bluuebunny/crossref_metadata_2025 huggingface dataset:
Leveraging Large Language Models in Gynecologic Oncology: A Systematic Review of Current Applications and Challenges
Authors: Mudrik Aya , Tsur Abraham , Nadkarni Girish N , Efros Orly , Glicksberg Benjamin S , Soffer Shelly , Klang Eyal
Published: August 2024

Rationale and Objectives

Over the past year, studies have been conducted to evaluate the performance of Large Language Models (LLMs), such as ChatGPT, in the fields of gynecologic oncology. This review aims to analyze the applications and risks associated with using LLMs in this specialized field.

Materials and Methods

This systematic review was performed in adherence to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, incorporating elements from the diagnostic test accuracy extension and the CHARMS checklist for reviews of prediction models. A systematic literature search was executed on July 17, 2024, across PubMed, Web of Science, and Scopus databases. We focused on identifying original research that integrates LLMs with gynecologic oncology. We assessed the risk of bias using the adapted QUADAS-2 criteria.

Results

Our search identified eight studies that met our criteria, focusing on healthcare education, clinical practice, and medical code generation. These studies revealed variability in ChatGPT’s performance across different applications. It excelled in genetic testing and counseling, achieving 97% accuracy rate. However, its performance in cervical cancer prevention was less robust, with an accuracy of 83%. While one study demonstrated ChatGPT’s high adherence to quality guidelines, another noted that established guidelines significantly outperformed ChatGPT’s outputs. Additionally, code generation using tools like Google Bard and RoBERTa have shown potential to improve accuracy in clinical predictions and quality assurance. For example, Natural Language Processing (NLP) assisted by RoBERTa (based on Google’s BERT model) has improved the prediction of residual disease in women with advanced epithelial ovarian cancer following cytoreductive surgery. Despite these advancements, challenges related to consistency, specificity, and personalization persist, underscoring the necessity for continuous enhancement of these technologies.

Conclusion

LLMs demonstrate inconsistent performance in gynecologic oncology. These findings emphasize the need for continuous evaluation of these models before they are implemented clinically.
Checklist to Support the Development and Implementation of AI in Clinical Settings
Authors: Owoyemi Ayomide , Osuchukwu Joanne , Salwei Megan , Boyd Andy
Published: August 2024

The integration of Artificial Intelligence (AI) in healthcare settings demands a nuanced approach that considers both technical performance and sociotechnical factors. Recognizing this, our study introduces the Clinical AI Sociotechnical Framework (CASoF), developed through literature synthesis, and refined via a Modified Delphi study involving global healthcare professionals. Our research identifies a critical gap in existing frameworks, which largely focus on either technical specifications or trial outcomes, neglecting the comprehensive sociotechnical dynamics essential for successful AI deployment in clinical environments. CASoF addresses this gap by providing a structured checklist that guides the planning, design, development, and implementation stages of AI systems in healthcare. The checklist emphasizes the importance of considering the value proposition, data integrity, human-AI interaction, technical architecture, organizational culture, and ongoing support and monitoring, ensuring that AI tools are not only technologically sound but also practically viable and socially adaptable within clinical settings. Our findings suggest that the successful integration of AI in healthcare depends on a balanced focus on both technological advancements and the socio-technical environment of clinical settings. CASoF represents a step forward in bridging this divide, offering a holistic approach to AI deployment that is mindful of the complexities of healthcare systems. The checklist aims to facilitate the development of AI tools that are effective, userfriendly, and seamlessly integrated into clinical workflows, ultimately enhancing patient care and healthcare outcomes.
A cell fractionation and quantitative proteomics pipeline to enable functional analyses of cotton fiber development
Authors: Lee Youngwoo , Rani Heena , Mallery Eileen L. , Szymanski Daniel B
Published: August 2024

Cotton fibers are aerial trichoblasts that employ a highly polarized diffuse growth mechanism to emerge from the developing ovule epidermis. After executing a complicated morphogenetic program, the cells reach lengths over 2 cm and serve as the foundation of a multi-billion-dollar textile industry. Important traits such as fiber diameter, length, and strength are defined by the growth patterns and cell wall properties of individual cells. At present, the ability to engineer fiber traits is limited by our lack of understanding regarding the primary controls governing the rate, duration, and patterns of cell growth. To gain insights into the compartmentalized functions of proteins in cotton fiber cells, we developed a label-free liquid chromatography mass spectrometry method for systems level analyses of fiber proteome. Purified fibers from a single locule were used to fractionate the fiber proteome into apoplast (APOT), membrane-associated (p200), and crude cytosolic (s200) fractions. Subsequently, proteins were identified, and their localizations and potential functions were analyzed using combinations of size exclusion chromatography, statistical and bioinformatic analyses. This method had good coverage of the p200 and apoplast fractions, the latter of which was dominated by proteins associated with particulate membrane-enclosed compartments. The apoplastic proteome was diverse, the proteins were not degraded, and some displayed distinct multimerization states compared to their cytosolic pool. This quantitative proteomic pipeline can be used to improve coverage and functional analyses of the cotton fiber proteome as a function of developmental time or differing genotypes.
Enhancement of response learning in male rats with intrastriatal infusions of a BDNF - TrkB agonist, 7,8-dihydroxyflavone
Authors: Gardner Robert S. , Ambalavanar Matthew T. , Gold Paul E. , Korol Donna L.
Published: August 2024

Enhancement of learning and memory by cognitive and physical exercise may be mediated by brain-derived neurotrophic factor (BDNF) acting at tropomyosin receptor kinase B (TrkB). Upregulation of BDNF and systemic administration of a TrkB agonist, 7,8-dihydroxyflavone (7,8-DHF), enhance learning of several hippocampus-sensitive tasks in rodents. Although BDNF and 7,8-DHF enhance functions of other brain areas too, these effects have mainly targeted non-cognitive functions. One goal of the present study was to determine whether 7,8-DHF would act beyond the hippocampus to enhance cognitive functions sensitive to manipulations of the striatum. Here, we examined the effects of intrastriatal infusions of 7,8-DHF on learning a striatum-sensitive response maze and on phosphorylation of TrkB receptors in 3-month-old male Sprague Dawley rats. Most prior studies of BDNF and 7,8-DHF effects on learning and memory have administered the drugs for days to months before assessing effects on cognition. A second goal of the present study was to determine whether a single drug treatment near the time of training would effectively enhance learning. Moreover, 7,8-DHF is often tested for its ability to reverse impairments in learning and memory rather than to enhance these functions in the absence of impairments. Thus, a third goal of this experiment was to evaluate the efficacy of 7,8-DHF in enhancing learning in unimpaired rats. In untrained rats, intrastriatal infusions of 7,8-DHF resulted in phosphorylation of TrkB receptors, suggesting that 7,8-DHF acted as a TrkB agonist and BDNF mimic. The findings that a single, intra-striatal infusion of 7,8-DHF 20 min before training enhanced response learning in rats suggest that, in addition to its trophic effects, BDNF modulates learning and memory through receptor mediated cell signaling events.
Phlorotannin richAscophyllum nodosumseaweed extract inhibits influenza infection
Authors: Mega Daniele F. , Sharma Parul , Kipar Anja , Hetzel Udo , Bramwell Chloe , Merritt Alan , Wright Samuel , Plummer Chris , Urbanowicz Richard A. , Stewart James P.
Published: August 2024

Seaweed derived compounds are a renewable resource utilised in the manufacturing and food industry. This study focuses on an Enriched seaweed extract (ESE) isolated fromAscophyllum nodosum.ESE was screened for antiviral activity by plaque reduction assays against influenza A viruses (IAV) H1N1 and H3N2 subtypes. Time of addition assays and FACS analysis were used to help determine the modes of action. The therapeutic potential of ESE was then explored using differentiated human bronchiole epithelial cells at the air liquid interphase and a murine model challenged with IAV. The data indicates ESE primarily interacts directly with virions, preventing virus cell binding. Interestingly, ESE also inhibits early and late stage of the influenza A lifecycle when treatment occurs after cell binding. This inhibitory effect appears to prevent internalisation of virus and release of progeny virus by targeting neuraminidase activity. Intranasal administration of ESE in mice infected with IAV reduced viral load in lung tissue. ESE may be a promising broad acting antiviral agent in the treatment of influenza infections.
Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Identities from Microglia
Authors: Du Siling , Drieu Antoine , Cheng Yumeng , Storck Steffen E. , Rustenhoven Justin , Mamuladze Tornike , Bhattarai Bishan , Brioschi Simone , Nguyen Khai , Ou Feiya , Cao Jay , Rodrigues Patrick F. , Smirnov Igor , DeNardo David , Ginhoux Florent , Cella Marina , Colonna Marco , Kipnis Jonathan
Published: August 2024

Microglia are thought to originate exclusively from primitive macrophage progenitors in the yolk sac (YS) and to persist throughout life without much contribution from definitive hematopoiesis. Here, using lineage tracing, pharmacological manipulation, and RNA-sequencing, we elucidated the presence and characteristics of monocyte-derived macrophages (MDMs) in the brain parenchyma at baseline and during microglia repopulation, and defined the core transcriptional signatures of brain-engrafted MDMs. Lineage tracing mouse models revealed that MDMs transiently express CD206 during brain engraftment as CD206+microglia precursors in the YS. We found that brain-engrafted MDMs exhibit transcriptional and epigenetic characteristics akin to meningeal macrophages, likely due to environmental imprinting within the meningeal space. Utilizing parabiosis and skull transplantation, we demonstrated that monocytes from both peripheral blood and skull bone marrow can repopulate microglia-depleted brains. Our results reveal the heterogeneous origins and cellular dynamics of brain parenchymal macrophages at baseline and in models of microglia depletion.
An Augmented Reality Visor for Intraoperative Visualization, Guidance and Temperature Monitoring using Fluorescence
Authors: Cipolato Oscar , Fauconneau Matthias , LeValley Paige J. , Nissler Robert , Suter Benjamin , Herrmann Inge K
Published: August 2024

Fluorescence-guided surgical techniques, including tumor resection and tissue soldering, are advancing the frontiers of surgical precision by offering enhanced control that minimizes tissue damage and improves recovery as well as outcomes. However, integrating the visualization of the fluorescent signal and temperature monitoring seamlessly into surgical workflows has not been fully realized and remains a challenge, thus limiting their effectiveness and wide-spread clinical adoption. To address this issue, we introduce an augmented reality (AR) visor designed to unite nanomaterial excitation along with fluorescence detection, and temperature monitoring during surgical procedures. The AR visor was evaluated using advanced fluorescent nanoparticles, such as indocyanine green-doped particles and single-walled carbon nanotubes. By consolidating fluorescence visualization, excitation monitoring, and precise temperature control into a single AR platform, we equip surgeons with a comprehensive view of both the surgical field and sub-surface conditions invisible to the naked eye. This integration notably improves the safety and efficacy of fluorescence-guided surgeries, as well as emerging technologies including laser tissue soldering, by ensuring the soldering temperature stays within therapeutic thresholds and the laser is accurately guided by real-time fluorescence signals. The presented technology not only enhances existing surgical techniques but also supports the development of new strategies and sensing technologies in areas where traditional methods fall short, marking significant progress in precision surgery, which could ultimately improve patient care.
The Neuroactive Potential of the Elderly Human Gut Microbiome is Associated with Mental Health Status
Authors: Calderón-Romero Paulina , Valderrama Benjamin , Bastiaanssen Thomaz , Lillo Patricia , Thumala Daniela , Clarke Gerard , Cryan John F , Slachevsky Andrea , González-Billault Christian , Court Felipe A.
Published: August 2024

Ageing is usually associated with physiological decline, increased mental health issues, and cognitive deterioration, alongside specific changes in the gut microbiome. However, the relationship between the neuroactive potential of the gut microbiome and mental health and cognition among the elderly remains less explored. This study examines a cohort of 153 older Chilean adults with cognitive complaints, assessing anthropometric data, mental health via five distinct tests, and gut microbiome composition through 16SV4 sequencing. Our findings reveal associations between anthropometric factors and depression scores in mental tests of participants with their gut microbiome composition. Notably, depression was associated with changes in the abundance ofLachnospiraceae Eubacterium xylanophilum groupandFusobacteriaceae Fusobacterium. Additionally, bacterial pathways involved in metabolising neuroactive compounds such as tryptophan, short-chain fatty acids, p-cresol, glutamate, and nitric oxide were associated with participant age, sex, and cognitive performance. Moreover, participants’ sex was associated with the neuroactive potential of specific bacteria, suggesting a role of the gut microbiome in sex-related mental health differences in the elderly. Together, to the best of our knowledge, this study demonstrates for the first time the association between the neuroactive potential of the human gut microbiome and mental health status in older individuals with cognitive complaints.
The spatial spread and the persistence of gene drives are affected by demographic feedbacks, density dependence and Allee effects
Authors: Kläy Léna , Girardin Léo , Calvez Vincent , Débarre Florence
Published: August 2024

Homing gene drive alleles bias their own transmission by converting wild-type alleles into drive alleles. If introduced in a natural population, they might fix within a relatively small number of generations, even if they are deleterious. No engineered homing gene drive organisms have been released in the wild so far, and modelling is essential to develop a clear understanding of the potential outcomes of such releases. We use deterministic models to investigate how different demographic features affect the spatial spread of a gene drive. Building on previous work, we first consider the effect of the intrinsic population growth rate on drive spread. We confirm that including demographic dynamics can change outcomes compared to a model ignoring changes in population sizes, because changes in population density can oppose the spatial spread of a drive. Secondly, we study the consequences of including an Allee effect, and find that it makes a population more prone to eradication following drive spread. Finally, we investigate the effects of the fitness component on which density dependence operates (fecundity or survival), and find that it affects the speed of drive invasion in space, and can accentuate the consequences of an Allee effect. These results confirm the importance of checking the robustness of model outcomes to changes in the underlying assumptions, especially if models are to be used for gene drive risk assessment.
A PthXo2B ortholog inXanthomonas oryzaepv oryzae strain IX-221 acts as a major virulence factor onindicarice without activating a Clade IIISWEETgene
Authors: Mishra Prashant , S Shakespear , Carpenter Sara C D , S Hamsa , S Vigi , N Anith K , Dash Prasanta K , Bogdanove Adam J , Rai Rhitu
Published: August 2024

To infect rice,Xanthomonas oryzaepv. oryzae (Xoo) deploys transcriptionactivator-likeeffectors (TALEs) that specifically bind and upregulate host “susceptibility” (S) genes. 34-amino acid (aa) repeats in TALEs interact one-to-one with DNA bases. Variation at positions 12 and 13 in each repeat, the repeat-variable diresidue (RVD), determine specificity. Some repeat variants shorter or longer than 34 aa can disengage to accommodate a single base deletion in the target sequence.OsSWEET11,13, and14are key S genes, targeted by different TALEs from diverseXoostrains.xa13is aSWEET11allele lacking the TALE binding site and thus conferring resistance.xa13is overcome by TALEs that activateSWEET13orSWEET14. We report here that anxa13-compatibleXoostrain, IX-221, from India, harbours an ortholog of theSWEET14-targeting TALE PthXo3 and two orthologs of theSWEET13-cognate PthXo2, each with one or two 36-aa repeats capable of disengaging. One of the PthXo2 orthologs, PthXo2BIX-221, has a repeat region identical to the previously characterized PthXo2BPXO61, except for a two amino acid difference near the end of the 19threpeat. Like PthXo2BPXO61, PthXo2BIX-221upregulatesSWEET13in japonica rice and noSWEETinindicarice, but unlike PthXo2BPXO61it nonetheless rendersindicarice susceptible, pointing to an alternativeSgene. Further, a designer TALE (dTALE) constructed using a standard, consensus sequence for each repeat and RVDs identical to those of PthXo2BIX-221failed to renderindicarice susceptible. Alignment of the PthXo2BIX-221repeats shows a departure from the consensus in each of two repeats carrying the RVD ‘NN’: the sequence ‘MAIAN’ in place of ‘VAIAS’ beginning at position 7. Together, the PthXo2BIX-221results thus suggest that non-RVD sequence variation affects TALE targeting profiles. More broadly, the presence of the three aberrant repeat-harbouring TALEs in IX-221 suggests that widespread deployment ofxa13in India resulted in strains super-equipped to overcome it, capable of activating multipleSWEETgenes and alleles as well as an apparent alternate S gene.
The “DDVF” motif used by viral and bacterial proteins to hijack RSK kinases evolved as a mimic of a short linear motif (SLiM) found in proteins related to the RAS-ERK MAP kinase pathway
Authors: Veinstein Martin , Stroobant Vincent , Michiels Thomas , Sorgeloos Frédéric
Published: August 2024

Proteins of pathogens such as cardioviruses, kaposi sarcoma-associated herpes virus, varicella zoster virus and bacteria of the genusYersiniawere previously shown to use a common “DDVF” (D/E-D/E-V-F) short linear motif (SLiM) to hijack cellular kinases of the RSK (p90 ribosomal S6 kinases) family. Remarkable conservation of the SLiM docking site in RSKs suggested a physiological role for this site. Using SLiM prediction tools and AlphaFold docking, we screened the human proteome for proteins that would interact with RSKs through a DDVF-like SLiM. Using co-immunoprecipitation experiments, we show that two candidates previously known as RSK partners, FGFR1 and SPRED2, as well as two candidates identified as novel RSK partners, GAB3 and CNKSR2 do interact with RSKs through a similar interface as the one used by pathogens, as was recently documented for SPRED2. Moreover, we show that FGFR1 employs a DSVF motif to bind RSKs and that phosphorylation of the serine in this motif increases RSK binding. FGFR1, SPRED2, GAB3 and CNKSR2 as well as other candidate RSK binders act upstream of RSK in the RAS-ERK MAP kinase pathway. Analysis of ERK activation in cells expressing a mutated form of RSK lacking the DDVF-docking site suggests that RSK might interact with the DDVF-like SLiM of several partners to provide a negative feed-back to the ERK MAPK pathway. Thus, through SLiM mimicry, pathogens not only retarget RSKs toward unconventional substrates but also likely compete with human proteins to alter the regulation of the RAS-ERK MAP kinase pathway.

Author Summary

Short linear motif (SLiM) are 3 to 10 amino acid-long protein sequences that can mediate the interaction with other proteins. We previously observed that highly unrelated pathogens, including viruses and bacteria, convergently evolved to hijack cellular enzymes of their host, through a common SLiM. In this work, we tested the hypothesis that the SLiM found in proteins of pathogens evolved to mimic a SLiM found in human proteins that regulate the cellular enzymes through the same interface. Protein-protein interactions mediated by SLiMs are often, low-affinity, transient interactions that are difficult to detect by conventional biochemical methods but that can nowadays be predicted with increasing confidence by artificial intelligence-based methods such as AlphaFold. Using such predictions, we identified several candidate human proteins and we confirmed experimentally that these proteins interact with the cellular enzymes the same way as pathogens’ proteins do. Identified proteins belong to the well-known RAS-ERK MAPK pathway which regulates important functions of the cell, suggesting that pathogens evolved to hijack this MAPK pathway by SLiM mimicry. By doing so, they can both dysregulate cellular physiology and hijack cellular enzymes to their own benefit.
RoAM: computational reconstruction of ancient methylomes and identification of differentially methylated regions
Authors: Mathov Yoav , Rosen Naomi , Leibson Chen , Meshorer Eran , Yakir Benjamin , Carmel Liran
Published: August 2024

Identifying evolutionary changes in DNA methylation bears a huge potential for unraveling adaptations that have occurred in modern humans. Over the past decade, computational methods to reconstruct DNA methylation patterns from ancient DNA sequences have been developed, allowing for the exploration of DNA methylation changes during the past hundreds of thousands of years of human evolution. Here, we introduce a new version of RoAM (Reconstruction of Ancient Methylation), a flexible tool that allows for the reconstruction of ancient methylomes, as well as the identification of differentially methylated regions between ancient populations. RoAM incorporates a series of filtering and quality control steps, resulting in highly reliable DNA methylation maps that exhibit similar characteristics to modern maps. To showcase RoAM’s capabilities, we used it to compare ancient methylation patterns between pre- and post-Neolithic revolution samples from the Balkans. Differentially methylated regions separating these populations are shown to be associated with genes related to regulation of sugar metabolism. Notably, we provide evidence for overexpression of the gene PTPRN2 in post-Neolithic revolution samples. PTPRN2 is a key regulator of insulin secretion, and our finding is compatible with hypoinsulinism in pre-Neolithic revolution hunter-gatherers. Additionally, we observe methylation changes in the genes EIF2AK4 and SLC2A5, which provide further evidence to metabolic adaptations to a changing diet during the Neolithic transition. RoAM offers powerful algorithms that position it as a key asset for researchers seeking to identify evolutionary regulatory changes through the lens of paleoepigenetics.
StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities
Authors: Heber Kerim , Tian Shuchang , Betancurt-Anzola Daniela , Koo Heejung , Bisanz Jordan E.
Published: August 2024

Background

Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level, standard methods for analysis of shotgun metagenomic sequencing do not account for ambiguous mapping between closely related strains, and other methods such as quantitative PCR (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing paired with a k-mer-based normalization strategy to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes.

Results

Bothin silico,and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy than other tools utilizing shotgun metagenomic sequencing reads and can resolve complex mixtures of highly related strains. Through experimental validation and benchmarking, we demonstrate that StrainR2’s accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification. Further, it is capable of scaling to communities of hundreds of strains and efficiently utilizes memory being capable of running both on personal computers and high-performance computing nodes.

Conclusions

Using shotgun metagenomic sequencing reads is a viable method for determining accurate strain-level abundances in synthetic communities using StrainR2.
FACT-(H3-H4) complex stimulates Pol α activity to coordinate DNA synthesis with nucleosome assembly
Authors: Zhang Wenshuo , Xu Jiawei , Yang Jiayi , Shi Guojun , Wu Jiale , Gao Ning , Feng Jianxun , Li Qing
Published: August 2024

Deficiencies in replication-coupled (RC) nucleosome assembly often lead to reduced DNA replication rate, but the precise mechanism underlying this process remains unsolved. Here, we discovered that H3-H4, but not H2A-H2B, mediates the interaction between FACT and the primase-polymerase complex DNA Pol α. This interaction stimulates the DNA polymerase activity of Pol α, and is indispensable for Okazaki fragment synthesis and replication fork progression. Moreover, the Pol1-N domain of Pol α provides a specific binding site for FACT and H3-H4. Furthermore, CAF-1 and Rtt106-mediated replication-coupled nucleosome assembly pathways regulate this interaction. Together, we propose that the FACT-(H3-H4)-Pol α interaction acts as a “Pre-Warning System” that regulates DNA replication, ensuring proper coordination between DNA synthesis and nucleosome assembly.
Mitochondrial Ca2+controls pancreatic cancer growth and metastasis by regulating epithelial cell plasticity
Authors: Weissenrieder Jillian S. , Peura Jessica , Paudel Usha , Bhalerao Nikita , Weinmann Natalie , Johnson Calvin , Wengyn Maximilian , Drager Rebecca , Furth Emma Elizabeth , Simin Karl , Ruscetti Marcus , Stanger Ben Z. , Rustgi Anil K. , Pitarresi Jason R. , Foskett J. Kevin
Published: August 2024

Endoplasmic reticulum to mitochondria Ca2+transfer is important for cancer cell survival, but the role of mitochondrial Ca2+uptake through the mitochondrial Ca2+uniporter (MCU) in pancreatic adenocarcinoma (PDAC) is poorly understood. Here, we show that increased MCU expression is associated with malignancy and poorer outcomes in PDAC patients. In isogenic murine PDAC models,Mcudeletion (McuKO) ablated mitochondrial Ca2+uptake, which reduced proliferation and inhibited self-renewal. Orthotopic implantation of MCU-null tumor cells reduced primary tumor growth and metastasis.Mcudeletion reduced the cellular plasticity of tumor cells by inhibiting epithelial-to-mesenchymal transition (EMT), which contributes to metastatic competency in PDAC. Mechanistically, the loss of mitochondrial Ca2+uptake reduced expression of the key EMT transcription factor Snail and secretion of the EMT-inducing ligand TGFβ. Snail re-expression and TGFβ treatment rescued deficits inMcuKOcells and restored their metastatic ability. Thus, MCU may present a therapeutic target in PDAC to limit cancer-cell-induced EMT and metastasis.
A synthetic cell-free pathway for biocatalytic upgrading of one-carbon substrates
Authors: Landwehr Grant M. , Vogeli Bastian , Tian Cong , Singal Bharti , Gupta Anika , Lion Rebeca , Sargent Edward H. , Karim Ashty S. , Jewett Michael C.
Published: August 2024

Biotechnological processes hold tremendous potential for the efficient and sustainable conversion of one-carbon (C1) substrates into complex multi-carbon products. However, the development of robust and versatile biocatalytic systems for this purpose remains a significant challenge. In this study, we report a hybrid electrochemical-biochemical cell-free system for the conversion of C1 substrates into the universal biological building block acetyl-CoA. The synthetic reductive formate pathway (ReForm) consists of five core enzymes catalyzing non-natural reactions that were established through a cell-free enzyme engineering platform. We demonstrate that ReForm works in a plug-and-play manner to accept diverse C1 substrates including CO2equivalents. We anticipate that ReForm will facilitate efforts to build and improve synthetic C1 utilization pathways for a formate-based bioeconomy.
Ion channels that mediate calcium-dependent control of spike patterns are spatially organized across the soma in relation to a cytoskeletal assembly
Authors: Sahu Giriraj , Greening Dylan , Nicola Wilten , Turner Ray W.
Published: August 2024

Sodium and potassium channels that regulate axonal spike propagation are highly organized at nodes of Ranvier by a spectrin-actin membrane periodic skeleton. STORM-TIRF microscopy was used to define the spatial organization over the soma of a complex of Cav1.3 calcium, RyR2, and IK potassium channels (CaRyK complex) that generate a slow AHP in hippocampal neurons. Nearest neighbor distance and non-negative matrix factorization analyses identified two spatial patterns as linear rows of 3-8 immuno-labeled clusters with 155 nm periodicity that extended to branchpoints, or as isolated clusters with 600-800 nm separation. The rows and isolated clusters for each of the CaRyK complex proteins closely overlapped with the patterns for spectrin βII and the actin linking proteins actinin I and II. Together the data reveal a close correspondence between the placement of CaRyK complex proteins and that of a net-like organization of spectrin βII across the soma. The regularity in the pattern of expression of these proteins at ER-PM junctions suggest their role as functional nodes of calcium- and calcium-gated potassium channels to control the pattern of spike output at the soma.
Structural basis of human 20S proteasome biogenesis
Authors: Zhang Hanxiao , Zhou Chenyu , Mohammad Zarith , Zhao Jianhua
Published: August 2024

New proteasomes are produced to accommodate increases in cellular catabolic demand and prevent the accumulation of cytotoxic proteins. Formation of the proteasomal 20S core complex relies on the function of the five chaperones PAC1-4 and POMP. To understand how these chaperones facilitate proteasome assembly, we tagged the endogenous chaperones using CRISPR/Cas gene editing and examined the chaperone-bound complexes by cryo-EM. We observed an early α-ring intermediate subcomplex that is stabilized by PAC1-4, which transitions to β-ring assembly upon dissociation of PAC3/PAC4 and rearrangement of the PAC1 N-terminal tail. Completion of the β-ring and dimerization of half-proteasomes repositions critical lysine K33 to trigger cleavage of the β pro-peptides, leading to the concerted dissociation of POMP and PAC1/PAC2 to yield mature 20S proteasomes. This study reveals structural insights into critical points along the assembly pathway of the human proteasome and provides a molecular blueprint for 20S biogenesis.
Top-down Proteomics for the Characterization and Quantification of Calreticulin Arginylation
Authors: Searfoss Richard M. , Liu Xingyu , Garcia Benjamin A. , Lin Zongtao
Published: August 2024

Arginylation installed by arginyltransferase 1 (ATE1) features an addition of arginine (Arg) to the reactive amino acids (e.g., Glu and Asp) at the proteinN-terminus or side chain. Systemic removal of arginylation after ATE1 knockout (KO) in mouse models resulted in heart defects leading to embryonic lethality. The biological importance of arginylation has motivated the discovery of arginylation sites on proteins using bottom-up approaches. While bottom-up proteomics is powerful in localizing peptide arginylation, it lacks the ability to quantify proteoforms at the protein level. Here we developed a top-down proteomics workflow for characterizing and quantifying calreticulin (CALR) arginylation. To generate fully arginylated CALR (R-CALR), we have inserted an R residue after the signaling peptide (AA1-17). Upon overexpression in ATE1 KO cells, CALR and R-CALR were purified by affinity purification and analyzed by LCMS in positive mode. Both proteoforms showed charge states ranging from 27-68 with charge 58 as the most intense charge state. Their MS2 spectra from electron-activated dissociation (EAD) showed preferential fragmentation at the proteinN-terminals which yielded sufficientcions facilitating precise localization of the arginylation sites. The calcium-binding domain (CBD) gave minimum characteristic ions possibly due to the abundant presence of >100 D and E residues. Ultraviolet photodissociation (UVPD) compared with EAD and ETD significantly improved the sequence coverage of CBD. This method can identify and quantify CALR arginylation at absence, endogenous (low), and high levels. To our knowledge, our work is the first application of top-down proteomics in characterizing post-translational arginylationin vitroandin vivo.
Dissecting the metabolic costs of up- and down-hill walking
Authors: Jessup Luke N. , Kelly Luke A. , Cresswell Andrew G. , Lichtwark Glen A.
Published: August 2024

Work- and collision-based models of locomotion are often used to describe the relationship between the body’s mechanical work requirements and metabolic energy expenditure. While work- and collision-based models do a reasonable job of relating mechanical work to metabolic cost at a system level, these models may not map to the underlying force and work demands of muscle, which directly affects energy expenditure. We collected motion capture, force, electromyography and ultrasound data from the main power producing muscles during uphill and downhill walking between +/− 15% grade. These data were used to evaluate a musculoskeletal modelling approach to simulate muscle force- and work-related costs that could be compared to metabolic power that we measured using indirect calorimetry. Muscle force-related costs (activation heat rate + maintenance heat rate) increased at steeper up- and down-hill grades and were moderately correlated with mean joint moments. Muscle work-related costs (mechanical work rate + shortening / lengthening heat rate) increased as grade became more positive and were strongly correlated with net joint work. Compared to traditional models, the inclusion of a term to account for muscle force-related costs should lead to a more explanatory cost model that maps directly to the mechanical demands of muscle.
Biomolecular condensates bridge experiment and theory of mass-conserving reaction-diffusion systems in phase separation
Authors: Li Cheng , Guo Man-Ting , He Xiaoqing , Liu Quan-Xing , Qi Zhi
Published: August 2024

Phase separation is crucial in biological processes and ecological resilience, yet experimental evidence supporting validity of mass-conserving reaction-diffusion (MCRD) models in describing phase separation remains rare. Here, we identified one type of biomolecular condensates – double-stranded DNA (dsDNA) and the human transcription factor p53 as forming dsDNA-protein interactive co-condensates (DPICs) as an experimental model, where dynamic DPICs evolve into droplet-like patterns through reversible autocatalytic biochemical reactions. Thus, we can use the MCRD model to describe this experimental system. The pattern formation depends on concentration of protein and dsDNA and their local nonlinear interactions, which were experimentally tested at meso-scale and integrated into an MCRD model. Our results provide direct evidence that the experimental data-driven MCRD models can reproduce the observed phase diagram and scaling-invariance coarsening patterns, thus, providing a compelling mechanism for phase-separation pattern in other systems.
The ameliorative effect ofC-Kitposhepatic endothelial Mertk deficiency on nonalcoholic steatohepatitis
Authors: Fu Seng-Wang , Gao Yu-Xuan , Li Hui-Yi , Ren Yi-Fan , Wu Jun-Cheng , Li Zheng-Hong , Xu Ming-Yi
Published: August 2024

Recently, Mer tyrosine kinase (Mertk) and KIT proto-oncogene (C-Kit) were reported play a role in liver sinusoidal endothelial cells (LSECs) in patients with nonalcoholic steatohepatitis (NASH). In this study, lower levels of C-Kit and higher levels of Mertk/p-Mertk were confirmed in steatotic LSECs and in the livers of patients and mice with NASH. C-Kit was suggested to negatively regulate Mertk signaling in steatotic LSECs. The steatotic LSECs in which Mertk was knocked down displayed high fenestration and reduced expression of procapillarized CD31/VN; showed antiangiogenic features and decreased expression of proangiogenic VEGF/ERK1/2; and exhibited intact mitophagy and upregulation of the Pink1/Parkin pathway. Bone marrow transplantation (BMT) ofC-Kitpos-BMCssh-Mertkto MCD mice could equivalently protect endothelial functions. Steatotic hepatocytes (HCs) or hepatic stellate cells (HSCs) cocultured with LSECssh-Mertkexhibited diminished lipid deposition; decreased expression of prolipogenic LXR/SREBP-1c, proinflammatory TNF-α/IL-6 and profibrotic α-SMA/ColI; and increased expression of prolipolytic FXR/ADPN. Similarly, the BMT ofC-Kitpos-BMCssh-Mertkto MCD mice ameliorated NASH.C-Kitpos-LSECs that underwent Mertk cleavage were found to limit NASH progression. Therefore, Mertk deficiency should be a novel therapeutic agent for restoring LSECs in patients with NASH.
Unraveling the Role of Viral Interference in Disrupting Biennial RSV Epidemics in Northern Stockholm
Authors: Li Ke , Hamrin Johan , Weinberger Daniel M. , Pitzer Virginia E.
Published: August 2024

Respiratory syncytial virus (RSV) primarily impacts infants and older adults, with seasonal winter outbreaks in temperate countries. Biennial cycles of RSV activity have also been identified in Northern Europe and some states in the United States. Delayed RSV activity was reported worldwide during the 2009 influenza pandemic, and a disrupted biennial pattern of RSV activity was observed in northern Stockholm following the pandemic. Biennial patterns shifted to early/large outbreaks in even-numbered years and late/small outbreaks in odd-numbered years. However, the mechanisms underpinning this change in pattern remain unknown. In this work, we constructed an age-stratified mechanistic model to explicitly test three factors that could lead to the change in RSV transmission dynamics: 1) birth rates, 2) temperatures, and 3) viral interference. By fitting the model to weekly RSV admission data over a 20-year period and comparing different models, we found that viral interference from influenza was the only mechanism that explained the shifted biennial pattern. Our work demonstrates the complex interplay between different respiratory viruses, providing evidence that supports the presence of interactions between the H1N1 pandemic influenza virus and RSV at the population level, with implications for future public health interventions.
Molecular Feature-Based Classification of Retroperitoneal Liposarcoma: A Prospective Cohort Study
Authors: Xiao Mengmeng , Li Xiangji , Bu Fanqin , Ma Shixiang , Yang Xiaohan , Chen Jun , Zhao Yu , Cananzi Ferdinando , Luo Chenghua , Min Li
Published: August 2024

Background

Retroperitoneal liposarcoma (RPLS) is a critical malignant disease with various clinical outcomes. However, the molecular heterogeneity of RPLS was poorly elucidated, and few biomarkers were proposed to monitor its progression.

Methods

RNA sequencing was performed on a training cohort of 88 RPLS patients to identify dysregulated genes and pathways using clusterprofiler. The GSVA algorithm was utilized to assess signaling pathways levels in each sample, and unsupervised clustering was employed to distinguish RPLS subtypes. Differentially expressed genes (DEGs) between RPLS subtypes were identified to construct a simplified dichotomous clustering via nonnegative matrix factorization. The feasibility of this classification was validated in a separate validation cohort (n=241) using immunohistochemistry (IHC) from the Retroperitoneal SArcoma Registry (RESAR). The study is registered withClinicalTrials.govunder numberNCT03838718.

Results

Cell cycle, DNA damage & repair, and Metabolism were identified as the most aberrant biological processes in RPLS, enabling the division of RPLS patients into two distinct subtypes with unique molecular signatures, tumor microenvironment, clinical features and outcomes (overall survival, OS and disease-free survival, DFS). A simplified RPLS classification based on representative biomarkers (LEP and PTTG1) demonstrated high accuracy (AUC>0.99), with patients classified as LEP+ and PTTG1-showing lower aggressive pathological composition ratio and fewer surgery times, along with better OS (HR=0.41,P<0.001) and DFS (HR=0.60,P=0.005).

Conclusions

Our study provided an ever-largest gene expression landscape of RPLS and established an IHC-based molecular classification that was clinically relevant and cost-effective for guiding treatment decisions.
Initial antigen encounter determines robust T-cell immunity against SARS-CoV-2 BA.2.86 variant three years later
Authors: Rubio Rocio , Yavlinsky Alexei , Escalera Zamudio Marina , Molinos-Albert Luis M , Martin Perez Carla , Pradenas Edwards , Canyelles Mar , Torres Celia , Tan Cedric , Swadling Leo , Ramirez-Morros Anna , Trinite Benjamin , Vidal-Alaball Josep , Aguilar Ruth , Ruiz-Comellas Anna , Blanco Julia , van Dorp Lucy , Balloux Francois , Dobano Carlota , Moncunill Gemma
Published: August 2024

Background The emergence of the hypermutated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) BA.2.86 variant raises significant concerns due to its potential to evade pre-existing immunity. Methods We measured cross-reactivity of neutralizing antibodies and T-cell responses to BA.2.86 in 52 previously exposed participants and investigated clinic-demographic and viral genetic determinants affecting T-cell responses. Findings We found that despite notable escape from neutralizing antibodies, T-cell responses remained generally preserved, albeit with a significant but small loss in T-cell cross-recognition (7.5 %, 14.2 % and 10.8 % average loss for IFN-g, IL-2 and IFN-g + IL-2, respectively, p < 0.05). This is consistent with the prediction of 6 out of 10 immunodominant T-cell epitopes (TCEs) altered by BA.2.86 lineage-defining mutations to have reduced peptide presentation. This effect is expected to be mitigated due to total TCEs across the genome. Remarkably, T-cell responses and cross-recognition were 3.5 (IFN-g), 2 (IL-2) and 2.4 (IFN-g + IL-2) times higher when first induced by natural infection rather than vaccination three years before, by increasing number of infections, and by ancestral/Delta than Omicron infections. Interpretation Our findings underscore the critical role and the factors influencing T-cell immunity against evolving SARS-CoV-2 variants, such as first antigen encounter (vaccination or infection), which is essential for developing effective control strategies against SARS-CoV-2 variants. Funding European Union (Horizon Europe), Fundacio Privada Daniel Bravo Andreu, Catalan Government (PERIS, CERCA), Spanish Ministry of Science, Rosetrees Trust, Pears Foundation.
Quality of Counselling, Exposure to Vaccination Messages and Caregivers’ Knowledge on the Uptake of Penta Vaccine in Six Northern Nigerian States
Authors: Alabi Matthew , Dougherty Leanne , Etim Eno-Obong , Adedimeji Adebola
Published: August 2024

Background

Pentavalent 3 (Penta-3) coverage for children aged 12-23 months is used as the prime substitute for determining vaccination coverage and monitoring the performance of the national immunization programme. However, the coverage for Penta 3 in Nigeria remains low. Quality interaction between caregivers and providers and access to appropriate information are associated with healthcare utilization and acceptance of recommended health behaviours. This study examines the quality of counselling (QOC), caregivers’ exposure to vaccination messages and child’s uptake of the Penta vaccine.

Methods

This was a cross-sectional study that utilized quantitative data obtained through a survey. Caregivers (n=561) of children aged 2-24 months accessing child vaccination services who received Penta vaccines at randomly selected health facilities (n=163) offering routine immunization (RI) services were surveyed. Penta uptake was coded as binary; hence, binary logistic regression was performed using Stata 14.

Result

We found that 56% of the caregivers received quality counselling. Although awareness of child vaccination was high (70%), two-thirds had poor exposure. The uptake of all three doses of Penta vaccine was 43%. Contextual factors associated with Penta uptake include caregivers’ knowledge of when a child should receive their first vaccination (aOR=2.08; 95% CI=1.01-4.29), sources of child vaccination messages, namely, place of worship (aOR=2.78; 95% CI=1.15-6.67), Community Health Workers CHW (aOR=1.95; 95% CI=1.14-3.34), community leader (aOR=2.21; 95% CI=1.11-4.41) and residence in the northwest region (aOR=2.60; 95% CI=1.51-4.48).

Conclusion

Given the low quality of counselling and the positive influence of religious and traditional leaders, interventions that prioritize strengthening patient-provider interaction and community structure are crucial for increasing child vaccination coverage in Nigeria.