tagged Ran-GEF dissociates from chromatin during spindle assembly but re-associates during meiotic anaphase. Meiotic spindle assembly occurred after auxin-induced degradation of Ran-GEF, but anaphase I was faster than controls and extrusion of the first polar body frequently failed. In search of a possible alternative pathway for spindle assembly, we found that soluble tubulin concentrates in the nuclear volume during germinal vesicle breakdown. We found that the concentration of soluble tubulin in the metaphase spindle region is enclosed by ER sheets which exclude cytoplasmic organelles including mitochondria and yolk granules. Measurement of the volume occupied by yolk granules and mitochondria indicated that volume exclusion would be sufficient to explain the concentration of tubulin in the spindle volume. We suggest that this concentration of soluble tubulin may be a redundant mechanism promoting spindle assembly near chromosomes.

Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis (kVR), capture structure-activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF-aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF-aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.

Cyanobacteria uniquely contain a primitive water-soluble carotenoprotein, the orange carotenoid protein (OCP). Nearly all extant cyanobacterial genomes contain genes for the OCP or its homologs, implying an evolutionary constraint for cyanobacteria to conserve its function. Genes encoding the OCP and its two constituent structural domains, the N-terminal domain, helical carotenoid proteins (HCPs), and its C-terminal domain, are found in the most basal lineages of extant cyanobacteria. These three carotenoproteins exemplify the importance of the protein for carotenoid properties, including protein dynamics, in response to environmental changes in facilitating a photoresponse and energy quenching. Here, we review new structural insights for these carotenoproteins and situate the role of the protein in what is currently understood about their functions.

Substantial evidence indicates that medical mistrust, resulting from experiences with discrimination and marginalisation, is a determinant of health disparities in minority populations. However, this research is largely limited to the US and other industrialised countries. To broaden our understanding of the role of medical mistrust on health-care decision making, we conducted a study on healthcare experiences and perceptions in a rural, underserved indigenous community in northwest Namibia (n = 86). Mixing semi-structured interview questions with the medical mistrust index (MMI), we aim to determine the relevance of the MMI in a non-industrialised population and compare index scores with reports of healthcare experiences. We find that medical mistrust is a salient concept in this community, mapping onto negative healthcare experiences and perceptions of discrimination. Reported healthcare experiences indicate that perceived incompetence, maltreatment and discrimination drive mistrust of medical personnel. However, reporting of recent healthcare experiences are generally positive. Our results indicate that the concept of medical mistrust can be usefully applied to communities in the Global South. These populations, like minority communities in the US, translate experiences of discrimination and marginalisation into medical mistrust. Understanding these processes can help address health disparities and aid in effective public health outreach in underserved populations.

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.

Synthetic biology enables the reprogramming of cellular functions for various applications. However, challenges in scalability and predictability persist due to context-dependent performance and complex circuit-host interactions. This study introduces an iModulon-based engineering approach, utilizing machine learning-defined co-regulated gene groups (iModulons) as design parts containing essential genes for specific functions. This approach identifies the necessary components for genetic circuits across different contexts, enhancing genome engineering by improving target selection and predicting module behavior. We demonstrate several distinct uses of iModulons: (i) discovery of unknown iModulons to increase protein productivity, heat tolerance and fructose utilization; (ii) an iModulon boosting approach, which amplifies the activity of specific iModulons, improved cell growth under osmotic stress with minimal host regulation disruption; (iii) an iModulon rebalancing strategy, which adjusts the activity levels of iModulons to balance cellular functions, significantly increased oxidative stress tolerance while minimizing trade-offs and (iv) iModulon-based gene annotation enabled natural competence activation by predictably rewiring iModulons. Comparative experiments with traditional methods showed our approach offers advantages in efficiency and predictability of strain engineering. This study demonstrates the potential of iModulon-based strategies to systematically and predictably reprogram cellular functions, offering refined and adaptable control over complex regulatory networks.

We discuss how epidemiology has been and can continue to be used to advance understanding of the links between urban areas and health informed by an existing urban-health conceptual framework. This framework considers urban areas as contexts for health, determinants of health and modifiers of health pathways, and part of a complex system that affects health. We highlight opportunities for descriptive epidemiology to inform the context of urban health, for example, by characterizing the social and physical environments that give rise to health and the actions that change those conditions. We then describe inferential tools for evaluating the impact of group-level actions (e.g., interventions, policies) on urban health, providing some examples, and describing assumptions and challenges. Finally, we discuss opportunities and challenges of applying systems thinking and methods to advance urban health. While different conceptual frames lead to different insights, each perspective demonstrates that urban health is a major and growing challenge. The effectiveness of urban health knowledge, action, and policy as the world continues to urbanize can be informed by applying and expanding upon research and surveillance methods described here.

How does one assess developmental change when the measures themselves change with development? Most developmental studies of word learning use either looking (infants) or pointing (preschoolers and older). With little empirical evidence of the relationship between the two measures, developmental change is difficult to assess. This paper analyzes 914 pointing, looking children (451 female, varied ethnicities, 2.5-6.5 years, dates: 2009-2019) in 36 word- or sound-learning experiments with two-alternative test trials. Looking proportions and pointing accuracy correlated strongly (r = .7). Counter to the "looks first" hypothesis, looks were not sensitive to incipient knowledge that pointing missed: when pointing is at chance, looking proportions are also. Results suggest one possible path forward for assessing continuous developmental change. Methodological best practices are discussed.

Primary cilia are membrane-covered microtubule-based structures that protrude from the cell surface and are critical for cell signaling and homeostasis during human development and adulthood. Dysregulation of cilia formation, length, and function can lead to a spectrum of human diseases and syndromes known as ciliopathies. Although some genetic and chemical screens have been performed to define important factors that modulate cilia biogenesis and length control, there are currently no clinical treatments that restore cilia length in patients. We report that the microtubule-targeting agent MI-181(mitotic inhibitor-181) is a potent modulator of cilia length and biogenesis. Treatment of retinal pigment epithelial-1 cells with MI-181 induced an increase in the average size of cilia and in the percent ciliated cells under nonstarved conditions. Importantly, MI-181 was effective at rescuing cilia length and ciliation defects in cells that had been treated with the intraflagellar transport inhibitor Ciliobrevin D or the O-GlcNAc transferase inhibitor OSMI-1. Most importantly, MI-181 induced an increase in cilia length and restored ciliation in cells with compromised shortened cilia at low nanomolar concentrations and did not show an inhibitory response at high concentrations. Therefore, MI-181 represents a lead molecule for developing drugs targeting ciliopathies characterized by shortened cilia.

BACKGROUND AND AIM[|]Traffic-Related Air Pollution (TrAP) adversely impacts human health, disproportionately harming disadvantaged communities. New technologies and infrastructure offer opportunities to reduce TrAP, but the health outcomes of individuals are not fully understood due to a lack of high-resolution models that grasp the complexities of transportation systems and their health implications amid evolving policies and technologies.[¤]METHOD[|]We introduce BEAM CORE (beam.lbl.gov), a high-resolution, agent-based transportation framework that simulates detailed passenger and freight activities. It captures interactions between transportation, land use, demographic and vehicle ownership changes at various scales. Validating crucial factors of emission modeling, including link-level VMT, speed and regional fleet in the San Francisco Bay Area’s nine counties, demonstrates its potential to be extended for assessing health outcomes from changes in TrAP.[¤]RESULTS[|]All major outputs from the BEAM CORE 2018 baseline have been calibrated and validated. Mode split and demographics align closely with census and survey data. Passenger and freight activities were validated against public and private data, with CO2 emissions corresponding to 3.67Mt/yr for medium/heavy-duty (MHD) and 22.79Mt/yr for all vehicles, demonstrating the model’s alignment with empirical data. The NOx, PM2.5 and PM10 from MHD exhaust, PM brake and tire wear are 14.8kt/yr, 424t/yr and 606.9t/yr under the 2018 baseline with high fractions of conventional vehicles, while the wide adoption of clean truck technologies under 2050 resulted in 87\%, 75\% and 56\% reductions respectively. BEAM CORE generates detailed fleet and activity data at high spatiotemporal resolution, enabling the integration with air quality models, including InMAP/AERMOD, to explore the causal pathway of health impacts from transport policy changes.[¤]CONCLUSIONS[|]We developed a sophisticated multi-dimensional transportation model for integration with advanced air quality, and health assessment models. It enables a thorough analysis of health impacts of transportation policies and technologies across diverse communities. It supports similar analyses in any area using local data.[¤]

Recent studies have implemented a calculated additive toxicity (CAT) approach that sums measured disinfection byproduct (DBP) concentrations weighted by their respective in vitro bioassay potencies to estimate their associated risk in disinfected waters. In this study, the CAT approach was used to systematically investigate 21 regulated and unregulated DBPs measured in drinking water at the household level. Water samples from the tap were collected from over 120 randomly selected participants supplied by eight public water systems using four distinct source water types, two types of disinfection processes, and across two seasons. The purpose of this study was to compare CAT using multiple biological end points, examine household variability, identify DBPs driving toxicity, and assess if current regulated DBPs are adequate predictors of unregulated DBPs. Our results support the significance of unregulated DBPs, particularly haloacetonitriles and iodoacetic acid, as drivers of toxicity. Simple linear models between regulated versus unregulated concentrations and CAT were overall weak with 67% considered poor (r 2 < 0.3). These results reveal that current regulatory monitoring approaches may not be adequately capturing true household exposure due to higher contribution of unregulated DBPs to CAT and poor predictability between regulated and unregulated DBP-mediated CAT.

Archaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly barcoded transposon libraries in the model methanogenic archaeon Methanococcus maripaludis and use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources in M. maripaludis including a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we inferred that M. maripaludis can utilize additional nitrogen sources including ʟ-glutamine, ᴅ-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize that it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP; group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale data set that can be used as a resource to further understand gene function and metabolism in the archaeal domain.IMPORTANCEArchaea are widespread in the environment, yet basic aspects of their biology remain underexplored. To address this, we apply randomly barcoded transposon libraries (RB-TnSeq) to the model archaeon Methanococcus maripaludis. RB-TnSeq coupled with high-throughput growth assays across over 100 unique conditions identified roles for previously uncharacterized genes, including several encoding proteins with domains of unknown function (DUFs). We also expand on our understanding of carbon and nitrogen metabolism and characterize a group IIId dissimilatory sulfite reductase-like protein as a functional sulfite reductase. This data set encompasses a wide range of additional conditions including stress, nitrogen fixation, amino acid supplementation, and autotrophy, thus providing an extensive data set for the archaeal community to mine for characterizing additional genes of unknown function.

California faces several serious direct and indirect climate exposures that can adversely affect public health, some of which are already occurring. The public health burden now and in the future will depend on atmospheric greenhouse gas concentrations, underlying population vulnerabilities, and adaptation efforts. Here, we present a structured review of recent literature to examine the leading climate risks to public health in California, including extreme heat, extreme precipitation, wildfires, air pollution, and infectious diseases. Comparisons among different climate-health pathways are difficult due to inconsistencies in study design regarding spatial and temporal scales and health outcomes examined. We find, however, that the current public health burden likely affects thousands of Californians each year, depending on the exposure pathway and health outcome. Further, while more evidence exists for direct and indirect proximal health effects that are the focus of this review, distal pathways (e.g., impacts of drought on nutrition) are more uncertain but could add to this burden. We find that climate adaptation measures can provide significant health benefits, particularly in disadvantaged communities. We conclude with priority recommendations for future analyses and solution-driven policy actions.

BackgroundPatients find technology tools to be more approachable for seeking sensitive health-related information, such as reproductive health information. The inventive conversational ability of artificial intelligence (AI) chatbots, such as ChatGPT (OpenAI Inc), offers a potential means for patients to effectively locate answers to their health-related questions digitally.ObjectiveA pilot study was conducted to compare the novel ChatGPT with the existing Google Search technology for their ability to offer accurate, effective, and current information regarding proceeding action after missing a dose of oral contraceptive pill.MethodsA sequence of 11 questions, mimicking a patient inquiring about the action to take after missing a dose of an oral contraceptive pill, were input into ChatGPT as a cascade, given the conversational ability of ChatGPT. The questions were input into 4 different ChatGPT accounts, with the account holders being of various demographics, to evaluate potential differences and biases in the responses given to different account holders. The leading question, "what should I do if I missed a day of my oral contraception birth control?" alone was then input into Google Search, given its nonconversational nature. The results from the ChatGPT questions and the Google Search results for the leading question were evaluated on their readability, accuracy, and effective delivery of information.ResultsThe ChatGPT results were determined to be at an overall higher-grade reading level, with a longer reading duration, less accurate, less current, and with a less effective delivery of information. In contrast, the Google Search resulting answer box and snippets were at a lower-grade reading level, shorter reading duration, more current, able to reference the origin of the information (transparent), and provided the information in various formats in addition to text.ConclusionsChatGPT has room for improvement in accuracy, transparency, recency, and reliability before it can equitably be implemented into health care information delivery and provide the potential benefits it poses. However, AI may be used as a tool for providers to educate their patients in preferred, creative, and efficient ways, such as using AI to generate accessible short educational videos from health care provider-vetted information. Larger studies representing a diverse group of users are needed.

Since extracellular vesicles (EVs) have emerged as a promising drug delivery system, diverse methods have been used to load them with active pharmaceutical ingredients (API) in preclinical and clinical studies. However, there is yet to be an engineered EV formulation approved for human use, a barrier driven in part by the intrinsic heterogeneity of EVs. API loading is rarely assessed in the context of single vesicle measurements of physicochemical properties but is likely administered in a heterogeneous fashion to the detriment of a consistent product. Here, we applied a suite of single-particle resolution methods to determine the loading of rhodamine 6G (R6G) surrogate cargo mimicking hydrophilic small molecule drugs across four common API loading methods: sonication, electroporation, freeze-thaw cycling and passive incubation. Loading efficiencies and alterations in the physical properties of EVs were assessed, as well as co-localization with common EV-associated tetraspanins (i.e., CD63, CD81 and CD9) for insight into EV subpopulations. Sonication had the highest loading efficiency, yet significantly decreased particle yield, while electroporation led to the greatest number of loaded API particles, albeit at a lower efficiency. Moreover, results were often inconsistent between repeated runs within a given method, demonstrating the difficulty in developing a rigorous loading method that consistently loaded EVs across their heterogeneous subpopulations. This work highlights the significance of how chosen quantification metrics can impact apparent conclusions and the importance of single-particle characterization of EV loading.

We present a new method to measure sub-microcurie activities of photon-emitting radionuclides in organs and lesions of small animals in vivo. Our technique, named the collimator-less likelihood fit, combines a very high sensitivity collimatorless detector with a Monte Carlo-based likelihood fit in order to estimate the activities in previously segmented regions of interest along with their uncertainties. This is done directly from the photon projections in our collimatorless detector and from the region of interest segmentation provided by an x-ray computed tomography scan. We have extensively validated our approach with 225Ac experimentally in spherical phantoms and mouse phantoms, and also numerically with simulations of a realistic mouse anatomy. Our method yields statistically unbiased results with uncertainties smaller than 20% for activities as low as ~111Bq (3nCi) and for exposures under 30 minutes. We demonstrate that our method yields more robust recovery coefficients when compared to SPECT imaging with a commercial pre-clinical scanner, specially at very low activities. Thus, our technique is complementary to traditional SPECT/CT imaging since it provides a more accurate and precise organ and tumor dosimetry, with a more limited spatial information. Finally, our technique is specially significant in extremely low-activity scenarios when SPECT/CT imaging is simply not viable.

Z-nucleic acid structures play vital roles in cellular processes and have implications in innate immunity due to their recognition by Zα domains containing proteins (Z-DNA/Z-RNA binding proteins, ZBPs). Although Zα domains have been identified in six proteins, including viral E3L, ORF112, and I73R, as well as, cellular ADAR1, ZBP1, and PKZ, their prevalence across living organisms remains largely unexplored. In this study, we introduce a computational approach to predict Zα domains, leading to the revelation of previously unidentified Zα domain-containing proteins in eukaryotic organisms, including non-metazoan species. Our findings encompass the discovery of new ZBPs in previously unexplored giant viruses, members of the Nucleocytoviricota phylum. Through experimental validation, we confirm the Zα functionality of select proteins, establishing their capability to induce the B-to-Z conversion. Additionally, we identify Zα-like domains within bacterial proteins. While these domains share certain features with Zα domains, they lack the ability to bind to Z-nucleic acids or facilitate the B-to-Z DNA conversion. Our findings significantly expand the ZBP family across a wide spectrum of organisms and raise intriguing questions about the evolutionary origins of Zα-containing proteins. Moreover, our study offers fresh perspectives on the functional significance of Zα domains in virus sensing and innate immunity and opens avenues for exploring hitherto undiscovered functions of ZBPs.

Recent studies have highlighted the essential role of RNA splicing, a key mechanism of alternative RNA processing, in establishing connections between genetic variations and disease. Genetic loci influencing RNA splicing variations show considerable influence on complex traits, possibly surpassing those affecting total gene expression. Dysregulated RNA splicing has emerged as a major potential contributor to neurological and psychiatric disorders, likely due to the exceptionally high prevalence of alternatively spliced genes in the human brain. Nevertheless, establishing direct associations between genetically altered splicing and complex traits has remained an enduring challenge. We introduce Spliced-Transcriptome-Wide Associations (SpliTWAS) to integrate alternative splicing information with genome-wide association studies to pinpoint genes linked to traits through exon splicing events. We applied SpliTWAS to two schizophrenia (SCZ) RNA-sequencing datasets, BrainGVEX and CommonMind, revealing 137 and 88 trait-associated exons (in 84 and 67 genes), respectively. Enriched biological functions in the associated gene sets converged on neuronal function and development, immune cell activation, and cellular transport, which are highly relevant to SCZ. SpliTWAS variants impacted RNA-binding protein binding sites, revealing potential disruption of RNA-protein interactions affecting splicing. We extended the probabilistic fine-mapping method FOCUS to the exon level, identifying 36 genes and 48 exons as putatively causal for SCZ. We highlight VPS45 and APOPT1, where splicing of specific exons was associated with disease risk, eluding detection by conventional gene expression analysis. Collectively, this study supports the substantial role of alternative splicing in shaping the genetic basis of SCZ, providing a valuable approach for future investigations in this area.

The contrast between the disruption of genome topology after cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome and chromatin accessibility at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic coexpression tendencies of cis-linked genes in single cells. Notably, cohesin loss induces widespread gene coactivation and chromatin co-opening tens of million bases apart in cis. Spatial genome and protein imaging reveals that cohesin prevents gene co-bursting along the chromosome and blocks spatial mixing of transcriptional hubs. Single-molecule imaging shows that cohesin confines the exploration of diverse enhancer and core promoter binding transcriptional regulators. Together, these results support that cohesin arranges nuclear topology to control gene coexpression in single cells.

Abstract: Since Nobel Laureate Arthur Ashkin first introduced the trapping and manipulation of microparticles using light, numerous studies have explored this technique not only for dielectric/metallic particles but also for organic matter. This advancement has significantly expanded the landscape of non-contact and non-invasive micromanipulation at the nanometric scale. However, micromanipulation of particles with a refractive index smaller than the host medium, n p < n m, proves challenging with Gaussian beams. To overcome this obstacle, a force known as thermocapillary, or the Marangoni force, has emerged as a straightforward trapping mechanism for bubbles in liquids. The Marangoni force results from the surface tension of bubbles, induced either thermally or chemically—by creating a temperature gradient or adding surfactants, respectively. The surface tension gradient on the liquid host induces tangential stress on the bubble wall, causing the bubble to move toward the region of lower surface tension, where it faces less opposing force. When the Marangoni force is generated by a laser beam’s temperature gradient, it becomes an exceptionally effective mechanism for the steady-state trapping and three-dimensional manipulation of bubbles, even with low optical power lasers. This force produces both longitudinal and transversal forces, resembling optical forces, creating a three-dimensional potential well capable of handling bubbles with radii of tens to hundreds of microns. This work provides guidance and demonstrates, both experimentally and theoretically, the step-by-step process of quasi-steady-state trapping and three-dimensional manipulation of bubbles through optothermal effects. The bubbles in question are tens of microns in size, significantly larger than those that optical tweezers can trap/manipulate. Furthermore, the study emphasizes the crucial role of the Marangoni force in this process, outlining its various advantages.

DDX3X regulates the translation of a subset of human transcripts containing complex 5' untranslated regions (5' UTRs). In this study, we developed the helicase activity reporter for translation (HART), which uses DDX3X-sensitive 5' UTRs to measure DDX3X-mediated translational activity in cells. To directly measure RNA structure in DDX3X-dependent mRNAs, we used SHAPE-MaP to determine the secondary structures present in DDX3X-sensitive 5' UTRs and then used HART to investigate how sequence alterations influence DDX3X sensitivity. Additionally, we identified residues 38-44 as potential mediators of DDX3X's interaction with the translational machinery. HART revealed that both DDX3X's association with the translational machinery and its helicase activity are required for its function in promoting the translation of DDX3X-sensitive 5' UTRs. These findings suggest DDX3X plays a crucial role in regulating translation through its interaction with the translational machinery during ribosome scanning and establish the HART reporter as a robust, lentivirally encoded, colorimetric measurement of DDX3X-dependent translation in cells.

Groundwater is the most ubiquitous source of liquid freshwater globally, yet its role in supporting diverse ecosystems is rarely acknowledged1,2. However, the location and extent of groundwater-dependent ecosystems (GDEs) are unknown in many geographies, and protection measures are lacking1,3. Here, we map GDEs at high-resolution (roughly 30 m) and find them present on more than one-third of global drylands analysed, including important global biodiversity hotspots4. GDEs are more extensive and contiguous in landscapes dominated by pastoralism with lower rates of groundwater depletion, suggesting that many GDEs are likely to have already been lost due to water and land use practices. Nevertheless, 53% of GDEs exist within regions showing declining groundwater trends, which highlights the urgent need to protect GDEs from the threat of groundwater depletion. However, we found that only 21% of GDEs exist on protected lands or in jurisdictions with sustainable groundwater management policies, invoking a call to action to protect these vital ecosystems. Furthermore, we examine the linkage of GDEs with cultural and socio-economic factors in the Greater Sahel region, where GDEs play an essential role in supporting biodiversity and rural livelihoods, to explore other means for protection of GDEs in politically unstable regions. Our GDE map provides critical information for prioritizing and developing policies and protection mechanisms across various local, regional or international scales to safeguard these important ecosystems and the societies dependent on them.

Reducing carbon dioxide (CO2) emissions urgently requires the large-scale deployment of carbon-capture technologies. These technologies must separate CO2 from various sources and deliver it to different sinks1,2. The quest for optimal solutions for specific source-sink pairs is a complex, multi-objective challenge involving multiple stakeholders and depends on social, economic and regional contexts. Currently, research follows a sequential approach: chemists focus on materials design3 and engineers on optimizing processes4,5, which are then operated at a scale that impacts the economy and the environment. Assessing these impacts, such as the greenhouse gas emissions over the plant's lifetime, is typically one of the final steps6. Here we introduce the PrISMa (Process-Informed design of tailor-made Sorbent Materials) platform, which integrates materials, process design, techno-economics and life-cycle assessment. We compare more than 60 case studies capturing CO2 from various sources in 5 global regions using different technologies. The platform simultaneously informs various stakeholders about the cost-effectiveness of technologies, process configurations and locations, reveals the molecular characteristics of the top-performing sorbents, and provides insights on environmental impacts, co-benefits and trade-offs. By uniting stakeholders at an early research stage, PrISMa accelerates carbon-capture technology development during this critical period as we aim for a net-zero world.

Hematopoietic stem cells and multipotential progenitors emerge in multiple, overlapping waves of fetal development. Some of these populations seed the bone marrow and sustain adult B- and T-cell development long-term after birth. However, others are present transiently, but whether they are vestigial or generate B and T cells that contribute to the adult immune system is not well understood. We now report that transient fetal progenitors distinguished by expression of low levels of the PU.1 transcription factor generated activated and memory T and B cells that colonized and were maintained in secondary lymphoid tissues. These included the small and large intestines, where they may contribute to the maintenance of gut homeostasis through at least middle age. At least some of the activated/memory cells may have been the progeny of B-1 and marginal zone B cells, as transient PU.1low fetal progenitors efficiently generated those populations. Taken together, our data demonstrate the potential of B- and T-cell progeny of transient PU.1low fetal progenitors to make an early and long-term contribution to the adult immune system.