5683099 research outputs found
Sort by
HLA-E/Mtb specific CD4+ and CD8+ T cells have a memory phenotype in individuals with TB infection.
No full textINTRODUCTION: Tuberculosis (TB) is the deadliest infectious disease worldwide and novel vaccines are urgently needed. HLA-E is a virtually monomorphic antigen presentation molecule and is not downregulated upon HIV co-infection. HLA-E restricted Mtb specific CD8+ T cells are present in the circulation of individuals with active TB (aTB) and Mtb infection (TBI) with or without HIV co-infection, making HLA-E restricted T cells interesting vaccination targets for TB. METHODS: Here, we performed in-depth phenotyping of HLA-E/Mtb specific and total T cell populations in individuals with TBI and in individuals with aTB or TBI and HIV using HLA-E/Mtb tetramers. RESULTS AND DISCUSSION: We show that HIV co-infection is the main driver in changing the memory distribution of HLA-E/Mtb specific CD4+ and CD8+ T cell subsets. HLA-E/Mtb specific CD4+ and CD8+ T cells were found to circulate with comparable frequencies in all individuals and displayed expression of KLRG1, PD-1 and 2B4 similar to that of total T cells. The presence of HLA-E/Mtb specific T cells in individuals with aTB and TBI highlights the potential of HLA-E as a vaccine target for TB
In preprints: oxygen and NFκB signals shift the timing of hindlimb formation.
No full textNo description supplie
A combined NMR and deep neural network approach for enhancing the spectral resolution of aromatic side chains in proteins.
No full textNuclear magnetic resonance (NMR) spectroscopy is an important technique for deriving the dynamics and interactions of macromolecules; however, characterizations of aromatic residues in proteins still pose a challenge. Here, we present a deep neural network (DNN), which transforms NMR spectra recorded on simple uniformly 13C-labeled samples to yield high-quality 1H-13C correlation maps of aromatic side chains. Key to the success of the DNN is the design of NMR experiments that produce data with unique features to aid the DNN produce high-resolution spectra. The methodology was validated experimentally on protein samples ranging from 7 to 40 kDa in size, where it accurately reconstructed multidimensional aromatic 1H-13C correlation maps, to facilitate 1H-13C chemical shift assignments and to quantify kinetics. More generally, we believe that the strategy of designing new NMR experiments in combination with customized DNNs represents a substantial advance that will have a major impact on the study of molecules using NMR in the years to come
Scaling OMERO for Histopathology and Beyond: Experiences from UCL
No full textThe Medical Imaging Research Software Group (MIRSG) within UCL’s Advanced Research Computing (ARC) Centre develops & supports research software & infrastructure for imaging.A core component is the provision of OMERO(Open Microscopy Environment) as a service, an open-source platform for managing, visualising & analysing microscopy data & metadata</p
A versatile platform for multispectralorganelle imaging and analysis
No full textPoster presented as part of the Crick BioImage Analysis Symposium 2025.Permission has been given by authors to upload to Crick Figshare.Copyright remains with the original authors.</p
How similar are the molecular mechanisms of yeast and metazoan genome replication initiation?
No full textDNA replication start sites are licensed for replication when two hexameric ring-shaped motors of the replicative helicase are loaded as an inactive double hexamer around duplex DNA. Activation requires untwisting of the double helix and ejection of one DNA strand from the central channel of each helicase ring. The process of replication initiation is best understood in yeast, thanks to reconstitution with purified yeast proteins, which allowed systematic structural analysis of the replication initiation process. Orthologs of most yeast replication factors have been identified in higher eukaryotes; however, reconstitution of metazoan replication initiation is still in its infancy, with double hexamer loading but not activation having been achieved. Nonetheless, artificial intelligence-driven structure prediction and cryo-EM studies on native complexes, combined with cell-based and cell-free approaches, are starting to provide insights into metazoan replication initiation mechanisms. Here, we describe the emerging picture
Dominance rank inference in mice via chemosensation
No full textSocial dominance hierarchies enable efficient resource allocation and conflict avoidance in animal communities.
1 Individuals can determine their relative status by tracking previous conflict outcomes, as seen in
aggression training2 and the winner effect,3,4 where successive wins increase the likelihood of future victories.
Repeated optogenetic stimulation of the dorsomedial prefrontal cortex (dmPFC) results in lasting
rank increases,5 suggesting that social rank is derived as a statistic of past outcomes. However, relative
rank could be assessed more efficiently by incorporating information about an opponent’s dominance status.
Pheromone signals, such as darcin, are enriched in the urine of dominant individuals,6–9 suggesting that hierarchical
behavior may integrate information about both own and opponent rank. Although prior studies
have explored the learning and neural representation of own rank,5,10,11 how opponent rank is detected
and encoded remains unclear. Here, we address this question in male mice using a tube test assay. We
show that stable hierarchies do not rely on fixed behavioral traits and that mice can infer the rank of unfamiliar
opponents by detecting scalable chemosensory rank cues. Sensory ablation experiments reveal that both
olfactory and vomeronasal cues are sufficient for rank assessment. Male mice thus use chemosensory signals
to infer dominance status during social interactions
Structural basis of Fanconi anemia pathway activation by FANCM.
No full textFANCM is crucial in genome maintenance, functioning in the Fanconi anemia (FA) pathway, alternative lengthening of telomeres (ALT), and replication fork protection. FANCM recognizes branched DNA structures and promotes their remodeling through ATP-dependent branch migration. The protein has emerged as a promising therapeutic target due to synthetic lethal interactions with BRCA1, SMARCAL1, and RAD52, and in ALT-positive cancers. Here we present crystal structures of FANCM's N-terminal ATP-dependent translocase domain (2.2 Å) and C-terminal FAAP24-bound region (2.4 Å), both complexed with branched DNA. Through structural analysis, biochemical reconstitution, and cellular studies, we demonstrate that FANCM employs two distinct mechanisms: an ATP-dependent branch migration activity essential for DNA damage survival, and a branched DNA-binding mode that enhances FANCD2-FANCI monoubiquitination through FA core complex interaction. The N-terminal translocase domain specifically recognizes DNA junctions through multiple key elements, while the C-terminal FAAP24-binding domain engages adjacent double-stranded DNA. Our results reveal how FANCM evolved from an ancient DNA repair motor into a sophisticated sensor that couples DNA damage recognition to selective pathway activation, providing a structural framework for developing targeted therapeutics
An Improved m6A-ELISA for quantifying N6-methyladenosine in Poly(A)-purified mRNAs
No full textN6-methyladenosine (m6A) is an abundant internal mRNA modification with roles in regulating cellular and organismal physiology, including development, differentiation, and disease. The deposition of m6A is highly regulated, with various m6A levels across different environmental conditions, cellular states, and cell types. Available methods for measuring bulk m6A levels are often time-consuming, have low throughput, and/or require specialized instrumentation or data analyses. Here, we present a detailed protocol for measuring bulk m6A levels in purified poly(A) RNA samples with m6A-ELISA using a standard-based approach. Critical steps of the protocol are highlighted and optimized, including poly(A) RNA quality controls and antibody specificity testing. The protocol is fast, scalable, adaptable, and cost-effective. It does not require specialized instrumentation, training, or skills in data analysis. We have successfully tested this protocol on mRNAs isolated from budding yeast and mouse cell lines
The DNA replication checkpoint prevents PCNA/RFC depletion to protect forks from HLTF-induced collapse in human cells
No full textThe DNA replication checkpoint is crucial for maintaining genome stability after genotoxic stress; without it, stalled DNA replication forks cannot restart normally, excess DNA replication origins are activated, DNA damage and single-stranded DNA (ssDNA) accumulate, S phase does not finish, and cells die. Preventing excess origin firing suppresses all these effects. Here, we show in human cells that when replication is not restrained by a functional checkpoint, excess DNA synthesis sequesters the processivity factor PCNA and its loader, replication factor C (RFC), preventing normal fork restart. Nascent DNA ends unprotected by RFC/PCNA are attacked by the helicase-like transcription factor (HLTF), causing irreversible replication fork collapse and hyperaccumulation of ssDNA. This explains how the checkpoint stabilizes stalled replication forks and has implications for how origin firing is normally coordinated with fork progression. Loss of HLTF suppresses fork collapse and cell lethality in checkpoint-deficient cells, which has implications for how resistance to anti-checkpoint therapies may arise