The rockefeller university

Aneuploidy in embryos poses a major barrier to successful human reproduction, contributing to nearly 50% of early miscarriages. Despite its high prevalence in human embryos, the molecular mechanisms regulating aneuploid cell fate during development remain poorly understood. This knowledge gap persists due to ethical constraints in human embryo research and the limitations of existing animal models. In this study, we identified the New World primate marmoset (Callithrix jacchus) as a suitable model for investigating aneuploidy. By calling copy number variants from single-cell RNA-sequencing data of marmoset embryonic cells, we identified heterogeneous aneuploidy, indicating chromosomal instability (CIN) in marmoset preimplantation embryos. Furthermore, marmoset aneuploidy displayed lineage-specific behavior during gastruloid differentiation, similar to humans, suggesting a conserved regulatory mechanism in lineage specification. To develop a more pluripotent cell line to study early specification, we established an efficient approach for generating na & iuml;ve-like marmoset pluripotent stem cells (cjPSCs). These cells resemble preimplantation epiblast-like cells and exhibit inherent CIN. Transcriptome analysis identified potential pathways contributing to aneuploidy during early embryogenesis, including the downregulation of cell cycle checkpoint signaling and the upregulation of autophagy pathways. Additionally, we found no significant effect of spontaneously occurring aneuploidy in cjPSCs on blastoid formation, suggesting that the consequences of aneuploidy become evident only after gastrulation, with preimplantation lineages exhibiting a higher tolerance for genomic instability. Unexpectedly, aneuploidy enhanced cavity formation during blastoid development, suggesting a potential role in facilitating efficient trophectoderm differentiation. Our findings validate the marmoset as a valuable model for studying CIN during early primate development and provide insight into the mechanisms underlying the prevalence of aneuploidy in primates. Na & iuml;ve-like cjPSCs recapitulate key phenotypic traits of early embryonic cells, providing a robust system for studying post-implantation aneuploid cell fates in vivo and serving as a foundation for future research in this field.

To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling >20 million cells from 623 mouse tissues across different life stages, sexes, and genotypes. This comprehensive dataset reveals >3000 different cellular states and >200 aging-associated cell populations. Our panoramic analysis uncovered organ-, lineage-, and sex-specific shifts in cellular dynamics during life-span progression. Moreover, we identify both systematic and organ-specific alterations in immune cell populations associated with aging. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte dependent. Our "cell-omics" strategy enhances comprehension of cellular aging and lays the groundwork for exploring the complex cellular regulatory networks in aging and aging-associated diseases.

Spinal cord injury (SCI) is a devastating condition with 250,000 to 500,000 new cases globally each year. Respiratory infections, e.g., pneumonia and influenza are the leading cause of death after SCI. Unfortunately, there is a poor understanding of how altered neuro-immune communication impacts an individual's outcome to infection. In humans and rodents, SCI leads to maladaptive changes in the spinal-sympathetic reflex (SSR) circuit which is crucial to sympathetic function. The cause of the impaired immune function may be related to harmful neuroinflammation which is detrimental to homeostatic neuronal function, aberrant plasticity, and hyperexcitable circuits. Soluble tumor necrosis factor (sTNF) is a pro-inflammatory cytokine that is elevated in the CNS after SCI and remains elevated for several months after injury. By pharmacologically attenuating sTNF in the CNS after SCI we were able to demonstrate improved immune function. Furthermore, when we investigated the specific cellular population which may be involved in altered neuro-immune communication we reported that excessive TNFR1 activity on excitatory INs promotes immune dysfunction. Furthermore, this observation is NFk beta dependent in VGluT2 + INs. Our data is the first report of a target within the CNS, TNFR1, that contributes to SCI-induced immune dysfunction after T9-SCI and is a potential avenue for future therapeutics.

Transitions across ecological boundaries, such as those separating freshwater from the sea, are major drivers of phenotypic innovation and biodiversity. Despite their importance to evolutionary history, we know little about the mechanisms by which such transitions are accomplished. To help shed light on these mechanisms, we generated the first high-quality, near-complete assembly and annotation of the genome of the American shad (Alosa sapidissima), an ancestrally diadromous (migratory between salinities) fish in the order Clupeiformes of major cultural and historical significance. Among the Clupeiformes, there is a large amount of variation in salinity habitat and many independent instances of salinity boundary crossing, making this taxon well-suited for studies of mechanisms underlying ecological transitions. Our initial analysis of the American shad genome reveals several unique insights for future study including: (i) that genomic repeat content is among the highest of any fish studied to date; (ii) that genome-wide heterozygosity is low and may be associated with range-wide population collapses since the 19th century; and (iii) that natural selection has acted on the branch leading to the diadromous genus Alosa. Our analysis suggests that functional targets of natural selection may include diet, particularly lipid metabolism, as well as cytoskeletal remodeling and sensing of salinity changes. Natural selection on these functions is expected in the transition from a marine to diadromous life history, particularly in the tolerance of nutrient- and ion-devoid freshwater. We anticipate that our assembly of the American shad genome will be used to test future hypotheses on adaptation to novel environments, the origins of diadromy, and adaptive variation in life history strategies, among others.

Many real-world data sets live on high-dimensional Stiefel and Grassmannian manifolds, V-k(R-N) and Gr(k, R-N), respectively, and benefit from projection onto lower-dimensional Stiefel (respectively, Grassmannian) manifolds. In this work, we propose an algorithm called principal Stiefel coordinates to reduce data dimensionality from V-k(R-N) to V-k(R-n) in an O(k)-equivariant manner (k <= n << N). We begin by observing that each element alpha is an element of V-n(R-N) defines an isometric embedding of V-k(R-n) into V-k(R-N). Next, we optimize for such an embedding map that minimizes data fit error by warm-starting with the output of principal component analysis (PCA) and applying gradient descent. Then we define a continuous and O(k)-equivariant map pi(alpha) that acts as a ''closest point operator" to project the data onto the image of V-k(R-n) in V-k(R-N) under the embedding determined by alpha, while minimizing distortion. Because this dimensionality reduction is O(k)-equivariant, these results extend to Grassmannian manifolds as well. Lastly, we show that the PCA output globally minimizes projection error in a noiseless setting, but that our algorithm achieves a meaningfully different and improved outcome when the data does not lie exactly on the image of a linearly embedded lower-dimensional Stiefel manifold as above. Multiple numerical experiments using synthetic and real-world data are performed.

QuestionCan investigators agree on morphological definitions and methods of assessment for lesions in clinical trials for hidradenitis suppurativa (HS)?FindingThrough a modified Delphi process involving expert dermatologists, consensus was achieved on 11 morphologic lesion definitions and on 16 of 18 statements guiding standardized HS lesion assessments.MeaningConsensus on detailed morphologic definitions to support classification of HS lesions and guidance that standardizes assessment of these lesions can be implemented in study protocols and investigator trainings with the goal of improving accuracy and reliability of investigator ratings in clinical trials for HS. This consensus statement establishes consensus-based morphological definitions of hidradenitis suppurativa (HS) lesions and guidance statements that standardize investigator lesion assessments for implementation in clinical trials. ImportanceAccurate classification and reliability in assessment for lesions of hidradenitis suppurativa (HS) by investigators is critical to the determination of responder status and to overall data quality in clinical trials.ObjectiveTo establish consensus-based morphological definitions of HS lesions and guidance statements that standardize investigator lesion assessments for implementation in clinical trials.Evidence ReviewHealth professionals (primarily dermatologists) with expertise in the measurement of HS disease activity as well as novice raters completed a preliminary questionnaire in which participants were asked to assess images of HS lesions and provide qualitative feedback on their decision making. Based on this feedback, detailed morphologic definitions for lesions and guidance statements that standardize lesion assessments were formulated and presented for consensus voting in 2 electronic Delphi surveys. A virtual group discussion after round 1 supported participants in round 2 voting.FindingsResponse rates were 84.7% (50 of 59), 86.0% (43 of 50), and 90.9% (40 of 44) in the preliminary, electronic Delphi round 1, and electronic Delphi round 2 surveys, respectively. Morphological definitions for 11 lesion types achieved the prespecified 70% consensus threshold, with 9 definitions reaching at least 90% agreement. After 2 electronic Delphi rounds, 16 of 18 guidance statements achieved the prespecified consensus threshold, with 13 statements receiving endorsement from more than 80% of participants. Two guidance statements related to assessment of tunneled plaques with multiple openings and assessment of scalp lesions failed to reach consensus.Conclusions and RelevanceCommon morphologic definitions and guidance that standardize assessment of HS lesions can be implemented in clinical trial protocols and investigator trainings with the goals of improving accuracy and reliability of investigator ratings.

Psychological stress and its sequelae pose a major challenge to public health. Immune activation is conventionally thought to aggravate stress-related mental diseases such as anxiety disorders and depression. Here, we sought to identify potentially beneficial consequences of immune activation in response to stress. We showed that stress led to increased interleukin (IL)-22 production in the intestine as a result of stress-induced gut leakage. IL-22 was both necessary and sufficient to attenuate stress-induced anxiety behaviors in mice. More specifically, IL-22 gained access to the septal area of the brain and directly suppressed neuron activation. Furthermore, human patients with clinical depression displayed reduced IL-22 levels, and exogenous IL- 22 treatment ameliorated depressive-like behavior elicited by chronic stress in mice. Our study thus identifies a gut-brain axis in response to stress, whereby IL-22 reduces neuronal activation and concomitant anxiety behavior, suggesting that early immune activation can provide protection against psychological stress.

A search is presented for an extended Higgs sector with two new particles, X and., in the process X ->phi phi ->(gamma gamma)(gamma gamma).Novel neural networks classify events with diphotons that are merged and determine the diphoton masses. The search uses LHC proton-proton collision data at root s = 13 TeV collected with the CMS detector, corresponding to an integrated luminosity of 138 fb(-1). No evidence of such resonances is seen. Upper limits are set on the production cross section for m(X) between 300 and 3000 GeV and m.=m(X) between 0.5% and 2.5%, representing the most sensitive search in this channel.

Human endogenous retroviruses (HERVs) occupy a large portion of the human genome. Most HERVs are transcriptionally silent, but they can be reactivated during pathological states such as viral infection and certain cancers. The HERV-K HML-2 clade includes elements that recently integrated have in the human germ line and often contain intact open reading frames that possibly support peptide and protein expression. Understanding HERV-K-host interactions and their potential as biomarkers is problematic due to the high similarity among different elements. Previously, we described a long-read single molecule real-time sequencing (PacBio) strategy to analyze HERV-K RNA expression profiles in different cell types. However, identifying HERV-K HML-2 proteins accurately is difficult without robust and reliable methods and reagents. Here we present a new approach to characterize the HML-2 elements that (a) are being translated and (b) produce enough protein to be detected and identified by mass spectrometry. Our data reveal that RNA expression profiling alone cannot accurately predict which HML-2 elements are responsible for protein production, as we observe several differences between the highest expressed RNAs and the elements that are the predominant source of HERV-K HML-2 protein synthesis. These studies represent an important advance toward untangling the complexity of HERV-K-host interactions.