bluuebunny/crossref_metadata_2025 huggingface dataset:
Consistency across multi-omics layers in a drug-perturbed gut microbial community
Authors: Wuyts Sander , Alves Renato , Zimmermann-Kogadeeva Maria , Nishijima Suguru , Blasche Sonja , Driessen Marja , Geyer Philipp E. , Hercog Rajna , Kartal Ece , Maier Lisa , Müller Johannes B. , Santamarina Sarela Garcia , Schmidt Thomas Sebastian B. , Sevin Daniel C. , Telzerow Anja , Treit Peter V. , Wenzel Tobias , Typas Athanasios , Patil Kiran R. , Mann Matthias , Kuhn Michael , Bork Peer
Published: January 2023

Multi-omics analyses are increasingly employed in microbiome studies to obtain a holistic view of molecular changes occurring within microbial communities exposed to different conditions. However, it is not always clear to what extent each omics data type contributes to our understanding of the community dynamics and whether they are concordant with each other. Here we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers, namely 16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics, and metabolomics. Using this controlled setting, we find that all omics methods with species resolution in their readouts are highly consistent in estimating relative species abundances across conditions. Furthermore, different omics methods complement each other in their ability to capture functional changes in response to the drug perturbations. For example, while nearly all omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control and metabolomics revealed a decrease in polysaccharide uptake, likely caused by Bacteroidota depletion. Taken together, our study provides insights into how multi-omics datasets can be utilised to reveal complex molecular responses to external perturbations in microbial communities.
The prospect of universal coronavirus immunity: a characterization of reciprocal and non-reciprocal T cell responses against SARS-CoV2 and common human coronaviruses
Authors: Soni Mithil , Migliori Edoardo , Fu Jianing , Assal Amer , Chan Hei Ton , Pan Jian , Khatiwada Prabesh , Ciubotariu Rodica , May Michael S. , Pereira Marcus , De Giorgi Valeria , Sykes Megan , Mapara Markus Y , Muranski Pawel
Published: January 2023

T cell immunity plays a central role in clinical outcomes of Coronavirus Infectious Disease 2019 (COVID-19). Therefore, T cell-focused vaccination or cellular immunotherapy might provide enhanced protection for immunocompromised patients. Pre-existing T cell memory recognizing SARS-CoV2 antigens antedating COVID-19 infection or vaccination, may have developed as an imprint of prior infections with endemic non-SARS human coronaviruses (hCoVs) OC43, HKU1, 229E, NL63, pathogens of “common cold”. In turn, SARS-CoV2-primed T cells may recognize emerging variants or other hCoV viruses and modulate the course of subsequent hCoV infections. Cross-immunity between hCoVs and SARS-CoV2 has not been well characterized. Here, we systematically investigated T cell responses against the immunodominant SARS-CoV2 spike, nucleocapsid and membrane proteins and corresponding antigens from α- and β-hCoVs among vaccinated, convalescent, and unexposed subjects. Broad T cell immunity against all tested SARS-CoV2 antigens emerged in COVID-19 survivors. In convalescent and in vaccinated individuals, SARS-CoV2 spike-specific T cells reliably recognized most SARS-CoV2 variants, however cross-reactivity against theomicronvariant was reduced by approximately 50%. Responses against spike, nucleocapsid and membrane antigens from endemic hCoVs were more extensive in COVID-19 survivors than in unexposed subjects and displayed cross-reactivity between α- and β-hCoVs. In some, non-SARS hCoV-specific T cells demonstrated a prominent non-reciprocal cross-reactivity with SARS-CoV2 antigens, whereas a distinct anti-SARS-CoV2 immunological repertoire emerged post-COVID-19, with relatively limited cross-recognition of non-SARS hCoVs. Based on this cross-reactivity pattern, we established a strategy forin-vitroexpansion of universal anti-hCoV T cells for adoptive immunotherapy. Overall, these results have implications for the future design of universal vaccines and cell-based immune therapies against SARS- and non-SARS-CoVs.
Calling pangenes from plant genome alignments confirms presence-absence variation
Authors: Contreras-Moreira Bruno , Saraf Shradha , Naamati Guy , Casas Ana M. , Amberkar Sandeep S. , Flicek Paul , Jones Andrew R. , Dyer Sarah
Published: January 2023

Consistent gene annotation in crops is becoming harder as genomes for new cultivars are frequently published. Gene sets from recently sequenced accessions have different gene identifiers to those on the reference accession, and might be of higher quality due to technical advances. For these reasons there is a need to define pangenes, which represent all known syntenic orthologues for a gene model and can be linked back to the original annotation sources. A pangene set effectively summarizes our current understanding of the coding potential of a crop and can be used to inform gene model annotation in new cultivars. Here we present an approach (get_pangenes) to identify and analyze pangenes that is not biased towards the reference annotation. The method involves computing Whole Genome Alignments (WGA), which are used to estimate gene model overlaps. After a benchmark onArabidopsis, rice, wheat and barley datasets, we find that minimap2 performs better than the GSAlign WGA algorithm. Our results show that pangenes recapitulate known phylogeny-based orthologies while adding extra core gene models in rice. More importantly, get_pangenes can also produce clusters of genome segments (gDNA) that overlap with gene models annotated in other cultivars. By lifting-over CDS sequences, gDNA clusters can help refine gene models across individuals and confirm or reject observed gene Presence-Absence Variation. A collection of flowering-related genes from the barley pangenome are discussed in detail. Documentation and source code are available athttps://github.com/Ensembl/plant-scripts.
The genetic architecture of the human skeletal form
Authors: Kun Eucharist , Javan Emily M. , Smith Olivia , Gulamali Faris , de la Fuente Javier , Flynn Brianna I. , Vajrala Kushal , Trutner Zoe , Jayakumar Prakash , Tucker-Drob Elliot M. , Sohail Mashaal , Singh Tarjinder , Narasimhan Vagheesh M.
Published: January 2023

The human skeletal form underlies our ability to walk on two legs, but unlike standing height, the genetic basis of limb lengths and skeletal proportions is less well understood. Here we applied a deep learning model to 31,221 whole body dual-energy X-ray absorptiometry (DXA) images from the UK Biobank (UKB) to extract 23 different image-derived phenotypes (IDPs) that include all long bone lengths as well as hip and shoulder width, which we analyzed while controlling for height. All skeletal proportions are highly heritable (∼40-50%), and genome-wide association studies (GWAS) of these traits identified 179 independent loci, of which 102 loci were not associated with height. These loci are enriched in genes regulating skeletal development as well as associated with rare human skeletal diseases and abnormal mouse skeletal phenotypes. Genetic correlation and genomic structural equation modeling indicated that limb proportions exhibited strong genetic sharing but were genetically independent of width and torso proportions. Phenotypic and polygenic risk score analyses identified specific associations between osteoarthritis (OA) of the hip and knee, the leading causes of adult disability in the United States, and skeletal proportions of the corresponding regions. We also found genomic evidence of evolutionary change in arm-to-leg and hip-width proportions in humans consistent with striking anatomical changes in these skeletal proportions in the hominin fossil record. In contrast to cardiovascular, auto-immune, metabolic, and other categories of traits, loci associated with these skeletal proportions are significantly enriched in human accelerated regions (HARs), and regulatory elements of genes differentially expressed through development between humans and the great apes. Taken together, our work validates the use of deep learning models on DXA images to identify novel and specific genetic variants affecting the human skeletal form and ties a major evolutionary facet of human anatomical change to pathogenesis.
Experiments in micro-patterned model membranes support the narrow escape theory
Authors: Meiser Elisabeth , Mohammadi Reza , Vogel Nicolas , Holcman David , Fenz Susanne F.
Published: January 2023

The narrow escape theory (NET) predicts the escape time distribution of Brownian particles confined to a domain with reflecting borders except for one small window. Applications include molecular activation events in cell biology and biophysics. Specifically, the mean first passage timecan be analytically calculated from the size of the domain, the escape window, and the diffusion coefficient of the particles. In this study, we systematically tested the NET in a disc by variation of the escape opening. Our model system consisted of micro-patterned lipid bilayers. For the measurement of, we imaged diffusing fluorescently-labeled lipids using single-molecule fluorescence microscopy. We overcame the lifetime limitation of fluorescent probes by re-scaling the measured time with the fraction of escaped particles. Experiments were complemented by matching stochastic numerical simulations. To conclude, we confirmed the NET predictionin vitroandin silicofor the disc geometry in the limit of small escape openings.

Significance Statement

In the biological context of a cell, a multitude of reactions are facilitated by diffusion. It is astonishing how Brownian motion as a cost-efficient but random process is mediating especially fast reactions. The formalism of the narrow escape theory is a tool to determine the average timescale of such processes to be completed (mean first passage time, MFPT) from the reaction space and diffusion coefficient. We present the systematic proof of this formalism experimentally in a bio-mimetic model system and by random walk simulations. Further, we demonstrate a straightforward solution to determine the MFPT from incomplete experimental traces. This will be beneficial for measurements of the MFPT, reliant on fluorescent probes, that have prior been inaccessible.
Stepwise molecular specification of excitatory synapse diversity on a target neuron
Authors: Paul Maëla A. , Sigoillot Séverine M. , Marti Léa , Delagrange Marine , Mailly Philippe , Selimi Fekrije
Published: January 2023

Brain function relies on the generation of a large variety of morphologically and functionally diverse, but specific, neuronal synapses. Here, we show that, initially, synapse formation on a common target neuron, the cerebellar Purkinje cells, involves a presynaptic secreted protein common for all types of excitatory inputs. The molecular program then evolves only in one of the inputs with the additional expression of a combination of presynaptic secreted proteins that specify the mature pattern of connectivity on the target. These results show that some inputs actively and gradually specify their synaptic molecular identity while others rely on the “original code”. Thus, the molecular specification of excitatory synapses, crucial for proper circuit function, is acquired in a stepwise manner during mouse postnatal development and obeys input-specific rules.
Uncursing winner’s curse: on-line monitoring of directed evolution convergence
Authors: Nemoto Takahiro , Ocari Tommaso , Planul Arthur , Tekinsoy Muge , Zin Emilia A. , Dalkara Deniz , Ferrari Ulisse
Published: January 2023

Directed evolution (DE) is a versatile protein-engineering strategy, successfully applied to a range of proteins, including enzymes, antibodies, and viral vectors. However, DE can be time-consuming and costly, as it typically requires many rounds of selection to identify desired mutants. Next-generation sequencing allows monitoring of millions of variants during DE and can be leveraged to reduce the number of selection rounds. Unfortunately the noisy nature of the sequencing data impedes the estimation of the performance of individual variants. Here, we propose ACIDES that combines statistical inference and in-silico simulations to improve performance estimation in DE by providing accurate statistical scores. We tested ACIDES first on a novel random-peptide-insertion experiment and then on several public datasets from DE of viral vectors and phage-display. ACIDES allows experimentalists to reliably estimate variant performanceon the flyand can aid protein engineering pipelines in a range of applications, including gene therapy.
Innovative Research Experiences for Underrepresented Undergraduates: A Collaborative STEM Research Program as a Pathway to Graduate School
Authors: Hacisalihoglu Gokhan
Published: January 2023

This paper aims to describe, reflect on, and explore the perceptions of underrepresented undergraduate researcher students towards the plantREU2 internship program of two universities (an HBCU and an R1 university) in Florida, USA. The plantREU2 internship program resulted from a collaboration between UF and FAMU and was located in UF main campus in Gainesville, Florida. A total of 17 students completed 10-week summer projects in plant biology. The program (PlantREU2) had a strong record of success. Over 40% of plantREU2 students co-authored a journal publication and received travel awards to attend Maize Genetics Conference. Furthermore, plantREU2 participants were significantly graduated within six years. The underrepresentation of minorities in STEM is a critical challenge. The findings of this study can be adapted similarly for underrepresented undergraduates. The vast majority of interns enrolled in post-graduate programs could therefore be a model to engage traditionally underrepresented students in STEM disciplines.
Transcription factor AhR regulates glutathione S-transferases (GSTs) conferring resistance tolambda-cyhalothrin inCydia pomonella
Authors: Hu Chao , Liu Yu-Xi , Zhang Shi-Pang , Wang Ya-Qi , Gao Ping , Li Yu-Ting , Yang Xue-Qing
Published: January 2023

Transcription factor aryl hydrocarbon receptor (AhR) can enhance insect resistance to insecticides by regulating the detoxification metabolic network. Our previous studies have confirmed that overexpression of cytochrome P450 monooxygenases (P450s) and glutathione S-transferases (GSTs) are both involved inlambda-cyhalothrin resistance inCydia pomonella. In this study, we report that AhR regulates GSTs thus conferringlambda-cyhalothrin resistance inC. pomonella. Spatiotemporal expression patterns indicated thatAhRgene ofC. pomonella(CpAhR) was highly expressed in the Malpighian tubules of larvae. Moreover, the expression ofCpAhRwas induced bylambda-cyhalothrin exposure and was up-regulated in alambda-cyhalothrin-resistant population. RNA interference (RNAi) of the expression ofCpAhRcould effectively decrease the relative expression level ofCpGSTe3and enzyme activity of GSTs, but not P450s, further reducing the tolerance of larvae tolambda-cyhalothrin. Furthermore, β-naphthoflavone (BNF), a novel agonist of AhR, can effectively increase the expression ofCpAhRand the activity of the GSTs enzyme, resulting in the enhancement of larvae tolerance tolambda-cyhalothrin. These results demonstrate thatlambda-cyhalothrin exposure can effectively activate the expression ofCpAhRand increase GSTs enzyme thus leading to the development of resistance tolambda-cyhalothrin, which enriches the theory of insecticide resistance regulation inC. pomonella.
CCR1 Mediates Müller Cell Activation and Photoreceptor Cell Death in Macular and Retinal Degeneration
Authors: Elbaz-Hayoun Sarah , Rinsky Batya , Hagbi-Levi Shira , Grunin Michelle , Chowers Itay
Published: January 2023

Mononuclear cells are involved in the pathogenesis of retinal diseases, including age-related macular degeneration (AMD). Here, we examined the mechanisms that underlie macrophage-driven retinal cell death. Monocytes were extracted from patients with AMD and differentiated into macrophages (hMdɸs), which were characterized based on proteomics, gene expression, andex vivoandin vivoproperties. Using bioinformatics, we identified the signaling pathway involved in macrophage-driven retinal cell death, and we assessed the therapeutic potential of targeting this pathway. We found that M2a hMdɸs were associated with retinal cell death in retinal explants and following adoptive transfer in a photic injury model. Moreover, M2a hMdɸs express several CCRI (C-C chemokine receptor type 1) ligands. Importantly, CCR1 was upregulated in Müller cells in models of retinal injury and aging, and CCR1 expression was correlated with retinal damage. Lastly, inhibiting CCR1 reduced photic-induced retinal damage, photoreceptor cell apoptosis, and retinal inflammation. These data suggest that hMdɸs, CCR1, and Müller cells work together to drive retinal and macular degeneration, suggesting that CCR1 may serve as a target for treating these sight-threatening conditions.
Identification of a novel enhancer essential forSatb1expression in TH2 cells and activated ILC2s
Authors: Nomura Aneela , Ohno-Oishi Michiko , Kobayashi Tetsuro , Seo Wooseok , Kakugawa Kiyokazu , Muroi Sawako , Yoshida Hideyuki , Endo Takaho A. , Moro Kazuyo , Taniuchi Ichiro
Published: January 2023

The genome organizer, special AT-rich binding protein-1 (SATB1) functions to globally regulate gene networks during primary T cells development and plays a pivotal role in lineage-specification in CD4+helper-, CD8+cytotoxic- and FOXP3+regulatory-T cell subsets. However, it remains unclear howSatb1gene expression is controlled, particularly in effector T cell function. Here, by using a novel reporter mouse strain expressing SATB1-Venus and genome editing, we have identified acis-regulatory enhancer, essential for maintainingSatb1expression specifically in TH2 cells. This enhancer is occupied by STAT6 and interacts withSatb1promoters through chromatin looping in TH2 cells. Reduction ofSatb1expression, by the lack of this enhancer, resulted in elevated IL-5 expression in TH2 cells. In addition, we found thatSatb1is induced in activated group 2 innate lymphoid cells (ILC2s) through this enhancer. Collectively, these results provide novel insights into howSatb1expression is regulated in TH2 cells and ILC2s during type 2 immune responses.
Aging Decreases the Precision of Visual Working Memory
Authors: Mohammadpour Esfahan Shahrzad , H.K Nili Mohammad-Hossein , Sanayei Mehdi , Rezayat Ehsan
Published: January 2023

Objectives

Working memory (WM) is a cognitive ability that enables us to hold information temporarily. As age increases during life, cognitive abilities such as WM performance decrease. Errors in WM tasks arise from different sources, such as decreasing precision and random response. In the current study, we investigated the effect of age on WM and elucidated sources of errors.

Method

A total of 102 healthy individuals aged 18 to 71, participated in the study. A face-based visual WM task was designed and performed. Responses were collected using a graded scale in a delayed match-to-sample reproduction task.

Results

The error of participants increased significantly as they aged. According to our analysis of the source of error, the standard deviation of error distribution increased considerably with age. However, there was no significant change in uniform probability with age. These observations were similar between male and female participants.

Conclusion

We found that WM performance declines through the lifespan. Investigating the sources of error, we found that the precision of WM decreased with age. This decline was monotonous without any particular age at which a significant drop-off occurred. The results also indicated that the probability of guessing the response as a measure of random response is not affected by age.
A generative model of electrophysiological brain responses to stimulation: an approach to study perceptual stability
Authors: Vidaurre Diego
Published: January 2023

Each brain response to a stimulus is, to a large extent, unique. However this variability, our perceptual experience feels stable. Standard decoding models, which utilise information across several areas to tap into stimuli representation and processing, are fundamentally based on averages. Therefore, they can focus precisely on the features that are most stable across stimulus presentations. But which are these features exactly is difficult to address in the absence of a generative model of the signal. Here, I introducegenephys, a generative model of brain responses to stimulation publicly available as a Python package that, when confronted with a decoding algorithm, can reproduce the structured patterns of decoding accuracy that we observe in real data. Using this approach, I characterise how these patterns may be brought about by the different aspects of the signal, which in turn may translate into distinct putative neural mechanisms. In particular, the model shows that the features in the data that support successful decoding —and, therefore, likely reflect stable mechanisms of stimulus representation— have an oscillatory component that spans multiple channels, frequencies and latencies of response; and an additive, slower response with a specific (cross-frequency) relation to the phase of the oscillatory component. At the individual trial level, still, responses are found to be highly variable, which can be due to various factors including phase noise and probabilistic activations.
An original potentiating mechanism revealed by the cryoEM structures of the human α7 nicotinic receptor in complex with nanobodies
Authors: Prevost Marie S. , Barilone Nathalie , Dejean De La Batie Gabrielle , Pons Stéphanie , Ayme Gabriel , England Patrick , Gielen Marc , Bontems François , Pehau-Arnaudet Gérard , Maskos Uwe , Lafaye Pierre , Corringer Pierre-Jean
Published: January 2023

The human α7 nicotinic receptor is a pentameric channel mediating cellular and neuronal communication. It has attracted considerable interest to design ligands for the treatment of neurological and psychiatric disorders. To develop a novel class of α7 ligands, we recently generated two nanobodies named E3 and C4 acting as positive and silent allosteric modulators respectively. Here, we solved the cryo-EM structures of the nanobody-receptor complexes. E3 and C4 bind to a common epitope involving two subunits at the apex of the receptor. They form by themselves a symmetric pentameric assembly that extends the extracellular domain. Unlike C4, the binding of E3 drives an active or desensitized conformation in the absence of orthosteric agonist, and mutational analysis shows a key contribution of a N-linked sugar moiety in mediating E3 potentiation. The nanobody E3, by remotely controlling the global allosteric conformation of the receptor, implements an original mechanism of regulation which opens new avenues for drug design.
Crystal structure of a mammalian CMTM6 and its interaction model with PD-L1
Authors: Zhang Senfeng , Xie Qingrong , Fu Chunting , Luo Yongbo , Sun Ziyi , Zhou Xiaoming
Published: January 2023

CKLF-like MARVEL transmembrane domain-containing protein 6 (CMTM6) is a master regulator of PD-L1. By binding PD-L1 at the plasma membrane and recycling endosomes, CMTM6 prevents the lysosomal degradation of PD-L1 and maintains its cell surface expression, thus stabilizing the inhibitory PD-1/PD-L1 axis. However, the mechanism of CMTM6/PD-L1 interaction is unknown. Here we report the first experimentally determined structure of CMTM6 from bovine. Combined with a low-resolution cryo-EM map, computational docking analysis and a protein binding assay an interaction model between CMTM6 and PD-L1 was proposed, providing a structural framework for the CMTM6 regulation on PD-L1.
Identification of two distinct phylogenomic lineages and model strains for the understudied cystic fibrosis lung pathogenBurkholderia multivorans
Authors: Parfitt Kasia M. , Green Angharad E. , Connor Thomas R. , Neill Daniel R. , Mahenthiralingam Eshwar
Published: January 2023

Burkholderia multivoransis the dominantBurkholderiapathogen recovered from lung infection in people with cystic fibrosis. However, as an understudied pathogen there are knowledge gaps in relation to its population biology, phenotypic traits and useful model strains. A phylogenomic study ofB. multivoranswas undertaken using a total of 283 genomes, of which 73 were sequenced and 49 phenotypically characterized as part of this study. Average nucleotide identity analysis (ANI) and phylogenetic alignment of core genes demonstrated that theB. multivoranspopulation separated into two distinct evolutionary clades, defined as lineage 1 (n= 58 genomes) and lineage 2 (n= 221 genomes). To examine the population biology ofB. multivorans, a representative subgroup of 77B. multivoransgenomes (28 from the reference databases and the 49-novel short-read genome sequences) were selected based on multilocus sequence typing (MLST), isolation source and phylogenetic placement criteria. Comparative genomics was used to identifyB. multivoranslineage-specific genes:ghrB_1in lineage 1, andglnM_2in lineage 2, and diagnostic PCRs targeting them successfully developed. Phenotypic analysis of 49 representativeB. multivoransstrains showed considerable variance with the majority of isolates tested being motile and capable of biofilm formation. A striking absence ofB. multivoransprotease activityin vitrowas observed, but no lineage-specific phenotypic differences demonstrated. Using phylogenomic and phenotypic criteria, three modelB. multivoransCF strains were identified, BCC0084 (lineage 1), BCC1272 (lineage 2a) and BCC0033 lineage 2b, and their complete genome sequences determined.B. multivoransCF strains BCC0033 and BCC0084, and the environmental reference strain, ATCC 17616, were all capable of short-term survival within a murine lung infection model. By mapping the population biology, identifying lineage-specific PCRs and model strains, we provide much needed baseline resources for future studies ofB. multivorans.
Computational mutagenesis by using AUTO-MUTE 2.0 to examine X-ray crystallography structures for p53 and the impact of its resolution on predictions
Authors: Sait Shaimaa , Vaisman Isoif
Published: January 2023

The mutation of P53 is found in 50% of all human cancers, affecting the protein structure conformation, which further impacts its function. Identifying the appropriate protein structure for future research has been challenging. Many X-ray crystallography structures exist in the Protein Data Bank (PDB) for a given protein. We compared two proteins with different resolutions to determine whether the differences between the two structures were statistically significant. The present study used mutagenesis to study two structures of the protein P53 with various resolutions to assess how the conformation of the protein changes upon mutation. We used an AUTO-MUTE 2.0, which is a computational geometry method based on the Delaunay tessellation for predicting protein structures. The current study compares the prediction results obtained from different predictive methods. We used logistic regression models and corresponding receiver operating characteristic (ROC) curves to model the differences between structures using the variables available at PDB. We conclude from this study that x-ray crystallography is a sensitive and advanced technique, and the resulting proteins at different resolutions are similar.
The myocardium utilizes Pdgfra-PI3K signaling to steer towards the midline during heart tube formation
Authors: Shrestha Rabina , McCann Tess , Saravanan Harini , Lieberth Jaret , Koirala Prashanna , Bloomekatz Joshua
Published: January 2023

Coordinated cell movement is a fundamental process in organ formation. During heart development, bilateral myocardial precursors collectively move towards the midline (cardiac fusion) to form the primitive heart tube. Along with extrinsic influences such as the adjacent anterior endoderm which are known to be required for cardiac fusion, we previously showed that the platelet-derived growth factor receptor alpha (Pdgfra) is also required. However, an intrinsic mechanism that regulates myocardial movement remains to be elucidated. Here, we uncover an essential intrinsic role in the myocardium for the phosphoinositide 3-kinase (PI3K) intracellular signaling pathway in directing myocardial movement towards the midline.In vivoimaging reveals that in PI3K-inhibited zebrafish embryos myocardial movements are misdirected and slower, while midline-oriented dynamic myocardial membrane protrusions become unpolarized. Moreover, PI3K activity is dependent on and genetically interacts with Pdgfra to regulate myocardial movement. Together our findings reveal an intrinsic myocardial steering mechanism that responds to extrinsic cues during the initiation of cardiac development.
Mitochondrial genes in the 22q11.2 deleted region regulate neural stem and progenitor cell proliferation
Authors: Campbell Philip D. , Lee Isaiah , Thyme Summer , Granato Michael
Published: January 2023

Microdeletion of a 3Mbp region encompassing 45 protein-coding genes at chromosome 22q11.2 (22q11.2DS) predisposes to multiple neurodevelopmental disorders and is one of the greatest genetic risk factors for schizophrenia. Defective mitochondrial function has been hypothesized to contribute to 22q11.2DS pathogenesis; however, which of the six mitochondrial genes contribute to neurodevelopmental phenotypes and their underlying mechanisms remain unresolved. To systematically test 22q11.2DS genes for functional roles in neurodevelopment and behavior, we generated genetic mutants for each of the 37 conserved zebrafish orthologs and performed high throughput behavioral phenotyping using seven behavioral assays. Through this unbiased approach, we identified five single-gene mutants with partially overlapping behavioral phenotypes. Two of these genes,mrpl40andprodha, encode for mitochondrial proteins and, similar to what we observed inmrpl40andprodhamutants, pharmacologic inhibition of mitochondrial function during development results in microcephaly. Finally, we show that bothmrpl40andprodhamutants display neural stem and progenitor cell phenotypes, with each gene regulating different neural stem cell populations. Combined, our results demonstrate a critical role for mitochondrial function in neural stem and progenitor cell populations in the developing vertebrate brain and provide compelling evidence that mitochondrial dysfunction during neurodevelopment is linked to brain volume and behavioral phenotypes observed in models of 22q11.2DS.
Sequence-to-sequence translation from mass spectra to peptides with a transformer model
Authors: Yilmaz Melih , Fondrie William E. , Bittremieux Wout , Melendez Carlo F. , Nelson Rowan , Ananth Varun , Oh Sewoong , Noble William Stafford
Published: January 2023

A fundamental challenge for any mass spectrometry-based proteomics experiment is the identification of the peptide that generated each acquired tandem mass spectrum. Although approaches that leverage known peptide sequence databases are widely used and effective for well-characterized model organisms, such methods cannot detect unexpected peptides and can be impractical or impossible to apply in some settings. Thus, the ability to assign peptide sequences to the acquired tandem mass spectra without prior information—de novopeptide sequencing—is valuable for gaining biological insights for tasks including antibody sequencing, immunopeptidomics, and metaproteomics. Although many methods have been developed to address thisde novosequencing problem, it remains an outstanding challenge, in part due to the difficulty of modeling the irregular data structure of tandem mass spectra. Here, we describe Casanovo, a machine learning model that uses a transformer neural network architecture to translate the sequence of peaks in a tandem mass spectrum into the sequence of amino acids that comprise the generating peptide. We train a Casanovo model from 30 million labeled spectra and demonstrate that the model outperforms several state-of-the-art methods on a cross-species benchmark dataset. We also develop a version of Casanovo that is fine-tuned for non-enzymatic peptides. Finally, we demonstrate that Casanovo’s superior performance improves the analysis of immunopeptidomics and metaproteomics experiments and allows us to delve deeper into the dark proteome.
Lytic/Lysogenic Transition as a Life-History Switch
Authors: Roughgarden Joan
Published: January 2023

The transition between lytic and lysogenic life cycles is the most important feature of the life history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density-dependence in bacterial growth is not needed.

The formula for the transition between lytic and lysogenic phases is termed the “fitness switch”. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic.

A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a “prophage lock”.

The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the “Piggyback-the-Winner” hypothesis than with the “Kill-the-Winner” hypothesis in virus ecology.
PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks
Authors: Stebliankin Vitalii , Shirali Azam , Baral Prabin , Chapagain Prem , Narasimhan Giri
Published: January 2023

The computational studies of protein binding are widely used to investigate fundamental biological processes and facilitate the development of modern drugs, vaccines, and therapeutics. Scoring functions aim to predict complexes that would be formed by the binding of two biomolecules and to assess and rank the strength of the binding at the interface. Despite past efforts, the accurate prediction and scoring of protein binding interfaces remain a challenge. The physics-based methods are computationally intensive and often have to trade accuracy for computational cost. The possible limitations of current machine learning (ML) methods are ineffective data representation, network architectures, and limited training data. Here, we propose a novel approach called PIsToN (evaluatingProtein bindingInterfaceswithTransformerNetworks) that aim to distinguish native-like protein complexes from decoys. Each protein interface is transformed into a collection of 2D images (interface maps), where each image corresponds to a geometric or biochemical property in which pixel intensity represents the feature values. Such a data representation provides atomic-level resolution of relevant protein characteristics. To buildhybridmachine learning models, additional empirical-based energy terms are computed and provided as inputs to the neural network. The model is trained on thousands of native and computationally-predicted protein complexes that contain challenging examples. The multi-attention transformer network is also endowed with explainability by highlighting the specific features and binding sites that were the most important for the classification decision. The developed PIsToN model significantly outperforms existing state-of-the-art scoring functions on well-known datasets.
AadT, a new weapon inAcinetobacter’sfight against antibiotics
Authors: Naidu Varsha , Shah Bhumika , Maher Claire , Paulsen Ian T. , Hassan Karl A.
Published: January 2023

A novel multidrug efflux pump, AadT from the Drug:H+antiporter 2 family, was discovered inAcinetobactermultidrug resistance plasmids. Here, we profiled the antimicrobial resistance potential and examined the distribution of this gene. Putative homologs of this efflux pump were encoded in manyAcinetobacterspecies and other Gram-negative species, and were genetically associated with novel variants ofadeAB(C), which encodes a major tripartite efflux pump inAcinetobacter. The AadT pump conferred decreased susceptibility to at least eight diverse antimicrobials, including antibiotics erythromycin, tetracycline; biocides chlorhexidine; and dyes ethidium bromide and DAPI. These results show that AadT is a new determinant in theAcinetobacterresistance arsenal and may cooperate with variants of AdeAB(C).
Efficient gene knockout and genetic interactions: the IN4MER CRISPR/Cas12a multiplex knockout platform
Authors: Anvar Nazanin Esmaeili , Lin Chenchu , Ma Xingdi , Wilson Lori L. , Steger Ryan , Sangree Annabel K. , Colic Medina , Wang Sidney H. , Doench John G. , Hart Traver
Published: January 2023

Genetic interactions mediate the emergence of phenotype from genotype, but initial technologies for combinatorial genetic perturbation in mammalian cells suffer from inefficiency and are challenging to scale. Recent focus on paralog synthetic lethality in cancer cells offers an opportunity to evaluate different approaches and improve on the state of the art. Here we report a meta-analysis of CRISPR genetic interactions screens, identifying a candidate set of background-independent paralog synthetic lethals, and find that the Cas12a platform provides superior sensitivity and assay replicability. We demonstrate that Cas12a can independently target up to four genes from a single guide array, and we build on this knowledge by constructing a genome-scale library that expresses arrays of four guides per clone, a platform we call ‘in4mer’. Our genome-scale human library, with only 49k clones, is substantially smaller than a typical CRISPR/Cas9 monogenic library while also targeting more than four thousand paralog pairs, triples, and quads. Proof of concept screens in four cell lines demonstrate discrimination of core and context-dependent essential genes similar to that of state-of-the-art CRISPR/Cas9 libraries, as well as detection of synthetic lethal and masking/buffering genetic interactions between paralogs of various family sizes, a capability not offered by any extant library. Importantly, the in4mer platform offers a fivefold reduction in the number of clones required to assay genetic interactions, dramatically improving the cost and effort required for these studies.
An RNA seq-based reference landscape of human normal and neoplastic brain
Authors: Arora Sonali , Szulzewsky Frank , Jensen Matt , Nuechterlein Nicholas , Pattwell Siobhan S , Holland Eric C
Published: January 2023

In order to better understand the relationship between normal and neoplastic brain, we combined five publicly available large-scale datasets, correcting for batch effects and applying Uniform Manifold Approximation and Projection (UMAP) to RNA-seq data. We assembled a reference Brain-UMAP including 702 adult gliomas, 802 pediatric tumors and 1409 healthy normal brain samples, which can be utilized to investigate the wealth of information obtained from combining several publicly available datasets to study a single organ site. Normal brain regions and tumor types create distinct clusters and because the landscape is generated by RNA seq, comparative gene expression profiles and gene ontology patterns are readily evident. To our knowledge, this is the first meta-analysis that allows for comparison of gene expression and pathways of interest across adult gliomas, pediatric brain tumors, and normal brain regions. We provide access to this resource via the open source, interactive online tool Oncoscape, where the scientific community can readily visualize clinical metadata, gene expression patterns, gene fusions, mutations, and copy number patterns for individual genes and pathway over this reference landscape.
IsoAnalytics: A Single-cell Proteomics Web Server
Authors: Palmer Suzette N. , Koh Andrew Y. , Zhan Xiaowei
Published: January 2023

Motivation

Single-cell proteomics provide unprecedented resolution to examine biological processes. Customized data analysis and facile data visualization are crucial for scientific discovery. Further, userfriendly data analysis and visualization software that is easily accessible for the general scientific community is essential.

Results

We have created a web server,IsoAnalytics, that gives users without computational or bioinformatics background the ability to directly analyze and interactively visualize data obtained from the Isoplexis single cell technology platform. We envision this open-sourced web server will increase research productivity and serve as a free, competitive alternative for single-cell proteomics research.

Contact

Andrew.Koh@utsouthwestern.eduandXiaowei.Zhan@utsouthwestern.edu

Availability

IsoAnalytics is free and available at:https://cdc.biohpc.swmed.edu/isoplexis/and is implemented in Python, with all major browsers supported. Code for IsoAnalytics is free and available at:https://github.com/zhanxw/Isoplexis_Data_Analysis.

Supplementary Information

Supplementary data are available atBioinformaticsonline.
The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma
Authors: Wilson Naomi G. , Hernandez-Leyva Ariel , Schwartz Drew J. , Bacharier Leonard B. , Kau Andrew L.
Published: January 2023

Asthma is a common allergic airway disease that develops in association with the human microbiome early in life. Both the composition and function of the infant gut microbiota have been linked to asthma risk, but functional alterations in the gut microbiota of older patients with established asthma remain an important knowledge gap. Here, we performed whole metagenomic shotgun sequencing of 95 stool samples from 59 healthy and 36 subjects with moderate-to-severe asthma to characterize the metagenomes of gut microbiota in children and adults 6 years and older. Mapping of functional orthologs revealed that asthma contributes to 2.9% of the variation in metagenomic content even when accounting for other important clinical demographics. Differential abundance analysis showed an enrichment of long-chain fatty acid (LCFA) metabolism pathways which have been previously implicated in airway smooth muscle and immune responses in asthma. We also observed increased richness of antibiotic resistance genes (ARGs) in people with asthma. One differentially abundant ARG was a macrolide resistance marker,ermF, which significantly co-occurred with theBacteroides fragilistoxin, suggesting a possible relationship between enterotoxigenicB. fragilis, antibiotic resistance, and asthma. Lastly, we found multiple virulence factor (VF) and ARG pairs that co-occurred in both cohorts suggesting that virulence and antibiotic resistance traits are co-selected and maintained in the fecal microbiota of people with asthma. Overall, our results show functional alterations via LCFA biosynthetic genes and increases in antibiotic resistance genes in the gut microbiota of subjects with moderate-to-severe asthma and could have implications for asthma management and treatment.
Altered hierarchical auditory predictive processing after lesions to the orbitofrontal cortex
Authors: Asko Olgerta , Blenkmann Alejandro O. , Leske Sabine L. , Foldal Maja Dyhre , Llorens Anaïs , Funderud Ingrid , Meling Torstein R. , Knight Robert T. , Endestad Tor , Solbakk Anne-Kristin
Published: January 2023

Orbitofrontal cortex (OFC) is classically linked to inhibitory control, emotion regulation and reward processing. Recent perspectives propose that the OFC also generates predictions about perceptual events, actions, and their outcomes. We tested the role of the OFC in detecting violations of prediction at two levels of abstraction (i.e., hierarchical predictive processing) by studying the event-related potentials (ERPs) of patients with focal OFC lesions (n = 12) and healthy controls (n = 14) while they detected deviant sequences of tones in a Local-Global paradigm. The structural regularities of the tones were controlled at two hierarchical levels by rules defined at a local (i.e.,between tones within sequences)and at a global (i.e.,between sequences) level. In OFC patients, ERPs elicited by standard tones were unaffected at both local and global levels compared to controls. However, patients showed an attenuated mismatch negativity (MMN) and P3a to local prediction violation, as well as a diminished MMN followed by a delayed P3a to the combined local and global level prediction violation. The subsequent P3b component to conditions involving violations of prediction at the level of global rules was preserved in the OFC group. Comparable effects were absent in patients with lesions restricted to the lateral PFC, which lends a degree of anatomical specificity to the altered predictive processing resulting from OFC lesion. Overall, the altered magnitudes and time courses of MMN/P3a responses after lesions to the OFC indicate that the neural correlates of detection of auditory regularity violation is impacted at two hierarchical levels of rule abstraction.

Highlights

Orbitofrontal lesions reduce auditory MMN to unpredicted tones at the local level (between tones within sequences) of the rule hierarchy in the Local-Global paradigm.

Orbitofrontal lesions also impact combined local and global (between sequences) level auditory deviance response, as manifested by diminished and delayed MMN and delayed P3a.
Assessment of Immunogenicity and Efficacy of CV0501 mRNA-based Omicron COVID-19 Vaccination in Small Animal Models
Authors: Roth Nicole , Gergen Janina , Kovacikova Kristina , Mueller Stefan O. , Ulrich Lorenz , Schön Jacob , Halwe Nico Joel , Fricke Charlie , Corleis Björn , Dorhoi Anca , Hoffmann Donata , Beer Martin , Maione Domenico , Petsch Benjamin , Rauch Susanne
Published: January 2023

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron and its subvariants (BA.2, BA.4, BA.5) represent the most commonly circulating variants of concern (VOC) in the coronavirus disease 2019 (COVID-19) pandemic in 2022. Despite high vaccination rates with approved SARS-CoV-2 vaccines encoding the ancestral spike (S) protein, these Omicron subvariants have collectively resulted in increased viral transmission and disease incidence. This necessitates the development and characterization of vaccines incorporating later emerging S proteins to enhance protection against VOC. In this context, bivalent vaccine formulations may induce broad protection against VOC and potential future SARS-CoV-2 variants. Here, we report preclinical data for a lipid nanoparticle (LNP)-formulated RNActive® N1-methylpseudouridine (N1mΨ) modified mRNA vaccine (CV0501) based on our second-generation SARS-CoV-2 vaccine CV2CoV, encoding the S protein of Omicron BA.1.

The immunogenicity of CV0501, alone or in combination with a corresponding vaccine encoding the ancestral S protein (ancestral N1mΨ), was first measured in dose-response and booster immunization studies performed in Wistar rats. Both monovalent CV0501 and bivalent CV0501/ancestral N1mΨ immunization induced robust neutralizing antibody titers against the BA.1, BA.2 and BA.5 Omicron subvariants, in addition to other SARS-CoV-2 variants in a booster immunization study.

The protective efficacy of monovalent CV0501 against live SARS-CoV-2 BA.2 infection was then assessed in hamsters. Monovalent CV0501 significantly reduced SARS-CoV-2 BA.2 viral loads in the airways, demonstrating protection induced by CV0501 vaccination. CV0501 has now advanced into human Phase 1 clinical trials (ClinicalTrials.govIdentifier:NCT05477186).