bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss-of-function mutation in Omicron variants reduces spike protein expression and attenuates SARS-CoV-2 infection
Authors: Vu Michelle N. , Alvarado R. Elias , Morris Dorothea R. , Lokugamage Kumari G. , Zhou Yiyang , Morgan Angelica L. , Estes Leah K. , McLeland Alyssa M. , Schindewolf Craig , Plante Jessica A. , Ahearn Yani P. , Meyers William M. , Murray Jordan T. , Crocquet-Valdes Patricia A. , Weaver Scott C. , Walker David H. , Russell William K. , Routh Andrew L. , Plante Kenneth S. , Menachery Vineet 
Published: April 2023

AbstractSARS-CoV-2 Omicron variants emerged in 2022 with >30 novel amino acid mutations in the spike protein alone. While most studies focus on receptor binding domain changes, mutations in the C-terminus of S1 (CTS1), adjacent to the furin cleavage site, have largely been ignored. In this study, we examined three Omicron mutations in CTS1: H655Y, N679K, and P681H. Generating a SARS-CoV-2 triple mutant (YKH), we found that the mutant increased spike processing, consistent with prior reports for H655Y and P681H individually. Next, we generated a single N679K mutant, finding reduced viral replicationin vitroand less diseasein vivo.Mechanistically, the N679K mutant had reduced spike protein in purified virions compared to wild-type; spike protein decreases were further exacerbated in infected cell lysates. Importantly, exogenous spike expression also revealed that N679K reduced overall spike protein yield independent of infection. Although a loss-of-function mutation, transmission competition demonstrated that N679K had a replication advantage in the upper airway over wild-type SARS-CoV-2 in hamsters, potentially impacting transmissibility. Together, the data show that N679K reduces overall spike protein levels during Omicron infection, which has important implications for infection, immunity, and transmission.
Benchmarking Uncertainty Quantification for Protein Engineering
Authors: Greenman Kevin P. , Amini Ava P. , Yang Kevin K. 
Published: April 2023

AbstractMachine learning sequence-function models for proteins could enable significant ad vances in protein engineering, especially when paired with state-of-the-art methods to select new sequences for property optimization and/or model improvement. Such methods (Bayesian optimization and active learning) require calibrated estimations of model uncertainty. While studies have benchmarked a variety of deep learning uncertainty quantification (UQ) methods on standard and molecular machine-learning datasets, it is not clear if these results extend to protein datasets. In this work, we implemented a panel of deep learning UQ methods on regression tasks from the Fitness Landscape Inference for Proteins (FLIP) benchmark. We compared results across different degrees of distributional shift using metrics that assess each UQ method’s accuracy, calibration, coverage, width, and rank correlation. Additionally, we compared these metrics using one-hot encoding and pretrained language model representations, and we tested the UQ methods in a retrospective active learning setting. These benchmarks enable us to provide recommendations for more effective design of biological sequences using machine learning.
Nucleosome reorganisation in breast cancer tissues
Authors: Jacob Divya R. , Guiblet Wilfried M. , Mamayusupova Hulkar , Shtumpf Mariya , Ciuta Isabella , Ruje Luminita , Gretton Svetlana , Bikova Milena , Correa Clark , Dellow Emily , Agrawal Shivam P. , Shafiei Navid , Drobysevskaja Anastasija , Armstrong Chris M. , Lam Jonathan D. G. , Vainshtein Yevhen , Clarkson Christopher T. , Thorn Graeme J. , Sohn Kai , Pradeepa Madapura M. , Chandrasekharan Sankaran , Brooke Greg N. , Klenova Elena , Zhurkin Victor B. , Teif Vladimir B. 
Published: April 2023

AbstractNucleosome repositioning in cancer is believed to cause many changes in genome organisation and gene expression. Understanding these changes is important to elucidate fundamental aspects of cancer. It is also important for medical diagnostics based on cell-free DNA (cfDNA), which originates from genomic DNA regions protected from digestion by nucleosomes. Here we have generated high resolution nucleosome maps in paired tumour and normal tissues from the same breast cancer patients using MNase-assisted histone H3 ChIP-seq and compared them with the corresponding cfDNA from blood plasma. This analysis has detected single-nucleosome repositioning at key regulatory regions in a patient-specific manner and common cancer-specific patterns across patients. The nucleosomes gained in tumour versus normal tissue were particularly informative of cancer pathways, with ∼20-fold enrichment at CpG islands, a large fraction of which marked promoters of genes encoding DNA-binding proteins. In addition, tumour tissues were characterised by a 5-10 bp decrease in the average distance between nucleosomes (nucleosome repeat length, NRL), which is qualitatively similar to the differences between pluripotent and differentiated cells. These effects were correlated with gene activity, DNA sequence repeats abundance, differential DNA methylation and binding of linker histone variants H1.4 and H1X. Our findings provide a new mechanistic understanding of nucleosome repositioning in tumour tissues that can be valuable for patient stratification and monitoring using liquid biopsies.
Metabolism of host lysophosphatidylcholine inPlasmodium falciparum-infected erythrocytes
Authors: Liu Jiapeng , Dapper Christie , Klemba Michael 
Published: April 2023

ABSTRACTThe human malaria parasitePlasmodium falciparumrequires exogenous fatty acids to support its growth during the pathogenic, asexual erythrocytic stage. Host serum lysophosphatidylcholine (LPC) is a significant fatty acid source, yet the metabolic processes responsible for the liberation of free fatty acids from exogenous LPC are unknown. Using a novel assay for LPC hydrolysis inP. falciparum-infected erythrocytes, we have identified small-molecule inhibitors of keyin situlysophospholipase activities. Competitive activity-based profiling and generation of a panel of single-to-quadruple knockout parasite lines revealed that two enzymes of the serine hydrolase superfamily, termed exported lipase (XL) 2 and exported lipase homolog (XLH) 4, are the dominant lysophospholipase activities in parasite-infected erythrocytes. The parasite ensures efficient exogenous LPC hydrolysis by directing these two enzymes to distinct locations: XL2 is exported to the erythrocyte, while XLH4 is retained within the parasite. While XL2 and XLH4 were individually dispensable with little effect on LPC hydrolysisin situ, loss of both enzymes resulted in a strong reduction in fatty acid scavenging from LPC, hyperproduction of phosphatidylcholine, and an enhanced sensitivity to LPC toxicity. Notably, growth of XL/XLH- deficient parasites was severely impaired when cultured in media containing LPC as the sole exogenous fatty acid source. Furthermore, when XL2 and XLH4 activities were ablated by genetic or pharmacologic means, parasites were unable to proliferate in human serum, a physiologically-relevant fatty acid source, revealing the essentiality of LPC hydrolysis in the host environment and its potential as a target for anti-malarial therapy.
CD45 limits Natural Killer cell development from common lymphoid progenitors
Authors: Guzman Lizeth G Meza , Hyland Craig D , Bidgood Grace M , Leong Evelyn , Shen Zihan , Goh Wilford , Kratina Tobias , Rautela Jai , Vince James E , Nicholson Sandra E , Huntington Nicholas D 
Published: April 2023

AbstractThe clinical development of Natural Killer (NK) cell-mediated immunotherapy marks a milestone in the development of new cancer therapies and has gained traction due to the intrinsic ability of the NK cell to target and kill tumour cells. To fully harness the tumour killing ability of NK cells, we need to improve NK cell persistence and overcome suppression of NK cell activation in the tumour microenvironment. The trans-membrane, protein tyrosine phosphatase CD45, regulates NK cell homeostasis, with genetic loss of CD45 in mice resulting in increased numbers of mature NK cells [1–3]. This suggests that CD45-deficient NK cells might display enhanced persistence following adoptive transfer. However, here we demonstrated that adoptive transfer of CD45-deficiency did not enhance NK cell persistence in mice, and instead, the homeostatic disturbance of NK cells in CD45-deficient mice stemmed from a developmental defect in the common lymphoid progenitor population. The enhanced maturation within the CD45-deficient NK cell compartment was intrinsic to the NK cell lineage, and independent of the developmental defect. CD45 is not a conventional immune checkpoint candidate, as systemic loss is detrimental to T and B cell development [4–6], compromising the adaptive immune system. Nonetheless, this study suggests that inhibition of CD45 in progenitor or stem cell populations may improve the yield ofin vitrogenerated NK cells for adoptive therapy.
The enemy of my enemy is my friend: a plausible defense mechanism against antagonism in bacterial communities
Authors: Sánchez-Gómez Laura , Santillán Moisés 
Published: April 2023

AbstractIn a recent work we studied an artificial bacterial community where resistant bacteria assisted sensitive bacteria in surviving in the presence of antagonistic bacteria. Typically, this behavior is attributed to lateral gene exchange. However, we identified evidence of a distinct mechanism, which operates on the principle of “the enemy of my enemy is my friend”. Here, we explore the viability of this mechanism by means of a reaction-diffusion mathematical model. Our findings suggest that this mechanism is feasible under specific circumstances, particularly when bacteria undergo significant metabolic changes at high population densities.Author summaryThe importance of studying the formation of bacterial communities cannot be overstated. Initially, it was believed that the environment alone determined the assembly of these communities, but recent research has demonstrated that interactions among members of the community also have a crucial impact. For instance, it has been observed in some cases that, even when susceptible bacteria are confronted with antagonism, they can survive with the aid of resistant bacteria. Lateral gene exchange is typically considered the underlying mechanism responsible for this phenomenon. However, we identified in a recent work an alternative mechanism that does not involve gene exchange but operates on the principle of “the enemy of my enemy is my friend”. Using a mathematical model, we examine the plausibility of this mechanism in a small artificial bacterial community. Our results indicate that this mechanism alone cannot account for all the experimental observations, but including the assumption that bacteria undergo significant metabolic changes at high concentrations may suffice.
Trypanosoma cruziVDU deubiquitinase mediates surface protein trafficking and infectivity
Authors: Souza-Melo Normanda , Brito Silva Nathalia , Malvezzi Amaranta Muniz , dos Santos Gregory Pedroso , Alcântara Laura Maria , de Lima Alcantara Carolina , da Cunha e Silva Narcisa Leal , Zoltner Martin , Field Mark C. , Schenkman Sergio 
Published: April 2023

AbstractUbiquitylation is a post-translational modification promoting protein degradation. Within the endomembrane system ubiquitylation marks proteins for lysosomal processing. Deubiquitinases (DUBs) cleave ubiquitin from modified proteins and, in the case of surface proteins, prevent lysosomal targeting and thus play a major role in controlling turnover. InTrypanosoma cruzi,the etiological agent of Chagas disease, acquisition of nutrients in parasites proliferating within the blood meal of insect vectors occurs via the cytostome, a unique structure connected to a long tubular cytopharynx. Contents are delivered to late endosomes and accumulate in reservosomes, equivalent to lysosomes. When starved,T. cruzidifferentiates into mammalian infective trypomastigotes, which are cell cycle arrested. Here we asked what roles ubiquitylation plays in this unique endocytic process by interrogation of theT. cruziortholog of VDU (von Hippel-Lindau-interacting deubiquitylating enzyme)/USP33 (ubiquitin-specific protease). We found that TcVDU expression level inversely correlated with transferrin endocytosis, and that overexpression led to a longer retention of the endocytic cargo near the cytostome. TcVDU itself was found enriched in the anterior region of the parasite, in proximity to endocytic cargo. Most importantly, TcVDU overexpression reduced parasite invasion capacity and led to increased release oftrans-sialidase. These alterations in the abundance of multiple surface proteins in TcVDU mutants indicate a key role of TcVDU in modulating theT. cruzisurface by affecting the endosomal traffic and consequently the host-parasite interface.Author summaryTrypanosoma cruziis the cause of Chagas disease that affects large populations of Central and South America. Disease is spreading to other continents due to poor control of blood transfusion from donors with chronic and undiagnosed infection, migration and drug treatment with limited performance and undesired side effects. Proliferating forms ofT. cruziacquire nutrients through the cytostome, a cell surface opening connected to a long tubular cytopharynx. Internalized material is endocytosed in the cytopharynx. This is distinct from other members of the Trypanosomatids, which endocytose material exclusively through the flagellar pocket. By using CRISPR gene editing and overexpression we demonstrated that a conserved deubiquitinase (VDU) is a key control element for traffic from the cytopharynx to endosomal compartments inT. cruzi. Changed levels of VDU modify endosomal traffic and largely impact the parasite surface, causing changes in infectivity.
Metabolic specialization drives reduced pathogenicity inPseudomonas aeruginosaCF clinical isolates
Authors: Pedersen Bjarke H. , Simões Filipa B. , Pogrebnyakov Ivan , Welch Martin , Johansen Helle Krogh , Molin Søren , La Rosa Ruggero 
Published: April 2023

AbstractMetabolism provides the foundation for all cellular functions. During persistent infections, in adapted pathogenic bacteria metabolism functions radically differently compared with more naïve strains. Whether this is simply a necessary accommodation to the persistence phenotype or if metabolism plays a direct role in achieving persistence in the host is still unclear. Here, we characterize a convergent shift in metabolic function(s) linked with the persistence phenotype duringPseudomonas aeruginosacolonization in the airways of people with cystic fibrosis. We show that clinically-relevant mutations in the key metabolic enzyme, pyruvate dehydrogenase, lead to a host-specialized metabolism together with a lower virulence and immune response recruitment. These changes in infection phenotype are mediated by impaired type III secretion system activity and by secretion of the antioxidant metabolite, pyruvate, respectively. Our results show how metabolic adaptations directly impinge on persistence and pathogenicity in this organism.
Matrigel inhibits elongation and drives endoderm differentiation in aggregates of mouse embryonic stem cells
Authors: Amel Atoosa , Goolam Mubeen 
Published: April 2023

AbstractModelling peri-implantation mammalian development using the self-organising properties of stem cells is a rapidly growing field that has advanced our understanding of cell fate decisions occurring in the early embryo. Matrigel, a basement membrane matrix, is a critical substrate used in various protocols for its efficacy in promoting stem cell growth and self-organization. However, its role in driving stem cell lineage commitment, and whether this effect is driven by biochemical or physical cues is not being clearly defined. Here, we grow embryoid bodies in suspension, Matrigel, and agarose, an inert polysaccharide, to attempt to decouple the physical and biochemical roles of Matrigel and better understand how it drives stem cell differentiation. We show that stem cell aggregates in Matrigel are hindered in their ability to elongate compared to those grown in agarose or in suspension indicating that prohibitive role in self-organisation. Aggregates in Matrigel are also driven to differentiate into endoderm with ectoderm differentiation inhibited. Furthermore, these effects are not due to the physical presence of Matrigel as the same effects are not witnessed in aggregates grown in agarose. Our results thus indicate that Matrigel has a significant and complex effect on the differentiation and morphology of embryoid bodies.
AHL10 phosphorylation determines RRP6L1 chromatin association and growth suppression during water stress
Authors: Wong Min May , Huang Xin-Jie , Bau Yu-Chiuan , Verslues Paul E. 
Published: April 2023

AbstractPhosphorylation of AHL10, one of the AT-hook family of plant-specific DNA binding proteins, is critical for growth suppression during moderate severity drought (low water potential, ψw) stress. To understand how AHL10 phosphorylation determines drought response, we identified putative AHL10 interacting proteins and further characterized interaction with RRP6L1, a protein involved in epigenetic regulation. RRP6L1 and AHL10 mutants, as well asahl10-1rrp6l1-2, had similar phenotype of increased growth maintenance during low ψw. Chromatin precipitation demonstrated that RRP6L1 chromatin association increased during low ψwstress and was dependent upon AHL10 phosphorylation. Transcriptome analyses showed that AHL10 and RRP6L1 have concordant effects on expression of stress- and development-related genes. Together these results indicate that stress signaling can act via AHL10 phosphorylation to control the chromatin association of the key regulatory protein RRP6L1. AHL10 and RRP6L1 interaction in meristem cells is part of a mechanism to down-regulate growth during low ψwstress. Interestingly, loss of AHL13, which is homologous to AHL10 and phosphorylated at similar C-terminal site, blocked the enhanced growth maintenance ofahl10-1. Thus, AHL10 and AHL13, despite their close homology, are not redundant but rather have distinct roles, likely related to the formation of AHL hetero-complexes.Summary StatementPhosphorylation ofArabidopsis thalianaAHL10 is important to control growth during drought stress, a function which is distinct from the closely related AHL13. One way that phosphorylation determines AHL10 function is by altering its ability to mediate chromatin recruitment of RRP6L1.
Transformers enable accurate prediction of acute and chronic chemical toxicity in aquatic organisms
Authors: Gustavsson Mikael , Käll Styrbjörn , Svedberg Patrik , Inda-Diaz Juan S. , Molander Sverker , Coria Jessica , Backhaus Thomas , Kristiansson Erik 
Published: April 2023

AbstractEnvironmental safety assessments, as mandated by many regulations, require that toxicity data is generated for up to three trophic levels, algae, aquatic invertebrates, and fish. Conducting these testsin vivois resource-intensive, time-consuming, and causes undue suffering. Computational methods are fast and cost-efficient alternatives, however, their adaptation in regulatory settings has been slow, both due to low accuracy and narrow applicability domains. Here we present a new method for predicting chemical toxicity based on molecular structure. The method is based on a transformer, capturing structural features associated with toxicity, followed by a deep neural network that predicts the corresponding effect concentrations. After training on data from tens of thousands of exposure experiments, the model shows high predictive performance for each of the three trophic levels. Compared to commonly used QSAR methods, the model has both a larger applicability domain and a considerably lower error. In addition, training the model on data that combines multiple types of effect concentrations further improves the performance. We conclude that transformer-based models have the potential to significantly advance computational predictions of chemical toxicity and makein silicoapproaches a more attractive alternative when compared to animal-based exposure experiments.
BREADR: An R Package for the Bayesian Estimation of Genetic Relatedness from Low-coverage Genotype Data
Authors: Rohrlach Adam B , Tuke Jonathan , Popli Divyaratan , Haak Wolfgang 
Published: April 2023

AbstractRobust and reliable estimates of how individuals are biologically related to each other are a key source of information when reconstructing pedigrees. In combination with contextual data, reconstructed pedigrees can be used to infer possible kinship practices in prehistoric populations. However, standard methods to estimate biological relatedness from genome sequence data cannot be applied to low coverage sequence data, such as are common in ancient DNA (aDNA) studies. Critically, a statistically robust method for assessing and quantifying the confidence of a classification of a specific degree of relatedness for a pair of individuals, using low coverage genome data, is lacking.In this paper we present the R-package BREADR (Biological RElatedness from Ancient DNA in R), which leverages the so-called pairwise mismatch rate, calculated on optimally-thinned genome-wide pseudo-haploid sequence data, to estimate genetic relatedness up to the second degree, assuming an underlying binomial distribution. BREADR also returns a posterior probability for each degree of relatedness, from identical twins/same individual, first-degree, second-degree or “unrelated” pairs, allowing researchers to quantify and report the uncertainty, even for particularly low-coverage data. We show that this method accurately recovers degrees of relatedness for sequence data with coverage as low as 0.04Xusing simulated data, and then compare the performance of BREADR on empirical data from Bronze Age Iberian human sequence data. The BREADR package is designed for pseudo-haploid genotype data, common in aDNA studies.