bluuebunny/crossref_metadata_2025 huggingface dataset:
Nipah virus from bats - another potential pandemic? Risk mapping the impact of anthropogenic and climate change on the transmission of Nipah virus infection to humans
Authors: Kumar Varsha Balachandra , Rooney Nicola J , Carr Andrew
Published: February 2022

The authors have withdrawn their manuscript as they are reviewing the study and the manuscript. Therefore, the authors do not wish this work to be cited as reference for the project. If you have anyquestions, please contact the corresponding author.
Estrogen receptor negative breast cancer incidence rates are similar in Ghanaian and Non-Hispanic Black women in the USA
Authors: Davis Lynn Brittny C , Figueroa Jonine , Awittor Fred Kwame , Ohene Oti Naomi O. , Edusei Lawrence , Titiloye Nicolas , Adjei Ernest , Addai Beatrice Wiafe , Adjei Robertson , Afriyie Lucy T. , Yarney Joel , Ansong Daniel , Wiafe Seth , Ahearn Thomas , Vanderpuye Verna , Dedey Florence , Brinton Louise A. , Awuah Baffour , Clegg-Lamptey Joe Nat , Abubakar Mustapha , Garcia-Closas Montserrat , Biritwum Richard , Graubard Barry I
Published: February 2022

Age-standardized incidence rates of estrogen receptor negative (ERN) breast cancers in the US are higher among Non-Hispanic Black (NHB) compared to Non-Hispanic White (NHW) women. We aimed to determine if incidence rates were similar between NHB and Ghanaians, given that a high proportion of NHB share West African genetic ancestry. We compared US rates (per 100,000 women) to those in Ghana, using data from US SEER, the Ghanaian census, and the Ghana Breast Health Study (GBHS), a population-based case-control study conducted between 2013-2015 in Accra and Kumasi. ERN age-standardized rates were similar among Ghanaian (40.7) and US NHB women (43.1), and both were higher compared to US NHW (24.0). Estrogen receptor-positive (ERP) rates were lower in Ghanaian (43.7) than US NHB (84.4), and highest in US NHW (128.5). Our data support higher ERN rates among women in Ghana similar to US NHB suggesting shared putative risk factors that require investigation.
Understanding the immunological landscape of England during SARS-CoV2 Omicron variant wave
Authors: Shingleton Joseph , Dyke Steven , Herrick Archie , Finnie Thomas
Published: February 2022

Understanding the scale of the threat posed by SARS-CoV2 B.1.1.529, or Omicron, variant formed a key problem in public health in the early part of 2022. Early evidence indicated that the variant was more transmissible and less severe than previous variants. As the virus was expected to spread quickly through the population of England, it was important that some understanding of the immunological landscape of the country was developed. This paper attempts to estimate the number of people with good immunity to the Omicron variant, defined as either recent infection with two doses of vaccine, or two doses of vaccine with a recent booster dose. To achieve this, we use a process of iterative proportional fitting to estimate the cell values of a contingency table, using national immunisation records and real-time model infection estimates as marginal values. Our results indicate that, despite the increased risk of immune evasion with the Omicron variant, a high proportion of England’s population had good immunity to the virus, particularly in older age groups. However, low rates of immunity in younger populations may allow endemic infection to persist for some time.
Seasonal dynamics and polyphenism of butterfly communities in the coastal plains of central Western Ghats, India
Authors: Naik Deepak , Rao R. Shyama Prasad , Kunte Krushnamegh , Mustak Mohammed S.
Published: February 2022

Long-term socioeconomic progress requires a healthy environment/ecosystem, but anthropogenic activities cause environmental degradation and biodiversity loss. Constant ecological monitoring is therefore necessary to assess the state of biodiversity and ecological health. However, baseline data is lacking even for ecologically sensitive regions such as the Western Ghats. We looked at the seasonality and polyphenism of butterflies of the central Western Ghats to get baseline population patterns on these charismatic taxa. We recorded 43118 individuals (175 species) using fortnightly time-constrained counts for two consecutive years, and found the peak abundance (49% of the total individuals) in post-monsoon period (Oct to Jan). The seasonal abundance was correlated with the overall increase in species richness. Habitat differences were stronger than seasonality as samples clustered based on sites. Several species also displayed polyphenism with distinct distributions of wet and dry season forms. Seasonal equitability and indicator species analysis showed distinct inter-species differences in seasonality patterns. This work provides key baseline data on the seasonal dynamics of butterflies of the Western Ghats in the context of climate change and conservation, and will help in future monitoring of this ecologically sensitive region using butterflies.
Intravesical BCG in patients with non-muscle invasive bladder cancer induces trained immunity and decreases respiratory infections
Authors: van Puffelen Jelmer H. , Novakovic Boris , van Emst Liesbeth , Kooper Denise , Zuiverloon Tahlita C.M. , Oldenhof Ursula T.H. , Witjes J. Alfred , Galesloot Tessel E. , Vrieling Alina , Aben Katja K.H. , Kiemeney Lambertus A.L.M. , Oosterwijk Egbert , Netea Mihai G. , Boormans Joost L. , van der Heijden Antoine G. , Joosten Leo A.B. , Vermeulen Sita H.
Published: February 2022

Bacillus Calmette-Guérin (BCG) is recommended as intravesical immunotherapy to reduce the risk of tumor recurrence in patients with non-muscle invasive bladder cancer (NMIBC). Currently, it is unknown whether intravesical BCG application induces trained immunity. Here, we found that intravesical BCG does induce trained immunity based on an increased production of TNF and IL-1β after heterologous ex-vivo stimulation of circulating monocytes 6- 12 weeks after intravesical BCG treatment; and a 37% decreased risk (OR 0.63 (95% CI 0.40- 1.01)) for respiratory infections in BCG-treated versus non-BCG-treated NMIBC patients. An epigenomics approach combining ChIP-sequencing and RNA-sequencing with in-vitro trained immunity experiments identified enhanced inflammasome activity in BCG-treated individuals. Finally, germline variation in genes that affect trained immunity was associated with recurrence and progression after BCG therapy in NMIBC, suggesting a link between trained immunity and oncological outcome.
Integrating phylogenetic and functional data in microbiome studies
Authors: Douglas Gavin M. , Hayes Molly G. , Langille Morgan G. I. , Borenstein Elhanan
Published: February 2022

Microbiome functional data are frequently analyzed to identify associations between microbial gene families and sample groups of interest. This is most often performed with approaches focused on the metagenome-wide relative abundance of microbial functions. Although such approaches can provide valuable insights, it is challenging to distinguish between different possible explanations for variation in community-wide functional profiles by considering functions alone. To help address this problem, we have developed a novel, phylogeny-aware framework to expand taxonomic balance tree-based approaches to identify enriched functions more robustly. The key focus of our approach, termed POMS, is on identifying functions that are consistently enriched in sample groups across independent taxonomic lineages. Based on simulated data we demonstrate that POMS can more accurately identify gene families that confer a selective advantage compared with commonly used differential abundance approaches. We also show that POMS can identify enriched functions in real-world metagenomics datasets that are potential targets of strong selection on multiple members of the microbiome. While this framework may not be able to identify all potential functional enrichments, the enrichments it does identify are more interpretable and conservative compared with those identified by existing differential abundance approaches. More generally, POMS is a novel approach for exploring microbiome functional data, which could be used to complement standard analyses. POMS is freely available as an R package at:https://github.com/gavinmdouglas/POMS.
Transcriptional response of a target plant to benzoxazinoid and diterpene allelochemicals highlights commonalities in detoxification
Authors: Knoch Eva , Kovács Judit , Deiber Sebastian , Shanmuganathan Reshi , Serra Núria Serra , Becker Claude , Schandry Niklas
Published: February 2022

Plants growing in proximity to other plants are exposed to a variety of metabolites that these neighbors release into the environment. Some species produce allelochemicals to inhibit growth of neighboring plants, which in turn have evolved ways to detoxify these compounds. In order to understand how the allelochemical-receiving target plants respond to chemically diverse compounds, we performed whole-genome transcriptome analysis ofArabidopsis thalianaexposed to either the benzoxazinoid derivative 2-amino-3H-phenoxazin-3-one (APO) or momilactone B. These two allelochemicals belong to two very different compound classes, benzoxazinoids and diterpenes, respectively, produced by different cereal crop species. Despite their distinct chemical nature, we observed similar molecular responses ofA. thalianato these allelochemicals. In particular, many of the same or closely related genes belonging to the three-phase detoxification pathway were upregulated in both treatments. Further, we observed an overlap between genes upregulated by allelochemicals and those involved in herbicide detoxification. Our findings highlight the overlap in the transcriptional response of a target plant to natural and synthetic phytotoxic compounds and illustrate how herbicide resistance could arise via pathways involved in plant-plant interaction.
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

During 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

Mutations 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 Statement

Partial 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

The 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

Current 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

Imaging 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.

Methods

The 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.

Results

OncoFAP 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.

Conclusions

177Lu-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

In 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

Autosomal 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

Pervasive 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

Uterine 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

Episodic 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

The 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

Recycling 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

It 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

Omics-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

Temperature 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.
Transcriptional profiling of transport mechanisms and regulatory pathways in rat choroid plexus
Authors: Andreassen Søren N. , Toft-Bertelsen Trine L. , Wardman Jonathan H. , Villadsen Rene , MacAulay Nanna
Published: February 2022

Background

Dysregulation of brain fluid homeostasis associates with brain pathologies in which fluid accumulation leads to elevated intracranial pressure. Surgical intervention remains standard care, since specific and efficient pharmacological treatment options are limited for pathologies with disturbed brain fluid homeostasis. Such lack of therapeutic targets originates, in part, from the incomplete map of the molecular mechanisms underlying cerebrospinal fluid (CSF) secretion by the choroid plexus.

Methods

The transcriptomic profile of rat choroid plexus was generated by RNA Sequencing (RNAseq) of whole tissue and epithelial cells captured by fluorescence-activated cell sorting (FACS), and compared to proximal tubules. The bioinformatic analysis comprised mapping to reference genome followed by filtering for type, location, and association with alias and protein function. The transporters and associated regulatory modules were arranged in discovery tables according to their transcriptional abundance and tied together in association network analysis.

Results

The transcriptomic profile of choroid plexus displays high similarity between sex and species (human, rat, and mouse) and lesser similarity to another secretory epithelium, the proximal tubules. The discovery tables provide lists of transport mechanisms that could participate in CSF secretion and suggest regulatory candidates.

Conclusions

With quantification of the transport protein abundance in choroid plexus and their potentially linked regulatory modules, we envision a molecular tool to devise rational hypotheses regarding future delineation of choroidal transport proteins involved in CSF secretion and their regulation. Our vision is to obtain pharmaceutical targets towards modulation of CSF production in pathologies involving disturbed brain water dynamics.
Photoreceptors generate neuronal diversity in their target field through a Hedgehog morphogen gradient in Drosophila
Authors: Bostock Matthew P. , Prasad Anadika R. , Donoghue Alicia , Fernandes Vilaiwan M.
Published: February 2022

Defining the origin of neuronal diversity is a major challenge in developmental neurobiology. The Drosophila visual system is an excellent paradigm to study how cellular diversity is generated. Photoreceptors from the eye disc grow their axons into the optic lobe and secrete Hedgehog (Hh) to induce the lamina, such that for every unit eye there is a corresponding lamina unit made up of post-mitotic precursors stacked into columns. Each differentiated column contains five lamina neuron types (L1-L5), making it the simplest neuropil in the optic lobe, yet how this diversity is generated was unknown. Here, we found that Hh pathway activity is graded along the distal-proximal axis of lamina columns and further determined that this gradient in pathway activity arises from a gradient of Hh ligand. We manipulated Hh pathway activity cell-autonomously in lamina precursors and non-cell autonomously by inactivating the Hh ligand, and by knocking it down in photoreceptors. These manipulations showed that different thresholds of activity specify unique cell identities, with more proximal cell types specified in response to progressively lower Hh levels. Thus, our data establish that Hh acts as a morphogen to pattern the lamina. Although, this is the first such report during Drosophila nervous system development, our work uncovers a remarkable similarity with the vertebrate neural tube, which is patterned by Sonic Hedgehog. Altogether, we show that differentiating neurons can regulate the neuronal diversity of their distant target fields through morphogen gradients.
HIV-1 Vpu restricts Fc-mediated effector functions in vivo
Authors: Prévost Jérémie , Anand Sai Priya , Rajashekar Jyothi Krishnaswamy , Richard Jonathan , Goyette Guillaume , Medjahed Halima , Gendron-Lepage Gabrielle , Chen Hung-Ching , Chen Yaozong , Horwitz Joshua A. , Grunst Michael W. , Zolla-Pazner Susan , Haynes Barton F. , Burton Dennis R. , Flavell Richard A. , Kirchhoff Frank , Hahn Beatrice H. , Smith Amos B. , Pazgier Marzena , Nussenzweig Michel C. , Kumar Priti , Finzi Andrés
Published: February 2022

Non-neutralizing antibodies (nnAbs) can eliminate HIV-1-infected cells via antibody-dependent cellular cytotoxicity (ADCC) and were identified as a correlate of protection in the RV144 vaccine trial. Fc-mediated effector functions of nnAbs were recently shown to alter the course of HIV-1 infection in vivo using a vpu-defective virus. Since Vpu is known to downregulate cell surface CD4, which triggers conformational changes in the viral envelope glycoprotein (Env), we ask whether the lack of Vpu expression was linked to the observed nnAbs activity. We found that restoring Vpu expression greatly reduces nnAb recognition of infected cells, rendering them resistant to ADCC responses. Moreover, administration of a nnAb in humanized mice reduces viral loads only in animals infected with a vpu-defective but not with a wildtype virus. Finally, nnAb Fc-effector functions are observed only on cells expressing Env in the “open” conformation. This work highlights the importance of Vpu-mediated evasion of humoral responses.
A model for the propagation of seizure activity in normal brain tissue
Authors: Depannemaecker Damien , Carlu Mallory , Bouté Jules , Destexhe Alain
Published: February 2022

Epilepsies are characterized by paroxysmal electrophysiological events and seizures, which can propagate across the brain. One of the main unsolved questions in epilepsy is how epileptic activity can invade normal tissue and thus propagate across the brain. To investigate this question, we propose three computational models at the neural network scale to study the underlying dynamics of seizure propagation, understand which specific features play a role, and relate them to clinical or experimental observations. We consider both the internal connectivity structure between neurons and the input properties in our characterization. We show that a paroxysmal input is sometimes controlled by the network while in other instances, it can entrain the network activity to itself produce paroxysmal activity, and thus will further propagate to efferent networks. We further show how the details of the network architecture are essential to determine this switch to a seizure-like regime. We investigated the nature of the instability involved and in particular found a central role for the inhibitory connectivity.

We propose a probabilistic approach to the propagative/non-propagative scenarios, which may serve as a guide to control the seizure by using appropriate stimuli.

Significance

Our computational study shows the specific role that the inhibitory population can have and the possible dynamics regarding the propagation of seizure-like behavior in three different neuronal networks. We find that both structural and dynamical aspects are important to determine whether seizure activity invades the network.

We show the existence of a specific time window favorable to the reversal of the seizure propagation by appropriate stimuli.
AFM Microfluidic Cantilevers as Weight Sensors for Live Single Cell Mass Measurements
Authors: Chien Chen-Chi , Jiang Jiaxin , Gong Bin , Li Tao , Gaitas Angelo
Published: February 2022

Reliably measuring small mass changes at the single-cell level is challenging. In this manuscript, we report the use of microfluidic cantilevers in liquid with sub-nanogram scale weight sensing capability for the measurement of cellular mass changes of living single cells. With this instrumentation, we were able to perform fast mass measurements within 3 minutes. We show results of mass measurements of polystyrene and metal beads of various sizes (smallest weight measured at 280 ± 95 pg) and live single-cell mass measurements in a physiologically relevant environment. We also performed finite element analysis to simulate and optimize the structural design and materials of cantilevers. Our simulation results indicate that using polymer materials, such as SU8 and polyimide, could improve the minimal detectable mass by 3-fold compared to conventional silicon cantilevers. The simulations also suggest that smaller dimensions of length, width, and thickness would improve the mass detection capability of microfluidic cantilevers.
Microglia reactivity entails microtubule remodeling from acentrosomal to centrosomal arrays
Authors: Rosito Maria , Sanchini Caterina , Gosti Giorgio , Moreno Manuela , De Panfilis Simone , Giubettini Maria , Debellis Doriana , Catalano Federico , Peruzzi Giovanna , Marotta Roberto , Indrieri Alessia , De Leonibus Elvira , De Stefano Maria Egle , Ragozzino Davide , Ruocco Giancarlo , Di Angelantonio Silvia , Bartolini Francesca
Published: February 2022

Microglia reactivity entails a large-scale remodeling of cellular geometry, but the role of the microtubule cytoskeleton during these changes remains unexplored. Here we show that reactive proinflammatory microglia provide a heretofore unique example of microtubule reorganization from a non-centrosomal array of parallel and stable microtubules to a radial array of more dynamic microtubules. While in the homeostatic state microglia nucleate microtubules at Golgi outposts, proinflammatory signaling induces recruitment of nucleating material nearby the centrosome and inhibition of centrosomal maturation enhances NLRP3 inflammasome activation and secretion of IL-1β. Our results demonstrate that a hallmark of microglia reactivity is a striking remodeling of the microtubule cytoskeleton and suggest that pericentrosomal microtubule nucleation may serve as a distinct marker of microglia activation as well as a novel target to modulate cytokine-mediated inflammatory responses in chronic disease and tissue injury.
Activation of Nedd4L Ubiquitin Ligase by FCHO2-generated Membrane Curvature
Authors: Sakamoto Yasuhisa , Uezu Akiyoshi , Kikuchi Koji , Suetsugu Shiro , Nakanishi Hiroyuki
Published: February 2022

The C2-WW-HECT domain ubiquitin ligase Nedd4L regulates sorting in endocytosis by mediating ubiquitination of cargo molecules, such as the epithelial sodium channel (ENaC). Defects in ENaC ubiquitination cause Liddle syndrome, a hereditary hypertension. Nedd4L is catalytically autoinhibited by an intramolecular interaction between the C2 and HECT domains, but the activation mechanism is poorly understood. Here, we show that Nedd4L is activated by membranes sculpted by FCHO2, a Bin-Amphiphysin-Rsv (BAR) domain protein that regulates endocytosis. We found that FCHO2 was required for Nedd4L-mediated ubiquitination and endocytosis of ENaC. Nedd4L co-localized with FCHO2 at clathrin-coated pits where it likely became activated. Nedd4L was specifically recruited to and activated by the FCHO2 BAR domain exogenously expressed in cells. Furthermore, we reconstitutedin vitroFCHO2-induced recruitment and activation of Nedd4L. Both the recruitment and activation were mediated by membrane curvature rather than protein–protein interactions. The Nedd4L C2 domain recognized a specific degree of membrane curvature that was generated by the FCHO2 BAR domain. Consequently, this curvature activated Nedd4L by relieving autoinhibition. Thus, we show for the first time a specific functionality (i.e., recruitment and activation of an enzyme regulating cargo sorting) of membrane curvature by a BAR domain protein.
The inner workings of replisome-dependent control of DNA damage tolerance
Authors: Zhang Tianpeng , Greenberg Roger A.
Published: February 2022

Genomic DNA is continuously challenged by endogenous and exogenous sources of damage. The resulting lesions may act as physical blocks to DNA replication, necessitating repair mechanisms to be intrinsically coupled to the DNA replisome machinery. DNA damage tolerance (DDT) is comprised of translesion synthesis (TLS) and template switch (TS) repair processes that allow the replisome to bypass of bulky DNA lesions and complete DNA replication. How the replisome orchestrates which DDT repair mechanism becomes active at replication blocks has remained enigmatic. In this issue of Genes & Development, Dolce and colleagues (pp. 167–179) report that parental histone deposition by replisome components Ctf4 and Dpb3/4 promotes TS while suppressing error-prone TLS. Deletion of Dpb3/4 restored resistance to DNA-damaging agents in ctf4Δ cells at the expense of synergistic increases in mutagenesis due to elevated TLS. These findings illustrate the importance of replisome-directed chromatin maintenance to genome integrity and the response to DNA-damaging anticancer therapeutics.
Human pre-mRNA 3′ end processing: reconstituting is believing
Authors: Yoon Yoseop , Shi Yongsheng
Published: February 2022

It is every biochemist's dream to reconstitute a biological process in vitro using defined components, because doing so not only reduces a biological phenomenon to one or a series of biochemical reactions, but also defines the minimal list of essential components. In this issue of Genes & Development, Boreikaite and colleagues (pp. 210–224) and Schmidt and colleagues (pp. 195–209) report their independent reconstitution of human pre-mRNA 3′ end processing.
Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
Authors: Li Qianru , Yang Haiwang , Stroup Emily K. , Wang Hongbin , Ji Zhe
Published: February 2022

We describe a low-input RNase footprinting approach for the rapid quantification of ribosome-protected fragments with as few as 1000 cultured cells. The assay uses a simplified procedure to selectively capture ribosome footprints based on optimized RNase digestion. It simultaneously maps cytosolic and mitochondrial translation with single-nucleotide resolution. We applied it to reveal selective functions of the elongation factor TUFM in mitochondrial translation, as well as synchronized repression of cytosolic translation after TUFM perturbation. We show the assay is applicable to small amounts of primary tissue samples with low protein synthesis rates, including snap-frozen tissues and immune cells from an individual's blood draw. We showed its feasibility to characterize the personalized immuno-translatome. Our analyses revealed that thousands of genes show lower translation efficiency in monocytes compared with lymphocytes, and identified thousands of translated noncanonical open reading frames (ORFs). Altogether, our RNase footprinting approach opens an avenue to assay transcriptome-wide translation using low-input samples from a wide range of physiological conditions.