bluuebunny/crossref_metadata_2025 huggingface dataset:
Medical and Cardiac Risk Stratification and Exercise Prescription in Persons With Cancer
Authors: Knowlton Sasha E. , Cristian Adrian , Orada Romer , Sokolof Jonas
Published: February 2024

Cancer patients are recommended to exercise at all stages of disease given the multiple health and functional benefits of physical activity. Certain safety precautions, including a preparticipation medical evaluation and periodic re-evaluations, should be undertaken before creating an exercise program based on individual cancer and treatment history. When designing an exercise program, physiatrists should use similar principles of frequency, intensity, timing, and type for cancer patients that are used for noncancer patients. Special attention to risks of cardiac and pulmonary disease along with risks of sarcopenia, thrombocytopenia, anemia, neutropenia, fracture risk, neurotoxicity, lymphedema, and metastases should be made. This article will outline these specific risks and necessary modifications to the exercise prescription for cancer patients that can be used to enable safe participation in recommended exercise.
Field recordings of transcranial magnetic stimulation in human brain postmortem models
Authors: Quesada Charles , Fauchon Camille , Pommier Benjamin , Bergandi Florian , Peyron Roland , Mertens Patrick , Garcia-Larrea Luis
Published: February 2024

Introduction:

The ability of repetitive transcranial magnetic stimulation (rTMS) to deliver a magnetic field (MF) in deep brain targets is debated and poorly documented.

Objective:

To quantify the decay of MF in the human brain.

Methods:

Magnetic field was generated by single pulses of TMS delivered at maximum intensity using a flat or angulated coil. Magnetic field was recorded by a 3D-magnetic probe. Decay was measured in the air using both coils and in the head of 10 postmortem human heads with the flat coil being positioned tangential to the scalp. Magnetic field decay was interpreted as a function of distance to the coil for 6 potential brain targets of noninvasive brain stimulation: the primary motor cortex (M1, mean depth: 28.5 mm), dorsolateral prefrontal cortex (DLPFC: 28 mm), secondary somatosensory cortex (S2: 35.5 mm), posterior and anterior insulae (PI: 38.5 mm; AI: 43.5 mm), and midcingulate cortex (MCC: 57.5 mm).

Results:

In air, the maximal MF intensities at coil center were 0.88 and 0.77 T for the flat and angulated coils, respectively. The maximal intracranial MF intensity in the cadaver model was 0.34 T, with a ∼50% decay at 15 mm and a ∼75% MF decay at 30 mm. The decay of the MF in air was similar for the flat coil and significantly less attenuated with the angulated coil (a ∼50% decay at 20 mm and a ∼75% MF decay at 45 mm).

Conclusions:

Transcranial magnetic stimulation coil MFs decay in brain structures similarly as in air, attenuation with distance being significantly lower with angulated coils. Reaching brain targets deeper than 20 mm such as the insula or Antérior Cingulate Cortex seems feasible only when using angulated coils. The abacus of MF attenuation provided here can be used to adjust modalities of deep brain stimulation with rTMS in future research protocols.
The Ability to Sustain Facial Expressions
Authors: Schutte Hilde , Bielevelt Freek , Emohamadian Hafsa , Muradin Marvick S.M. , Bleys Ronald L.A.W. , Rosenberg Antoine J.W.P.
Published: February 2024

To gain more insight into facial muscle function, imaging during action would be optimal. Magnetic resonance imaging is highly suitable for visualizing facial muscles. However, magnetic resonance imaging requires the individual to remain as still as possible for a while. Knowledge of the ability to sustain facial expressions is requisite before scanning individuals. This could help adapting the scanning protocol to obtain optimal quality of imaging the muscles in action. A study, including 10 healthy volunteers, was done to perceive the extent of movement while holding facial expressions of smiling and pouting. During 6 minutes, 3-dimensional photographs were taken every consecutive minute while the participants maintained their facial expressions as motionless as possible. The movement was objectified by creating distance maps between the 2 models and calculating the Root Mean Square using the software 3DMedX. The results showed that most movements occurred in the first minute, with a decrease of the intensity of the expression. After the first minute, the expression, although less intense, could be held stable. This implies that magnetic resonance imaging scanning during facial expression is possible, provided that the scanning starts after the first minute has elapsed. In addition, results demonstrated that more slackening of the muscles while smiling compared with pouting.
The Development, Implementation, and Evaluation of a Geriatric Disaster Nursing Simulation Intervention With Supportive Debriefing
Authors: Jin Joo-Young , Choi Yun-Jung
Published: February 2024

Introduction

Geriatric disaster nursing simulation curriculum use scenarios with trauma-based topics that may contribute to lack of psychological safety in learners. This learning condition lowers students' self-efficacy, so supportive debriefing is needed to provide psychological safety for learners. The aims of this study are to develop and apply a geriatric disaster nursing simulation and to evaluate the effectiveness of a supportive debriefing model on psychological safety, learning self-efficacy, and counseling self-efficacy.

Methods

A geriatric nursing simulation scenario, checklists, and a standardized patient were developed based on the Analysis-Design-Development-Implementation-Evaluation model. Nursing students were recruited as participants and randomly assigned to either the experimental group, conventional group, or control group. All 3 groups participated in the same geriatric disaster nursing simulation scenario, after which the experimental group used a supportive debriefing model—the SENSE (share-explore-notice-support-extend) model. The conventional group used a common debriefing model, the GAS (gathering-analyzing-summarizing) model, and the control group received simple comments with no debriefing model. The effects of the debriefing models on psychological safety, learning self-efficacy, and counseling self-efficacy were measured by self-report questionnaires. The aggregate scores of the measures were 222 for counseling self-efficacy, 70 for learning self-efficacy, and 50 for psychological safety. Higher scores within these measures corresponded to heightened capabilities.

Results

The mean score of counseling self-efficacy in the SENSE model group was significantly increased after the simulation with the supportive debriefing from 142.80 ± 11.43 to 164.53 ± 15.48 (Z = −3.411, P = 0.001). In addition, the SENSE model group and the GAS model group had significantly higher scores in counseling self-efficacy, learning self-efficacy, and psychological safety than those of the control group. However, the SENSE model group had a significantly higher score in psychological safety than that of the GAS model group.

Conclusions

The SENSE debriefing model is recommended as a supportive debriefing model to foster students' psychological safety in disaster nursing simulations.
Infratemporal abscess: a rare complication of a common procedure
Authors: Kotagiri Rajesh , Repp Matthew L. , Kim Michael H. , Stipho Faissal
Published: February 2024

The infratemporal fossa (ITF) is an anatomically complex cavity that houses a variety of muscular and neurovascular structures at the base of the skull. Infections involving the ITF, though uncommon, can be fatal due to the difficulties of accessing this anatomical space and its proclivity to evolve into a cavernous venous thrombosis (CVT). As a result, a multi-disciplinary approach involving several surgical and medical subspecialists is often warranted. We present a case of an infratemporal fossa abscess (IFA) after wisdom teeth extraction with a very complicated clinical course and a distinct microbiologic profile.
Identification of novel tail-anchored membrane proteins integrated by the bacterial twin-arginine translocase
Authors: Gallego-Parrilla José Jesús , Severi Emmanuele , Chandra Govind , Palmer Tracy
Published: February 2024

The twin-arginine protein transport (Tat) system exports folded proteins across the cytoplasmic membranes of prokaryotes and the energy transducing-membranes of plant thylakoids and mitochondria. Proteins are targeted to the Tat machinery by N-terminal signal peptides with a conserved twin-arginine motif, and some substrates are exported as heterodimers where the signal peptide is present on one of the partner proteins. A subset of Tat substrates is found in the membrane. Tat-dependent membrane proteins usually have large globular domains and a single transmembrane helix present at the N- or C-terminus. Five Tat substrates that have C-terminal transmembrane helices have previously been characterized in the model bacterium Escherichia coli. Each of these is an iron–sulfur cluster-containing protein involved in electron transfer from hydrogen or formate. Here we have undertaken a bioinformatic search to identify further tail-anchored Tat substrates encoded in bacterial genomes. Our analysis has revealed additional tail-anchored iron–sulfur proteins associated in modules with either a b-type cytochrome or a quinol oxidase. We also identified further candidate tail-anchored Tat substrates, particularly among members of the actinobacterial phylum, that are not predicted to contain cofactors. Using reporter assays, we show experimentally that six of these have both N-terminal Tat signal peptides and C-terminal transmembrane helices. The newly identified proteins include a carboxypeptidase and a predicted protease, and four sortase substrates for which membrane integration is a prerequisite for covalent attachment to the cell wall.
Tuft cells transdifferentiate to neural-like progenitor cells in the progression of pancreatic cancer
Authors: Salas-Escabillas Daniel J. , Hoffman Megan T. , Moore Jacee S. , Brender Sydney M. , Wen Hui-Ju , Benitz Simone , Davis Erick T. , Long Dan , Wombwell Allison M. , Steele Nina G. , Sears Rosalie C. , Matsumoto Ichiro , DelGiorno Kathleen E. , Crawford Howard C.
Published: February 2024

Pancreatic ductal adenocarcinoma (PDA) is partly initiated through the transdifferentiation of acinar cells to metaplastic ducts that act as precursors of neoplasia and cancer. Tuft cells are solitary chemosensory cells not found in the normal pancreas but arise in metaplasia and neoplasia, diminishing as neoplastic lesions progress to carcinoma. Metaplastic tuft cells (mTCs) function to suppress tumor progression through communication with the tumor microenvironment, but their fate during progression is unknown. To determine the fate of mTCs during PDA progression, we have created a lineage tracing model that uses a tamoxifen-inducible tuft-cell specific Pou2f3CreERT/+driver to induce transgene expression, including the lineage tracer tdTomato or the oncogeneMyc. mTC lineage trace models of pancreatic neoplasia and carcinoma were used to follow mTC fate. We found that mTCs, in the carcinoma model, transdifferentiate into neural-like progenitor cells (NRPs), a cell type associated with poor survival in PDA patients. Using conditional knock-out and overexpression systems, we found thatMycactivity in mTCs is necessary and sufficient to induce this Tuft-to-Neuroendocrine-Transition (TNT).
Distinct sets of molecular characteristics define tumor-rejecting neoantigens
Authors: Adams Anngela C. , Macy Anne M. , Borden Elizabeth S. , Herrmann Lauren M. , Brambley Chad A. , Ma Tao , Li Xing , Hughes Alysia , Roe Denise J. , Mangold Aaron R. , Buetow Kenneth H. , Wilson Melissa A. , Baker Brian M. , Hastings Karen Taraszka
Published: February 2024

Challenges in identifying tumor-rejecting neoantigens limit the efficacy of neoantigen vaccines to treat cancers, including cutaneous squamous cell carcinoma (cSCC). A minority of human cSCC tumors shared neoantigens, supporting the need for personalized vaccines. Using a UV-induced mouse cSCC model which recapitulated the mutational signature and driver mutations found in human disease, we found that CD8 T cells constrain cSCC. Two MHC class I neoantigens were identified that constrained cSCC growth. Compared to the wild-type peptides, one tumor-rejecting neoantigen exhibited improved MHC binding and the other had increased solvent accessibility of the mutated residue. Across known neoantigens that do not impact MHC binding, structural modeling of the peptide/MHC complexes indicated that increased solvent accessibility, which will facilitate TCR recognition of the neoantigen, distinguished tumor-rejecting from non-immunogenic neoantigens. This work reveals characteristics of tumor-rejecting neoantigens that may be of considerable importance in identifying optimal vaccine candidates in cSCC and other cancers.
Quantitative model and physical mechanisms of iRBC membrane curling during egress of malaria parasites
Authors: Gorkavyi N. , Parmeggiani A. , Kajava A. V.
Published: February 2024

Egress of malaria merozoites from infected red blood cells (iRBC) is a critical step in the parasite’s life cycle. The egress is accompanied by the formation of a pore in the erythrocyte membrane, followed by an outward curling of the membrane around the pore, resulting in a complete eversion of the erythrocyte membrane, pushing the parasites away. Despite the well-documented steps of the egress, the detailed mechanism and source of energy for such a spectacular eversion of iRBC remains largely unknown. In this paper, we consider a biophysical model based on the energetics of the egress process that includes both viscous dissipation and energy consumption for the formation of the rim around the pore in iRBC. We show that viscosity does not play a significant role in iRBC eversion and we hypothesize that this process is controlled by lateral lipid diffusion. The model is supported by quantitative estimates and is in good agreement with known experimental data.
ChemGLaM: Chemical-Genomics Language Models for Compound-Protein Interaction Prediction
Authors: Koyama Takuto , Tsumura Hayato , Matsumoto Shigeyuki , Okita Ryunosuke , Kojima Ryosuke , Okuno Yasushi
Published: February 2024

Abstract

Accurate prediction of compound-protein interaction (CPI) is of great importance for drug discovery. For creating generalizable CPI prediction deep learning (DL) models, the expansion of CPI data through experimental validation is crucial. However, the cost associated with these experimental validations is a bottleneck. Recently developed large language models (LLMs) such as chemical language models (CLMs) and protein language models (PLMs) have emerged as foundation models, demonstrating high generalization performance in various tasks involving compounds and proteins. Inspired by this, we propose a chemical-genomics language model, ChemGLaM, for predicting compound-protein interactions. ChemGLaM is based on the 2 independent language models, MoLFormer for compounds and ESM-2 for proteins, and fine-tuned for the CPI datasets using an interaction block with a cross-attention mechanism. ChemGLaM is capable of predicting interactions between unknown compounds and proteins with higher accuracy than existing CPI prediction models, demonstrating that combining the independently pre-trained foundation models is effective for obtaining sophisticated representation of compound-protein interactions. Furthermore, visualizing the learned cross-attention map can offer explainable insights into the mechanism of compound-protein interaction. This study emphasizes the potential of integrating the independent foundation models for the tasks of multi-modality such as CPI prediction.
MobileLAMP: A portable, low-cost, open-source device for isothermal nucleic acid amplification
Authors: Bhupathi Mohini , Hegde Smitha , Devarapu Ganga Chinna Rao , Molloy Jennifer C
Published: February 2024

1

Isothermal amplification-based methods for pathogen DNA or RNA detection offer high sensitivity, rapid detection, and the potential for deployment in remote fields and home testing. Consequently, they are emerging as alternatives to PCR and saw a surge in research activity and deployment for the rapid detection of SARS-CoV-2 during the Covid-19 pandemic. The most common isothermal DNA detection methods rely on minimal reagents for DNA amplification and simple hardware that can maintain isothermal conditions and read-out a fluorescent or colorimetric signal. Many researchers globally are working on improving these components based on diverse end-user needs. In this work, we have recognized the need for an open-source hardware device for isothermal amplification, composed of off-the-shelf components that are easily accessible in any part of the world, is easily manufacturable in a distributed and scalable way using 3D printing, and that can be powered using a wide diversity of batteries and power sources. We demonstrate the easy assembly of our device design and demonstrate its efficacy using colorimetric LAMP for both RNA and DNA targets.
Predicting the macrovascular contribution to resting-state fMRI functional connectivity at 3 Tesla: A model-informed approach
Authors: Zhong Xiaole Z. , Polimeni Jonathan R. , Chen J. Jean
Published: February 2024

Macrovascular biases have been a long-standing challenge for fMRI, limiting its ability to detect spatially specific neural activity. Recent experimental studies, including our own (Huck et al., 2023; Zhong et al., 2023), found substantial resting-state macrovascular BOLD fMRI contributions from large veins and arteries, extending into the perivascular tissue at 3 T and 7 T. The objective of this study is to demonstrate the feasibility of predicting, using a biophysical model, the experimental resting-state BOLD fluctuation amplitude (RSFA) and associated functional connectivity (FC) values at 3 Tesla. We investigated the feasibility of both 2D and 3D infinite-cylinder models as well as macrovascular anatomical networks (mVANs) derived from angiograms. Our results demonstrate that: 1) with the availability of mVANs, it is feasible to model macrovascular BOLD FC using both the mVAN-based model and 3D infinite-cylinder models, though the former performed better; 2) biophysical modelling can accurately predict the BOLD pairwise correlation near to large veins (with R2ranging from 0.53 to 0.93 across different subjects), but not near to large arteries; 3) compared with FC, biophysical modelling provided less accurate predictions for RSFA; 4) modelling of perivascular BOLD connectivity was feasible at close distances from veins (with R2ranging from 0.08 to 0.57), but not arteries, with performance deteriorating with increasing distance. While our current study demonstrates the feasibility of simulating macrovascular BOLD in the resting state, our methodology may also apply to understanding task-based BOLD. Furthermore, these results suggest the possibility of correcting for macrovascular bias in resting-state fMRI and other types of fMRI using biophysical modelling based on vascular anatomy.
Gel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates
Authors: Meng Zhaowei , Saei Amir Ata , Zhang Xuepei , Lyu Hezheng , Gharibi Hassan , Lundström Susanna L , Végvári Ákos , Gaetani Massimiliano , Zubarev Roman A.
Published: February 2024

Here we present a high-throughput virtual top-down proteomics approach that restores the molecular weight (MW) information in shotgun proteomics, and demonstrate its utility in studying proteolytic events in programmed cell death. With Gel-Assisted Proteome Position Integral Shift (GAPPIS), we quantified over 7000 proteins in staurosporine-induced apoptotic HeLa cells and identified 89 proteins exhibiting in a statistically significant manner at least two of the following features: 1) a negative MW shift; 2) an elevated ratio in a pair of a semi-tryptic and tryptic peptide, 3) a negative shift in the standard deviation of MW estimated for different peptides, and 4) a negative shift in skewness of the same data. Of these proteins, 60 molecules were novel caspase 3 substrates. Further analysis identified the preferred cleavage sites consistent with the known caspase cleavages after the DXXD motif. As a powerful tool for high-throughput MW analysis simultaneously with the conventional expression analysis, GAPPIS assay can prove useful in studying a broad range of biological processes involving proteolytic events.
Transient Impairment in Microglial Function Causes Sex-Specific Deficits in Synaptic and Hippocampal Function in Mice Exposed to Early Adversity
Authors: Ahmed Sahabuddin , Polis Baruh , Jamwal Sumit , Sanganahalli Basavaraju G. , MacDowell Kaswan Zoe , Islam Rafiad , Kim Dana , Bowers Christian , Giuliano Lauryn , Biederer Thomas , Hyder Fahmeed , Kaffman Arie
Published: February 2024

Abnormal development and function of the hippocampus are two of the most consistent findings in humans and rodents exposed to early life adversity, with males often being more affected than females. Using the limited bedding (LB) paradigm as a rodent model of early life adversity, we found that male adolescent mice that had been exposed to LB exhibit significant deficits in contextual fear conditioning and synaptic connectivity in the hippocampus, which are not observed in females. This is linked to altered developmental refinement of connectivity, with LB severely impairing microglial-mediated synaptic pruning in the hippocampus of male and female pups on postnatal day 17 (P17), but not in adolescent P33 mice when levels of synaptic engulfment by microglia are substantially lower. Since the hippocampus undergoes intense synaptic pruning during the second and third weeks of life, we investigated whether microglia are required for the synaptic and behavioral aberrations observed in adolescent LB mice. Indeed, transient ablation of microglia from P13-21, in normally developing mice caused sex-specific behavioral and synaptic abnormalities similar to those observed in adolescent LB mice. Furthermore, chemogenetic activation of microglia during the same period reversed the microglial-mediated phagocytic deficits at P17 and restored normal contextual fear conditioning and synaptic connectivity in adolescent LB male mice. Our data support an additional contribution of astrocytes in the sex-specific effects of LB, with increased expression of the membrane receptor MEGF10 and enhanced synaptic engulfment in hippocampal astrocytes of 17-day-old LB females, but not in LB male littermates. This finding suggests a potential compensatory mechanism that may explain the relative resilience of LB females. Collectively, these studies highlight a novel role for glial cells in mediating sex-specific hippocampal deficits in a mouse model of early-life adversity.
Investigating T cell Recruitment in Atherosclerosis using a novel Human 3D Tissue-Culture Model reveals the role of CXCL12 in intraplaque neovessels
Authors: Parma Laura , Sachs Nadja , Li Zhaolong , Merchant Kevin , Sobczak Nikola , Slütter Bram , Maegdefessel Lars , Weber Christian , Duchene Johan , Megens Remco T.A.
Published: February 2024

Background

Development of effective treatments for atherosclerosis requires new models that better predict the human immune response. Although T cells are abundant in human atherosclerotic lesions and play a key role in the pathogenesis, the mechanism involved in plaque infiltration remains ill defined.

Methods

We developed a three-dimensional tissue-culture model to study leukocyte recruitment to human atherosclerotic plaques. In this study, human atherosclerotic plaques obtained during carotid endarterectomy surgery were co-cultured with patient-matching T cells. Exogenous T cells were stained using a multi-factor staining strategy, which involved intracellular fluorescent cell tracker dyes combined with nuclear labels. Flow cytometry was used to assess the presence of the labeled cells within the plaques, and microscopic analysis was performed to examine their localization.

Results

Flow cytometry and microscopy cell-tracking analysis demonstrated that exogenous T cells successfully migrated into atherosclerotic plaques. Furthermore, infiltrated CD8+T cells displayed a significant increase of CD69 expression, indicating their activation within the tissue. Blocking chemokine receptors, particularly CXCR4, significantly impaired T cell infiltration, demonstrating that exogenous CD8+T cells invade plaques through chemotactic migration. Surprisingly, 3D microscopy combined with optical tissue clearing strategy revealed that CXCL12, the sole ligand of CXCR4, mainly accumulated in intraplaque neovessels. Single-cell RNA sequencing (scRNAseq) analysis further confirmed that endothelial cells from intraplaque neovessels were the primary source for CXCL12. Additionally, exogenous T cells were found within and in proximity to these neovessels, suggesting that the CXCL12/CXCR4 axis regulates T cell recruitment through intraplaque neovessels.

Conclusions

Overall, these findings shed new light on the mechanism of action of CXCL12 in atherosclerosis and demonstrated the potential of the model to advance our understanding of leukocyte accumulation in human atherosclerosis and assist in testing novel pharmacological therapies.
Optical Control of Cell-Surface and Endomembrane-Exclusive β-Adrenergic Receptor Signaling
Authors: Thotamune Waruna , Ubeysinghe Sithurandi , Shrestha Kendra K. , Mostafa Mahmoud Elhusseiny , Young Michael C. , Karunarathne Ajith
Published: February 2024

Beta-adrenergic receptors (βARs) are G protein-coupled receptors (GPCRs) that mediate catecholamine-induced stress responses, such as heart rate increase and bronchodilation. In addition to signals from the cell surface, βARs also broadcast non-canonical signaling activities from the cell interior membranes (endomembranes). Dysregulation of these receptor pathways underlies severe pathological conditions. Excessive βAR stimulation is linked to cardiac hypertrophy, leading to heart failure, while impaired stimulation causes compromised fight or flight stress responses and homeostasis. In addition to plasma membrane βAR, emerging evidence indicates potential pathological implications of deeper endomembrane βARs, such as inducing cardiomyocyte hypertrophy and apoptosis, underlying heart failure. However, the lack of approaches to control their signaling in subcellular compartments exclusively has impeded linking endomembrane βAR signaling with pathology. Informed by the β1AR-catecholamine interactions, we engineered an efficiently photo-labile, protected hydroxy β1AR pro-ligand (OptoIso) to trigger βAR signaling at the cell surface, as well as exclusive endomembrane regions upon blue light stimulation. Not only does OptoIso undergo blue light deprotection in seconds, but it also efficiently enters cells and allows examination of G protein heterotrimer activation exclusively at endomembranes. In addition to its application in the optical interrogation of βARs in unmodified cells, given its ability to control deep organelle βAR signaling, OptoIso will be a valuable experimental tool.
Importin-β specific nuclear transport defects recapitulate phenotypic and transcriptional alterations seen in neurodegeneration
Authors: Plessis-Belair Jonathan , Ravano Kathryn , Han Ellen , Janniello Aubrey , Molina Catalina , Sher Roger
Published: February 2024

Defects in Nucleocytoplasmic transport have been implicated as an important neurodegenerative pathway in ALS/FTD. Here, we show that aNemfR86Smutation results in the disruption of NCT bothin vitroandin vivo. These disruptions are specific to Importin-β nuclear import, and result in the nuclear loss and cytoplasmic gain of NEMF, Importin-β, and TDP-43. We show that a transient nuclear import block is capable of inducing the mis-localization of TDP-43 and is associated with altered transcriptional expression of ALS, FTD, and AD/ARD genes. Taken together, these findings show that disrupted Importin-β nuclear import, whether through genetic forms such asNemfmutations, or through pharmacological inhibition, is the primary driver of TDP-43 pathology, disease-related transcriptional alterations, and neurodegeneration.
Feed-forward stimulation of CAMK2 by the oncogenic pseudokinase PEAK1 generates a therapeutically ‘actionable’ signalling axis in triple negative breast cancer
Authors: Yang Xue , Ma Xiuquan , Zhao Tianyue , Croucher David R , Nguyen Elizabeth V. , Clark Kimberley C. , Hu Changyuan , Latham Sharissa L , Bayly-Jones Charles , Nguyen Viet Chi Bao , Budnar Srikanth , Shin Sung-Young , Nguyen Lan K. , Cotton Thomas R. , Chüeh Anderly C. , Sian Terry C C Lim Kam , Stratton Margaret M. , Ellisdon Andrew M. , Daly Roger J
Published: February 2024

The PEAK family of pseudokinases, comprising PEAK1-3, are signalling scaffolds that play oncogenic roles in several poor prognosis human cancers, including triple negative breast cancer (TNBC). However, therapeutic targeting of pseudokinases is challenging due to their lack of catalytic activity. To address this, we screened for PEAK1 effectors by affinity purification and mass spectrometry, identifying calcium/calmodulin-dependent protein kinase 2 (CAMK2)D and CAMK2G. PEAK1 promoted CAMK2D/G activation in TNBC cells via a novel feed-forward mechanism involving PEAK1/PLCγ1/Ca2+signalling and direct binding via a consensus CAMK2 interaction motif in the PEAK1 N-terminus. In turn, CAMK2 phosphorylated PEAK1 to enhance association with PEAK2, which is critical for PEAK1 oncogenic signalling. To achieve pharmacologic targeting of PEAK1/CAMK2, we repurposed RA306, a second generation CAMK2 inhibitor under pre-clinical development for treatment of cardiovascular disease. RA306 demonstrated on-target activity against CAMK2 in TNBC cells and inhibited PEAK1-enhanced migration and invasionin vitro. Moreover, RA306 significantly attenuated TNBC xenograft growth and blocked metastasis in a manner mirrored by CRISPR-mediated PEAK1 ablation. Overall, these studies establish PEAK1 as a critical cell signalling nexus, identify a novel mechanism for regulation of Ca2+signalling and its integration with tyrosine kinase signals, and identify CAMK2 as a therapeutically ‘actionable’ target downstream of PEAK1.
Pangenomic landscapes shape the genetic circuit performance in aStutzerimonasbiodesign toolkit
Authors: Chan Dennis Tin Chat , Bernstein Hans C.
Published: February 2024

Implementation of identical biodesign strategies into different species often results in different performance, a process called the “chassis effect”. Our current understanding of how cellular host context underpins its ability to be engineered is lacking and closing this knowledge gap will greatly improve the rational design of microorganisms. Here, we combined global differential gene expression analysis and pangenomics to uncover how genome structure and function relates to the observed chassis effect of an engineered genetic inverter device operating in six closely relatedStutzerimonashosts. The differential expression of the core genome, gene clusters shared between all hosts, was found to be the main source of significant concordance to the observed device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes related to denitrification and efflux pumps were among the most differentially expressed gene clusters in response to the engineered device. This study establishes that the effectiveness of synthetic gene circuits can be traced along differences in closely related microbial hosts that each represent unique hardware options for biodesign.
Adaptation of human cell populations to different levels of centriole amplification involves a two-step response
Authors: Dias Louro Marco António , Peneda Catarina , Bank Claudia , Bettencourt-Dias Mónica
Published: February 2024

Centrioles are the main components of cilia and centrosomes, which play a central role in cell proliferation and signalling. Their number is strictly regulated. Centriole amplification, or the presence of extra centrioles, often occurs in tumours and leads to aneuploidy and altered signalling and has been associated with cancer development and malignancy. Negative selection of cells with extra centrioles prevents numerical errors from expanding in the population, resulting in an overproduction-selection balance. However, how chronic perturbation of key centriolar regulators affect centriole number dynamics is poorly described.

PLK4, a key regulator of centriole biogenesis, is often overexpressed in cancer and is associated with worse prognosis in breast cancer. Here we show that centriole amplification cannot be sustained in cultured MCF10A breast cells exposed to low and high levels of chronic PLK4 overexpression. We observed a short-term response in which negative selection and reduction in PLK4 mRNA limit centriole amplification. This was followed by long-term adaptation in which a rise in PLK4 mRNA levels was decoupled from accumulation of the protein at the centrosome. Furthermore, adaptation was dose-dependent. Populations evolved in low-overexpression conditions retained the ability to generate extra centrioles when PLK4 was further overexpressed, whereas centriole overproduction was irreversibly inhibited in populations evolved under high PLK4 overexpression. Taken together, our data reveal a two step mode of centriole number regulation and suggest that differences in the level of PLK4 overexpression may condition cancer evolution.
Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera Soda Pans, Zimbabwe
Authors: Mangoma Ngonidzashe , Zhou Nerve , Ncube Thembekile
Published: February 2024

The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe. This ecosystem has not been studied despite its unique geochemistry and potential as a habitat for unique microorganisms. Metagenomic DNA from the soda pan was sequenced using the DNA Nanoball Sequencing (DNBSEQR) technique. Sequence analysis, done on the Knowledgebase (KBase) platform, involved quality assessment, read assembly, contig binning, and MAG extraction. The MAGs were subjected to taxonomic placement, phylogenetic profiling and functional annotation in order to establish their possible ecological roles in the soda pan ecosystem. A total of 16 bacterial MAGs of medium to high quality were recovered, all distributed among five phyla dominated byProteobacteriaandFirmicutes. Of the ten MAGs that were taxonomically classified up to genus level, five of them belonged to the halophilic/ haloalkaliphilic generaAlkalibacterium, Vibrio, Thioalkalivibrio, CecembiaandNitrincola. Functional profiling revealed the use of diverse carbohydrate-metabolising pathways among the MAGs, with glycolysis and the pentose phosphate pathways appearing to be key pathways in this ecosystem. Several MAGs harboured both sulphur/ sulphate reduction and respiratory pathways, suggesting a possible mechanism of energy generation through sulphur/ suphate respiration. In conclusion, this study revealed a highly taxonomically and functionally diverse microbial community in the soda pans, dominated by halophilic and haloalkaliphilic bacteria.
Ligand binding determines proteolytic stability ofVibrioLuxR/HapR quorum sensing transcription factors
Authors: Rasal Tanmaya A. , Mallery Caleb P. , Brockley Matthew W. , Brown Laura C. , Paczkowski Jon E. , van Kessel Julia C.
Published: February 2024

InVibriospecies, quorum sensing signaling culminates in the production of a TetR-type master transcription factor collectively called the LuxR/HapR family, which regulates genes required for colonization and infection of host organisms. These proteins possess a solvent accessible putative ligand binding pocket. However, a native ligand has not been identified, and the role of ligand binding in LuxR/HapR function inVibrionaceaeis unknown. To probe the role of the ligand binding pocket, we utilize the small molecule thiophenesulfonamide inhibitor PTSP (3-phenyl-1-(thiophen-2-ylsulfonyl)-1H-pyrazole) that we previously showed targets LuxR/HapR proteins. Amino acid conservation in the ligand binding pocket determines the specificity and efficacy of PTSP inhibition acrossVibriospecies. Here, we used structure-function analyses to identify PTSP-interacting residues in the ligand binding pocket of SmcR – theVibrio vulnificusLuxR/HapR homolog – that are required for PTSP inhibition of SmcR activityin vivo. Forward genetic screening combined with X-ray crystallography structural determination of SmcR bound to PTSP identified substitutions at eight residues that were sufficient to reduce or eliminate PTSP-mediated SmcR inhibition. Small-angle X-ray scattering and computational modeling determined that PTSP drives allosteric unfolding at the N-terminal DNA binding domain. We discovered that SmcR is degraded by the ClpAP protease in the presence of PTSPin vivo; substitution of key PTSP-interacting residues stabilized or increased SmcR levels in the cell. This mechanism of inhibition is observed for all thiophenesulfonamide compounds tested and against otherVibriospecies. We conclude that thiophenesulfonamides specifically bind in the ligand binding pocket of LuxR/HapR proteins, promoting protein degradation and thereby suppressing downstream gene expression, implicating ligand binding as a mediator of LuxR/HapR protein stability and function to govern virulence gene expression inVibriopathogens.

SIGNIFICANCE

LuxR/HapR proteins were discovered in the 1990s as central regulators of quorum sensing gene expression and later discovered to be conserved in all studiedVibriospecies. LuxR/HapR homologs regulate a wide range of genes involved in pathogenesis, including but not limited to genes involved in biofilm production and toxin secretion. As archetypal members of the broad class of TetR-type transcription factors, each LuxR/HapR protein has a predicted ligand binding pocket. However, no ligand has been identified for LuxR/HapR proteins that control their function as regulators. Here, we used LuxR/HapR-specific chemical inhibitors to determine that ligand binding drives proteolytic degradationin vivo, the first demonstration of LuxR/HapR function connected to ligand binding for this historical protein family.
Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB
Authors: Manthei Kelly A. , Munson Lia M. , Nandakumar Jayakrishnan , Simmons Lyle A.
Published: February 2024

ABSTRACT

Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacteriumBacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ- family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3’-5’ DNA exonuclease. We show that Leu113 aids in coordinating the 3’ end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC- induced DNA adducts.

GRAPHICAL ABSTRACT
Brain-handedness associations depend on how and when handedness is measured
Authors: Tejavibulya Link , Horien Corey , Fredricks Carolyn , Ficek-Tani Bronte , Westwater Margaret L. , Scheinost Dustin
Published: February 2024

Hand preference is ubiquitous, intuitive, and often simplified to right- or left-handed. Accordingly, differences between right- and left-handed individuals in the brain have been established. Nevertheless, considering handedness as a binarized construct fails to capture the variability of brain-handedness associations across different domains or activities. Further, many cultures, environments, and generations impose right-handed norms, and handedness preferences can change over the lifespan. As a result, brain-handedness associations may depend onhowandwhenhandedness is measured. We used two large datasets, the Human Connectome Project-Development (HCP-D; n=465; age=5-21 years) and Human Connectome Project-Aging (HCP-A; n=368; age=36-100 years), to explore handedness preferences and brain-handedness associations. Nine items from the Edinburgh Handedness Inventory were associated with resting-state functional connectomes. We show that brain-handedness associations differed across the two cohorts. Moreover, these differences depended on the way handedness was measured. Given that brain-handedness associations differ across handedness measures and datasets, we caution against a one-size-fits-all approach to neuroimaging studies of this complex trait.
Deep Learning Based Models for Preimplantation Mouse and Human Development
Authors: Proks Martin , Salehin Nazmus , Brickman Joshua M
Published: February 2024

The rapid growth of single-cell transcriptomic technology has produced an increasing number of datasets for both embryonic development and in vitro pluripotent stem cell derived models. This avalanche of data about pluripotency and the process of lineage specification has meant it has become increasingly difficult to define specific cell types or states and compare these to in vitro differentiation. Here we utilize a set of deep learning (DL) tools to integrate and classify multiple datasets. This allows for the definition of both mouse and human embryo cell types, lineages and states, thereby maximising the information one can garner from these precious experimental resources. Our approaches are built on recent initiatives for large scale human organ atlases, but here we focus on the difficult to obtain and process material that spans early mouse, and in particular, human development. Using publicly available data for these stages, we test different deep learning approaches and develop both a model to classify cell types in an unbiased fashion and define the set of genes required to identify lineages, cell types and states. We have used our predictions to probe pluripotent stem cell models for both mouse and human development, showcasing the importance of this resource as a dynamic reference for early embryogenesis.
Immuno-Scanning Electron Microscopy of Islet Primary Cilia
Authors: Sviben Sanja , Polino Alexander J. , Melena Isabella , Hughes Jing W.
Published: February 2024

The definitive demonstration of protein localization on primary cilia has been a challenge for cilia biologists. Primary cilia are solitary thread-like projections that contain specialized protein composition, but as the ciliary structure overlays the cell membrane and other cell parts, the identity of ciliary proteins are difficult to ascertain by conventional imaging approaches like immunofluorescence microscopy. Surface scanning electron microscopy combined with immuno-labeling (immuno-SEM) bypasses some of these indeterminacies by unambiguously showing protein expression in the context of the 3D ultrastructure of the cilium. Here we apply immuno-SEM to specifically identify proteins on the primary cilia of mouse and human pancreatic islets, including post-translationally modified tubulin, intraflagellar transport (IFT) 88, the small GTPase Arl13b, as well as subunits of axonemal dynein. Key parameters in sample preparation, immuno-labeling, and imaging acquisition are discussed to facilitate similar studies by others in the cilia research community.
Probing fractal spatiotemporal inhomogeneity in a quantum walk
Authors: Pires Marcelo A. , Naves Caio B. , Soares-Pinto Diogo O. , Queirós Sílvio M. Duarte
Published: February 2024

We investigate the transport and entanglement properties exhibited by quantum walks with coin operators concatenated in a space-time fractal structure. Inspired by recent developments in photonics, we choose the paradigmatic Sierpinski gasket. The 0-1 pattern of the fractal is mapped into an alternation of the generalized Hadamard-Fourier operators. This two-state coin-operator approach overcomes the intricacies caused by the utilization of high-dimensional coin operators required in prior studies of discrete-time quantum walks on fractals. In fulfilling the blank space on the analysis of the impact of inhomogeneity in quantum walk properties, specifically, fractal deterministic inhomogeneity, our results show a robust effect of entanglement enhancement as well as an interesting road to superdiffusive spreading with a tunable scaling exponent attaining robust superdiffusion, subballistic though. Explicitly, with this fractal approach it is possible to obtain an increase in quantum entanglement with reduced impact on standard quantum walk theoretical spreading. Alongside those features, we analyze further properties such as the degree of interference and visibility. The present model corresponds to an application of fractals in an experimentally viable setting, namely, the building block for the construction of photonic patterned structures.

Published by the American Physical Society
2024
Dynamical and kinematical X-ray diffraction in a bent crystal
Authors: Malkov Dmitry M. , Punegov Vasily
Published: February 2024

Numerical modeling of kinematical and dynamical X-ray diffraction in a bent crystal was performed on the basis of two approaches to integrating the Takagi–Taupin equations, and using two-dimensional recurrence relations. Within the framework of kinematical diffraction, a new equation is obtained that describes the distribution of diffracted intensity inside a bent crystal. The time taken for numerical calculations based on this equation is significantly reduced in comparison with the use of algorithms of the dynamical diffraction theory. The simulation shows for the first time that, for strongly bent crystals, the maximum value of the diffraction intensity is formed inside the deformed structure and not on its surface. In the case of strong bending of the crystal structure, the deviation of the X-ray beam from the Bragg angle does not change the diffraction pattern but shifts it along the lateral direction. The results of calculations of diffraction in a strongly bent crystal based on the equations of dynamical and kinematical diffraction coincide, while the computations for weakly bent crystals differ. The possibility of estimating the primary extinction length of a bent crystal as a function of the bending radius is shown. In the case of kinematical diffraction in bent crystalline microsystems, a new method has been developed to calculate X-ray reciprocal-space mapping.