bluuebunny/crossref_metadata_2025 huggingface dataset:
Neural Correlates of Different Randomization Tasks
Authors: Guseva Maja , Bogler Carsten , Allefeld Carsten , Ziya Ece Büşra , Haynes John-Dylan
Published: March 2024

In some cases, when we are making decisions, the available choices can appear to be equivalent. When this happens, our choices appear not to be constrained by external factors and instead we can believe to be selecting “randomly”. Furthermore, randomness is sometimes even explicitly required by task conditions such as in random sequence generation (RSG) tasks. This is a challenging task that involves the coordination of multiple cognitive processes, which can include the inhibition of habitual choice patterns and monitoring of the running choice sequence.

It has been shown that random choices are strongly influenced by the way they are instructed. This raises the question whether the brain mechanisms underlying random selection also differ between different task instructions. To assess this, we measured brain activity while participants were engaging in three different variations of a sequence generation task: Based on previous work, participants were instructed to either (1) “generate a random sequence of choices”, (2) “simulate a fair coin toss”, or (3) “choose freely”.

Our results reveal a consistent frontoparietal activation pattern that is shared across all tasks. Specifically, increased activity was observed in bilateral inferior and right middle frontal gyrus, left pre-supplementary motor area, bilateral inferior parietal lobules and portions of anterior insular cortex in both hemispheres. Activity in the mental coin toss condition was higher in right dorsolateral prefrontal cortex, left (pre-) supplementary motor area, a portion of right inferior frontal gyrus, bilateral superior parietal lobules and bilateral anterior insula. Additionally, our multivariate analysis revealed a distinct region in the right frontal pole to be predictive of the outcome of choices, but only when randomness was explicitly instructed.

These results emphasize that different randomization tasks involve both shared and unique neural mechanisms. Thus, even seemingly similar randomization behavior can be produced by different neural pathways.
On the contribution of genetic heterogeneity to complex traits
Authors: Liu Hai-Jun , Swarts Kelly , Xu Shuhua , Yan Jianbing , Nordborg Magnus
Published: March 2024

Genetic heterogeneity, where different alleles or loci are responsible for similar phenotypes, reduces the power of genome-wide association studies and can cause misleading results. Although many striking examples have been identified, the general importance of genetic heterogeneity for complex traits is unclear. Here, we use a novel interpretative machine-learning approach to look for evidence of genetic heterogeneity in plants and humans. Our approach helps identify new loci/alleles influencing trait variation in several agriculturally important species, and we show that at least 6% of maize eQTL, half of them newly identified, exhibit evidence of allelic heterogeneity. Finally, we search for evidence of synthetic associations in human GWAS data, and find that as many as 3–5% may be affected. Our results highlight the need to take genetic heterogeneity seriously, and provide a simple approach for doing so.
Behavior and alpha-band oscillations reveal cross-modal interactions between chemosensory and auditory processing
Authors: Klatt Laura-Isabelle , Hucke Christine
Published: March 2024

The perceived location of a sound can be mislocated towards a spatially discordant but temporally synchronous visual stimulus. This is referred to as the spatial ventriloquist effect. However, whether chemosensory cues can similarly bias sound localization remains largely unaddressed. Hence, the present EEG study adopted a dynamic sound localization paradigm with concurrent bimodal odorant stimulation. Participants heard sequences of sounds varying in location. After each sound, participants made a two-alternative forced choice localization judgment (left vs. right). Critically, in a subset of occasions, but unbeknown to the participants, the sounds originated from a central location. Furthermore, in the first half of the sequence, sound presentation could be accompanied by a task-irrelevant, trigeminally potent odorant in the left, right, or both nostril(s). Auditory-only trials and birhinal stimulation served as controls. For central sounds in the second half of the sequence, the proportion of right-ward responses increased with right-nostril stimulation but decreased with left-nostril stimulation relative to the control conditions, showing an after-effect of odorant stimulation for ambiguous sound cues. This odorant-induced localization bias diminished with increasing spatial discernability of the sounds. On the contrary, alpha power lateralization, a correlate of auditory spatial attention, was most susceptible to odorant stimulation when the spatial disparity between the senses was largest, as reflected in diminished alpha lateralization for incongruent chemosensory-sound stimulation. No such effect was present in a multivariate decoding analysis of alpha power. We discuss the present findings in light of cross-modal interactions and a proposed common attentional control system between the senses.
Immediate glucose signaling transmitted via the vagus nerve in gut-brain neural communication
Authors: Yamada Serika , Natsubori Akiyo , Harada Kazuki , Tsuboi Takashi , Monai Hiromu
Published: March 2024

Sucrose consumption is influenced by certain gut-brain signaling mechanisms. Among these, one pathway involves neuropod cells, which form synaptic connections with the vagus nerve, leading to the immediate activation of central dopaminergic pathways. This study explored the role of the frontal cortex in its process. We found that the vagus nerve’s immediate activation is mediated by the sodium-glucose cotransporter 1 (SGLT1) of neuropod cells after the intragastric glucose injection in mice. Also, we showed that the involvement of both astrocytes and neurons in the frontal cortex via D2 and D1 dopamine receptors, respectively, by in vivo Ca2+imaging. Finally, we revealed that psychological stress, which induces a reduction in sucrose preference, significantly diminishes the activation levels of both the vagus nerve and the frontal cortex. These findings highlight the role of a comprehensive gut-brain network in modulating sucrose preference, involving neuropod cells, the vagus nerve, and the frontal cortex.

Graphical abstract
MegaKG: Toward an explainable knowledge graph for early drug development
Authors: Dong Jianqiang , Liu Junwu , Wei Yifan , Huang Peilin , Wu Qiong
Published: March 2024

In biomedical research, the utilization of Knowledge Graph (KG) has proven valuable in gaining deep understanding of various processes. In this study, we constructed a comprehensive biomedical KG, named as MegaKG, by integrating a total of 23 primary data sources, which finally consisted of 188, 844 nodes/entities and 9, 165, 855 edges/relations after stringent data processing. Such a massive KG can not only provide a holistic view of the entities of interest, but also generate insightful hypotheses on unknown relations by applying AI computations. We focused on the interplay of the key elements in drug development, such as genes, diseases and drugs, and aimed to facilitate practical applications that could benefit early drug development in industries. More importantly, we placed much emphasis on the exploitability of the predictions generated by MegaKG. This may greatly help researchers to assess the feasibility or design appropriate downstream validation experiments, making AI techniques more than just black-box models. In this regard, NBFNet was adopted, which combines the advantages of both traditional path-based methods and more recently developed GNN-based ones. Performance evaluation experiments indicated superior results by MegaKG. We also conducted real case studies to validate its practical utility in various scenarios, including target prediction, indication extension and drug repurposing. All these experiments highlighted the potential of MegaKG as a valuable tool in driving innovation and accelerating drug development in pharmaceutical industry.
The Hyaluronan Synthase isoforms direct distinct patterns of fibroblast activation linked to fibrosis progression versus resolution following renal ischaemia
Authors: Grigorieva Irina , Midgley Adam , Brown Charlotte , Chevez Gilda , Williams Aled , Manetta-Jones Dominic , Bowen Timothy , Chan Deva , Plaas Anna , Chevez Rafael , Steadman Robert , Khalid Usman , Meran Soma
Published: March 2024

Background

The stroma plays a key role during renal development and in regeneration after injury. However, following injury, the stroma expands driving progressive fibrosis. Hyaluronan (HA) is a glycosaminoglycan that is absent in healthy kidney stroma but highly expressed in disease. To understand strategies to modulate stromal HA towards therapeutic advantage, this study compares HA and HA Synthase (HAS) enzyme expression in kidney development, health, disease, and recovery.

Methods

Rats underwent ischaemia reperfusion injury (IRI) with/without ischaemic preconditioning (IPC) and kidneys histologically analysed. Kidneys from C57BL/6 embryos and HAS1/3-/-mice were also analysed and parallel mechanistic cell studies performed using primary human fibroblasts.

Results

In health, stromal HA was absent from the renal cortex. HAS1 was expressed in some epithelial cells, whilst HAS2 was not expressed. Following IRI there was increased stromal HA in areas of chronic fibrosis, alongside increased HAS2 (but not HAS1) expression. In contrast, during development prominent stromal HA matrices were evident in areas of tubular generation, with strong HAS1 (not HAS2) expression. Following IPC+IRI, stromal HA and HAS2 were attenuated; whilst HAS1+cells expanded but were distinct from α-SMA+myofibroblasts. Cell studies demonstrated that HAS1+fibroblasts had a functionally distinct phenotype, with enhanced migration and FAP expression but attenuated α-SMA, EDA-FN and COL1A1 expression, whereas HAS2+fibroblasts demonstrated a classic α-SMA+contractile myofibroblast phenotype with high EDA-FN and COL1A1.

Conclusions

HA is a key regulator of stromal fibroblast heterogeneity, with HAS1 and HAS2 defining phenotypically distinct populations that may influence divergent renal outcomes following injury.

SIGNIFICANCE STATEMENT

Hyaluronan (HA) is a matrix glycosaminoglycans that is absent in healthy kidney cortex but demonstrates increased expression in the renal stroma during progressive fibrosis. This study makes comparisons of HA accumulation, localisation, and HA Synthase (HAS) protein expression during kidney development, in health, following ischaemic kidney injury and during renal recovery. The study identifies that different HAS isoenzymes (HAS1 and HAS2) mediate distinct functional fibroblast phenotypesin vitroand are localised in distinct stromal localisations and cell sub-populationsin vivo. The data provides interesting insights into HA dependent regulation of fibroblast stromal heterogeneity and identifies thenovelfinding that HAS1 defines cell populations that are associated with kidney recovery following ischaemic injury and are protective against progressive renal fibrosis.
Large-scale RNA-seq mining reveals ciclopirox triggers TDP-43 cryptic exons
Authors: Sinha Irika R. , Sandal Parker S. , Burns Grace D. , Mallika Aswathy Peethambaran , Irwin Katherine E. , Cruz Anna Lourdes F. , Wang Vania , Rodríguez Josué Llamas , Wong Philip C. , Ling Jonathan P.
Published: March 2024

Nuclear clearance and cytoplasmic aggregation of TDP-43 in neurons, initially identified in ALS-FTD, are hallmark pathological features observed across a spectrum of neurodegenerative diseases. We previously found that TDP-43 loss-of-function leads to the transcriptome-wide inclusion of deleterious cryptic exons in brains and biofluids post-mortem as well as during the presymptomatic stage of ALS-FTD, but upstream mechanisms that lead to TDP-43 dysregulation remain unclear. Here, we developed a web-based resource (SnapMine) to determine the levels of TDP-43 cryptic exon inclusion across hundreds of thousands of publicly available RNA sequencing datasets. We established cryptic exon inclusion across a variety of human cells and tissues to provide ground truth references for future studies on TDP-43 dysregulation. We then explored studies that were entirely unrelated to TDP-43 or neurodegeneration and found that ciclopirox olamine (CPX), an FDA-approved antifungal, can trigger the inclusion of TDP-43-associated cryptic exons in a variety of mouse and human primary cells. CPX induction of cryptic exon occurs via heavy metal toxicity and oxidative stress, suggesting that similar vulnerabilities could play a role in neurodegeneration. Our work demonstrates how diverse datasets can be linked through common biological features and underscores that public archives of sequencing data represent a vastly underutilized resource with tremendous potential for uncovering novel insights into complex biological mechanisms and diseases.
Lineage-tracing reveals an expanded population of NPY neurons in the inferior colliculus
Authors: Silveira Marina A. , Herrera Yoani N. , Beebe Nichole L. , Schofield Brett R. , Roberts Michael T.
Published: March 2024

Growing evidence suggests that neuropeptide signaling shapes auditory computations. We previously showed that neuropeptide Y (NPY) is expressed in the inferior colliculus (IC) by a population of GABAergic stellate neurons and that NPY regulates the strength of local excitatory circuits in the IC. NPY neurons were initially characterized using the NPY-hrGFP reporter mouse, in which hrGFP expression indicates NPY expression at the time of assay, i.e., an expression-tracking approach. However, studies in other brain regions have shown that NPY expression can vary based on a range of factors, suggesting that the NPY-hrGFP mouse might miss NPY neurons not expressing NPY proximal to the experiment date. Here, we hypothesized that neurons with the ability to express NPY represent a larger population of IC GABAergic neurons than previously reported. To test this hypothesis, we used a lineage-tracing approach to irreversibly tag neurons that expressed NPY at any point prior to the experiment date. We then compared the physiological and anatomical features of neurons labeled with this lineage-tracing approach to our prior data set, revealing a larger population of NPY neurons than previously found. In addition, we used optogenetics to test the local connectivity of NPY neurons and found that NPY neurons routinely provide inhibitory synaptic input to other neurons in the ipsilateral IC. Together, our data expand the definition of NPY neurons in the IC, suggest that NPY expression might be dynamically regulated in the IC, and provide functional evidence that NPY neurons form local inhibitory circuits in the IC.
The importance of visual and chemical cues in infection detection and avoidance in a freshwater fish
Authors: Côté Ariane , Binning Sandra A.
Published: March 2024

The characteristics of infected animals, including their smell, appearance, behaviour or sound, can greatly differ from those of uninfected conspecifics. These differences can serve as cues to recognize and avoid infected individuals to minimize the risk of infection. Avoidance of infected conspecifics is a risk-sensitive behaviour that can be influenced by various factors such as sensory cues and environmental parasite load, which both remain poorly understood in fish. We investigated the ability of two populations of wild caught pumpkinseed sunfish (Lepomis gibbosus) to distinguish between conspecifics infected with parasitic worms versus uninfected individuals in two-choice experiments using visual and chemical cues separately. One population was from a lake without parasites (parasite naive) whereas the other population originated from a lake with a high prevalence of trematode and cestode worms (parasite experienced). Both populations preferred to be with conspecifics, regardless of their infection level, over being alone when given visual cues but avoided conspecifics and remained alone when given chemical cues, suggesting that visual and chemical cues are not redundant. Neither population showed any preference between infected and uninfected conspecifics when given visual cues. However, in the presence of chemical cues, there was a great interindividual variation: some fish preferred uninfected conspecifics while others preferred infected ones. On average, naive fish avoided infected conspecifics whereas experienced fish did not show any preferences, suggesting that fish from lakes with high prevalence of infection habituate to infection cues. We suggest that pumpkinseeds use chemical rather than visual cues to discriminate between infected and uninfected conspecifics and make a shoaling decision. Our study highlights the importance of considering different sensory cues as well as parasite load when studying avoidance and shoaling behaviours, especially in a time of modifying sensory landscape and parasites abundance of freshwater ecosystems through global changes.
Evaluation of Plant- and Microbial-Derived Protein Hydrolysates as Substitutes for Fetal Bovine Serum in Cultivated Seafood Cell Culture Media
Authors: Amirvaresi Arian , Ovissipour Reza
Published: March 2024

This study seeks to explore alternatives by substituting or reducing the conventional 10% serum concentration in Zebrafish embryonic stem cell (ESC) growth media with protein hydrolysates sourced from peas, mushrooms, yeast, and algae. Notably, algae exhibited the highest protein content, optimal amino acid balance, and favorable functional properties. When applied at concentrations ranging from 1 to 10 mg/mL, all protein hydrolysates demonstrated pro-apoptotic effects and inhibited cell growth, particularly when used in conjunction with 10% serum. However, concentrations ranging from 0.001 to 0.1 mg/mL displayed anti-apoptotic properties and promoted cell proliferation. The study found that media containing 1% or 2.5% serum, along with 0.01 mg/mL of protein hydrolysates, supported cell growth effectively. Lactate Dehydrogenase (LDH) Activity served as an indicator of cell health and integrity under the specified conditions of protein hydrolysate supplementation. Cells cultured in serum-free media exhibited significantly decreased cell membrane integrity (P < 0.05) compared to those in regular media or media containing low serum (1% and 2.5%) along with low concentrations (0.01 mg/mL) of protein hydrolysates. Furthermore, analysis of Greenhouse Gas emissions (GHG) suggested that media formulations containing 1% serum combined with low concentrations of protein hydrolysates present a sustainable approach for cell-based seafood production.
Uncertainty in Thermosensory Expectations Enhances an Illusion of Pain
Authors: Ehmsen Jesper Fischer , Nikolova Niia , Christensen Daniel Elmstrøm , Banellis Leah , Brændholt Malthe , Courtin Arthur S. , Kraenge Camilla E. , Mitchell Alexandra G. , Deolindo Camila Sardeto , Steenkjær Christian , Vejlø Melina , Mathys Christoph , Allen Micah G. , Fardo Francesca
Published: March 2024

The human brain has a remarkable ability to learn and update its beliefs about the world. Here, we investigate how thermosensory learning shapes our subjective experience of temperature and the misperception of pain in response to harmless thermal stimuli. Through computational modeling, we demonstrate that the brain uses a probabilistic predictive coding scheme to update beliefs about temperature changes based on their uncertainty. We find that these expectations directly modulate the perception of pain in the thermal grill illusion. Quantitative microstructural brain imaging revealed that the myeloarchitecture and iron content of the somatosensory cortex, the posterior insula and the amygdala reflect inter-individual variability in computational parameters related to learning and the degree to which uncertainty modulates illusory pain perception. Our findings offer a new framework to explain how the brain infers pain from innocuous thermal inputs. Our model has important implications for understanding the etiology of thermosensory symptoms in chronic pain conditions.
Glycoengineered recombinant alpha1-antitrypsin results in comparablein vitroandin vivoactivities to human plasma-derived protein
Authors: Rocamora Frances , Schoffelen Sanne , Arnsdorf Johnny , Toth Eric A. , Abdul Yunus , Cleveland Thomas E. , Bjørn Sara Petersen , Min Wu Mina Ying , McElvaney Noel G. , Voldborg Bjørn Gunnar Rude , Fuerst Thomas R. , Lewis Nathan E.
Published: March 2024

Alpha-1-antitrypsin (A1AT) is a multifunctional, clinically important, high value therapeutic glycoprotein that can be used for the treatment of many diseases such as alpha-1-antitrypsin deficiency, diabetes, graft-versus-host-disease, cystic fibrosis and various viral infections. Currently, the only FDA-approved treatment for A1AT disorders is intravenous augmentation therapy with human plasma-derived A1AT. In addition to its limited supply, this approach poses a risk of infection transmission, since it uses therapeutic A1AT harvested from donors. To address these issues, we sought to generate recombinant human A1AT (rhA1AT) that is chemically and biologically indistinguishable from its plasma-derived counterpart using glycoengineered Chinese Hamster Ovary (geCHO-L) cells. By deleting nine key genes that are part of the CHO glycosylation machinery and expressing the human ST6GAL1 and A1AT genes, we obtained stable, high producing geCHO-L lines that produced rhA1AT having an identical glycoprofile to plasma-derived A1AT (pdA1AT). Additionally, the rhA1AT demonstratedin vitroactivity andin vivohalf-life comparable to commercial pdA1AT. Thus, we anticipate that this platform will help produce human-like recombinant plasma proteins, thereby providing a more sustainable and reliable source of therapeutics that are cost-effective and better-controlled with regard to purity, clinical safety and quality.
On the recovery of malformed horseshoe crabs across multiple moulting stages
Authors: Bicknell Russell D. C. , Cuomo Carmela
Published: March 2024

Malformed horseshoe crabs have been documented for over a century. However, most of these records are anecdotal observations of often striking morphologies recorded in isolation. There is therefore little understanding of how malformations are manifested and how they can develop in the group. Here we consider the moult sequences of three extantLimulus polyphemusindividuals to explore different patterns of malformation development. One specimen with an injured telson demonstrates a gradual recovery of the telson section over three moulting events. The second individual demonstrates a fused thoracetron-telson articulation with a hole for the telson. This individual shows consistent growth of a reduced telson across moults. The third individual shows a thoracetronic injury incurred during at least moult-stage 7 that shows no evidence of recovery over five moulting stages. These records illustrate that horseshoe crab malformation recovery is far more complicated than previously thought. This also suggests that unless an exoskeletal section has functional morphological importance (i.e., the telson), the region is unlikely to recover from an older malformation. From a conservation standpoint, the ability or inability to fully recover from injury affects a horseshoe crab’s ability to survive and/or reproduce in the wild particularly if the injury affects the telson. Given the global decline in horseshoe crab populations and conservation efforts underway, the extent of injuries in extant populations of horseshoe crabs may affect population recovery and should be considered.
CXCR2-mediated recruitment of adaptive NK cells with NKG2C/HLA-E dependent antigen-specific memory enhances tumor killing in ovarian cancer
Authors: Sun Yizhe , Rodgers-Furones Andrea , Gultekin Okan , Khare Shruti , Neo Shi Yong , Shi Wenyang , Galceran Lidia Moyano , Lam Kong-Peng , Dasgupta Ramanuj , Fuxe Jonas , Salehi Sahar , Lehti Kaisa , Sarhan Dhifaf
Published: March 2024

Natural killer (NK) cells have emerged as promising effectors in cancer immunotherapy due to their ability to recognize and eliminate tumor cells. To investigate the immunological memory and tumor reactivity of adaptive (a)NK cells in the context of desmoplastic tumors, we used human ovarian cancer as a model. Throughin vitroculture systems resembling dendritic cell (DC)-mediated T cell activation, we demonstrated that aNK cells exhibit antigen-specific cytotoxic responses and memory generation towards ovarian tumor antigens. Furthermore, mature DCs presenting tumor-associated antigens induced the expansion of aNK cells, suggesting antigen-specific proliferation. Single-cell transcriptomics revealed a distinct genetic signature of aNK cells in tumor samples, characterized by a cytotoxic phenotype and interactions with myeloid cells, particularly DCs. The spatial analysis confirmed the intratumoral presence of aNK cells, with higher abundance in the tumor nest compared to conventional (c)NK cells. Functional assays demonstrated the cytotoxicity of expanded aNK cells against autologous ovarian tumors, accompanied by an activated receptor profile. Importantly, aNK cells displayed antigen-specific memory responses towards primary tumors, maintaining specificity over time. Blockade of NKG2C and HLA-E influenced aNK cell recall responses, indicating their roles in the adaptive NK cell immune memory. Additionally, CXCR2 was essential for efficient aNK cell migration toward tumors. These findings shed light on the therapeutic potential of aNK cells in ovarian cancer immunotherapy, highlighting their ability to develop immunological memory and effectively eradicate tumor cells.
Learning and actioning general principles of cancer cell drug sensitivity
Authors: Carli Francesco , Di Chiaro Pierluigi , Morelli Mariangela , Arora Chakit , Bisceglia Luisa , De Oliveira Rosa Natalia , Cortesi Alice , Franceschi Sara , Lessi Francesca , Di Stefano Anna Luisa , Santonocito Orazio , Pasqualetti Francesco , Aretini Paolo , Miglionico Pasquale , Diaferia Giuseppe R. , Giannotti Fosca , Liò Pietro , Duran-Frigola Miquel , Mazzanti Chiara Maria , Natoli Gioacchino , Raimondi Francesco
Published: March 2024

High-throughput screening platforms for the profiling of drug sensitivity of hundreds of cancer cell lines (CCLs) have generated large datasets that hold the potential to unlock targeted, anti-tumor therapies.

In this study, we leveraged these datasets to create predictive models of cancer cells drug sensitivity. To this aim we trained explainable machine learning algorithms by employing cell line transcriptomics to predict the growth inhibitory potential of drugs. We used large language models (LLMs) to expand descriptions of the mechanisms of action (MOA) for each drug starting from available annotations, which were matched to the semantically closest pathways from reference knowledge bases. By leveraging this AI-curated resource, and the interpretability of our model, we demonstrated that pathways enriched for genes crucial for prediction often matched known drug-MOAs and essential genes, suggesting that our models learned the molecular determinants of drug response. Furthermore, we demonstrated that by incorporating only LLM-curated genes associated with MOAs, we enhanced the predictive accuracy of our drug models.

To enhance translatability to a clinical setting, we employed a pipeline to align bulk RNAseq from CCLs, used for training the models, to those from patient samples, used for inference. We proved the effectiveness of our approach on TCGA samples, where patients’ best scoring drugs matched those prescribed for their cancer type. We further showed its usefulness by predicting and experimentally validating effective drugs for the patients of two highly lethal solid tumors, i.e. pancreatic cancer and glioblastoma.

In summary, our method facilitates the inference and interpretation of cancer cell line drug sensitivity and holds potential to effectively translate them into new cancer therapeutics.

Highlights

-Interpretable drug-response prediction models were trained on large scale pharmacogenomics data sets (i.e. GDSC and PRISM).

-Large language models were used to enhance the curation of biological pathways associated to drugs MOA

-Unbiased interpretation of the models demonstrated learning of drug MOAsandgene essentiality

-Inference of TCGA cohort samples recovered mono- and combination cancer drug prescriptions and indicate potential repurposing candidates.

-Drug candidates predicted from bulk RNAseq samples of pancreatic cancer and glioblastoma were experimentally validated.
SKP2-mediated FBXO2 proteasomal degradation drives hepatocellular carcinoma progression via stabilizing Hsp47
Authors: Xue Cailin , Yang Fei , Bao Guojian , Yan Jiawu , Fu Rao , Zhang Minglu , Ding Jialu , Feng Jiale , Han Jianbo , Qin Xihu , Su Hua , Sun Beicheng
Published: March 2024

Accumulating studies highlight that dysregulated E3 ubiquitin ligases are associated with the onset and advancement of cancers. Nevertheless, the impact and mechanism of most E3 ubiquitin ligases on tumorigenesis and tumor metastasis remain poorly understood. Here, we show that loss of FBXO2, an E3 ubiquitin ligase, accelerates hepatocellular carcinoma (HCC) tumor growth and metastasis to the lung through stabilizing heat shock protein 47 (Hsp47). Downregulation of FBXO2, caused by DNA-PKcs-medicated phosphorylation at serine 17 and E3 ligase SKP2-mediated ubiquitination at lysine 79 and subsequent proteasomal degradation, is observed in tumor tissues compared to their parallel non-tumor tissues resected from patients with HCC. Patients whose tumors are enriched for SKP2 or Hsp47 or express low levels of FBXO2 have poor median survival compared to those whose tumors have reversed levels of SKP2, FBXO2 and Hsp47. Together, FBXO2 acts as a tumor suppressor in HCC development. The components of the SKP2-FBXO2-Hsp47 axis provide newly prognostic and therapeutic factors for anti-HCC.
APP and β-amyloid modulate protein aggregation and dissociation from recycling endosomal and exosomal membranes
Authors: Singh Preman J. , Verma Bhavna , Wells Adam , Mendes Cláudia C. , Dunn Dali , Chen Ying-Ni , Oh Jade , Blincowe Lewis , Wainwright S. Mark , Fischer Roman , Fan Shih-Jung , Harris Adrian L. , Goberdhan Deborah C. I. , Wilson Clive
Published: March 2024

Secretory proteins frequently aggregate into non-soluble dense-core granules (DCGs) in recycling endosome-like compartments prior to release. By contrast, aberrantly processed Aβ-peptides derived from Amyloid Precursor Protein (APP) form pathological amyloidogenic aggregations in late-stage Alzheimer’s Disease (AD) after secretion. By examining livingDrosophilaprostate-like secondary cells, we show both APP and Aβ-peptides affect normal DCG biogenesis. These cells generate DCGs and secreted nanovesicles called Rab11-exosomes within enlarged recycling endosomes. The fly APP homologue, APP-like (APPL), associates with Rab11-exosomes and the compartmental limiting membrane, from where its extracellular domain controls protein aggregation. Proteolytic release of this membrane-associated domain permits aggregates to coalesce into a large central DCG. Mutant Aβ-peptide expression, likeApplloss-of-function, disrupts this assembly step and compartment motility, and increases lysosomal targeting, mirroring pathological events reported in early-stage AD. Our data therefore reveal a physiological role for APP in membrane-dependent protein aggregation, which when disrupted, rapidly triggers AD-relevant intracellular pathologies.
Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex
Authors: Yanagisawa Tatsuo , Murayama Yuko , Ehara Haruhiko , Goto Mie , Aoki Mari , Sekine Shun-ichi
Published: March 2024

The 5’-3’ exoribonuclease Rat1 (or Xrn2) plays a pivotal role in termination of mRNA transcription by eukaryotic RNA polymerase II (RNAPII). Rat1 forms a complex with its partner proteins, Rai1 and Rtt103, and acts as a “torpedo” to bind transcribing RNAPII and dissociate DNA/RNA from it. Here we report the cryo-electron microscopy structures of a Rat1-Rai1-Rtt103 complex and three Rat1-Rai1-associated RNAPII complexes (type-1, type-1b, and type-2) from the yeastKomagataella phaffii. The Rat1-Rai1-Rtt103 complex structure revealed that Rat1 and Rai1 form a heterotetramer, with a single Rtt103 bound between two Rai1 molecules. In the type-1 complex, Rat1-Rai1 forms a heterodimer and directly binds to the RNA exit site of transcribing RNAPII to extract RNA into the Rat1 nuclease active site. This interaction changes the RNA path in favor of termination (the “pre-termination” state). The type-1b and type-2 complexes have no bound DNA/RNA, likely representing the “post-termination” states. These structures shed light on the mechanism of eukaryotic mRNA transcription termination.
ORCA: Predicting replication origins in circular prokaryotic chromosomes
Authors: van Meel Zoya , Baaijens Jasmijn A.
Published: March 2024

The proximity of genes to the origin of replication plays a key role in replication and transcription-related processes in bacteria. Computational prediction of potential origin locations has an important role in origin discovery, critically reducing experimental costs. We present ORCA (Origin of RepliCation Assessment) as a fast and lightweight tool for the visualisation of nucleotide disparities and the prediction of the location of replication origins. ORCA uses the analysis of nucleotide disparities,dnaA-box regions, and target gene positions to find potential origin sites, and has a random forest classifier to predict which of these sites are likely origins. ORCA’s prediction and visualization capabilities make it a valuablein silicomethod to assist in experimental determination of replication origins. ORCA is written in Python-3.11, works on any operating system with minimal effort, and can process large databases. Full implementation details are provided in the supplementary material and the source code is freely available on GitHub:https://github.com/ZoyavanMeel/ORCA.
Force Reserve Predicts Compensation in Reaching Movement with Induced Shoulder Strength Deficit
Authors: Faity Germain , Barradas Victor R. , Schweighofer Nicolas , Mottet Denis
Published: March 2024

Following events such as fatigue or stroke, individuals often move their trunks forward during reaching, leveraging a broader muscle group even when only arm movement would suffice. In previous work, we showed the existence of a ‘force reserve’ — a phenomenon where individuals, when challenged with a heavy weight, adjusted their motor coordination to preserve approximately 40% of their shoulder’s force. Here, we investigated if such reserve can predict hip, shoulder, and elbow movements and torques resulting from an induced shoulder strength deficit. We engaged 20 healthy participants in a reaching task with incrementally heavier dumbbells, analyzing arm and trunk movements via motion capture and joint torques through inverse dynamics. We simulated these movements using an optimal control model of a 3-degree-of-freedom upper body, contrasting three cost functions: traditional sum of squared torques, a force reserve function incorporating a nonlinear penalty, and a normalized torque function. Our results demonstrate a clear increase in trunk movement correlated with heavier dumbbell weights, with participants employing compensatory movements to maintain a shoulder force reserve of approximately 40% of maximum torque. Simulations showed that while traditional and reserve functions accurately predicted trunk compensation, only the reserve function effectively predicted joint torques under heavier weights. These findings suggest that compensatory movements are strategically employed to minimize shoulder effort and distribute load across multiple joints in response to weakness. We discuss the implications of the force reserve cost function in the context of optimal control of human movements and its relevance for understanding of compensatory movements post-stroke.

NEW & NOTEWORTHY

Our study reveals key findings on compensatory movements during upper limb reaching tasks under shoulder strength deficits, as observed post-stroke. Using heavy dumbbells with healthy volunteers, we demonstrate how forward trunk displacement conserves around 40% of shoulder strength reserve during reaching. We show that an optimal controller employing a cost function combining squared motor torque and a nonlinear penalty for excessive muscle activation outperforms traditional controllers in predicting torques and compensatory movements in these scenarios.
Synaptic function and sensory processing in ZDHHC9-associated neurodevelopmental disorder: a mechanistic account
Authors: Ianov Vitanov Rebeca , Achterberg Jascha , Akarca Danyal , Astle Duncan E. , Baker Kate
Published: March 2024

Loss-of-functionZDHHC9variants are associated with X-linked intellectual disability (XLID), rolandic epilepsy (RE) and developmental language difficulties. This study integrates human neurophysiological data with a computational model to identify a potential neural mechanism explainingZDHHC9-associated differences in cortical function and cognition. Magnetoencephalography (MEG) data was collected during an auditory roving oddball paradigm from eight individuals with aZDHHC9loss-of-function variant (ZDHHC9 group) and seven age-matched individuals without neurological or neurodevelopmental difficulties (control group). Evoked responses to auditory stimulation were larger in amplitude and showed a later peak latency in the ZDHHC9 group but demonstrated normal stimulus-specific properties. Magnetic mismatch negativity (mMMN) amplitude was also increased in the ZDHHC9 group, reflected by stronger neural activation during deviant processing relative to the standard. A recurrent neural network (RNN) model was trained to mimic recapitulate group-level auditory evoked responses, and subsequently perturbed to test the hypothesised impact ofZDHHC9-driven synaptic dysfunction on neural dynamics. Results of model perturbations showed that reducing inhibition levels by weakening inhibitory weights recapitulates the observed group differences in evoked responses. Stronger reductions in inhibition levels resulted in increased peak amplitude and peak latency of RNN prediction relative to the pre-perturbation predictions. Control experiments in which excitatory connections were strengthened by the same levels did not result in consistently stable activity or AEF-like RNN predictions. Together, these results suggest that reduced inhibition is a plausible mechanism by which loss of ZDHHC9 function alters cortical dynamics during sensory processing.

Abstract Figure

Graphical Abstract

In the current study, we employed a bottom-up approach to study the impact of synaptic-level alterations associated withZDHHC9variants on cortical function in healthy andZDHHC9-deficient participants. To achieve this, a recurrent neural network model was developed to recapitulate MEG-derived auditory evoked responses and subsequently perturbed in order to determine effects on resulting dynamics. We show that reduced network inhibition recapitulates empirical observations, specifically increased response amplitudes, delayed peak latencies and increased mismatch negativity. These results offered a mechanistic account on the impact ofZDHHC9-associated synaptic alterations on auditory processing.
Elucidating microRNA-34a organisation within Human Argonaute-2 by DNP MAS NMR
Authors: Dasgupta Rubin , Becker Walter , Petzold Katja
Published: March 2024

Understanding mRNA regulation by microRNA (miR) relies on the structural understanding of the RNA-induced silencing complex (RISC). Here, we elucidate the structural organisation of miR-34a, deregulated in various cancers, in hAgo2, effector protein in RISC, using guanosine-specific isotopic labelling and dynamic nuclear polarisation (DNP)-enhanced solid-state NMR. Homonuclear correlation experiments revealed that the non-A-form helical conformation of miR-34a increases when incorporated into hAgo2 and then bound to SIRT1 mRNA compared to the free hairpin or the free duplex formed with mRNA. Nucleotide-specific information of the of C2’- and C3’-endo sugar puckering can be obtained from the C8 – C1’ correlation with varying distributions, revealing a trapping of different confirmations upon freezing. C3’-endo puckering was predominantly observed for the seed, while C2’-endo for the central region and a mixture of both elsewhere. These observations provide insights into the molecular dynamic basis of miR-based mRNA regulation, while also providing a proof-of-concept that experiments under cryogenic conditions, e.g. at 90K, can trap and with that reveal frozen dynamic states, using methods such as (DNP-enhanced) solid-state NMR or Cryo-EM
Open Educational Resources for distributed hands-on teaching in molecular biology
Authors: Cerda Ariel , Aravena Alejandro , Zapata Valentina , Arce Anibal , Araya Wladimir , Gallardo Domingo , Aviles Javiera , Quero Francisco , Nuñez Isaac , Matute Tamara , Navarro Felipe , Ferrando Valentina , Blanco Marta , Velozo Sebastian , Rodriguez Sebastian , Aguilera Sebastian , Chateau Francisco , Molloy Jennifer C , Aidelberg Guy , Lindner Ariel B. , Castro Fernando , Cremades Pablo , Ramirez-Sarmiento Cesar , Federici Fernan
Published: March 2024

Open Educational Resources (OER), freely accessible learning, teaching and research materials, have been proposed as key enabling tools to achieve inclusive knowledge societies and equitable access to education. Here, we describe novel OER consisting of low cost and locally produced public domain biological reagents, open source hardware and free software collaborative notebooks to teach LAMP DNA amplification, RT-PCR RNA detection, enzyme kinetics and fluorescence imaging. These resources have been distributed nationwide to students’ homes as a lab-in-a-box, i.e. remote teaching during the pandemic lockdowns, as well as in the form of personalized learning environments during in-person teaching after the opening of teaching laboratories. All the protocols and design files are available under open source licenses.
A RALF-Brassinosteroid morpho-signaling circuit regulates Arabidopsis hypocotyl cell shape
Authors: Biermann David , von Arx Michelle , Xhelilaj Kaltra , Sere David , Stegmann Martin , Wolf Sebastian , Zipfel Cyril , Gronnier Julien
Published: March 2024

Plant cells survey and modulate their cell wall to control their shape and anisotropic growth. Signaling mediated by the plant steroid hormones brassinosteroids (BR) plays a central role in coordinating cell wall status and cell growth, and alterations in the cell wall BR feedback loop leads to life-threatening defects in tissue and cellular integrity. How the status of the cell wall is relayed to BR signaling remains largely unclear. Increasing evidence shows that RAPID ALKALANIZATION FACTORs (RALFs), a class of secreted peptides, play structural and signaling roles at the cell surface. Here we show that perception of RALF23 promotes the formation and signaling of the main BR receptor complex formed by BRASSINOSTEROID INSENSITIVE 1 (BRI1) and BRI1 BRASSINOSTEROID INSENSITIVE1 BRASSINOSTEROID ASSOCIATED KINASE 1 (BAK1). The loss of the plasma membrane localized RALF receptor complex FERONIA (FER) LORELEI LIKE GPI anchor protein 1 (LLG1) leads to defects in cell expansion and anisotropy, as well as uncontrolled BRI1 BAK1 complex formation and signaling. RALF23 bioactivity relies on pectin status and its perception induces changes in pectin composition and the activity of pectin-modifying enzymes. Our observations suggest a model in which RALF23 functions as a cell wall informed signaling cue initiating a feedback loop that solicits BR signaling, modifies the cell wall, and coordinates cell morphogenesis.
Live Cell Fluorescence Microscopy – An End-to-End Workflow for High-Throughput Image and Data Analysis
Authors: Zahumensky Jakub , Malinsky Jan
Published: March 2024

Fluorescence microscopy images of biological samples contain valuable information but require rigor-ous analysis for accurate and reliable determination of changes in protein localization, fluorescence intensity and morphology of the studied objects. Traditionally, cells for microscopy are immobilized using chemicals, which can introduce stress. Analysis often focuses only on colocalization and in-volves manual segmentation and measurement, which are time-consuming and can introduce bias. Our new workflow addresses these issues by gently immobilizing cells using a small agarose block on a microscope cover glass. This approach is suitable for cell-walled cells (yeast, fungi, plants, bacteria), facilitates their live imaging under conditions close to their natural environment and enables the addi-tion of chemicals during time-lapse experiments. The primary focus of the protocol is on the presented analysis workflow, which is applicable to virtually any cell type – we describe cell segmentation using the Cellpose software followed by automated analysis of a multitude of parameters using custom-written Fiji (ImageJ) macros. The results can be easily processed using the provided R markdown scripts or available graphing software. Our method facilitates unbiased batch analysis of large datasets, improving the efficiency and accuracy of fluorescence microscopy research.

The reported sample preparation protocol and Fiji macros were used in our recent publications:Microbiol Spectr(2022), DOI: 10.1128/spectrum.01961-22;Microbiol Spectr(2022), DOI: 10.1128/spectrum.02489-22;J Cell Sci(2023), DOI: 10.1242/jcs.260554.

Graphical overview

From fluorescence microscopy to numbers and plots – a generalized workflow
The ER-phagy receptor FAM134B is targeted bySalmonellaTyphimurium to promote infection
Authors: Gatica Damián , Alsaadi Reham M. , Hamra Rayan El , Mueller Rudolf , Miyazaki Makoto , Sad Subash , Russell Ryan C.
Published: March 2024

Macroautophagy/autophagy is a key catabolic-recycling pathway that can selectively target damaged organelles or invading pathogens for degradation. The selective autophagic degradation of the endoplasmic reticulum (hereafter referred to as ER-phagy) is a homeostatic mechanism, controlling ER size, the removal of misfolded protein aggregates, and organelle damage. ER-phagy is also stimulated by pathogen infection. However, the link between ER-phagy and bacterial infection remains poorly understood, as are the mechanisms evolved by pathogens to escape the effects of ER-phagy. Here, we show thatSalmonella entericaserovar Typhimurium inhibits ER-phagy by targeting the ER-phagy receptor FAM134B, leading to a pronounced increase inSalmonellaviability after invasion.Salmonellaprevents FAM134B oligomerization, which is required for efficient ER-phagy. FAM134B knock-out raises intracellularSalmonellanumber, while FAM134B activation reducesSalmonellaburden. Additionally, we found thatSalmonellatargets FAM134B through the bacterial effector SopF to enhance intracellular survival through ER-phagy inhibition. Furthermore, FAM134B knock-out mice infected withSalmonellapresented severe intestinal damage and increased bacterial burden. These results provide new mechanistic insight into the interplay between ER-phagy and bacterial infection, highlighting a key role for FAM134B in innate immunity.