Dual-role transcription factors stabilize intermediate expression levels.

Precise control of gene expression levels is essential for normal cell functions, yet how they are defined and tightly maintained, particularly at intermediate levels, remains elusive. Here, using a series of newly developed sequencing, imaging, and functional assays, we uncover a class of transcription factors with dual roles as activators and repressors, referred to as condensate-forming level-regulating dual-action transcription factors (TFs). They reduce high expression but increase low expression to achieve stable intermediate levels. Dual-action TFs directly exert activating and repressing functions via condensate-forming domains that compartmentalize core transcriptional unit selectively. Clinically relevant mutations in these domains, which are linked to a range of developmental disorders, impair condensate selectivity and dual-action TF activity. These results collectively address a fundamental question in expression regulation and demonstrate the potential of level-regulating dual-action TFs as powerful effectors for engineering controlled expression levels.

Cellular architecture of human brain metastases.

Brain metastasis (BrM) is the most common form of brain cancer, characterized by neurologic disability and an abysmal prognosis. Unfortunately, our understanding of the biology underlying human BrMs remains rudimentary. Here, we present an integrative analysis of >100,000 malignant and non-malignant cells from 15 human parenchymal BrMs, generated by single-cell transcriptomics, mass cytometry, and complemented with mouse model- and in silico approaches. We interrogated the composition of BrM niches, molecularly defined the blood-tumor interface, and revealed stromal immunosuppressive states enriched with infiltrated T cells and macrophages. Specific single-cell interrogation of metastatic tumor cells provides a framework of 8 functional cell programs that coexist or anticorrelate. Collectively, these programs delineate two functional BrM archetypes, one proliferative and the other inflammatory, that are evidently shaped through tumor-immune interactions. Our resource provides a foundation to understand the molecular basis of BrM in patients with tumor cell-intrinsic and host environmental traits.

TCR+/BCR+ dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes.

Ahmed and colleagues recently described a novel hybrid lymphocyte expressing both a B and T cell receptor, termed double expresser (DE) cells. DE cells in blood of type 1 diabetes (T1D) subjects were present at increased numbers and enriched for a public B cell clonotype. Here, we attempted to reproduce these findings. While we could identify DE cells by flow cytometry, we found no association between DE cell frequency and T1D status. We were unable to identify the reported public B cell clone, or any similar clone, in bulk B cells or sorted DE cells from T1D subjects or controls. We also did not observe increased usage of the public clone VH or DH genes in B cells or in sorted DE cells. Taken together, our findings suggest that DE cells and their alleged public clonotype are not enriched in T1D. This Matters Arising paper is in response to Ahmed et al. (2019), published in Cell. See also the response by Ahmed et al. (2021), published in this issue.

The THO Complex Coordinates Transcripts for Synapse Development and Dopamine Neuron Survival.

Synaptic vesicle and active zone proteins are required for synaptogenesis. The molecular mechanisms for coordinated synthesis of these proteins are not understood. Using forward genetic screens, we identified the conserved THO nuclear export complex (THOC) as an important regulator of presynapse development in C. elegans dopaminergic neurons. In THOC mutants, synaptic messenger RNAs are retained in the nucleus, resulting in dramatic decrease of synaptic protein expression, near complete loss of synapses, and compromised dopamine function. CRE binding protein (CREB) interacts with THOC to mark synaptic transcripts for efficient nuclear export. Deletion of Thoc5, a THOC subunit, in mouse dopaminergic neurons causes severe defects in synapse maintenance and subsequent neuronal death in the substantia nigra compacta. These cellular defects lead to abrogated dopamine release, ataxia, and animal death. Together, our results argue that nuclear export mechanisms can select specific mRNAs and be a rate-limiting step for neuronal differentiation and survival.

The 3D-Evo Space: Evolution of Gene Expression and Alternative Splicing Regulation.

Animal species present relatively high levels of gene conservation, and yet they display a great variety of cell type and tissue phenotypes. These diverse phenotypes are mainly specified through differential gene usage, which relies on several mechanisms. Two of the most relevant mechanisms are regulated gene transcription, usually referred to as gene expression (rGE), and regulated alternative splicing (rAS). Several works have addressed how either rGE or rAS contributes to phenotypic diversity throughout evolution, but a back-to-back comparison between the two molecular mechanisms, specifically highlighting both their common regulatory principles and unique properties, is still missing. In this review, we propose an innovative framework for the unified comparison between rGE and rAS from different perspectives: the three-dimensional (3D)-evo space. We use the 3D-evo space to comprehensively (a) review the molecular basis of rGE and rAS (i.e., the molecular axis), (b) depict the tissue-specific phenotypes they contribute to (i.e., the tissue axis), and (c) describe the determinants that drive the evolution of rGE and rAS programs (i.e., the evolution axis). Finally, we unify the perspectives emerging from the three axes by discussing general trends and specific examples of rGE and rAS tissue program evolution.

Brain Repair by Cell Replacement via In Situ Neuronal Reprogramming.

Neurodegenerative diseases, characterized by progressive neural loss, have been some of the most challenging medical problems in aging societies. Treatment strategies such as symptom management have little impact on disease progression, while intervention with specific disease mechanisms may only slow down disease progression. One therapeutic strategy that has the potential to reverse the disease phenotype is to replenish neurons and rebuild the pathway lost to degeneration. Although it is generally believed that the central nervous system has lost the capability to regenerate, increasing evidence indicates that the brain is more plastic than previously thought, containing perhaps the biggest repertoire of cells with latent neurogenic programs in the body. This review focuses on key advances in generating new neurons through in situ neuronal reprogramming, which is tied to fundamental questions regarding adult neurogenesis, cell source, and mechanisms for neuronal reprogramming, as well as the ability of new neurons to integrate into the existing circuitry.

High Amount of Transcription Factor IRF8 Engages AP1-IRF Composite Elements in Enhancers to Direct Type 1 Conventional Dendritic Cell Identity.

Development and function of conventional dendritic cell (cDC) subsets, cDC1 and cDC2, depend on transcription factors (TFs) IRF8 and IRF4, respectively. Since IRF8 and IRF4 can each interact with TF BATF3 at AP1-IRF composite elements (AICEs) and with TF PU.1 at Ets-IRF composite elements (EICEs), it is unclear how these factors exert divergent actions. Here, we determined the basis for distinct effects of IRF8 and IRF4 in cDC development. Genes expressed commonly by cDC1 and cDC2 used EICE-dependent enhancers that were redundantly activated by low amounts of either IRF4 or IRF8. By contrast, cDC1-specific genes relied on AICE-dependent enhancers, which required high IRF concentrations, but were activated by either IRF4 or IRF8. IRF8 was specifically required only by a minority of cDC1-specific genes, such as Xcr1, which could distinguish between IRF8 and IRF4 DNA-binding domains. Thus, these results explain how BATF3-dependent Irf8 autoactivation underlies emergence of the cDC1-specific transcriptional program.

Stress-induced transcriptional memory accelerates promoter-proximal pause release and decelerates termination over mitotic divisions.

Heat shock instantly reprograms transcription. Whether gene and enhancer transcription fully recover from stress and whether stress establishes a memory by provoking transcription regulation that persists through mitosis remained unknown. Here, we measured nascent transcription and chromatin accessibility in unconditioned cells and in the daughters of stress-exposed cells. Tracking transcription genome-wide at nucleotide-resolution revealed that cells precisely restored RNA polymerase II (Pol II) distribution at gene bodies and enhancers upon recovery from stress. However, a single heat exposure in embryonic fibroblasts primed a faster gene induction in their daughter cells by increasing promoter-proximal Pol II pausing and by accelerating the pause release. In K562 erythroleukemia cells, repeated stress refined basal and heat-induced transcription over mitotic division and decelerated termination-coupled pre-mRNA processing. The slower termination retained transcripts on the chromatin and reduced recycling of Pol II. These results demonstrate that heat-induced transcriptional memory acts through promoter-proximal pause release and pre-mRNA processing at transcription termination.

Promoting sustainable smallholder farming via multistakeholder collaboration.

Transforming smallholder farms is critical to global food security and environmental sustainability. The science and technology backyard (STB) platform has proved to be a viable approach in China. However, STB has traditionally focused on empowering smallholder farmers by transferring knowledge, and wide-scale adoption of more sustainable practices and technologies remains a challenge. Here, we report on a long-term project focused on technology scale-up for smallholder farmers by expanding and upgrading the original STB platform (STB 2.0). We created a formalized and standardized process by which to engage and collaborate with farmers, including integrating their feedback via equal dialogues in the process of designing and promoting technologies. Based on 288 site-year of field trials in three regions in the North China Plain over 5 y, we find that technologies cocreated through this process were more easily accepted by farmers and increased their crop yields and nitrogen factor productivity by 7.2% and 28.1% in wheat production and by 11.4% and 27.0% in maize production, respectively. In promoting these technologies more broadly, we created a "one-stop" multistakeholder program involving local government agencies, enterprises, universities, and farmers. The program was shown to be much more effective than the traditional extension methods applied at the STB, yielding substantial environmental and economic benefits. Our study contributes an important case study for technology scale-up for smallholder agriculture. The STB 2.0 platform being explored emphasizes equal dialogue with farmers, multistakeholder collaboration, and long-term investment. These lessons may provide value for the global smallholder research and practitioners.

Harnessing developmental cues for cardiomyocyte production.

Developmental research has attempted to untangle the exact signals that control heart growth and size, with knockout studies in mice identifying pivotal roles for Wnt and Hippo signaling during embryonic and fetal heart growth. Despite this improved understanding, no clinically relevant therapies are yet available to compensate for the loss of functional adult myocardium and the absence of mature cardiomyocyte renewal that underlies cardiomyopathies of multiple origins. It remains of great interest to understand which mechanisms are responsible for the decline in proliferation in adult hearts and to elucidate new strategies for the stimulation of cardiac regeneration. Multiple signaling pathways have been identified that regulate the proliferation of cardiomyocytes in the embryonic heart and appear to be upregulated in postnatal injured hearts. In this Review, we highlight the interaction of signaling pathways in heart development and discuss how this knowledge has been translated into current technologies for cardiomyocyte production.

Bioinspired shape shifting of liquid-infused ribbed sheets.

The recent emergence of stimuli-responsive, shape-shifting materials offers promising applications in fields as different as soft robotics, aeronautics, or biomedical engineering. Targeted shapes or movements are achieved from the advantageous coupling between some stimulus and various materials such as liquid crystalline elastomers, magnetically responsive soft materials, swelling hydrogels, etc. However, despite the large variety of strategies, they are strongly material dependent and do not offer the possibility to choose between reversible and irreversible transformations. Here, we introduce a strategy applicable to a wide range of materials yielding systematically reversible or irreversible shape transformations of soft ribbed sheets with precise control over the local curvature. Our approach-inspired by the spore-releasing mechanism of the fern sporangium-relies on the capillary deformation of an architected elastic sheet impregnated by an evaporating liquid. We develop an analytical model combining sheet geometry, material stiffness, and capillary forces to rationalize the onset of such deformations and develop a geometric procedure to inverse program target shapes requiring fine control over the curvature gradient. We finally demonstrate the potential irreversibility of the transformation by UV-curing a photosensitive evaporating solution and show that the obtained shells exhibit enhanced mechanical stiffness.

Fisheries subsidies reform in China.

Subsidies are widely criticized in fisheries management for promoting global fishing capacity growth and overharvesting. Scientists worldwide have thus called for a ban on "harmful" subsidies that artificially increase fishing profits, resulting in the recent agreement among members of the World Trade Organization to eliminate such subsidies. The argument for banning harmful subsidies relies on the assumption that fishing will be unprofitable after eliminating subsidies, incentivizing some fishermen to exit and others to refrain from entering. These arguments follow from open-access governance regimes where entry has driven profits to zero. Yet many modern-day fisheries are conducted under limited-access regimes that limit capacity and maintain economic profits, even without subsidies. In these settings, subsidy removal will reduce profits but perhaps without any discernable effect on capacity. Importantly, until now, there have been no empirical studies of subsidy reductions to inform us about their likely quantitative impacts. In this paper, we evaluate a policy reform that reduced fisheries subsidies in China. We find that China's subsidy reductions accelerated the rate at which fishermen retired their vessels, resulting in reduced fleet capacity, particularly among older and smaller vessels. Notably, the reduction of harmful subsidies was only partly responsible for reducing fleet capacity; an increase in vessel retirement subsidies was also a necessary driver of capacity reduction. Our study demonstrates that the efficacy of removing harmful subsidies depends on the policy environment in which removals occur.

Convalescent Plasma and the US Expanded Access Program: A Personal Narrative.

Between early April 2020 and late August 2020, nearly 100,000 patients hospitalized with SARS-CoV2 infections were treated with COVID-19 convalescent plasma (CCP) in the US under the auspices of an FDA-authorized Expanded Access Program (EAP) housed at the Mayo Clinic. Clinicians wishing to provide CCP to their patients during that 5-month period early in the COVID pandemic had to register their patients and provide clinical information to the EAP program. This program was utilized by some 2,200 US hospitals located in every state ranging from academic medical centers to small rural hospitals and facilitated the treatment of an ethnically and socio-economically diverse cross section of patients. Within 6 weeks of program initiation, the first signals of safety were found in 5,000 recipients of CCP, supported by a later analysis of 20,000 recipients (Joyner et al. in J Clin Invest 130:4791-4797, 2020a; Joyner et al. in Mayo Clin Proc 95:1888-1897, 2020b). By mid-summer of 2020, strong evidence was produced showing that high-titer CCP given early in the course of hospitalization could lower mortality by as much as a third (Joyner et al. in N Engl J Med 384:1015-1027, 2021; Senefeld et al. in PLoS Med 18, 2021a). These data were used by the FDA in its August decision to grant Emergency Use Authorization for CCP use in hospitals. This chapter provides a personal narrative by the principal investigator of the EAP that describes the events leading up to the program, some of its key outcomes, and some lessons learned that may be applicable to the next pandemic. This vast effort was a complete team response to a crisis and included an exceptional level of collaboration both inside and outside of the Mayo Clinic. Writing just 4 years after the initiation of the EAP, this intense professional effort, comprising many moving parts, remains hard to completely understand or fully explain in this brief narrative. As Nelson Mandela said of the perception of time during his decades in prison, "the days seemed like years, and the years seemed like days."

PDIA3 orchestrates effector T cell program by serving as a chaperone to facilitate the non-canonical nuclear import of STAT1 and PKM2.

Dysregulated T cell activation underpins the immunopathology of rheumatoid arthritis (RA), yet the machineries that orchestrate T cell effector program remain incompletely understood. Herein, we leveraged bulk and single-cell RNA sequencing data from RA patients and validated protein disulfide isomerase family A member 3 (PDIA3) as a potential therapeutic target. PDIA3 is remarkably upregulated in pathogenic CD4 T cells derived from RA patients and positively correlates with C-reactive protein level and disease activity score 28. Pharmacological inhibition or genetic ablation of PDIA3 alleviates RA-associated articular pathology and autoimmune responses. Mechanistically, T cell receptor signaling triggers intracellular calcium flux to activate NFAT1, a process that is further potentiated by Wnt5a under RA settings. Activated NFAT1 then directly binds to the Pdia3 promoter to enhance the expression of PDIA3, which complexes with STAT1 or PKM2 to facilitate their nuclear import for transcribing T helper 1 (Th1) and Th17 lineage-related genes, respectively. This non-canonical regulatory mechanism likely occurs under pathological conditions, as PDIA3 could only be highly induced following aberrant external stimuli. Together, our data support that targeting PDIA3 is a vital strategy to mitigate autoimmune diseases, such as RA, in clinical settings.

One model for the learning of language.

A major goal of linguistics and cognitive science is to understand what class of learning systems can acquire natural language. Until recently, the computational requirements of language have been used to argue that learning is impossible without a highly constrained hypothesis space. Here, we describe a learning system that is maximally unconstrained, operating over the space of all computations, and is able to acquire many of the key structures present in natural language from positive evidence alone. We demonstrate this by providing the same learning model with data from 74 distinct formal languages which have been argued to capture key features of language, have been studied in experimental work, or come from an interesting complexity class. The model is able to successfully induce the latent system generating the observed strings from small amounts of evidence in almost all cases, including for regular (e.g., an , [Formula: see text], and [Formula: see text]), context-free (e.g., [Formula: see text], and [Formula: see text]), and context-sensitive (e.g., [Formula: see text], and xx) languages, as well as for many languages studied in learning experiments. These results show that relatively small amounts of positive evidence can support learning of rich classes of generative computations over structures. The model provides an idealized learning setup upon which additional cognitive constraints and biases can be formalized.

Encouraging voluntary government action via a solar-friendly designation program to promote solar energy in the United States.

SignificanceDue to market and system failures, policies and programs at the local level are needed to accelerate the renewable energy transition. A voluntary environmental program (VEP), such as SolSmart, can encourage local governments to adopt solar-friendly best practices. Unlike previous research, this study uses a national sample, more recent data, and a matched control group for difference-in-differences estimation to quantify the causal impact of a VEP in the public, rather than private, sector. We offer empirical evidence that SolSmart increased installed solar capacity and, with less statistical significance, the number of solar installations. The results inform the design of sustainability-focused VEPs and future research to understand the causal pathways between local governments' voluntary actions and solar market development.

Cardiac maturation.

The heart undergoes a dynamic maturation process following birth, in response to a wide range of stimuli, including both physiological and pathological cues. This process entails substantial re-programming of mitochondrial energy metabolism coincident with the emergence of specialized structural and contractile machinery to meet the demands of the adult heart. Many components of this program revert to a more "fetal" format during development of pathological cardiac hypertrophy and heart failure. In this review, emphasis is placed on recent progress in our understanding of the transcriptional control of cardiac maturation, encompassing the results of studies spanning from in vivo models to cardiomyocytes derived from human stem cells. The potential applications of this current state of knowledge to new translational avenues aimed at the treatment of heart failure is also addressed.

Running a successful STEMM summer program: A week-by-week guide.

While some established undergraduate summer programs are effective across many institutions, these programs may only be available to some principal investigators or may not fully address the diverse needs of incoming undergraduates. This article outlines a 10-week science, technology, engineering, mathematics, and medicine (STEMM) education program designed to prepare undergraduate students for graduate school through a unique model incorporating mentoring dyads and triads, cultural exchanges, and diverse activities while emphasizing critical thinking, research skills, and cultural sensitivity. Specifically, we offer a straightforward and adaptable guide that we have used for mentoring undergraduate students in a laboratory focused on mitochondria and microscopy, but which may be customized for other disciplines. Key components include self-guided projects, journal clubs, various weekly activities such as mindfulness training and laboratory techniques, and a focus on individual and cultural expression. Beyond this unique format, this 10-week program also seeks to offer an intensive research program that emulates graduate-level experiences, offering an immersive environment for personal and professional development, which has led to numerous achievements for past students, including publications and award-winning posters.

Empowering STEM students: A university-wide mentorship program fostering retention and belonging.

In the face of a challenging climate STEM (Science, Technology, Engineering and Mathematics) higher education that is resistant to Diversity, Equity, and Inclusion efforts aimed to increase and retain students from historically excluded groups (HEGs), there is a critical need for a support structure to ensure students from HEGs continue to be recruited retained. The Biology Undergraduate and Master's Mentorship Program (BUMMP) embodies this commitment to fostering scientific identity, efficacy, and a sense of belonging for first-generation and historically underserved undergraduate and master's students at UC San Diego. The mission of BUMMP is to cultivate a sense of belonging, instill confidence, and nurture a strong scientific identity amongst all its participants. At its core, the three pillars of BUMMP are (1) mentorship, (2) professional development, and (3) research. Quality mentorship is provided where students receive personal guidance from faculty, graduate students, postdocs, and industry leaders in navigating their career pathways. Complementing mentorship, BUMMP provides paid research opportunities and prioritizes professional development by offering workshops designed to enhance students' professional skills. These three pillars form the backbone of BUMMP, empowering students from all backgrounds and ensuring their retention and persistence in STEM. So far, we've served over 1350 mentees, collaborated with 809 mentors, and had over 180 mentees actively engaged in BUMMP-sponsored research activities. The primary focus of this paper is to provide a programmatic guideline for the three pillars of BUMMP: mentorship, professional development, and research. This will offer a blueprint for other institutions to establish similar mentorship programs. Additionally, the paper highlights the impact of the BUMMP program and surveyed mentees who have participated in the mentorship and research component of BUMMP. We showed that mentorship and research experience enhance students' sense of belonging, science identity, and science efficacy, which are key predictors of retention and persistence in pursuing a STEM career. Overall, BUMMP's expansive efforts have made a tremendous impact at UC San Diego and will continue to foster a community of future leaders who will be prepared to make meaningful contributions to the scientific community and beyond.

Twenty Years of Get With The Guidelines-Stroke: Celebrating Past Successes, Lessons Learned, and Future Challenges.

The Get With The Guidelines-Stroke program which, began 20 years ago, is one of the largest and most important nationally representative disease registries in the United States. Its importance to the stroke community can be gauged by its sustained growth and widespread dissemination of findings that demonstrate sustained increases in both the quality of care and patient outcomes over time. The objectives of this narrative review are to provide a brief history of Get With The Guidelines-Stroke, summarize its major successes and impact, and highlight lessons learned. Looking to the next 20 years, we discuss potential challenges and opportunities for the program.