bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genome ofGallaecimonas pentaromativoransstrain 10A, isolated from a Pacific oyster, reveals the potential for hydrocarbon degradation and CRISPR-Cas defense
Authors: Gouin Yasmine , Wilcockson Adam , Zhong Kevin Xu , Chan Amy M. , Suttle Curtis A. 
Published: October 2024

AbstractBacteria in the genusGallaecimonasare known for their ability to breakdown complex hydrocarbons, making them of particular ecological and biotechnological significance. However, few species have been isolated to date, and their ecological distribution has yet to be examined. Here, we report a novel bacterium in the genusGallaecimonas, designated asG. pentaromativoransstrain 10A, which was isolated from a Pacific oyster (Magallana gigas, a.k.a.Crassostrea gigas) collected from a farm experiencing a mass mortality event in British Columbia, Canada.G. pentaromativoransstrain 10A is a rod-shaped, motile bacterium and has a circular genome of 4,322,156 bp encoding 3,928 protein-coding sequences (CDS). Phylogenetic analysis showed that strain 10A is closely related to members ofG. pentaromativorans.Like otherGallaecimonasmembers, strain 10A harbours specific pathways involved in degrading polycyclic aromatic hydrocarbons (PAHs) and xenobiotic compounds, producing biosurfactants, and assimilating nitrate and sulfate; however, it is uniquely equipped with an additional 166 genes belonging to 147 protein families, including a putativehigB-higAthat likely contributes to enhanced stress response. Strain 10A also possesses clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems (CRISPR-Cas), prevalent inGallaecimonas(detected in three out of four species), implying a potential defense mechanism against exogenous mobile genetic elements such as plasmids and viruses. We also mined publicly available databases to establish the widespread distribution of bacteria in the genusGallaecimonasin seawater, sediments, and freshwater across latitude, suggesting its versatility and importance to environmental processes. Ultimately, this study demonstrates that the genome ofGallaecimonas pentaromativoransstrain 10A, isolated from a diseased Pacific oyster, encodes for a suite of putative functions, including oil degradation, xenobiotic breakdown, biosurfactants production, assimilatory nitrate and sulfate reduction, and viral defense. This plasticity and breadth in metabolic function help to explain the cosmopolitan distribution of members of this genus.
PIRATE: Plundering AlphaFold Predictions to Automate Protein Engineering
Authors: Richardson Graham , Kopec Jola , Esposito Carmen , James Tim 
Published: October 2024

AbstractAn important characteristic for many proteins is the presence of flexible loops or linkers known as intrinsically disordered regions. One downside to many of the state-of-the-art disorder prediction approaches is that they require significant computational time for each inference. Here, we introduce three novel surrogate models trained on AlphaFold2 predictions that rapidly encode local, regional, and global structural properties directly from primary sequence. We combined the outputs from these surrogate models, in an approach we term PIRATE, and show that this approach approximates the performance of AlphaFold2 for disorder prediction. Additionally, we show that PIRATE is much more sensitive to the effects of point mutants on disorder at distal sites than many current disorder prediction methods. Furthermore, we show that in the context of a greedy exploration algorithm, PIRATE’s ability to evaluate differences between point mutants makes it ideal for automating disorder-related protein engineering tasks.
Diversity and evolution of Radiolaria: Beyond the stars of the ocean
Authors: Sandin Miguel M. , Renaudie Johan , Suzuki Noritoshi , Not Fabrice 
Published: October 2024

AbstractSince Ernst Haeckel and the Challenger expedition (1872-1876), Radiolaria have been known as ubiquitous and abundant star-shaped oceanic plankton. Their exquisite biomineralized skeletons have left an extensive fossil record which is extremely valuable for biostratigraphic and paleo-environmental research. In contemporary oceans, there is growing evidence that Radiolaria are significant contributors to marine food webs and global biogeochemical cycles. Here we provide a comprehensive morpho-molecular framework to assess the extant diversity, biogeography and evolutionary history of Radiolaria. Our analyses reveal that half of radiolarian diversity is morphologically undescribed, with a large part forming three hyper-diverse environmental clades, named Rad-A, Rad-B and Rad-C. We suggest that most of this undescribed diversity likely comprises skeleton-less life forms or endosymbionts, explaining their elusive nature. Phylogenetic analyses highlight the need for major revision of high-level Radiolaria taxonomy, including placement of the Collodaria within the order Nassellaria. Fossil calibration of a molecular clock revealed the first appearance of Radiolaria ∼760 million years ago (Ma), the development of the skeleton in the early Paleozoic (∼500 Ma) and the onset of photosymbiotic relationships during the mid to late Mesozoic (∼140 Ma), related to geological periods of oligotrophy and anoxia. The results presented here provide an extensive and robust framework for developing new perspectives on early eukaryotic diversification, paleo-environmental impacts on plankton evolution, and marine microbial ecology in rapidly evolving ecosystems.
Co-cultivation with Azolla affects the metabolome of whole rice plant beyond canonical inorganic nitrogen fertilization
Authors: Consorti Elena , Costarelli Alma , Cannavò Sara , Cerri Martina , Valeri Maria Cristina , Reale Lara , Saccomano Antonietta , Paleni Chiara , Gregis Veronica , Kater Martin M. , Brilli Federico , Paolocci Francesco , Ghirardo Andrea 
Published: October 2024

AbstractAzolla spp. are floating ferns used for centuries as biofertilizers to enrich the soil with inorganic nitrogen and improve rice yields. In this study, rice plants were grown together with Azolla by maintaining a low and constant concentration of inorganic nitrogen. We employed a combination of non-targeted metabolomics, chemometrics, and molecular networking to dissect the impact of Azolla co-cultivation on the metabolome of rice roots-and leaves. Our analyses revealed that Azolla releases a broad range of metabolites in the culture medium, mainly comprising small peptides and flavonoids. Moreover, in rice co-cultivated with Azolla, we observed a systematic response in the upregulation of metabolites that started from the roots and, over time, shifted to the leaves. During the early stages of co-cultivation, Azolla led to the accumulation of small peptides, lipids, and carbohydrates in roots, and flavonoid glycosides and carbohydrates in leaves of rice. Consistent with these results, transcriptomics analysis of rice roots indicated significant changes in the expression of genes coding for small peptide and lipid transporters, and genes involved in amino acid salvage and biosynthesis. Overall, our study highlights novel growth-promoting effects of Azolla on rice which could facilitate the development of sustainable techniques to increase yields.HighlightsThe aquatic fern Azolla synthesizes and releases a broad range of growth promoting metabolites (i.e. small peptides) that can be absorbed by the roots of co-cultivated rice plants
Quantifying small GTPase activation status using a novel fluorescence HPLC-based assay
Authors: Araki Makoto , Kasuya Yukika , Yoshimoto Kaho , Katada Toshiaki , Kontani Kenji 
Published: October 2024

AbstractSmall GTPases play crucial roles in cellular signaling pathways, with their activation states tightly regulated between GDP-bound inactive and GTP-bound active forms. Dysregulation of these nucleotide-binding states, such as in oncogenic RAS, is implicated in diseases like cancer. Accurately quantifying these states in cells is thus crucial for deciphering their functional roles and regulatory mechanisms. However, current methods do not fully meet the necessary sensitivity and versatility, limiting their effectiveness in small GTPase analysis. Here, we present a highly sensitive HPLC-based assay with fluorescence detection (Fluor-HPLC), enabling precise quantification of guanine nucleotide-binding states in small GTPases. Applying this technique, we successfully quantified the guanine nucleotide-binding states of RHEB and KRAS at their endogenous expression levels. We demonstrated the utility of Fluor-HPLC by elucidating RHEB activation dynamics in response to insulin stimulation and amino acid availability. Furthermore, integration of Fluor-HPLC with syngeneic mouse models provided insights into KRAS activation dynamics in tumor tissues and evaluated the effectiveness of targeted therapeutics. Overall, this versatile method paves the way for investigating activation states and regulatory mechanisms of various small GTPases, potentially accelerating our understanding of their roles in cellular processes and disease pathogenesis.
Brain Structural Organization Revealed by Unbiased Cell-Type Distribution Clustering
Authors: Muñoz-Castañeda Rodrigo , Palaniswamy Ramesh , Palmer Jason , Drewes Rhonda , Elowsky Corey , Hirokawa Karla E. , Cain Nicholas , Venkataraju Kannan Umadevi , Harris Julie A. , Osten Pavel 
Published: October 2024

ABSTRACTCell type composition across brain regions is a crucial anatomical factor shaping both local and long-range brain circuits. In this study, we employed single-cell resolution imaging of the mouse brain, combined with automated computational analyses, to map the distribution of thirty cell types defined by unique gene marker expressions across the entire brain. Leveraging Cre recombinase mouse models for cell type labeling, we generated a comprehensive atlas of cell-type-specific distributions throughout the male and female brain. This analysis revealed that major anatomical brain areas can be characterized by distinct cell-type composition signatures. Furthermore, these distributions provide a powerful framework for identifying and refining the boundaries of different brain regions through unbiased clustering of whole-brain cell density data. This includes mapping of cortical areas and layers, hippocampal subregions, and thalamic and hypothalamic nuclei. Our findings suggest that cell type composition is intricately linked to the structural organization of the brain, with even subtle variations potentially contributing to distinct, brain region-specific brain functions.
Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems
Authors: Novak Vlastimil , Andeer Peter F. , King Eoghan , Calabria Jacob , Fitzpatrick Connor , Kelm Jana M. , Wippel Kathrin , Kosina Suzanne M. , Daum Chris , Zane Matt , Yadav Archana , Chen Mingfei , Russ Dor , Adams Catharine A. , Owens Trenton K. , Lee Bradie , Ding Yezhang , Sordo Zineb , Chakraborty Romy , Roux Simon , Deutschbauer Adam M. , Ushizima Daniela , Zengler Karsten , Arsova Borjana , Dangl Jeffery L. , Schulze-Lefert Paul , Watt Michelle , Vogel John P. , Northen Trent R. 
Published: October 2024

AbstractInter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grassBrachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure whereParaburkholderiasp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability ofParaburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.
Transcriptome-based identification of long noncoding RNAs (lncRNAs) across the genome ofAnopheles gambiae
Authors: Xu Jiannong , Hu Kai , Riehle Michelle M. , Khadka Vedbar S. 
Published: October 2024

AbstractAnopheles gambiaeis a primary malaria vector mosquito in Africa. RNA-seq based transcriptome analysis has been widely used to study gene expression underlying mosquito life traits such as development, reproduction, immunity, metabolism, and behavior. While it is well known that long non-coding RNAs (lncRNAs) are expressed ubiquitously in transcriptomes across metazoans, lncRNAs remain relatively underexplored in mosquitoes including their identity, expression profiles, and biological functions. In this study, publicly available RNA-seq datasets were leveraged to identify lncRNAs across diverse contexts, including whole mosquitoes, mosquito cells or tissues including midguts, salivary glands, and hemocytes, as well as under different physiological conditions including sugar-feeding, blood-feeding, bacterial challenges, andPlasmodiuminfections. Across this pool of transcriptomes, 2684 unique lncRNA genes, comprising 4082 transcripts, were identified. Following their identification, these lncRNA genes were integrated into the mosquito transcriptome annotation, which was then used as a reference to analyze both mRNAs and lncRNAs for transcriptional dynamics in different conditions. Like mRNAs, lncRNAs exhibited context-dependent expression patterns. Co-expression networks constructed using weighted gene co-expression network analysis (WGCNA) highlighted the interconnections among lncRNAs and mRNAs. Furthermore, we identified polysome-associated lncRNAs within polysome-captured transcripts, suggesting their involvement in translation regulation and coding capacity for micropeptides. A published ChIP-seq dataset was explored to correlate epigenetic signatures with transcriptional activities of lncRNAs. Overall, our analysis demonstrated that lncRNAs are transcribed alongside mRNAs in various biological contexts. Given their prevalence in the transcriptome, incorporating lncRNAs into transcriptome analyses will enhance our understanding of their functions, shedding light on their regulatory roles inAn. gambiaebiology.
Development and validation of a computational tool to predict treatment outcomes in cells from High-Grade Serous Ovarian Cancer patients
Authors: Cortesi Marilisa , Liu Dongli , Powell Elyse , Barlow Ellen , Warton Kristina , Giordano Emanuele , Ford Caroline E. 
Published: October 2024

AbstractTreatment of High-Grade Serous Ovarian Cancer (HGSOC) is often ineffective due to frequent late-stage diagnosis and development of resistance to therapy. Timely selection of the most effective (combination of) drug(s) for each patient would improve outcomes, however the tools currently available to clinicians are poorly suited to the task.We here present a computational simulator capable of recapitulating cell response to treatment in ovarian cancer. The technical development of the in silico framework is described, together with its validation on both cell lines and patient-derived laboratory models. A calibration procedure to identify the parameters that best recapitulate each patient’s response is also presented.Our results support the use of this tool in preclinical research, to provide relevant insights into HGSOC behaviour and progression. They also provide a proof of concept for its use as a personalised medicine tool and support disease monitoring and treatment selection.
A minimally guided organoid model for cross-species comparisons of cerebellar development
Authors: Guglielmi Luca , Lloyd-Davies-Sánchez Daniel , González Martínez José , Lancaster Madeline A. 
Published: October 2024

AbstractThe human cerebellum has undergone significant evolutionary expansion compared to other species, contributing to both motor and cognitive skills. However, the mechanisms underlying this process remain largely unknown as interrogating human cerebellar development alongside other species has to date been unfeasible. To address this, we developed a minimally guided cerebellar organoid protocol that combines unguided neural induction with precise temporal calibration of posteriorizing morphogens. This approach effectively overrides default telencephalic fate in cerebral organoids and induces stable cerebellar identities. Cerebellar organoids derived from both human and mouse ESCs exhibit species-specific size differences at comparable developmental stages and show robust induction of cerebellar master regulators and progenitor cell types. This model provides a powerful tool for investigating the mechanisms underlying cerebellar development in the context of both evolution and disease.
Divergence and parallelism in two tropical drosophilids simultaneously invading a desert environment
Authors: El-Sabrout Ahmed M. , Moreno Céline , Temperville Mélody , Ferreira Erina A. , Ogereau David , Hassani Issa Mze , Bastide Héloïse , Abou-Youssef Amira Y. , Yassin Amir 
Published: October 2024

AbstractInvasive species have once been called a ‘grand experiment in evolution’ but natural replicates of such experiments are often scarce. In particular, whether the rapid adaptation to the new environment involves genetic predisposition in the ancestral range or mainly occurs via post-introductory selection on a genetically variable propagule remains unknown. Here, we investigate the parallel adaptation of two drosophilid species of the genusZaprionus,Z. indianus(the African fig fly) andZ. tuberculatus, to contrasting agrarian and desert environments following their introduction in Egypt during the last four decades. Field collection unraveled distinct spatial distribution of the two species. Population genomics analyses showed correlated differentiation levels at orthologous genes before and after introduction in both species. Nonetheless, phenotypic analyses revealed distinct fruit preference and desiccation resistance between both species as well as between introduced and nativeZ. tuberculatuspopulations. Hence, despite signals of genomic parallelism, ecological divergence between the two species likely facilitates their co-existence in the introduced regions. Our results provide a significant step towards understanding the mechanisms underlying the simultaneous invasive success of both species, which have also recently invaded the Americas and Europe, and of which one at least is a notorious pest.
Unlearning Virus Knowledge Toward Safe and Responsible Mutation Effect Predictions
Authors: Li Mingchen , Zhou Bingxin , Tan Yang , Hong Liang 
Published: October 2024

AbstractPre-trained deep protein models have become essential tools in fields such as biomedical research, enzyme engineering, and therapeutics due to their ability to predict and optimize protein properties effectively. However, the diverse and broad training data used to enhance the generalizability of these models may also inadvertently introduce ethical risks and pose biosafety concerns, such as the enhancement of harmful viral properties like transmissibility or drug resistance. To address this issue, we introduce a novel approach using knowledge unlearning to selectively remove virus-related knowledge while retaining other useful capabilities. We propose a learning scheme, PROEDIT, for editing a pre-trained protein language model toward safe and responsible mutation effect prediction. Extensive validation on open benchmarks demonstrates that PROEDIT significantly reduces the model’s ability to enhance the properties of virus mutants without compromising its performance on non-virus proteins. As the first thorough exploration of safety issues in deep learning solutions for protein engineering, this study provides a foundational step toward ethical and responsible AI in biology.
Traction force generation in motile malaria parasites is modulated by thePlasmodiumadhesin TLP
Authors: Ripp Johanna , Probst Dimitri , Singer Mirko , Schwarz Ulrich S. , Frischknecht Friedrich 
Published: October 2024

AbstractPlasmodiumsporozoites are the highly polarized and motile forms of the malaria parasite that are transmitted by mosquitoes to the vertebrate hosts. Sporozoites use myosin molecular motors to generate retrograde flow of actin filaments. These are linked to plasma-membrane spanning adhesins, which in turn bind to the extracellular environment, resulting in forward directed gliding motility. The gliding motility machine of sporozoites leads to high speeds in the range of micrometer per second, which are essential for efficient migration in the skin. Yet, it is not clear how the individual parts of the machinery work together to generate force during migration. Sporozoites are elongated and curved cells and move on circular tracksin vitro. Sporozoites lacking the adhesin thrombospondin related anonymous protein (TRAP) like protein, TLP, can still migrate in the skin, but at a lower level. TLP lacking sporozoites generate a lower force on the dorsal (non-substrate facing) surface as measured by laser tweezers. Here we use traction force microscopy to investigate motile sporozoites and the forces they produce during migration on their ventral surface. Both wild type andtlp(-)sporozoites show distinct foci of force generation, buttlp(-)sporozoites generating overall lower forces. Our findings demonstrate that TLP is an important element of the force-generating machinery during sporozoite gliding motility.
OpenExo: An Open-Source Modular Exoskeleton to Augment Human Function
Authors: Williams Jack R. , Cuddeback Chance F. , Fang Shanpu , Colley Daniel , Enlow Noah , Cox Payton , Pridham Paul , Lerner Zachary F. 
Published: October 2024

AbstractWhile the field of wearable robotic exoskeletons is rapidly expanding, there are several barriers to entry that discourage many from pursuing research in this area, ultimately hindering growth. Chief among these are the lengthy and costly development time to get an exoskeleton from conception to implementation and the necessity for a broad set of expertise. Additionally, many exoskeletons are designed for a specific utility (e.g., ankle plantarflexor assistance) and are confined to the laboratory environment, limiting the flexibility of the designed system to adapt to answer new questions and explore new domains. To address these barriers, we present OpenExo, an open-source modular untethered exoskeleton framework that provides access to all aspects of the design process including (1) software, (2) electronics, (3) hardware, and (4) control schemes. To demonstrate the utility of this exoskeleton framework, we performed benchtop and experimental validation testing with the system across multiple configurations including (1) hip-only incline assistance, (2) ankle-only indoor and outdoor assistance, (3) hip-and-ankle load-carriage assistance, and (4) elbow-only weightlifting assistance. All aspects of the software architecture, electrical components, hip and Bowden-cable transmission designs, and control schemes are freely available for other researchers to access, use, and modify when looking to address research questions in the field of wearable exoskeletons. Our hope is that OpenExo will rapidly accelerate the development and testing of new exoskeleton designs and control schemes, while simultaneously encouraging others, including those who would have been turned away from entering the field, to explore new and unique research questions.One-Sentence SummaryWe present an open-source, open-hardware exoskeleton to aid in accelerating the growth of robotic exoskeleton research.