bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the ribosome function from the structures of non-arrested ribosome nascent chain complexes
Authors: Syroegin Egor A. , Aleksandrova Elena V. , Polikanov Yury S. 
Published: February 2022

ABSTRACTDuring protein synthesis, the growing polypeptide chain threads through the nascent peptide exit tunnel that spans the body of the large ribosomal subunit while simultaneously acting as a modulator of ribosomal activity by itself or by sensing various small molecules, such as metabolites or antibiotics appearing in the tunnel. While arrested ribosome nascent chain complexes (RNCCs) have been extensively studied structurally, little attention has been given to the RNCCs that represent the functionally active state of the ribosome. This is in part due to the lack of a simple and reliable procedure for the large-scale preparation of peptidyl-tRNAs. Here we report a new chemoenzymatic approach based on native chemical ligation reaction for the facile synthesis of stably linked peptidyl-tRNAs that were used to determine several structures of RNCCs in the functional pre-attack state of the peptidyl transferase center (PTC) at the highest resolution available to date. These structures reveal a previously unknown role of the ribosome in stabilization of the growing polypeptide within the PTC and suggest an extended entropic trap model that mechanistically rationalizes how ribosome acts with comparable efficiencies upon a multitude of possible growing peptides having various sequences. Our structures also provide new insights into the mechanism of PTC functioning and explain what makes ribosome a versatile catalyst.
Structural and functional determinants inferred from deep mutational scans
Authors: Bajaj Priyanka , Manjunath Kavyashree , Varadarajan Raghavan 
Published: February 2022

ABSTRACTMutations that affect protein binding to a cognate partner primarily occur either at buried residues or at exposed residues directly involved in partner binding. Distinguishing between these two categories based solely on mutational phenotypes is challenging. The bacterial toxin CcdB kills cells by binding to DNA Gyrase. Cell death is prevented by binding to its cognate antitoxin CcdA, at an extended interface that partially overlaps with the GyrA binding site. Using the CcdAB toxin-antitoxin (TA) system as a model, a comprehensive site-saturation mutagenesis library of CcdB was generated in its native operonic context. The mutational sensitivity of each mutant was estimated by evaluating the relative abundance of each mutant in two strains, one resistant and the other sensitive to the toxic activity of the CcdB toxin, through deep sequencing. The ability to bind CcdA was inferred through a RelE reporter gene assay, since the CcdAB complex binds to its own promoter, repressing transcription. By analysing mutant phenotypes in the CcdB sensitive, CcdB resistant and RelE reporter strains, it was possible to assign residues to buried, CcdA interacting or GyrA interacting sites. A few mutants were individually constructed, expressed, and biophysically characterised to validate molecular mechanisms responsible for the observed phenotypes. Residues inferred to be important for antitoxin binding, are also likely to be important for rejuvenating CcdB from the CcdB-Gyrase complex. Therefore, even in the absence of structural information, when coupled to appropriate genetic screens, such high-throughput strategies can be deployed for predicting structural and functional determinants of proteins.Broader Impact StatementPartial loss-of-function mutations predominantly occur either at buried-site or exposed, active-site residues. We report a facile method to identify multiple binding sites for different interacting partners for a protein, and distinguish them from buried site and exposed non active-site residues, solely from mutational data.
Molecular Signatures and Cellular Diversity During Mouse Habenula Development
Authors: van de Haar Lieke L. , Riga Danai , Boer Juliska E. , Adolfs Youri , Sieburgh Thomas E. , van Dijk Roland E. , Watanabe Kyoko , van Kronenburg Nicky C.H. , Broekhoven Mark H. , Posthuma Danielle , Meye Frank J. , Basak Onur , Pasterkamp R. Jeroen 
Published: February 2022

SUMMARYThe habenula plays a key role in various motivated and pathological behaviors and is composed of molecularly distinct neuron subtypes. Despite progress in identifying mature habenula neuron subtypes, how these subtypes develop and organize into functional brain circuits remains largely unknown. Here we performed single-cell transcriptional profiling of mouse habenular neurons at critical developmental stages instructed by detailed three-dimensional anatomical data. Our data reveal cellular and molecular trajectories during embryonic and postnatal development leading to different habenular subtypes. Further, based on this analysis our work establishes the distinctive functional properties and projection target of a previously uncharacterized subtype of Cartpt+ habenula neurons. Finally, we show how comparison of single-cell transcriptional profiles and GWAS data links specific developing habenular subtypes to psychiatric disease. Together, our study begins to dissect the mechanisms underlying habenula neuron subtype-specific development and creates a framework for further interrogation of habenular development in normal and disease states.
An Improved Linear Mixed Model for Multivariate Genome-Wide Association Studies
Authors: Wang Dan , Teng Jun , Zhao Changheng , Zhang Xinhao , Tang Hui , Fan Xinzhong , Xu Shizhong , Zhang Qin , Ning Chao 
Published: February 2022

AbstractCurrent methods of multivariate analysis require complete multivariate phenotypes from each individual and have a computational time complexity of O(n2) per SNP, where n is the sample size. We develop an efficient genomic multivariate analysis tool (GMAT) for genome-wide association studies of multiple correlated traits. The new method can handle incomplete multivariate data with missing records and reduce the time complexity to O(n) per SNP. Simulation studies based on known genotypes and phenotypes of actual populations show that GMAT has increased the statistical power with a proper control of false positivity for association studies compared to the conventional linear mixed model (LMM) that removes individuals with incomplete records. Applications to a balanced donkey data and an unbalanced yeast data show that the computational efficiency of the new method has been increased about tens of times faster than the conventional LMM analysis. The GMAT package can be downloaded at https://github.com/chaoning/GMAT.
A novel dimeric FAP-targeting small molecule-radio conjugate with high and prolonged tumour uptake
Authors: Galbiati Andrea , Zana Aureliano , Bocci Matilde , Millul Jacopo , Elsayed Abdullah , Mock Jacqueline , Neri Dario , Cazzamalli Samuele 
Published: February 2022

ABSTRACTImaging procedures based on small molecule-radio conjugates (SMRCs) targeting fibroblast activation protein (FAP) have recently emerged as a powerful tool for the diagnosis of a wide variety of tumours. However, the therapeutic potential of radiolabeled FAP-targeting agents is limited by their short residence time in neoplastic lesions. In this work, we present the development and in vivo characterization of BiOncoFAP, a new dimeric FAP-binding motif with extended tumour residence time and favorable tumour-to-organ ratio.MethodsThe binding properties of BiOncoFAP and its monovalent OncoFAP analogue were assayed against recombinant hFAP. Preclinical experiments with [177Lu]Lu-OncoFAP-DOTAGA (177Lu-OncoFAP) and [177Lu]Lu-BiOncoFAP-DOTAGA (177Lu-BiOncoFAP) were performed in mice bearing FAP-positive HT-1080 tumours.ResultsOncoFAP and BiOncoFAP displayed comparable sub-nanomolar dissociation constants towards hFAP in solution, but the bivalent BiOncoFAP bound more avidly to the target immobilized on solid supports. In a comparative biodistribution study, 177Lu-BiOncoFAP exhibited a more stable and prolonged tumour uptake than 177Lu-OncoFAP (∼20% ID/g vs ∼4% ID/g, at 24h p.i., respectively). Notably, 177Lu-BiOncoFAP showed favorable tumour-to-organ ratios with low kidney uptake. Both 177Lu-OncoFAP and 177Lu-BiOncoFAP displayed potent anti-tumour efficacy when administered at therapeutic doses in tumour bearing mice.Conclusions177Lu-BiOncoFAP is a promising candidate for radioligand therapy of cancer, with favorable in vivo tumour-to-organ ratio, long tumour residence time and potent anti-cancer efficacy.
Novel Mathematical Model Based on Cellular Automata for Study of Alzheimer’s Disease Progress
Authors: Jafari Niloofar , Sarbaz Yashar , Ebrahimi-kalan Abbas , Golabi Faegheh 
Published: February 2022

AbstractIn recent years, extensive research has been done for the prediction, treatment, and recognition of Alzheimer’s disease (AD). Among these scientific works, mathematical modeling of AD is an efficient way to study the influence of various parameters such as drugs on AD progression. This paper proposes a novel model based on Cellular Automata (CA), a powerful collection of colored cells, for the investigation of AD progress. In our model, the synapses of each neuron have been considered as square cells located around the central cell. The key parameter for the progression of AD in our model is the amount of amyloid-β (Aβ), which is calculated by differential rate equations of the Puri-Li model. Based on the proposed model in this article, we introduce a new definition of AD Rate for a M × L-neuron network, which can be expanded for the whole space of the hippocampus. To better illustrate the mechanism of this model, we simulate a 3×3 neuron network and discuss the obtained results. Our numerical results show that the variations of some parameters have a great effect on AD progress. For instance, it is obtained that AD Rate is more sensitive to astroglia variations, in comparison to microglia variations. The presented model can improve the scientist's insight into the progress of AD, which will assist them to effectively consider the influence of various parameters on AD.
Closely related type II-C Cas9 orthologs recognize diverse PAMs
Authors: Wei Jingjing , Hou Linghui , Liu Jingtong , Gao Siqi , Qi Tao , Sun Shuna , Wang Yongming 
Published: February 2022

AbstractAutosomal dominant diseases can be treated by allele-specific disruption of mutant alleles. If the missense mutation generates a novel protospacer-adjacent motif (PAM), CRISPR-Cas9 can distinguish mutant alleles from wild-type alleles by a PAM-specific approach. Therefore, it is crucial to develop a CRISPR toolbox capable of recognizing multiple PAMs. Here, by using a GFP-activation assay, we tested the activities of 29 type II-C orthologs closely related to Nme1Cas9, 25 of which are active in human cells. These orthologs recognize diverse PAMs with variable length and nucleotide preference, including purine-rich, pyrimidine-rich, and mixed purine and pyrimidine PAMs. We characterized in depth the activity and specificity of Nsp2Cas9. We also generated a chimeric Cas9 nuclease that recognizes a simple N4C PAM, representing the most relaxed PAM preference for compact Cas9s to date. These Cas9 nucleases significantly enhance our ability to perform allele-specific genome editing.
Antisense non-coding transcription represses the PHO5 model gene at the level of promoter chromatin structure
Authors: Novačić Ana , Menéndez Dario , Ljubas Jurica , Barbarić Slobodan , Stutz Françoise , Soudet Julien , Stuparević Igor 
Published: February 2022

AbstractPervasive transcription of eukaryotic genomes generates non-coding transcripts with regulatory potential. We examined the effects of non-coding antisense transcription on the regulation of expression of the yeast PHO5 gene, a paradigmatic case for gene regulation through promoter chromatin remodeling. A negative role for antisense transcription at the PHO5 gene locus was demonstrated by leveraging the level of overlapping antisense transcription through specific mutant backgrounds, expression from a strong promoter in cis, and use of the CRISPRi system. Furthermore, we showed that enhanced elongation of PHO5 antisense leads to a more repressive chromatin conformation at the PHO5 gene promoter, which is more slowly remodeled upon gene induction. The negative effect of antisense transcription on PHO5 gene transcription is mitigated upon inactivation of the histone deacetylase Rpd3, showing that PHO5 antisense RNA acts via histone deacetylation. This regulatory pathway leads to Rpd3-dependent decreased recruitment of the RSC chromatin remodeling complex to the PHO5 gene promoter upon induction of antisense transcription. Overall, the data in this work reveal an additional level in the complex regulatory mechanism of PHO5 gene expression by showing antisense transcription-mediated repression at the level of promoter chromatin structure remodeling.
Dynamic changes in uterine NK cell subset frequency and function over the menstrual cycle and pregnancy
Authors: Whettlock Emily M , Woon Ee Von , Cuff Antonia O , Browne Brendan , Johnson Mark R , Male Victoria 
Published: February 2022

AbstractUterine Natural Killer cells (uNK) play an important role in promoting successful pregnancy by regulating trophoblast invasion and spiral artery remodelling in the first trimester. Recently, single cell RNA sequencing (scRNAseq) on first trimester decidua showed that uNKs can be divided into three subsets, which may have different roles in pregnancy. Here we present an integration of previously published scRNAseq datasets, together with novel flow cytometry data to interrogate the frequency, phenotype and function of uNK1-3 in seven stages of the reproductive cycle (menstrual, proliferative, secretory phases; first, second, third trimester; and postpartum). We found that uNK1 and −2 peak in the first trimester, but by the third trimester the majority of uNK are uNK3. All three subsets are most able to degranulate and produce cytokines during the secretory phase of the menstrual cycle and express KIR2D molecules, which allow them to interact with HLA-C expressed by placental extravillous trophoblast cells, at the highest frequency during the first trimester. Taken together, our findings suggest that uNK are particularly active and able to interact with placental cells at the time of implantation, and that uNK1 and 2 may be particularly involved in these processes. Our findings are the first to establish how uNK frequency and function changes dynamically across the healthy reproductive cycle. This serves as a platform from which the relationship between uNK function and impaired implantation and placentation can be investigated. This will have important implications for the study of subfertility, recurrent miscarriage, pre-eclampsia and pre-term labour.
Pattern reinstatement and attentional control: overlapping processes during episodic long-term memory retrieval
Authors: Sabo Melinda , Schneider Daniel 
Published: February 2022

AbstractEpisodic long-term memory (eLTM) retrieval involves the reinstatement of neural patterns from the encoding phase. However, recent evidence suggests that comparable effects on cortical activity patterns can also be linked to attentional control processes on the level of memory representations. The current investigation assesses these two processes independently based on alpha-beta-band activity in the electroencephalogram (EEG). During encoding, subjects were presented with an object on a certain position on the screen and had to imagine it on a new position. In each trial, either the task-irrelevant presentation position or the task- relevant imagination position was lateralized. In the retrieval phase, subjects first made an old/new judgement based on centrally presented objects and then reported the imagination position. Pattern reinstatement should be reflected in similar lateralized alpha-beta activity during encoding and retrieval. Conversely, the influence of attentional control processes during retrieval would be associated with the suppression of alpha-beta power contralateral to the to-be-reported imagination position and with the increase of activity contralateral to the irrelevant presentation position. Our results support this latter pattern. This shows that an experimental differentiation between selective attention and pattern reinstatement processes is necessary when studying the neural basis of eLTM retrieval on cortical level.
Structural basis for the activation and ligand recognition of the human oxytocin receptor
Authors: Waltenspühl Yann , Ehrenmann Janosch , Vacca Santiago , Thom Cristian , Medalia Ohad , Plückthun Andreas 
Published: February 2022

AbstractThe small cyclic neuropeptide hormone oxytocin (OT) and its cognate receptor play a central role in the regulation of social behaviour and sexual reproduction. Here we report the single-particle cryo-electron microscopy structure of the active oxytocin receptor (OTR) in complex with its cognate ligand oxytocin. Our structure provides high-resolution insights into the OT binding mode, the OTR activation mechanism as well as the subtype specificity within the oxytocin/vasopressin receptor family.
GCNA is a histone binding protein required for spermatogonial stem cell maintenance
Authors: Ribeiro Jonathan , Crossan Gerry P. 
Published: February 2022

AbstractRecycling and de-novo deposition of histones during DNA replication is a critical challenge faced by eukaryotic cells and is coordinated by histone chaperones. However, little is known about how tissue-specific histone chaperones function to maintain tissue homeostasis. Here we show that Germ Cell Nuclear Acidic protein (GCNA), a germ cell specific protein in adult mice, can bind histones and purified GCNA exhibits histone chaperone activity. GCNA associates with the DNA replication machinery and supports progression through S-phase in murine spermatogonial stem cells (SSCs). Whilst GCNA is dispensable for embryonic germ cell development, it is required for the maintenance of the SSC pool and for long-term production of sperm. Our work describes the role of a germ cell specific histone chaperone in SSCs maintenance in mice. These findings provide a mechanistic basis for the male infertility observed in patients carrying mutations in the GCNA locus.
Cochlear theta activity oscillates in phase opposition during interaural attention
Authors: Köhler Moritz Herbert Albrecht , Weisz Nathan 
Published: February 2022

AbstractIt is widely established that sensory perception is a rhythmic process as opposed to a continuous one. In the context of auditory perception this effect is only established on a cortical and behavioral level. Yet, the unique architecture of the auditory sensory system allows its primary sensory cortex to modulate the processes of its sensory receptors at the cochlear level. Previously, we could demonstrate the existence of a genuine cochlear theta (~6 Hz) rhythm that is modulated in amplitude by intermodal selective attention. As the study’s paradigm was not suited to assess attentional effects on the oscillatory phase of cochlear activity the question whether attention can also affect the temporal organization of the cochlea’s ongoing activity remained open. The present study utilizes an interaural attention paradigm to investigate ongoing otoacoustic activity during a stimulus-free cue-target interval and an omission period of the auditory target in humans. We were able to replicate the existence of the cochlear theta rhythm. Importantly, we found significant phase opposition between the two ears and attention conditions of anticipatory as well as cochlear oscillatory activity during target presentation. Yet, the amplitude was unaffected by interaural attention. These results are the first to demonstrate that intermodal and interaural attention deploy different aspects of excitation and inhibition at the first level of auditory processing. While intermodal attention modulates the level of cochlear activity, interaural attention modulates the timing.
Decoding mechanism of action and susceptibility to drug candidates from integrated transcriptome and chromatin state
Authors: Carraro Caterina , Bonaguro Lorenzo , Schulte-Schrepping Jonas , Horne Arik , Oestreich Marie , Warnat-Herresthal Stefanie , Helbing Tim , Franco Michele De , Händler Kristian , Mukherjee Sach , Ulas Thomas , Gandin Valentina , Göttlich Richard , Aschenbrenner Anna C. , Schultze Joachim L. , Gatto Barbara 
Published: February 2022

AbstractOmics-based technologies are driving major advances in precision medicine but efforts are still required to consolidate their use in drug discovery. In this work, we exemplify the use of multi-omics to support the development of 3-chloropiperidines (3-CePs), a new class of candidate anticancer agents. Combined analyses of transcriptome and chromatin accessibility elucidated the mechanisms underlying sensitivity to test agents. Further, we implemented a new versatile strategy for the integration of RNA-seq and ATAC-seq data, able to accelerate and extend the standalone analyses of distinct omic layers. This platform guided the construction of a perturbation-informed basal signature able to predict cancer cell lines’ sensitivity and to further direct compound development against specific tumor types. Overall, this approach offered a scalable pipeline to support the early phases of drug discovery, understanding of mechanism and potentially inform the positioning of therapeutics in the clinic.
The cellular coding of temperature in the mammalian cortex
Authors: Vestergaard M. , Carta M. , Poulet J.F.A. 
Published: February 2022

SummaryTemperature is a fundamental sensory modality separate from touch, with dedicated receptor channels and primary afferent neurons for cool and warm (Blix, 1882; Filingeri, 2016; Vriens et al., 2014). Unlike other modalities, however, the cortical encoding of temperature remains mysterious, with very few cortical neurons reported that respond to non-painful temperature and the presence of a ‘thermal cortex’ is debated (Bokiniec et al., 2018; Craig et al., 2000; Hellon et al., 1973; Milenkovic et al., 2014; Tsuboi et al., 1993). Using widefield and two-photon calcium imaging in the mouse forepaw system, here we identify cortical neurons that respond to cooling and/or warming with distinct spatial and temporal response properties. Surprisingly, we observed a representation of cool, but not warm, in the primary somatosensory cortex, but cool and warm in the posterior insular cortex (pIC). The representation of thermal information in pIC is robust, somatotopicallyarranged and reversible manipulations show a profound impact on thermal perception. Intriguingly, despite being positioned along the same one-dimensional sensory axis, the encoding of cool and warm is distinct, both in highly- and broadly- tuned neurons. Together, our results show that pIC contains the primary cortical representation of skin temperature and may help explain how the thermal system generates sensations of cool and warm.