The rockefeller university

Oxytocin, an evolutionarily conserved neuropeptide, plays a crucial role in various physiological and behavioural processes, offering potential therapeutic benefits for several psychiatric and neurodevelopmental conditions. Despite its promise, oxytocin research has been marked by inconsistent results concerning its therapeutic applications and underlying mechanisms. Performing a systematic review and meta-analysis is a popular approach to shed light on mixed findings in a body of literature; however, they can become quickly outdated as new evidence becomes available. Given these challenges, research on the links between oxytocin and biobehavioural outcomes is ideally positioned for the adoption of 'living' meta-analyses, which allow for the continuous integration of new data and updated conclusions. Here we introduce the Active Monitoring of Oxytocin Research Evidence (AMORE) platform (https://amore-project.org), which is a hub that aggregates articles and materials associated with living meta-analyses for biobehavioural oxytocin research in humans. Developed through consensus among 24 expert researchers, a standardized framework was established that either requires or recommends practices ensuring transparency and rigor in living meta-analyses featured on the AMORE platform. Overall, AMORE has been designed to advance human oxytocin biobehavioural research by the timely integration of emerging evidence through transparent living meta-analyses. To date, two living meta-analysis projects at different stages of publication are hosted on AMORE, demonstrating the platform's practical application.

The complement system is a central component of innate and shaping adaptive responses. Deficiencies in complement proteins, whether inherited or acquired, predispose to severe infections, particularly with encapsulated bacteria such as Neisseria meningitidis and Streptococcus pneumoniae. Although rare, inherited defects affect different pathways and may also present with autoimmune or renal diseases. Diagnosis relies on functional and quantitative assays, especially in patients with earlyonset or recurrent infections. Complement inhibition, introduced with eculizumab and expanded to agents targeting C3, Factor B, or Factor D, has transformed the management of complement-mediated disorders but unmasked novel infectious risks, including meningococcal disease and invasive fungal infections.

Immunodeficient mice, particularly the NOD.Cg-Prkdc scid Il2rg tm1Wjl /SzJ (NSG) strain and other non-obese diabetic (NOD)-derived lines are widely used in biomedical research due to their profound immunosuppression, which enables stable engraftment of human cells and tissues with minimal rejection. Despite their broad utility, these models exhibit unique immunologic and anatomic features and are predisposed to infectious and noninfectious diseases that may confound experimental outcomes and limit translational relevance. This review summarizes current knowledge on spontaneous, infectious, and experimentally induced lesions in NSG and related strains. These mice characteristically display hypoplastic lymphoid organs, including the spleen, thymus, and lymph nodes, due to a near-complete absence of lymphocytes. Spontaneous background lesions include splenic osseous metaplasia, neurodegeneration, pancreatic mastocytosis, cochlear degeneration, intervertebral disk disease, skull hyperostosis, and pancreatic duct cysts, among others. Common spontaneous neoplasms include lymphomas, osteosarcomas, and mammary gland tumors. Due to their immunodeficient status, NSG and NOD-derived mice are also highly susceptible to opportunistic infections, such as Corynebacterium bovis, Chlamydia muridarum, Clostridioides difficile, and mouse kidney parvovirus. In humanized models, engraftment of human immune cells can result in distinctive syndromes, including xenogeneic graft-versus-host disease, post-transplant lymphoproliferative disorders, and chimeric myeloid cell hyperactivation syndrome, which can impact study outcomes and lead to mortality and morbidity. This review is intended as a resource for comparative pathologists to become familiar with these widely used immunodeficient mice, so they can interpret strain-specific lesions and recognize experimental confounders in these mouse models.

Nucleoside-modified messenger RNA (mRNA) vaccines elicit protective antibodies through their ability to promote T follicular helper (Tfh) cell differentiation. The lipid nanoparticles (LNPs) of mRNA vaccines possess inherent adjuvant activity. However, the extent to which the nucleoside-modified mRNA is sensed and contributes to Tfh cell responses remains undefined. Herein, we deconvolute the signals induced by LNPs and mRNA that instruct dendritic cells (DCs) to promote Tfh cell differentiation. We demonstrate that the mRNA drives the production of type I interferons, which act on DCs to enhance their maturation and Tfh cell differentiation, and favors plasma cells and memory B cell responses. In parallel, LNPs, which allow for mRNA uptake by DCs within the draining lymph node, also modulate Tfh cell responses by shaping the localization of CD25+ DCs. Our work unravels distinct adjuvant features of mRNA and LNPs necessary for the induction of Tfh cells, with implications for rational vaccine design.

Replicative senescence is a powerful tumor suppressor pathway that curbs proliferation of human cells when a few critically-short telomeres activate the DNA damage response (DDR). We show that ATM is the sole DDR kinase responsible for the induction and maintenance of replicative senescence and that ATM inhibition can induce normal cell divisions in senescent cells. Compared to non-physiological atmospheric (similar to 20%) oxygen, primary fibroblast cells grown at physiological (3%) oxygen were more tolerant to critically short telomeres, explaining their extended replicative lifespan. We show that this tolerance is due to attenuation of the ATM response to double-strand breaks (DSBs) and unprotected telomeres. Our data indicate that the reduced ATM response to DSBs at 3% oxygen is due to increased ROS, which induces disulfide crosslinked ATM dimers that do not respond to DSBs. This regulation of cellular lifespan through attenuation of ATM at physiological oxygen has implications for tumor suppression through telomere shortening.

'Intrinsic immunity' is often used to refer to mechanisms of host defense operating in nonleukocytic cells. This term can refer to the intrinsic capacity of an individual cell to fend off invading microbes without help from other cells or of a group of similar cells to fend off invading microbes without help from other cell types. The intrinsic capacity of individual cells to defend themselves against invading microbes without assistance has received little attention and is the topic of this review. We also focus on nonleukocytic cells and on humans, the only species in which intrinsic immunity has been shown by genetic means to be essential for homeostasis in natural conditions at wholebody level. We review recent progress in our understanding of the type I interferon-independent intrinsic immunity of individual nonleukocytic cells, as inferred from human inborn errors of intrinsic immunity manifesting as infection or autoinflammation.

The recent Society for Molecular Biology and Evolution Satellite Meeting on De Novo Gene Birth, hosted at Texas A&M University on November 6 to 9, 2023, represented the first-ever opportunity for scientists studying the evolution and biology of de novo genes to gather through a dedicated meeting and discuss about groundbreaking discoveries in this emerging and exciting field of gene evolution. In this perspective, we discuss recent advances and major open questions in de novo gene emergence and evolution that were presented at the SMBE satellite meeting, as well as some of the key recent findings published before or since the conference. These key themes include de novo gene identification, function, and evolution, what we are learning about de novo genes from experimental analyses of random peptides, de novo gene birth and microproteins, and the role of de novo genes in human disease.

Pseudomonas aeruginosa is a leading cause of nosocomial infections, including pneumonia and urinary tract infections, and the primary cause of morbidity and mortality in cystic fibrosis patients. The emergence of multidrug-resistant strains makes these infections life-threatening. To overcome this challenge, lysocins can be employed as novel antipseudomonals. Lysocins use components of the pyocin antimicrobial system to deliver bacteriophage lysins to their peptidoglycan substrate in Pseudomonas. Peptidoglycan cleavage causes membrane destabilization, cytoplasmic leakage, and disruption of the proton motive force, thereby killing the cell. In our previous proof-of-concept study, the PyS2-GN4 lysocin killed only one-third of P. aeruginosa strains due to the targeted receptor. This limitation can now be circumvented by engineering second-generation lysocins that bind and translocate through highly conserved Pseudomonas-specific receptors. One lysocin, PyS5-I-GN4, uses a single domain from pyocin S5 to deliver the GN4 lysin through the conserved ferric pyochelin transporter, consequently killing 95% of multidrug-resistant clinical isolates tested. Importantly, PyS5-I-GN4 displayed antibiofilm properties and was bactericidal in serum and lung surfactant. Serum inactivation observed for lysins is not seen for lysocins, making this approach more effective for treating systemic Gram-negative bacterial infections. Despite its broadened pseudomonal strain coverage, PyS5-I-GN4 demonstrated narrow-spectrum antibacterial activity toward P. aeruginosa only and lacked cytotoxicity toward human cells. A single dose of lysocin was protective and reduced bacteria multiple log10-fold in the lungs and secondary organs in a neutropenic murine lung infection model. These findings support lysocins as therapeutics for P. aeruginosa and provide insight into designing future constructs for other Gram-negative pathogens.

Eukaryotic ribosomal small subunit (SSU) assembly requires the SSU processome, a nucleolar precursor containing the RNA chaperone U3 small nucleolar RNA (snoRNA). The underlying molecular mechanisms of SSU processome maturation, remodelling, disassembly and RNA quality control, and the transitions between states remain unknown owing to a paucity of intermediates1, 2-3. Here we report 16 native SSU processome structures alongside genetic data, revealing how two helicases, the Mtr4-exosome and Dhr1, are controlled for accurate and unidirectional ribosome biogenesis. Our data show how irreversible pre-ribosomal RNA degradation by the redundantly tethered RNA exosome couples the transformation of the SSU processome into a pre-40S particle, during which Utp14 can probe evolving surfaces, ultimately positioning and activating Dhr1 to unwind the U3 snoRNA and initiate nucleolar pre-40S release. This study highlights a paradigm for large dynamic RNA-protein complexes in which irreversible RNA degradation drives compositional changes and communicates these changes to govern enzyme activity while maintaining overall quality control.

Antibodies play a crucial role in adaptive immunity. They develop as B cell receptors (BCRs): membrane-bound forms of antibodies that are expressed on the surfaces of B cells. BCRs are refined through affinity maturation, a process of somatic hypermutation (SHM) and natural selection, to improve binding to an antigen. Computational models of affinity maturation have developed from two main perspectives: molecular evolution and language modeling. The molecular evolution perspective focuses on nucleotide sequence context to describe mutation and selection; the language modeling perspective involves learning patterns from large data sets of protein sequences. In this paper, we compared models from both perspectives on their ability to predict the course of antibody affinity maturation along phylogenetic trees of BCR sequences. This included models of SHM, models of SHM combined with an estimate of selection, and protein language models. We evaluated these models for large human BCR repertoire data sets, as well as an antigen-specific mouse experiment with a pre-rearranged cognate naive antibody. We demonstrated that precise modeling of SHM, which requires the nucleotide context, provides a substantial amount of predictive power for predicting the course of affinity maturation. Notably, a simple nucleotide-based convolutional neural network modeling SHM outperformed state-of-the-art protein language models, including one trained exclusively on antibody sequences. Furthermore, incorporating estimates of selection based on a custom deep mutational scanning experiment brought only modest improvement in predictive power. To support further research, we introduce EPAM (Evaluating Predictions of Affinity Maturation), a benchmarking framework to integrate evolutionary principles with advances in language modeling, offering a road map for understanding antibody evolution and improving predictive models.