The rockefeller university

RNAs are remarkably versatile molecules that can fold into intricate three-dimensional (3D) structures to perform diverse cellular and viral functions. Despite their biological importance, relatively few RNA 3D structures have been solved, and our understanding of RNA structure-function relationships remains in its infancy. This limitation partly arises from challenges posed by RNA's complex conformational landscape, characterized by structural flexibility, formation of multiple states, and a propensity to misfold. Recently, cryoelectron microscopy (cryo-EM) has emerged as a powerful tool for the visualization of conformationally dynamic RNA- only 3D structures. However, RNA's characteristics continue to pose challenges. We discuss experimental methods developed to overcome these hurdles, including the engineering of modular modifications that facilitate the visualization of small RNAs, improve particle alignment, and validate structural models.

Chromothripsis describes the catastrophic shattering of mis-segregated chromosomes trapped within micronuclei. Although micronuclei accumulate DNA double-strand breaks and replication defects throughout interphase, how chromosomes undergo shattering remains unresolved. Using CRISPRCas9 screens, we identify a non-canonical role of the Fanconi anemia (FA) pathway as a driver of chromothripsis. Inactivation of the FA pathway suppresses chromosome shattering during mitosis without impacting interphase-associated defects within micronuclei. Mono-ubiquitination of FANCIFANCD2 by the FA core complex promotes its mitotic engagement with under-replicated micronuclear chromosomes. The structure-selective SLX4-XPF-ERCC1 endonuclease subsequently induces largescale nucleolytic cleavage of persistent DNA replication intermediates, which stimulates POLD3-dependent mitotic DNA synthesis to prime shattered fragments for reassembly in the ensuing cell cycle. Notably, FA-pathway-induced chromothripsis generates complex genomic rearrangements and extra- chromosomal DNA that confer acquired resistance to anti-cancer therapies. Our findings demonstrate how pathological activation of a central DNA repair mechanism paradoxically triggers cancer genome evolution through chromothripsis.

Pain management in amphibians is an emerging field of veterinary medicine with only a limited number of analgesics studied for their efficacy. The African-clawed frog, Xenopus laevis, is a popular animal model in research due to its oocyte morphology and embryonic development. We investigated analgesic effects of 2 formulations of meloxicam (standard and extended release [ER]) along with their pharmacokinetics and potential toxicity in this species. Adult female African-clawed frogs (n = 6/group) received either standard (0.2, 0.4, 1, or 5 mg/kg) or ER meloxicam (0.6, 1.2, 3, or 15 mg/kg) injected into the dorsal lymph sac. The acetic acid test (AAT) was performed at -1, 1, 6, 12, 24, 48, and 72 h postadministration to evaluate pain response. In addition, a subset of frogs (n = 2/group) were euthanized 72 h postinjection and submitted for necropsy. There were no significant differences in AAT with both formulations compared with saline control. No signs of meloxicam-induced toxicity with either formulation was present in histology. A pharmacokinetic study was conducted for both the standard and ER formulation of meloxicam at 5 and 15 mg/kg, respectively. Results were consistent with the fact that both formulations of meloxicam were readily absorbed with the standard plasma concentrations peaking at 20.40 mu g/mL at 2 h and ER plasma concentration at 30.4 mu g/mL at 12 h. The elimination half-life was only determinable for standard formulation (7.74 h). According to the AAT, both formulations of meloxicam did not provide effective analgesia in adult female Xenopus laevis despite reaching high plasma concentrations.

Two-particle correlations are presented for K-S(0), Lambda, and (Lambda) over bar strange hadrons as a function of relative momentum in lead-lead collisions at a nucleon-nucleon center-of-mass energy of 5.02 TeV. The dataset corresponds to an integrated luminosity of 0.607 nb(-1) and was collected using the CMS detector at the CERN LHC. These correlations are sensitive to quantum statistics and to final-state interactions between the particles. The source size extracted from the (KSKS0)-K-0 correlations is found to decrease from 4.6 to 1.6 fm in going from central to peripheral collisions. Strong interaction scattering parameters (i.e., scattering length and effective range) are determined from the Lambda K-S(0) and Lambda Lambda (including their charge conjugates) correlations using the Lednicky-Lyuboshitz model and are compared to theoretical and other experimental results.

How do neural circuits coordinate multiple behavioral responses to a single sensory cue? Here, we investigate how sweet taste drives appetitive behaviors in Drosophila, , including feeding, locomotor suppression, spatial preference, and associative learning. We find that neural circuits mediating different innate responses to sugar are partially overlapping and diverge at the second and third layers. Connectomic analyses reveal distinct subcircuits that mediate different behaviors. Connectome-based simulations of neuronal activity predict that second-order sugar neurons act synergistically to promote downstream activity and that bitter input overrides the sugar circuit through multiple pathways acting at third- and fourth-order neurons. Consistent with the latter prediction, optogenetic experiments suggest that bitter input inhibits third- and fourth-order sugar neurons to override the sugar pathway, whereas hunger and diet act earlier in the circuit to modulate behavior. Together, these studies provide insight into how circuits are organized to drive diverse behavioral responses to a single stimulus.

A search for electroweak production of a single vectorlike T quark in association with a bottom (b) quark in the all-hadronic decay channel is presented. This search uses proton-proton collision data at root s = 13 TeV collected by the CMS experiment at the CERN LHC during 2016-2018, corresponding to an integrated luminosity of 138 fb(-1). The T quark is assumed to have charge 2/3 and decay to a top (t) quark and a Higgs (H) or Z boson. Hadronic decays of the t quark and the H or Z boson are reconstructed from the kinematic properties of jets, including those containing b hadrons. No deviation from the standard model prediction is observed in the reconstructed tH and tZ invariant mass distributions. The 95% confidence level upper limits on the product of the production cross section and branching fraction of a T quark produced in association with a b quark and decaying via tH or tZ range from 1260 to 68 fb for T quark masses of 600-1200 GeV.

A search for Higgs boson pair (HH) production in association with a vector boson V (W or Z boson) is presented. The search is based on proton-proton collision data at a center-of-mass energy of 13 TeV, collected with the CMS detector at the LHC, corresponding to an integrated luminosity of 138 fb(-1). Both hadronic and leptonic decays of V bosons are used. The leptons considered are electrons, muons, and neutrinos. The HH production is searched for in the b (b) over barb (b) over bar decay channel. An observed (expected) upper limit at 95% confidence level of VHH production cross section is set at 294 (124) times the standard model prediction. Constraints are also set on the modifiers of the Higgs boson trilinear self-coupling, k(lambda), assuming k(2V) = 1, and vice versa on the coupling of two Higgs bosons with two vector bosons, k(2V). The observed (expected) 95% confidence intervals of these coupling modifiers are -37.7 < k(lambda) < 37.2 (-30.1 < k(lambda) < 28.9) and -12.2 < k(2V) < 13.5 (-7.2 < k(2V) < 8.9), respectively.

Despite therapeutic efficacy observed with immune checkpoint blockade in advanced melanoma, many tumors do not respond to treatment, representing a need for new therapies. Here, we have generated chimeric antigen receptor (CAR) T cells targeting TYRP1, a melanoma differentiation antigen expressed on the surface of melanomas, including rare acral and uveal melanomas. TYRP1-targeted CART cells demonstrate antigen-specific activation and cytotoxic activity in vitro and in vivo against human melanomas independent of the MHC alleles and expression. In addition, the toxicity to pigmented normal tissues observed with T lymphocytes expressing TYRP1-targeted TCRs was not observed with TYRP1-targeted CAR T cells. Anti-TYRP1 CAR T cells provide a novel means to target advanced melanomas, serving as a platform for the development of similar novel therapeutic agents and as a tool to interrogate the immunobiology of melanomas.

The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE similar to 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons similar to 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.

In eukaryotes, the leading strand DNA is synthesized by Pol epsilon and the lagging strand by Pol delta. These replicative polymerases have higher processivity when paired with the DNA clamp PCNA. While the structure of the yeast Pol epsilon catalytic domain has been determined, how Pol epsilon interacts with PCNA is unknown in any eukaryote, human or yeast. Here we report two cryo-EM structures of human Pol epsilon-PCNA-DNA complex, one in an incoming nucleotide bound state and the other in a nucleotide exchange state. The structures reveal an unexpected three-point interface between the Pol epsilon catalytic domain and PCNA, with the conserved PIP (PCNA interacting peptide)-motif, the unique P-domain, and the thumb domain each interacting with a different protomer of the PCNA trimer. We propose that the multi-point interface prevents other PIP-containing factors from recruiting to PCNA while PCNA functions with Pol epsilon. Comparison of the two states reveals that the finger domain pivots around the [4Fe-4S] cluster-containing tip of the P-domain to regulate nucleotide exchange and incoming nucleotide binding. In eukaryotes, the leading strand DNA polymerase Pol epsilon synthesises the DNA with higher processivity when in complex with the DNA clamp PCNA. Here, the authors report two cryo-EM structures of human Pol epsilon bound to the PCNA clamp and a DNA substate, revealing the conformational changes associated with incoming nucleotide binding.