The rockefeller university

Spatial refugia offered by structurally complex habitats mitigate high rates of predation for many aquatic and terrestrial prey species. These refuges are particularly important for small juvenile marine invertebrates, for which predation often represents the greatest cause of mortality. When the availability or quality of habitat landscapes and refugia are diminished by natural or anthropogenic forces, prey populations face further risk. In this study, we examined the utilization of alternative types of submerged aquatic vegetation (SAV) by juvenile bay scallops, Argopecten irradians, in a system where their historical habitat of eelgrass, Zostera marina, has largely disappeared. We found that scallops settled on and remained attached, above the bottom, to 9 species of macroalgae, 6 of which were fine filamentous or fleshy red algae. Macroalgae thus serve as suitable substrates for scallop larval settlement and early juvenile life, clearly important to successful population rebuilding that occurred following commencement of our restoration efforts. However, the much smaller maximum observed size (2-9 mm) and calculated duration of attachment (5-27 days) of scallops in the canopy of red macroalgae were considerably lower than those previously reported for eelgrass and the green macroalgae Codium fragile. With scallops dropping sooner to the bottom from red macroalgae, at smaller sizes, they are accessible to greater numbers of predator species/sizes and higher rates of predation (as shown in supporting laboratory experiments). Furthermore, this transition occurs well before scallops have undergone an ontogenetic shift to evasive swimming or have grown to reach a refuge in larger size. Fine filamentous red macroalgae, in which juvenile scallops demonstrated the highest frequency of attachment in this study and among the shortest duration in the canopy, now predominate in many areas of the Peconic Bays, New York, where eelgrass was formerly widespread. This apparent habitat degradation/replacement is thus acting to compress the length of time scallops are able to utilize a spatial refuge from predation at a critical life history stage, with potential cascading ontogenetic impacts on the use of a subsequent behavioral refuge and possible negative demographic consequences. Few prior studies have revealed such clear impacts of this kind resulting from habitat loss.

The Christchurch mutation (R136S) in the APOE3 (E3S/S) gene is associated with attenuated tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high amyloid burden in the carrier. However, the molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse Apoe with wild-type human APOE3 or APOE3S/S on a tauopathy background. The R136S mutation decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in hippocampal theta and gamma power. Additionally, the R136S mutation reduced interferon responses to tau pathology in both mouse and human microglia, suppressing cGAS-STING pathway activation. Treating E3 tauopathy mice with a cGAS inhibitor protected against tau-induced synaptic loss and induced transcriptomic alterations similar to the R136S mutation across brain cell types. Thus, suppression of the microglial cGAS-STING-interferon (IFN) pathway plays a central role in mediating the protective effects of R136S against tauopathy.

The original 100.3 Mb reference genome for Caenorhabditis elegans, generated from the wild-type laboratory strain N2, has been crucial for analysis of C. elegans since 1998 and has been considered complete since 2005. Unexpectedly, this long-standing reference was shown to be incomplete in 2019 by a genome assembly from the N2-derived strain VC2010. Moreover, genetically divergent versions of N2 have arisen over decades of research and hindered reproducibility of C. elegans genetics and genomics. Here we provide a 106.4 Mb gap-free, telomere-to-telomere genome assembly of C. elegans, generated from CGC1, an isogenic derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier assemblies come from repeat regions, unique additions to the genome are also found. Of 19,972 protein-coding genes in the N2 assembly, 19,790 (99.1%) encode products that are unchanged in the CGC1 assembly. The CGC1 assembly also may encode 183 new protein-coding and 163 new ncRNA genes. CGC1 thus provides both a completely defined reference genome and corresponding isogenic wild-type strain for C. elegans, allowing unique opportunities for model and systems biology.

Background Recent advances in machine learning have revolutionized medical imaging. Currently, identifying brown adipose tissue (BAT) relies on manual identification and segmentation on Fluorine-(18) fluorodeoxyglucose positron emission tomography/computed tomography (F-18-FDG PET/CT) scans. However, the process is time-consuming, especially for studies involving a large number of cases, and is subject to bias due to observer dependency. The introduction of machine learning algorithms, such as the PET/CT algorithm implemented in the TriDFusion (3DF) Image Viewer, represents a significant advancement in BAT detection. In the context of cancer care, artificial intelligence (AI)-driven BAT detection holds immense promise for rapid and automatic differentiation between malignant lesions and non-malignant BAT confounds. By leveraging machine learning to discern intricate patterns in imaging data, this study aims to advance the automation of BAT recognition and provide precise quantitative assessment of radiographic features. Results We used a semi-automatic, threshold-based 3DF workflow to segment 317 PET/CT scans containing BAT. To minimize manual edits, we defined exclusion zones via machine-learning-based CT organ segmentation and used those organ masks to assign each volume of interest (VOI) to its anatomical site. Three physicians then reviewed and corrected all segmentations using the 3DF contour panel. The final, edited masks were used to train an nnU-Net V2 model, which we subsequently applied to 118 independent PET/CT scans. Across all anatomical sites, physicians reviewed the network's automated segmentations to be approximately 90% accurate. Conclusion Although nnU-Net V2 effectively identified BAT from PET/CT scans, training an AI model capable of perfect BAT segmentation remains a challenge due to factors such as PET/CT misregistration and the absence of visible BAT activity across contiguous slices.

Pregnancy brings about profound changes in the mammary gland to prepare for lactation, yet immunocyte changes that accompany this rapid remodeling are incompletely understood. We comprehensively analyzed mammary T cells, revealing a marked increase in CD4+ and CD8+ T effector cells, including an expansion of T cell receptor (TCR)alpha beta+CD8 alpha alpha+ cells, in pregnancy and lactation. T cells were localized in the mammary epithelium, resembling intraepithelial lymphocytes (IELs) typically found in mucosal tissues. Similarity to mucosal tissues was substantiated by demonstrating partial dependence on microbial cues, T cell migration from the intestine to the mammary gland in late pregnancy and shared TCR clonotypes between intestinal and mammary tissues, including intriguing public TCR families. Putative counterparts of mammary IELs were found in human breast and milk. Mammary IELs are thus poised to manage the transition from a nonmucosal tissue to a mucosal barrier during lactogenesis.

Genetic investigation in Mendelian skin disorders featuring generalized or localized skin scaling and redness, known as the ichthyoses, has revealed novel pathways relevant to epidermal integrity, barrier function, and desquamation. Here, we show that a recurrent de novo missense variant in EMP2 (epithelial membrane protein 2), which encodes a cell surface tetraspan protein in the growth- arrest specific 3 (GAS3)/peripheral myelin protein 22 (PMP22) family, is associated with a Mendelian skin disorder in the progressive symmetric erythrokeratoderma spectrum. The disorder features severely thickened, red, and scaly skin at sites of wound healing or repetitive movement including on the face, genitals, flexural areas, and the palms and soles. EMP2 has previously been shown to directly associate with focal adhesion kinase, which links cell junction forces to signaling pathways relevant to proliferation, migration, and wound healing. Using single- cell spatial transcriptomics in affected tissue, we found ectopic suprabasal activation of signaling pathways downstream of receptor tyrosine kinases including epidermal growth the key role of EMP2 in epidermal differentiation and proliferation.

Traditional chemical screens have focused on a single assay per screen, making them labor intensive and costly. Here, we combined a chemical screen with single-cell RNA sequencing (scRNA-seq) to perform Chemical Perturb-seq (ChemPerturb-seq), enabling a systematic analysis of the molecular changes of human beta cells upon individual small molecule treatments. Using this platform, we performed an in vivo barcoded screen and discovered a small molecule cocktail, including beta-lipotropin 61-91, insulin growth factor-1, and prostaglandin E2, with which preconditioning human beta cells and primary islets significantly enhanced function and survival when transplanted subcutaneously to female, but not to male, mice. We identified two additional molecules, serotonin and histamine, that promote islet function when transplanted subcutaneously to male mice using ChemPerturb-seq. Such small molecule cocktails could be applied to improve the current FDA-approved islet transplantation procedure. Finally, we developed an artificial intelligence (AI)-powered website, ChemPerturbDB, which provides user-friendly open access analysis of the extensive ChemPerturb-seq dataset.

Biomolecular condensates are key features of intracellular compartmentalization(1,2). As the most prominent nuclear condensate in eukaryotes, the nucleolus is a multiphase liquid-like structure in which ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps to form the small (SSU) and large (LSU) ribosomal subunits(3-5). However, how rRNA processing is coupled to the layered organization of the nucleolus is poorly understood owing to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. By generating synthetic nucleoli in cells using an engineered rDNA plasmid system, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.

Epidermal stem cells produce the skin's barrier that excludes pathogens and prevents dehydration. Hair follicle stem cells (HFSCs) are dedicated to bursts of hair regeneration, but upon injury, they can also reconstruct, and thereafter maintain, the overlying epidermis. How HFSCs balance these fate choices to restore physiologic function to damaged tissue remains poorly understood. Here, we uncover serine as an unconventional, non-essential amino acid that impacts this process. When dietary serine dips, endogenous biosynthesis in HFSCs fails to meet demands (and vice versa), slowing hair cycle entry. Serine deprivation also alters wound repair, further delaying hair regeneration while accelerating re-epithelialization kinetics. Mechanistically, we show that HFSCs sense each fitness challenge by triggering the integrated stress response, which acts as a rheostat of epidermal-HF identity. As stress levels rise, skin barrier restoration kinetics accelerate while hair growth is delayed. Our findings offer potential for dietary and pharmacological intervention to accelerate wound healing.