bluuebunny/crossref_metadata_2025 huggingface dataset:
morphoHeart: a novel quantitative tool to perform integrated 3D morphometric analyses of heart and ECM morphology during embryonic development
Authors: Sánchez-Posada Juliana , Noël Emily S
Published: February 2024

Heart development involves the complex structural remodelling of a linear heart tube into an asymmetrically looped and ballooned organ. Previous studies have associated regional expansion of extracellular matrix (ECM) space with tissue morphogenesis during development. We have developedmorphoHeart, an 3D image tissue segmentation and morphometry software which delivers the first integrated 3D visualisation and multiparametric analysis of both heart and ECM morphology in live embryos.morphoHeartreveals that the ECM undergoes regional dynamic expansion and reduction during cardiac development, concomitant with chamber-specific morphological maturation. We usemorphoHeartto demonstrate that regionalised ECM expansion driven by the ECM crosslinker Hapln1a promotes atrial lumen expansion during heart development. Finally, we have developed a GUI that allows the morphometric analysis tools ofmorphoHeartto be applied toz-stack images of any fluorescently-labelled tissue.
Prevalence and genotypes ofChlamydia psittaciin pet birds of Hong Kong
Authors: Ko Jackie Cheuk Kei , Choi Yannes Wai Yan , Poon Emily Shui Kei , Wyre Nicole , Go Jennifer Le Lin , Poon Leo Lit Man , Sin Simon Yung Wa
Published: February 2024

Psittacosis, or parrot fever, is a zoonotic disease caused byChlamydiaspecies associated with birds. One of the causative agents of the disease isChlamydia psittaci, which is often carried by psittacine and can be highly pathogenic and virulent to humans. In Hong Kong, a city with high population density, psittacosis is a notifiable disease with over 60% of cases in the last decade resulting in hospitalization. However, the source of transmission ofC. psittaciand its prevalence in pet birds in Hong Kong are currently unknown. To evaluate the risks of psittacosis transmission through pet birds, we tested the presence ofC. psittaciand determined its genotypes in samples obtained from 516 captive birds from households, pet shops, and a veterinary hospital in Hong Kong. Results revealed that five samples (0.97%), collected from budgerigars and cockatiels, wereC. psittaci-positive, while 80% of them were obtained from pet shops. The identified strains belonged to genotype A and were closely related to the strain SP15 that was previously discovered in mainland China. Our study highlights the need for genotypingChlamydiaspecies in psittacosis patients to understand their source(s) of origin.
Assessment of the Histone Mark-based Epigenomic Landscape in Human Myometrium at Term Pregnancy
Authors: Wu San-Pin , Quiroz Elvis , Wang Tianyuan , Redecke Skylar Montague , Xu Xin , Lin Lin , Anderson Matthew L. , DeMayo Francesco J.
Published: February 2024

The myometrium plays a critical role during pregnancy as it is responsible for both the structural integrity of the uterus and force generation at term. Emerging studies in mice indicate a dynamic change of the myometrial epigenome and transcriptome during pregnancy to ready the contractile machinery for parturition. However, the regulatory systems underlying myometrial gene expression patterns throughout gestation remain largely unknown. Here we investigated human term pregnant nonlabor myometrial biopsies for transcriptome, enhancer histone mark cistrome, and chromatin conformation pattern mapping. More than thirty-thousand putative enhancers with H3K27ac and H3K4me1 double positive marks were identified in the myometrium. Enriched transcription factor binding motifs include known myometrial regulators AP-1, STAT, NFkB, and PGR among others. Putative myometrial super enhancers are mostly colocalized with progesterone receptor occupying sites and preferentially associated with highly expressing genes, suggesting a conserved role of PGR in regulating the myometrial transcriptome between species. In human myometrial specimens, inferred PGR activities are positively correlated with phospholipase C like 2 (PLCL2)mRNA levels, supporting that PGR may act through this genomic region to promotePLCL2expression. PGR overexpression facilitatedPLCL2gene expression in myometrial cells. Using CRISPR activation, we assessed the functionality of a PGR putative enhancer 35-kilobases upstream of the contractile-restrictive genePLCL2. In summary, results of this study serve as a resource to study gene regulatory mechanisms in the human myometrium at the term pregnancy stage for further advancing women’s health research.
Directed evolution of a bacterial leucyl tRNA in mammalian cells for enhanced noncanonical amino acid mutagenesis
Authors: Huang Rachel L. , Jewel Delilah , Kelemen Rachel E. , Pham Quan , Wang Shu , Roy Soumya Jyoti Singha , Huang Zeyi , Levinson Samantha D. , Sundaresh Bharathi , Miranda Suyen Espinoza , Van Opijnen Tim , Chatterjee Abhishek
Published: February 2024

TheE. colileucyl-tRNA synthetase (EcLeuRS)/tRNAEcLeupair has been engineered to genetically encode a structurally diverse group of enabling noncanonical amino acids (ncAAs) in eukaryotes, including those with bioconjugation handles, environment-sensitive fluorophores, photocaged amino acids, and native post-translational modifications. However, the scope of this toolbox in mammalian cells is limited by the poor activity of tRNAEcLeu. Here, we overcome this limitation by evolving tRNAEcLeudirectly in mammalian cells using a virus-assisted selection scheme. This directed evolution platform was optimized for higher throughput such that the entire acceptor stem of tRNAEcLeucould be simultaneously engineered, which resulted in the identification of several variants with remarkably improved efficiency for incorporating a wide range of ncAAs. The advantage of the evolved leucyl tRNAs was demonstrated by expressing ncAA mutants in mammalian cells that were challenging to express before using the wild-type tRNAEcLeu, by creating viral vectors that facilitated ncAA mutagenesis at a significantly lower dose, and by creating more efficient mammalian cell lines stably expressing the ncAA-incorporation machinery.
Glutathione metabolism impacts fungal virulence by modulating the redox environment
Authors: Black Braydon , da Silva Leandro Buffoni Roque , Hu Guanggan , Qu Xianya , Smith Daniel F. Q. , Magaña Armando Alcázar , Horianopoulos Linda C. , Caza Mélissa , Attarian Rodgoun , Foster Leonard J. , Casadevall Arturo , Kronstad James W.
Published: February 2024

Pathogens must overcome the hostile conditions of their hosts to survive, proliferate and cause disease. The fungal pathogenCryptococcus neoformansis particularly adept at mitigating challenges in the host environment and has developed an arsenal of defense mechanisms to evade oxidative and nitrosative agents released by phagocytic cells during infection. Among these mechanisms, melanin production is crucially linked to both fungal virulence and defense against harmful free radicals that facilitate host innate immunity and clearance of invading pathogens. Here, we employed comparative global metabolomics to demonstrate that metabolism of the antioxidant glutathione (GSH) is inextricably linked to redox-active processes that facilitate melanin production, and that genetic perturbations in GSH biosynthesis affect fungal growth and virulence in a murine model of cryptococcosis. Furthermore, we show that disruption of GSH biosynthesis leads to overaccumulation of reducing and acidic compounds in the extracellular environment of mutant cells. These changes not only impacted melanin formation but also influenced titan cell and urease production as well as survival in macrophages. Overall, these findings highlight the importance of redox homeostasis and metabolic compensation in pathogen adaptation to the host environment and suggest new avenues for antifungal drug development.
Inhibition of Indirect Pathway Activity Causes Abnormal Decision-Making In a Mouse Model of Impulse Control Disorder in Parkinson’s Disease
Authors: Zhuang Xiaowen , Lemak Julia , Sridhar Sadhana , Nelson Alexandra B.
Published: February 2024

Healthy action selection relies on the coordinated activity of striatal direct and indirect pathway neurons. In Parkinson’s disease (PD), in which loss of midbrain dopamine neurons is associated with progressive motor and cognitive deficits, this coordination is disrupted. Dopamine replacement therapy can remediate motor symptoms, but can also cause impulse control disorder (ICD), which is characterized by pathological gambling, hypersexuality, and/or compulsive shopping. The cellular and circuit mechanisms of ICD remain unknown. Here we developed a mouse model of PD/ICD, in which ICD-like behavior was assayed with a delay discounting task. We found that in parkinsonian mice, the dopamine agonist pramipexole drove more pronounced delay discounting, as well as disrupted firing in both direct and indirect pathway neurons. We found that chemogenetic inhibition of indirect pathway neurons in parkinsonian mice drove similar phenotypes. Together, these findings provide a new mouse model and insights into ICD pathophysiology.
TUnA: An uncertainty aware transformer model for sequence-based protein-protein interaction prediction
Authors: Ko Young Su , Parkinson Jonathan , Liu Cong , Wang Wei
Published: February 2024

Protein-protein interactions (PPIs) are important for many biological processes, but predicting them from sequence data remains challenging. Existing deep learning models often cannot generalize to proteins not present in the training set, and do not provide uncertainty estimates for their predictions. To address these limitations, we present TUnA, a Transformer-based uncertainty aware model for PPI prediction. TUnA uses ESM-2 embeddings with Transformer encoders and incorporates a Spectral-normalized Neural Gaussian Process. TUnA achieves state-of-the-art performance and, importantly, evaluates uncertainty for unseen sequences. We demonstrate that TUnA’s uncertainty estimates can effectively identify the most reliable predictions, significantly reducing false positives. This capability is crucial in bridging the gap between computational predictions and experimental validation.
The Generalized Haldane (GH) model of genetic drift resolving the many paradoxes of molecular evolution
Authors: Ruan Yongsen , Wang Xiaopei , Hou Mei , Huang Liying , Diao Wenjie , Tracy Miles , Xu Shuhua , Liufu Zhongqi , Wen Haijun , Wu Chung-I
Published: February 2024

Genetic drift, the random changes in frequencies of neutral variants, is the fundamental force of molecular evolution. However, the standard Wright-Fisher (WF) model of random sampling in population of sizeNonly partially defines genetic drift with 1/Nor 1/Ne(Nebeing a function of varyingN’s). In parallel, JBS Haldane (1927) proposed the branching process for genetic drift, whereby each gene copy is transmitted toKdescendants with the mean and variance ofE(K) andV(K). WhereasNis externally imposed on the standard and modified WF models, the Haldane model can be generalized (hence, the GH model) for regulatingN’s internally as a function ofE(K). The determination ofN, as well as the broader definition of genetic drift based onV(K), enables the GH model to account for many paradoxes of molecular evolution. They include: i) Genetic drift may often become stronger asNbecomes larger; ii) The two sexes experience drift differently; iii) Genetic drift operates on advantageous mutations is independent ofN; iv) Irresolution and paradoxes emerge in multi-copy gene systems (viruses, mitochondria, etc.) whereby genetic drift happens within and between individuals. We show how a GH model can resolve these paradoxes that elude the WF models. By integrating their results, GH models may supplant the WF models of genetic drift for the ever more complex biological systems.
Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages
Authors: Zeng Tao , Cao Yongqing , Yin Jianmei , Feng Peishi , Tian Yong , Sun Hanxue , Gu Tiantian , Zong Yibo , Ma Xueying , Zhao Zelong , Chen Li , Xu Wenwu , Han Wei , Lu Lizhi
Published: February 2024

Tibetan animals have several unique advantages owing to the harsh ecological conditions under which they live. Tibetan mammals have been studied extensively. However, understanding of the advantages and underlying mechanisms of the representative high-latitude bird, the Tibetan chicken (Gallus gallus, TC), remains limited. The gut microbiota of animals has been conclusively shown to be closely related to both host health and host environmental adaptation. This study aimed to explore the relationships between the cecal microbiome and the advantages of TCs based on comparisons among three populations: native TCs residing on the plateau, domestic TCs living in the plain, and one native plain species. Metatranscriptomic sequencing revealed a significant enrichment of active Bacteroidetes but a loss of active Firmicutes in native TCs. Additionally, the upregulated expression of genes in the cecal microbiome of native TCs showed enriched pathways related to energy metabolism, glycan metabolism, and the immune response. Furthermore, the expression of genes involved in the biosynthesis of short-chain fatty acids (SCFAs) and secondary bile acids (SBAs) was upregulated in the cecal microbiome of native TCs. Data from targeted metabolomics further confirmed elevated levels of certain SCFAs and SBAs in the cecum of native TCs. Based on the multi-omics association analysis, we proposed that the higher ratio of active Bacteroidetes/Firmicutes may be attributed to the efficient energy metabolism and stronger immunological activity of native TCs. Our findings provide a better understanding of the interactions between gut microbiota and highland adaptation, and novel insights into the mechanisms by which Tibetan chickens adapt to the plateau hypoxic environment.

IMPORTANCE

The composition and function of the active cecal microbiome were significantly different between the plateau Tibetan chicken population and the plain chicken population. Higher expression genes related to energy metabolism and immune response were found in the cecal microbiome of the plateau Tibetan chicken population. The cecal microbiome in the plateau Tibetan chicken population exhibited higher biosynthesis of short-chain fatty and secondary bile acids, resulting in higher cecal content of these metabolites. The active Bacteroidetes/Firmicutes ratio in the cecal microbiome may contribute to the high-altitude adaptive advantage of the plateau Tibetan chicken population.
Simple prerequisite of presequence for mitochondrial protein import in the unicellular red algaCyanidioschyzon merolae
Authors: Hirata Riko , Mogi Yuko , Takahashi Kohei , Nozaki Hisayoshi , Higashiyama Tetsuya , Yoshida Yamato
Published: February 2024

Mitochondrial biogenesis relies on hundreds of proteins which are derived from genes encoded in the nucleus. According to characteristic properties of N-terminal targeting peptides (TP) and multi-step authentication by the protein translocase called the TOM complex, nascent polypeptides satisfying the requirements are imported into mitochondria. However, it has not been investigated whether the eukaryotic cell with a simple proteome and a single mitochondrion in a cell has a similar or simpler complexity of presequence requirements for mitochondrial protein import as other eukaryotes with multiple mitochondria. Based on the amino acid compositions of putative mitochondrial TP sequences in the unicellular red algaCyanidioschyzon merolae, we designed the synthetic TP (synTP) and confirmed that synTP-fused mVenus were translocated into the mitochondrionin vivo. Through a series of experimental evaluations using modified synTPs, we showed that functional TP must have some basic residues, at least one, and compose the specific amino acid composition, but the physicochemical properties of net charge, hydrophobicity and hydrophobic moment are not strictly determined inC. merolae. Combined with the simple composition of the TOM complex inC. merolae, our results suggest that a regional positive charge in TP would be recognized and verified solely by TOM22 as a single-step authentication for mitochondrial protein import inC. merolae. The simple authentication mechanism indicates that theC. merolaecell, with its simple cell structure and genome, would not need to increase the cryptographic complexity of the lock-and-key for mitochondrial protein import.
Proteomic comparison of epidemic AustralianBordetella pertussisbiofilm cells
Authors: Suyama Hiroki , Luu Laurence Don Wai , Zhong Ling , Raftery Mark J. , Lan Ruiting
Published: February 2024

Bordetella pertussiscauses whooping cough, a severe respiratory infectious disease. Studies have compared the currently dominant single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele,ptxP3) and previously dominant SNP cluster II (ptxP1) strains as planktonic cells. Since biofilm formation is linked withB. pertussispathogenesisin vivo, this study compared the biofilm formation capabilities of representative strains of cluster I and cluster II. Confocal laser scanning microscopy found that the cluster I strain had a denser biofilm structure compared to the cluster II strain. Differences in protein expression of the biofilm cells were then compared using Tandem Mass Tagging (TMT) and high-resolution multiple reaction monitoring (MRM-hr). In total, 1453 proteins were identified of which 40 proteins had significant differential expression between the two strains in biofilm conditions. Of particular interest was a large increase in expression of energy metabolism proteins (cytochrome proteins PetABC and BP3650) in the cluster I strain. When the expression of these proteins was compared between 6 additional strains from each cluster, it was found that the protein expression varied between all strains. These findings suggest that there are large levels of individual proteomic diversity betweenB. pertussisstrains in biofilm conditions despite the highly conserved genome of the species. Overall, this study revealed visual differences in biofilm structure betweenB. pertussisstrains and highlighted strain specific variation in protein expression that dominate potential cluster specific changes that may be linked with the dominance of cluster I strains.

Importance

Bordetella pertussiscauses whooping cough. The currently circulating cluster I strains have taken over previously dominant cluster II strains. It is important to understand the reasons behind the evolution to develop new strategies against the pathogen. Recent studies have shown thatB. pertussiscan form biofilms during infection. This study compared the biofilm formation capabilities of a cluster I and a cluster II strain and identified visual differences in the biofilms. The protein expression between these strains grown in biofilms were compared and proteins identified with varied expression were measured with additional strains from each cluster. It was found that despite the highly conserved genetics of the species, there was varied protein expression between the additional strains. This study highlights that strain specific variation in protein expression during biofilm conditions that may dominate the cluster specific changes that may be linked to the dominance of cluster I strains.
Fine-tuning BERT models to extract transcriptional regulatory interactions of bacteria from biomedical literature
Authors: Varela-Vega Alfredo , Posada-Reyes Ali-Berenice , Méndez-Cruz Carlos-Francisco
Published: February 2024

Abstract

Curation of biomedical literature has been the traditional approach to extract relevant biological knowledge; however, this is time-consuming and demanding. Recently, Large language models (LLMs) based on pre-trained transformers have addressed biomedical relation extraction tasks outperforming classical machine learning approaches. Nevertheless, LLMs have not been used for the extraction of transcriptional regulatory interactions between transcription factors and regulated elements (genes or operons) of bacteria, a first step to reconstruct a transcriptional regulatory network (TRN). These networks are incomplete or missing for many bacteria. We compared six state-of-the-art BERT architectures (BERT, BioBERT, BioLinkBERT, BioMegatron, BioRoBERTa, LUKE) for extracting this type of regulatory interactions. We fine-tuned 72 models to classify sentences in four categories:activator,repressor,regulator, andno relation. A dataset of 1562 sentences manually curated from literature ofEscherichia coliwas utilized. The best model of LUKE architecture obtained a relevant performance in the evaluation dataset (Precision: 0.8601, Recall: 0.8788, F1-Score Macro: 0.8685, MCC: 0.8163). An examination of model predictions revealed that the model learned different ways to express the regulatory effect. The model was applied to reconstruct a TRN ofSalmonellaTyphimurium using 264 complete articles. We were able to accurately reconstruct 82% of the network. A network analysis confirmed that the transcription factor PhoP regulated many genes (uppermost degree), some of them responsible for antimicrobial resistance. Our work is a starting point to address the limitations of curating regulatory interactions, especially for the reconstruction of TRNs of bacteria or diseases of biological interest.
Multilevel proteomic profiling of colorectal adenocarcinoma cell differentiation to characterize an intestinal epithelial model
Authors: Fekete Emily EF , Wang Angela , Creskey Marybeth , Cummings Sarah E , Lavoie Jessie R , Ning Zhibin , Li Jianjun , Figeys Daniel , Chen Rui , Zhang Xu
Published: February 2024

Emergent advancements on the intestinal microbiome for human health and disease treatment necessitates well-defined intestinal cellular models to study and rapidly assess host, microbiome, and drug interactions. This study characterized molecular alterations during Caco-2 cell differentiation, an epithelial intestinal model, using quantitative multi-omic approaches. We demonstrated that both spontaneous and medium-induced cellular differentiations displayed similar protein and pathway changes, including the down-regulation of proteins related to translation and proliferation, and up-regulation of proteins related to cell adhesion, molecule binding and metabolic pathways. Acetyl-proteomics revealed decreased histone acetylation and increased acetylation in proteins associated with mitochondria functions in differentiated cells. Butyrate-containing differentiation medium accelerates differentiation, with earlier up-regulation of proteins related to differentiation and host-microbiome interactions. These results emphasize the controlled progression of Caco-2 differentiation toward a specialized intestinal epithelial-like cell. This further enhances their characterization, establishing their suitability for facilitating the effective evaluation of risk and quality in microbiome-directed therapeutics.
Gene Therapy Mediates Therapeutic Improvement in Cardiac Hypertrophy and Survival in a Murine Model ofMYBPC3-Associated Cardiomyopathy
Authors: Greer-Short Amara , Greenwood Anna , Leon Elena C. , Qureshi Tawny Neal , von Kraut Konor , Wong Justin , Reid Christopher A. , Cheng Ze , Easter Emilee , Yang Jin , Ho Jaclyn , Steltzer Stephanie , Budan Ana , Cho Marie , Feathers Charles , Chung Tae Won , Rodriguez Neshel , Jones Samantha , Alleyne-Levy Chris , Liu Jun , Jing Frank , Prince William S. , Lin JianMin , Ivey Kathryn N. , Tingley Whittemore G. , Hoey Timothy , Lombardi Laura M.
Published: February 2024

Background

Hypertrophic cardiomyopathy (HCM) affects an estimated 600,000 people in the U.S. and is the leading cause of sudden cardiac arrest in those under 18. Loss-of-function mutations inMyosin Binding Protein C3,MYBPC3, are the most common genetic cause of HCM. The majority ofMYBPC3mutations causative for HCM result in truncations. The sarcomeric pathophysiology of the majority of HCM patients withMYBPC3mutations appears to be due to haploinsufficiency, as the total amount of MYBPC3 protein incorporated into sarcomeres falls significantly below normal.

Methods

A clear path for the treatment of haploinsufficiency is the restoration of the insufficient gene product; in this case wild-type MYBPC3. To achieve this, we engineered an AAV vector (TN-201) with superior properties for mediating cardiomyocyte-selective expression of MYBPC3 after systemic delivery.

Results

We have demonstrated for the first time with AAV gene therapy the ability of both a mouse surrogate and TN-201, which encodes human MYBPC3 to reverse cardiac hypertrophy and systolic dysfunction and to improve diastolic dysfunction and survival in a symptomatic MYBPC3-deficient murine model of disease. Dose-ranging efficacy studies exhibited restoration of wild-type MYBPC3 protein levels and saturation of cardiac improvement at the clinically relevant dose of 3E13 vg/kg, outperforming a previously published construct. Further, we have established stable cardiac benefit for greater than one year post-injection, as well as reversal of cardiac dysfunction even in late-stage models of disease.

Conclusions

Our data suggest that by restoring MYBPC3 to the sarcomere, TN-201 has the potential to slow and even reverse the course of the disease in patients withMYBPC3-associated HCM.
Interactive visualisation of raw nanopore signal data with Squigualiser
Authors: Samarakoon Hiruna , Liyanage Kisaru , Ferguson James M. , Parameswaran Sri , Gamaarachchi Hasindu , Deveson Ira W.
Published: February 2024

Nanopore sequencing measures ionic current during the translocation of DNA, RNA or protein molecules through a nanoscale protein pore. This raw current signal data can be ‘basecalled’ into sequence information and has the potential to identify other diverse molecular features, such as base modifications, secondary structures, etc. Despite the unique properties and potential utility of nanopore signal data, there are currently limited options available for signal data visualisation. To address this, we have developedSquigualiser, a toolkit for intuitive, interactive visualisation of sequence-aligned signal data, which currently supports both DNA and RNA sequencing data from Oxford Nanopore Technologies (ONT) instruments. A series of methodological innovations enable efficient alignment of raw signal data to a reference genome/transcriptome with single-base resolution.Squigualisergenerates an interactive signal browser view (HTML file), in which the user can navigate across a genome/transcriptome region and customise the display. Multiple independent reads are integrated into a signal ‘pileup’ format and different datasets can be displayed as parallel tracks to facilitate their comparison.Squigualiserprovides the most sophisticated framework for nanopore signal data visualisation to date and will catalyse new advances in signal analysis. We provideSquigualiseras an open-source tool for the nanopore community:https://github.com/hiruna72/squigualiser
A pangenome analysis of ESKAPE bacteriophages: the underrepresentation may impact machine learning models
Authors: Lee Jeesu , Hunter Branden , Shim Hyunjin
Published: February 2024

Bacteriophages are the most prevalent biological entities in the biosphere. However, limitations in both medical relevance and sequencing technologies have led to a systematic underestimation of the genetic diversity within phages. This underrepresentation not only creates a significant gap in our understanding of phage roles across diverse biosystems but also introduces biases in computational models reliant on these data for training and testing. In this study, we focused on publicly available genomes of bacteriophages infecting high-priority ESKAPE pathogens to show the extent and impact of this underrepresentation. First, we demonstrate a stark underrepresentation of ESKAPE phage genomes within the public genome and protein databases. Next, a pangenome analysis of these ESKAPE phages reveals extensive sharing of core genes among phages infecting the same host. Furthermore, genome analyses and clustering highlight close nucleotide-level relationships among the ESKAPE phages, raising concerns about the limited diversity within current public databases. Lastly, we uncover a scarcity of unique lytic phages and phage proteins with antimicrobial activities against ESKAPE pathogens. This comprehensive analysis of the ESKAPE phages underscores the severity of underrepresentation and its potential implications. This lack of diversity in phage genomes may restrict the resurgence of phage therapy and cause biased outcomes in data-driven computational models due to incomplete and unbalanced biological datasets.
Phylogeny predicts tolerance in aquatic animals for only a minority of chemicals
Authors: Coleman Alice L. , Edmands Suzanne
Published: February 2024

There are substantial gaps in our empirical knowledge of the effects of chemical exposure on aquatic life that are unlikely to be filled by traditional laboratory toxicity testing alone. One possible alternative of generating new toxicity data is cross-species extrapolation (CSE), a statistical approach in which existing data are used to predict the effect of a chemical on untested species. Some CSE models use relatedness as a predictor of chemical sensitivity, but relatively little is known about how strongly shared evolutionary history influences sensitivity across all chemicals. To address this question, we conducted a survey of phylogenetic signal in the toxicity data from aquatic animal species for a large set of chemicals using a phylogeny inferred from taxonomy. Strong phylogenetic signal was present in just six of thirty-two toxicity datasets, and there were no clear shared properties among those datasets with strong signal. Strong signal was rare even among chemicals specifically developed to target insects, meaning that these chemicals may be equally lethal to non-target taxa, including chordates. When signal was strong, distinct patterns of sensitivity were evident in the data, which may be informative when assembling toxicity datasets for regulatory use. Although strong signal does not appear to manifest in aquatic toxicity data for most chemicals, we encourage additional phylogenetic evaluations of toxicity data in order to guide the selection of CSE tools and as a means to explore the patterns of chemical sensitivity across the broad diversity of life.
Circadian clocks in human cerebral organoids
Authors: Rzechorzek Nina M , Sutcliffe Magdalena A , Mihut Andrei , Baranes Koby , Karam Nuzli , Sánchez Daniel Lloyd-Davies , Peak-Chew Sew Y , Zeng Aiwei , Poulin Noah , Seinkmane Estere , Karim Kaiser , Proctor Christopher M , Kotter Mark , Lancaster Madeline A , Beale Andrew D
Published: February 2024

Circadian rhythms result from cell-intrinsic timing mechanisms that impact health and disease1,2. To date, however, neural circadian research has largely focused on the hypothalamic circuitry of nocturnal rodents3. Whether circadian rhythms exist in human brain cells is unknown. Here we showbona fidecircadian rhythms in human neurons, glia, cerebral organoids, and cerebral organoid slices (ALI-COs)4–8. Human neural circadian rhythms are synchronised by physiological timing cues such as glucocorticoids and daily temperature cycles, and these rhythms are temperature-compensated across the range of normal human brain temperatures9. Astrocyte rhythms are phase-advanced relative to other cultures and they modulate neuronal clock responses to temperature shift. Cerebral organoid rhythms are more robust at physiological brain temperatures; the relative amplitude of these rhythms increases over time in culture and their resetting capacity recapitulates key neurodevelopmental transitions in glucocorticoid signalling10–14. Remarkably, organoid post-transcriptional bioluminescent clock reporter rhythms are retained even when those of their putative transcriptional drivers are indiscernible15, and electrophysiology recordings confirm circadian rhythms in functional activity of monocultures, organoids, and ALI-COs. Around one third of the cerebral organoid proteome and phosphoproteome are circadian-rhythmic, with temporal consolidation of disease-relevant neural processes. Finally, we show that human brain organoid rhythms can be modulated and disrupted by commonly used brain-permeant drugs and mistimed cortisol exposure, respectively. Our results demonstrate that human brain cells and tissues develop their own circadian oscillations and that canonical mechanisms of the circadian clockwork may be inadequate to explain these rhythmic phenomena. 2D and 3D human neural cultures represent complementary and tractable models for exploring the emergence, disruption, and mechanics of the circadian neural clockwork, with important implications for chronobiology, brain function, and brain health.
Busted: maternal modifiers of the triploid block involved in seed size control
Authors: Akinmusola Ruth Y. , Kilsby Harvey , Wilkins Catherine-Axa , Cevik Volkan , Scott Rod , Doughty James
Published: February 2024

The triploid block leads to seed abortion in crosses involving tetraploid Col-0 pollen. The genetic basis underlying this phenomenon is established in the endosperm and attributed to parental genomic imprinting. This research utilised the genetic variation in Arabidopsis to identify the genomic regions harbouring the maternal modifiers of the triploid block to produce viable large seeds. Distinct chromosomal regions were identified in Bla-1 and Tsu-0 accessions. The Bla-1 maternal modifier maps to theTTG2locus at the lower end of chromosome 2 to produce large viable seeds in response to a triploid block. Tsu-0 accession, on the other hand, recruits theTTG1locus on the upper arm of chromosome 5 as a maternal modifier of the triploid block.TTG1andTTG2mutations significantly increased the proportion of large viable seeds in interploidy crosses. Both genes are involved in transcriptional regulation in the flavonoid biosynthesis pathway. However, to regulate seed size in diploids,TTG1functions synergistically with auxin but does so independently ofTTG2. This work contributed to the genetic framework for theTTG1andTTG2seed size roles.

HIGHLIGHTS

Different Arabidopsis accessions recruit maternal modifiers to repress Col-killing in F1triploids.

These maternal modifiers may operate in the same pathway, such as the flavonoid biosynthesis pathway or other interconnected pathways such as auxin.

TTG1andTTG2generally increase F1triploid survival but in an accession-dependent manner.

TTG1differentially exhibits a strong positive additive interaction with auxin to increase diploid seed size.

TheTTG1/TTG2roles in diploid seed size control appear to have diverged somewhere in the auxin branch of the flavonoid biosynthesis pathway.
Ovarian disrupting effects and mechanisms of long- and short-chain per- and polyfluoroalkyl substances in mice
Authors: Pattarawat Pawat , Zhan Tingjie , Fan Yihan , Zhang Jiyang , Yang Hilly , Zhang Ying , Moyd Sarahna , Douglas Nataki C. , Urbanek Margrit , Buckley Brian , Burdette Joanna , Zhang Qiang , Kim Ji-Yong Julie , Xiao Shuo
Published: February 2024

Background

The extensive use of per- and polyfluoroalkyl substances (PFAS) has led to environmental contamination and bioaccumulation. Previous research linked PFAS exposure to female reproductive disorders, but the mechanism remains elusive. Further, most studies focused on legacy long-chain PFOA and PFOS, yet the reproductive impacts of other long-chain PFAS and short-chain alternatives are rarely explored.

Objectives

We investigated the effects and mechanisms of long- and short-chain PFAS on the ovary and associated ovarian functions.

Methods

A 3Din vitroovarian follicle culture system and anin vivomouse model, together with approaches of reverse transcription-quantitative polymerase chain reaction, enzyme-linked immunosorbent assay, RNA-sequencing, pharmacological treatment,in situzymography, histology,in situhybridization, analytical chemistry, and benchmark dose modeling (BMD), were used to test environmentally relevant exposure levels of six long- and short-chain PFAS on follicle maturation, hormone secretion, and ovulation.

Results

In vitroexposure revealed that long-but not short-chain PFAS interfered with gonadotropin-dependent follicle maturation, ovulation, and hormone secretion. Mechanistically, long-chain perfluorononanoic acid (PFNA) acted as a peroxisome proliferator-activated receptor gamma (PPARγ) agonist in granulosa cells to disrupt follicle-stimulating hormone (FSH)-dependent follicle maturation, luteinizing hormone (LH)-stimulated ovulation, and associated gene regulatory pathways.In vivomouse exposure confirmed the ovarian accumulation of PFNA and the mechanism of PPARγ-mediated ovarian toxicities of PFNA observedin vitro. The BMD analysis ofin vitroandin vivoresults suggested human relevant exposure levels of long-chain PFAS in our study pose an extra risk of ovarian defects, with follicular rupture as the most sensitive endpoint.

Discussion

Usingin vitrofollicle culture andin vivomouse models, we discovered that long-chain PFAS interfere with gonadotropin-dependent follicle maturation, hormone secretion, and ovulation, posing a non-negligible risk to women’s reproductive health including anovulation, irregular menstrual cycles, and sub- or infertility.
Antibody-Drug Conjugates Targeting the EGFR Ligand Epiregulin Elicit Robust Anti-Tumor Activity in Colorectal Cancer
Authors: Jacob Joan , Anami Yasuaki , High Peyton , Liang Zhengdong , Subramanian Shraddha , Ghosh Sukhen C. , AghaAmiri Solmaz , Guernsey-Biddle Cara , Tran Ha , Rowe Julie H. , Azhdarinia Ali , Tsuchikama Kyoji , Carmon Kendra S.
Published: February 2024

As colorectal cancer (CRC) remains a leading cause of cancer-related death, identifying therapeutic targets and approaches is essential to improve patient outcomes. The EGFR ligand epiregulin (EREG) is highly expressed in RAS wildtype and mutant CRC with minimal expression in normal tissues, making it an attractive target for antibody-drug conjugate (ADC) development. In this study, we produced and purified an EREG monoclonal antibody (mAb), H231, that had high specificity and affinity for human and mouse EREG. H231 also internalized to lysosomes, which is important for ADC payload release. ImmunoPET andex vivobiodistribution studies showed significant tumor uptake of89Zr-labeled H231 with minimal uptake in normal tissues. H231 was conjugated to either cleavable dipeptide or tripeptide chemical linkers attached to the DNA-alkylating payload duocarmycin DM, and cytotoxicity of EREG ADCs was assessed in a panel of CRC cell lines. EREG ADCs incorporating tripeptide linkers demonstrated the highest potency in EREG-expressing CRC cells irrespective of RAS mutations. Preclinical safety and efficacy studies showed EREG ADCs were well-tolerated, neutralized EGFR pathway activity, caused significant tumor growth inhibition or regression, and increased survival in CRC cell line and patient-derived xenograft models. These data suggest EREG is a promising target for the development of ADCs for treating CRC and other cancer types that express high levels of EREG. While the efficacy of clinically approved anti-EGFR mAbs are largely limited by RAS mutational status, EREG ADCs may show promise for both RAS mutant and wildtype patients, thus improving existing treatment options.

Significance:EREG-targeting antibody-drug conjugates demonstrate acceptable safety and robust therapeutic efficacy in RAS mutant and wildtype colorectal cancer, suggesting their potential as an alternative to EGFR-targeted therapy to benefit a broader patient population.
SpacerPlacer: Ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions
Authors: Fehrenbach Axel , Mitrofanov Alexander , Alkhnbashi Omer S. , Backofen Rolf , Baumdicker Franz
Published: February 2024

Bacteria employ CRISPR-Cas systems for defense by integrating invader-derived sequences, termed spacers, into the CRISPR array, which constitutes an immunity memory. While spacer deletions occur randomly across the array, newly acquired spacers are predominantly integrated at the leader end. Consequently, spacer arrays can be used to derive the chronology of spacer insertions.

Reconstruction of ancestral spacer acquisitions and deletions could help unravel the coevolution of phages and bacteria, the evolutionary dynamics in microbiomes, or track pathogens. However, standard reconstruction methods produce misleading results by overlooking insertion order and joint deletions of spacers.

Here, we present SpacerPlacer, a maximum likelihood-based ancestral reconstruction approach for CRISPR array evolution. We used SpacerPlacer to reconstruct and investigate ancestral deletion events of 4565 CRISPR arrays, revealing that spacer deletions occur 374 times more frequently than mutations and are regularly deleted jointly, with an average of 2.7 spacers. Surprisingly, we observed a decrease in the spacer deletion frequency towardsbothends of the reconstructed arrays. While the resulting trailer-end conservation is commonly observed, a reduced deletion frequency is now also detectable towards the variable leader end. Finally, our results point to the hypothesis that frequent loss of recently acquired spacers may provide a selective advantage.
The SAS Chromatin-Remodeling Complex Mediates Inflorescence-Specific Chromatin Accessibility for Transcription Factor Binding
Authors: Guo Jing , Liu Zhen-Zhen , Su Yin-Na , He Xin-Jian
Published: February 2024

While the role of transcription factors in flower development is well understood, the impact of chromatin remodeling on this process remains largely unclear. We conducted a comprehensive analysis to investigate the coordination of the SAS, BAS, and MAS-type SWI/SNF chromatin-remodeling complexes with transcription factors to regulate chromatin accessibility and gene transcription during flower development inArabidopsis thaliana. Our findings indicate that the SAS complex binds to numerous genes related to flower development and is responsible for establishing chromatin accessibility of these genes during flower development. In contrast, the BAS and MAS complexes exhibit minimal involvement in regulating the accessibility of these genes. The SAS-bound genomic regions and the SAS-dependent accessible regions are enriched with sites occupied by multiple MADS family transcription factors involved in flower development. Furthermore, we found that the SAS-dependent accessibility is indispensable for the genomic binding of the MADS transcription factor AP1 at these regions. This study highlights the dynamic role of the SAS complex in modulating the genomic binding of transcription factors during plant development.

One-sentence summary

The SAS-type SWI/SNF complex regulates Inflorescence-specific chromatin accessibility at distal promoter and upstream intergenic regions, thereby facilitating the binding of transcription factors involved in flower development.
Predicting species invasiveness with genomic data: is Genomic Offset related to establishment probability?
Authors: Camus Louise , Gautier Mathieu , Boitard Simon
Published: February 2024

Predicting the risk of establishment and spread of populations outside their native range represents a major challenge in evolutionary biology. Various methods have recently been developed to estimate population (mal)adaptation to a new environment with genomic data via so-called Genomic Offset (GO) statistics. These approaches are particularly promising for studying invasive species, but have still rarely been used in this context. Here, we evaluated the relationship between GO and the estab-lishment probability of a population in a new environment using both in silico and empirical data. First, we designed invasion simulations to evaluate the ability to predict establishment probability of two GO computation methods (Geometric GO and Gradient Forest) under several conditions. Additionally, we aimed to evaluate the interpretability of absolute Geometric GO values, which the-oretically represent the adaptive genetic distance between populations from distinct environments. Second, utilizing public real data from the crop pest speciesBactrocera tryoni, a fruit fly native from Northern Australia, we computed GO between “source” populations and a diverse range of locations within invaded areas. This practical application of GO within the context of a biological invasion underscores its potential in providing insights and guiding recommendations for future invasion risk assessment. Overall, our results suggest that GO statistics represent good predictors of the estab-lishment probability and may thus inform invasion risk, although the influence of several factors on prediction performance (e.g. propagule pressure or admixture) will need further investigation.
The Rift Valley fever (RVF) vaccine candidate 40Fp8 shows an extreme attenuation in IFNARKO mice following intranasal inoculation
Authors: Borrego Belén , Alonso Celia , Moreno Sandra , de la Losa Nuria , Sánchez-Cordón Pedro J. , Brun Alejandro
Published: February 2024

Rift Valley fever (RVF) is an important zoonotic viral disease affecting several species of domestic and wild ruminants, causing major economic losses and dozens of human deaths in various geographical areas of Africa, where it is endemic. Although it is not present in Europe, there is a risk of its introduction and spread linked to globalisation and climate change. At present, the only measure that could help to prevent the disease is vaccination of flocks in areas at risk of RVF. Available live attenuated vaccines are an effective means of controlling the disease, but their use is often questioned due to residual virulence, particularly in susceptible hosts such as pregnant sheep. On the other hand, no vaccine is currently licensed for use in humans. The development of safe and effective vaccines is therefore a major area of research.

In previous studies, we selected under selective mutagenic pressure a highly attenuated RVFV 56/74 virus variant called 40Fp8. This virus showed an extremely attenuated phenotype in both wild-type and immunodeficient A129 (IFNARKO) mice, yet was still able to induce protective immunity after a single inoculation, thus supporting its use as a safe, live attenuated vaccine. To further investigate its safety, in this work we have analysed the attenuation level of 40Fp8 in immunosuppressed mice (A129) when administered by the intranasal route, and compared it with other attenuated RVF viruses that are the basis of vaccines in use or in development. Our results show that 40Fp8 has a much higher attenuated level than these other viruses and confirm its potential as a candidate for safe RVF vaccine development.

Author Summary

Vaccines that use attenuated viruses are highly effective in terms of providing protection, duration, breadth, and quality of the immune response. However, they may pose a risk to immunosuppressed individuals or in certain situations, such as during pregnancy. It is therefore important to analyze the residual virulence of attenuated vaccines to ensure their safety. In this work, we analysed the safety of the RVF virus vaccine variant 40Fp8 developed in our laboratory. We studied its effect on immunodeficient mice and used a more aggressive route of administration such as the intranasal delivery route. To assess the degree of attenuation of 40Fp8, we compared it with other attenuated prototype RVF vaccines. The results clearly demonstrate that 40Fp8 is highly attenuated, and its residual virulence level is extremely low compared to other vaccine viruses tested.