The rockefeller university

In view of changing climatic conditions and disappearing natural resources such as fertile soil and water, exploring alternatives to today's industrial monocrop farming becomes essential. One promising farming practice is intercropping (IC), in which two or more crop species are grown together. Many experiments have shown that, under certain circumstances, IC can decrease soil erosion and fertilizer use, improve soil health and land management, while preserving crop production levels. However, there have been no quantitative approaches to predict, design, and control appropriate IC implementation for given particular environmental and farming conditions, and to assess its robustness. Here, we develop such an approach, based on methods and concepts developed in data science and systems biology. Our dataset groups the results of 2258 IC experiments, involving 274 pairs of 69 different plants. The data include 4 soil characteristics and 5 environmental and farming conditions, together with 8 traits for each of the two intercropped plants. We performed a dimensional reduction of the resulting 25-dimensional variable space and showed that, from a few quantities, one can predict IC yield relative to sole cultivation with good accuracy. For given environmental conditions, our computational approach can help to choose a companion plant and appropriate farming practices. It also indicates how to estimate the robustness of IC to external perturbations. This approach, together with its results, can be viewed as an initial step toward "systems agriculture," which would ultimately develop systems of multiple plant grown together in appropriately designed and controlled settings.

Hidradenitis suppurativa (HS) is a chronic, debilitating inflammatory skin disease characterized by keratinized epithelial tunnels that grow deeply into the dermis. Here, we examined the immune microenvironment within human HS lesions. Multi-omics profiling and multiplexed imaging identified tertiary lymphoid structures (TLSs) near HS tunnels. These TLSs were enriched with proliferative T cells, including follicular helper (Tfh), regulatory (Treg), and pathogenic T cells ( IL17A + and IFNG +), alongside extensive clonal expansion of plasma cells producing antibodies reactive to keratinocytes. HS fibroblasts express CXCL13 or CCL19 in response to immune cytokines. Using a microfluidic system to mimic TLS on a chip, we found that HS fibroblasts critically orchestrated lymphocyte aggregation via tumor necrosis factor alpha (TNF-a)-CXCL13 and TNF-a-CCL19 feedback loops with B and T cells, respectively; early TNF-a blockade suppressed aggregate initiation. Our findings provide insights into TLS formation in the skin, suggest therapeutic avenues for HS, and reveal mechanisms that may apply to other autoimmune settings, including Crohn's disease.

Early time-restricted eating (eTRE) is a dietary strategy that restricts caloric intake to the first 6-8 h of the day and can effect metabolic benefits independent of weight loss. However, the extent of these benefits is unknown. We conducted a randomized crossover feeding study to investigate the weight-independent effects of eTRE on glycemic variation, multiple time-in-range metrics, and levels of inflammatory markers. Ten adults with prediabetes were randomized to eTRE (8-h feeding window, 80% of calories consumed before 14:00 h) or usual feeding (50% of calories consumed after 16:00 h) for 1 week followed by crossover to the other schedule. Using continuous glucose monitoring, we showed that eTRE decreased glycemic variation (mean amplitude of glycemic excursion) and time in hyperglycemia greater than 140 mg/dL without affecting inflammatory markers (erythrocyte sedimentation rate and C-reactive protein). These data implicate eTRE as a candidate dietary intervention for the weight-independent management of dysglycemia in high-risk individuals.

Common variable immunodeficiency (CVID) is one of the most common groups of human inborn errors of immunity. In addition to infections resulting from insufficient levels of immunoglobulins and antibodies, a signifi cant proportion of patients develop autoimmune cytopenias, especially immune thrombocytopenia, hemolytic anemia, or neutropenia. They may be the initial manifestation of CVID in a patient who has not had significant infections, and similar episodes may recur at intervals over time. Treatment of these hematologic complications includes the use of corticosteroids or other medications, often including rituximab; splenectomy is discouraged. Here we outline the overall occurrence of these blood cytopenias in a cohort of 408 patients, as well as the clinical and genetic associations noted in these individuals.

The molecular mechanism by which inborn errors of the human RNA lariat-debranching enzyme 1 (DBR1) underlie brainstem viral encephalitis is unknown. We show here that the accumulation of RNA lariats in human DBR1-deficient cells interferes with stress granule (SG) assembly, promoting the proteasome degradation of at least G3BP1 and G3BP2, two key components of SGs. In turn, impaired assembly of SGs, which normally recruit PKR, impairs PKR activation and activity against viruses, including HSV-1. Remarkably, the genetic ablation of PKR abolishes the corresponding antiviral effect of DBR1 in vitro. We also show that Dbr1Y17H/Y17H mice are susceptible to similar viral infections in vivo. Moreover, cells and brain samples from Dbr1Y17H/Y17H mice exhibit decreased G3BP1/2 expression and PKR phosphorylation. Thus, the debranching of RNA lariats by DBR1 permits G3BP1/2- and SG assembly-mediated PKR activation and cell-intrinsic antiviral immunity in mice and humans. DBR1-deficient patients are prone to viral disease because of intracellular lariat accumulation, which impairs G3BP1/2- and SG assembly-dependent PKR activation.

ZAP is an antiviral protein that binds to and depletes viral RNA, which is often distinguished from vertebrate host RNA by its elevated CpG content. Two ZAP cofactors, TRIM25 and KHNYN, have activities that are poorly understood. Here, we show that functional interactions between ZAP, TRIM25 and KHNYN involve multiple domains of each protein, and that the ability of TRIM25 to multimerize via its RING domain augments ZAP activity and specificity. We show that KHNYN is an active nuclease that acts in a partly redundant manner with its homolog N4BP1. The ZAP N-terminal RNA binding domain constitutes a minimal core that is essential for antiviral complex activity, and we present a crystal structure of this domain that reveals contacts with the functionally required KHNYN C-terminal domain. These contacts are remote from the ZAP CpG binding site and would not interfere with RNA binding. Based on our dissection of ZAP, TRIM25 and KHNYN functional anatomy, we could design artificial chimeric antiviral proteins that reconstitute the antiviral function of the intact authentic proteins, but in the absence of protein domains that are otherwise required for activity. Together, these results suggest a model for the RNA recognition and action of ZAP-containing antiviral protein complexes.

Identifying the scaling rules describing ecological patterns across time and space is a central challenge in ecology. Taylor's law of fluctuation scaling, which states that the variance of a population's size or density is proportional to a positive power of the mean size or density, has been widely observed in population dynamics and characterizes variability in multiple scientific domains. However, it is unclear if this phenomenon accurately describes ecological patterns across many orders of magnitude in time, and therefore links otherwise disparate observations. Here, we use water clarity observations from 10,531 days of high-frequency measurements in 35 globally distributed lakes, and lower-frequency measurements over multiple decades from 6342 lakes to test this unknown. We focus on water clarity as an integrative ecological characteristic that responds to both biotic and abiotic drivers. We provide the first documentation that variations in ecological measurements across diverse sites and temporal scales exhibit variance patterns consistent with Taylor's law, and that model coefficients increase in a predictable yet non-linear manner with decreasing observation frequency. This discovery effectively links high-frequency sensor network observations with long-term historical monitoring records, thereby affording new opportunities to understand and predict ecological dynamics on time scales from days to decades.

Detecting viral infection is a key role of the innate immune system. The genomes of some RNA viruses have a high CpG dinucleotide content relative to most vertebrate cell RNAs, making CpGs a molecular marker of infection. The human zinc- finger antiviral protein (ZAP) recognizes CpG, mediates clearance of the foreign CpG-rich RNA, and causes attenuation of CpG-rich RNA viruses. While ZAP binds RNA, it lacks enzymatic activity that might be responsible for RNA degradation and thus requires interacting cofactors for its function. One of these cofactors, KHNYN, has a predicted nuclease domain. Using biochemical approaches, we found that the KHNYN NYN domain is a single- stranded RNA ribonuclease that does not have sequence specificity and digests RNA with or without CpG dinucleotides equivalently in vitro. We show that unlike most KH domains, the KHNYN KH domain does not bind RNA. Indeed, a crystal structure of the KH region revealed a double-KH domain with a negatively charged surface that accounts for the lack of RNA binding. Rather, the KHNYN C- terminal domain (CTD) interacts with the ZAP RNA- binding domain (RBD) to provide target RNA specificity. We define a minimal complex composed of the ZAP RBD and the KHNYN NYN-CTD and use a fluorescence polarization assay to propose a model for how this complex interacts with a CpG dinucleotide- containing RNA. In the context of the cell, this module would represent the minimum ZAP and KHNYN domains required for CpG- recognition and ribonuclease activity essential for attenuation of viruses with clusters of CpG dinucleotides.

Social elective egg freezing (EEF) is now widely used globally but in many countries is unaffordable to many women because of high costs and lacking insurance coverage. Efforts to reduce costs, therefore, are of importance. Surprisingly, a simple, well-defined and practical approach ensuring optimal outcomes for EEF has, however, so-far not been published. We, therefore, conducted a narrative review of the literature for relevant articles regarding the different steps of ovarian stimulation (OS) in the EEF process, in order to define such a standard protocol. This review revealed that in order to maximize oocyte yields with minimal number of OS cycles - while ensuring patient safety - a multiple-dose GnRH antagonist protocol with a daily gonadotropin dose of 300 IU appears best, unless patients demonstrate a polycystic ovarian phenotype, suggestive of likely high responses. The initial gonadotropin should be recFSH, while LH supplementation should be co-administered with the addition of GnRH antagonist. Final follicular maturation should be triggered by GnRH agonist trigger, with a dual trigger (1000-1500 IU hCG) considered for suboptimal responders to GnRH agonist trigger, optionally with Cabergoline to mitigate ovarian hyperstimulation syndrome (OHSS) in high responders.

Melanoma arising in association with a blue nevus (BN) is rare but has molecular similarities to uveal melanoma (UM), including GNAQ/11 mutations. Tebentafusp was recently approved for UM based on improved overall survival in a phase 3 study. We hypothesized that tebentafusp may be active in BN-associated melanoma. Here, we present a case of metastatic BN-associated melanoma with rapid response and similar to 1 year of disease control on tebentafusp. We also explore molecular and histological features of secondary resistance. Our case highlights that PD-1-resistant melanomas should be screened for GNAQ/11 mutations, as tebentafusp may be a treatment option in this extremely rare disease.