bluuebunny/crossref_metadata_2025 huggingface dataset:
Skin metatranscriptomics reveals landscape of variation in microbial activity and gene expression across the human body
Authors: Chia Minghao , Ng Amanda , Ravikrishnan Aarthi , Mohamed Naim Ahmad Nazri , Wearne Stephen , Common John , Nagarajan Niranjan
Published: December 2024

The skin microbiome plays an important role in immune homeostasis and skin health, and yet our understanding of in vivo microbial gene activity is hindered by the lack of a robust, non-invasive protocol for metatranscriptomics across skin sites. Circumventing the challenges of low microbial biomass, host contamination, and RNA stability, we developed a clinically tractable skin metatranscriptomics workflow that provides high technical reproducibility of profiles (Pearson r>0.95), uniform coverage across gene bodies, and strong enrichment of microbial mRNAs (2.5-40x;). Applying this protocol to a cohort of healthy adults (n=27) across five different skin sites (n=102, paired metatranscriptomes and metagenomes), identified a striking divergence between transcriptomic and genomic abundances, with Staphylococcus species and the skin fungi Malassezia having an outsized contribution to the metatranscriptomic landscape at most sites despite their modest representation in metagenomes. Species-level analysis showed skin site-specific enrichment of gene expression (e.g. increased levels of secreted fungal phospholipase C on cheeks relative to scalp), and revealed how key pathways were transcriptionally active in vivo (e.g. propionate and 4-aminobutyrate metabolism, potentially impacting skin barrier function). Gene-level analysis identified diverse antimicrobial genes transcribed by skin commensals in situ, including several uncharacterized bacteriocins, some of which are expressed at levels comparable to known antimicrobial genes. Correlation of microbial gene expression with organismal abundances uncovered >20 genes that putatively mediate interactions between microbes (e.g. a secreted Malassezia restricta protein with strongly negative in vivo association with Cutibacterium acnes; Spearman Rho>0.7). This work showcases the potential for leveraging skin metatranscriptomics to identify microbes whose activities play an outsized role in the community, and for uncovering pivotal microbial pathways and biomarkers linked to skin health and disease.
Genomic network analysis characterizes genetic architecture and identifies trait-specific biology
Authors: Thorp Jackson G. , Gerring Zachary F. , Reay William R. , Derks Eske M. , Grotzinger Andrew D.
Published: December 2024

Pervasive genetic overlap across human complex traits necessitates developing multivariate methods that can parse pleiotropic and trait-specific genetic signals. Here, we introduce Genomic Network Analysis (GNA), an analytic framework that applies the principles of network modelling to estimates of genetic overlap derived from genome-wide association study (GWAS) summary statistics. The result is a genomic network that describes the conditionally independent genetic associations between traits that remain when controlling for shared signal with the broader network of traits. Graph theory metrics provide added insight by formally quantifying the most important traits in the genomic network. GNA can discover additional trait-specific pathways by incorporating gene expression or genetic variants into the network to estimate their conditional associations with each trait. Extensive simulations establish GNA is well-powered for most GWAS. Application to a diverse set of traits demonstrate that GNA yields critical insight into the genetic architecture that demarcate genetically overlapping traits at varying levels of biological granularity.
Autoimmune side-effect of immunotherapy in lung cancer treatment revealed from large-scale cohort
Authors: Sun Yan , Yang Shihao
Published: December 2024

Although immune checkpoint inhibitors have illustrated strong benefits in patient survival and have been widely acknowledged in treating lung cancer, they may be subject to increased risk of immune-related adverse effects (irAEs). Although existing literature have studied the mechanisms of irAEs of immunotherapy, it is difficult to quantify such effect, especially at a large-scale real-world population level. In this paper, the autoimmune-related risk of multiple immune checkpoint inhibitors is compared with that of chemotherapy based on Medicaid and CHIP TAF (T-MSIS Analytic File) data of over 100,000 patient samples from 2012 to 2018. Results show that the irAEs of immunotherapy is significantly higher than chemotherapy in both unadjusted and adjusted samples from the dataset. Analysis on subpopulation and specific disease types further shows that certain immunotherapy treatments are associated with higher risk of irAEs, and the risk of certain autoimmune diseases may vary. We also illustrate the robustness of our conclusion through additional sensitivity analysis, confirming the necessity of keeping track of autoimmune side effects of immune checkpoint inhibitors for medicine researchers. Our methods are also available to evaluate effectiveness and side effects of novel therapies at a large-scale population level.
The oncogene SLC35F2 is a high-specificity transporter for the micronutrients queuine and queuosine
Authors: Burtnyak Lyubomyr , Yuan Yifeng , Pan Xiaobei , Gunaratne Lankani , d’Almeida Gabriel Silveira , Martinelli Maria , Reed Colbie , Garcia Jessie Fernandez , Patel Bhargesh Indravadan , Marquez Isaac , Ehrenhofer-Murray Ann E. , Swairjo Manal A. , Alfonzo Juan D. , Green Brian D. , Kelly Vincent P. , de Crécy-Lagard Valérie
Published: December 2024

The nucleobase queuine (q) and its nucleoside queuosine (Q) are micronutrients derived from bacteria that are acquired from the gut microbiome and/or diet in humans. Following cellular uptake, Q is incorporated at the wobble base (position 34) of tRNAs with a GUN anticodon, which is important for efficient translation. Early studies suggested that cytosolic uptake of queuine is mediated by a selective transporter that is regulated by mitogenic signals, but the identity of this transporter has remained elusive. Here, through a cross-species bioinformatic search and genetic validation, we have identified the solute carrier family member SLC35F2 as a unique transporter for both queuine and queuosine inSchizosaccharomyces pombeandTrypanosoma brucei. Furthermore, gene disruption in HeLa cells revealed that SLC35F2 is the sole transporter for queuosine in HeLa cells (Km174 nM) and a high-affinity transporter for the queuine nucleobase (Km67 nM), with the presence of another low-affinity transporter (Km259 nM) in these cells. Competition uptake studies show that SLC35F2 is not a general transporter for other canonical ribonucleobases or ribonucleosides, but selectively imports q and Q. The identification of SLC35F2, an oncogene, as the transporter of both q and Q advances our understanding of how intracellular levels of queuine and queuosine are regulated and how their deficiency contributes to a variety of pathophysiological conditions, including neurological disorders and cancer.

Significance Statement

The discovery of SLC35F2 as the eukaryotic transporter of queuine and queuosine is key to understanding how these micronutrients are salvaged from the human gut and distributed to different body tissues. Queuosine modification of tRNAs enhances the accuracy and efficiency of codon-anticodon pairing and regulates a range of biological and pathophysiological states, including oxidative stress responses, cancer, learning, memory, and gut homeostasis.
Remission spectroscopy resolves the mode of action of bedaquiline within living mycobacteria
Authors: Harrison Suzanna H , Walters Rowan C , Cheung Chen-Yi , Springett Roger J , Cook Gregory M , Osman Morwan M , Blaza James N
Published: December 2024

Bedaquiline, an ATP synthase inhibitor, is the spearhead of transformative therapies against drug-resistantMycobacterium tuberculosis. Beyond causing a cellular energetic crisis, differentin vivomechanisms of action have been proposed. Here, we apply remission spectroscopy to measure the electron-occupancy of the energy-transducing cytochromes within the mycobacterial and human bioenergetic systems as they power living cells. We find no evidence for bedaquiline’s protonophoric or ionophoric uncoupling activity but observe sub-second redirection of electron flux to the cytochromebdoxidase, Cyd, bypassing the respiratory control ATP synthase imposes on the electron transport chain. We find that bedaquiline does not affect human mitochondrial function. Overall, we explain how bedaquiline works, why different models for its action developed, and the mechanisms underlying bedaquiline’s synergy in combination regimes.
Cardiac Applications of CRISPR/AAV-Mediated Precise Genome Editing
Authors: Zheng Yanjiang , Mayourian Joshua , King Justin S. , Li Yifei , Bezzerides Vassilios J. , Pu William T. , VanDusen Nathan J.
Published: December 2024

The ability to efficiently make precise genome edits in somatic tissues will have profound implications for gene therapy and basic science. CRISPR/Cas9 mediated homology-directed repair (HDR) is one approach that is commonly used to achieve precise and efficient editing in cultured cells. Previously, we developed a platform capable of delivering CRISPR/Cas9 gRNAs and donor templates viaadeno-associatedvirus to induceHDR(CASAAV-HDR). We demonstrated that CASAAV-HDR is capable of creating precise genome editsin vivowithin mouse cardiomyocytes at the neonatal and adult stages. Here, we report several applications of CASAAV-HDR in cardiomyocytes. First, we show the utility of CASAAV-HDR for disease modeling applications by using CASAAV-HDR to create and precisely tag two pathological variants of the titin gene observed in cardiomyopathy patients. We used this approach to monitor the cellular localization of the variants, resulting in mechanistic insights into their pathological functions. Next, we utilized CASAAV-HDR to create another mutation associated with human cardiomyopathy, arginine 14 deletion (R14Del) within the N-terminus of Phospholamban (PLN). We assessed the localization of PLN-R14Del and quantified cardiomyocyte phenotypes associated with cardiomyopathy, including cell morphology, activation of PLN via phosphorylation, and calcium handling. After demonstrating CASAAV-HDR utility for disease modeling we next tested its utility for functional genomics, by targeted genomic insertion of a library of enhancers for a massively parallel reporter assay (MPRA). We show that MPRAs with genomically integrated enhancers are feasible, and can yield superior assay sensitivity compared to tests of the same enhancers in an AAV/episomal context. Collectively, our study showcases multiple applications forin vivoprecise editing of cardiomyocyte genomes via CASAAV-HDR.
Conservation of function without conservation of amino acid sequence in intrinsically disordered transcriptional activation domains
Authors: LeBlanc Claire , Stefani Jordan , Soriano Melvin , Lam Angelica , Zintel Marissa A. , Kotha Sanjana R. , Chase Emily , Pimentel-Solorio Giovani , Vunnum Aditya , Flug Katherine , Fultineer Aaron , Hummel Niklas , Staller Max V.
Published: December 2024

Protein function is canonically believed to be more conserved than amino acid sequence, but this idea is only well supported in folded domains, where highly diverged sequences can fold into equivalent 3D structures. In contrast, intrinsically disordered protein regions (IDRs) do not fold into a stable 3D structure, thus it remains unknown when and how function is conserved for IDRs that experience rapid amino acid sequence divergence. As a model system for studying the evolution of IDRs, we examined transcriptional activation domains, the regions of transcription factors that bind to coactivator complexes. We systematically identified activation domains on 502 orthologs of the transcriptional activator Gcn4 spanning 600 MY of fungal evolution. We find that the central activation domain shows strong conservation of function without conservation of sequence. This conservation of function without conservation of sequence is facilitated by evolutionary turnover (gain and loss) of key acidic and aromatic residues, the positions most important for function. This high sequence flexibility of functional orthologs mirrors the physical flexibility of the activation domain coactivator interaction interface, suggesting that physical flexibility enables evolutionary plasticity. We propose that turnover of short functional elements, sometimes individual amino acids, is a general mechanism for conservation of function without conservation of sequence during IDR evolution.
Lineage–specific amino acids define functional attributes of the protomer-protomer interfaces for the Rad51 and Dmc1 recombinases
Authors: Petassi Mike , Shin Yeonoh , Jessop Aidan M. , Morse Katherine , Kim Stefan Y. , Matei Razvan , Raina Vivek B. , Greene Eric C.
Published: December 2024

Most eukaryotes possess two Rad51/RecA family DNA recombinases that are thought to have arisen from an ancient gene duplication event: Rad51, which is expressed in both mitosis and meiosis; and Dmc1, which is only expressed in meiosis. To explore the evolutionary relationship between these recombinases, here, we present high-resolution CryoEM structures ofS. cerevisiaeRad51 filaments andS. cerevisiaeDmc1 filaments bound to ssDNA, which reveal a pair of stacked interfacial aromatic amino acid residues that are nearly universally conserved in Rad51 but are absent from Dmc1. We use a combination of bioinformatics, genetic analysis of natural sequence variation, and deep mutational analysis to probe the functionally tolerated sequence space for these stacked aromatic residues. Our findings demonstrate that the functional landscape of the interfacial aromatic residues within the Rad51 filament is highly constrained. In contrast, the amino acids at the equivalent positions within the Dmc1 filament exhibit a broad functional landscape. This work helps highlight the distinct evolutionary trajectories of these two eukaryotic recombinases, which may have contributed to their functional and mechanistic divergence.

AUTHOR SUMMARY

Most eukaryotic organisms have two closely related proteins, Rad51 and Dmc1, that are needed for different aspects of genetic recombination. These proteins may have evolved from a single gene that was duplicated during the early evolution of eukaryotes. Rad51 is active during both normal cell division (mitosis) and sexual reproduction (meiosis), while Dmc1 is only active during meiosis. To better understand how these proteins are related, we studied their three-dimensional structures using high resolution cryogenic electron microscopy. Our findings show that Rad51 has a specific set of conserved amino acids located at the protein interfaces, but this set of amino acids is different in Dmc1. We used a series of genetic approaches to analyze how these amino acids affect the proteins’ function. Our results show that Rad51 has a strict set of rules governing the identify of these amino acids, whereas Dmc1 does not. This research sheds light on how Rad51 and Dmc1 have evolved differently, leading to distinct functions in genetic recombination.
Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding
Authors: Zhang Yingxue , Alshammari Eid , Sobota Jacob , Spellmon Nicolas , Perry Emerson , Cao Tianxin , Mugunamalwaththa Thamarahansi , Smith Sheila , Brunzelle Joseph , Wu Gensheng , Stemmler Timothy , Jin Jianping , Li Chunying , Yang Zhe
Published: December 2024

Allosteric regulation allows proteins to dynamically respond to environmental cues by modulating activity at sites away from the catalytic center. Despite its importance, the SET-domain protein lysine methyltransferase superfamily has been understudied. Here, we present four crystal structures of SMYD2, a unique family member with a MYND domain. Our findings reveal a novel allosteric binding site with high conformational plasticity and promiscuity, capable of binding peptides, proteins, PEG, and small molecules. This site exhibits positive cooperativity with substrate binding, influencing catalytic activity. Mutations here significantly alter substrate affinity, changing the enzyme’s kinetic profile. Specificity studies show interaction with PARP1 but not histones, suggesting targeted regulation. Interestingly, this site’s function remains unaffected by active site changes, indicating unidirectional mechanisms. Our discovery provides novel insights into SMYD2’s biochemical regulation and lays the foundation for broader research on allosteric control in lysine methyltransferases. Given SMYD2’s role in various cancers, this work opens exciting avenues for designing specific allosteric inhibitors with reduced off-target effects.
Development and clinical application of a methylated ctDNA assay in the preoperative risk classification of resectable colon cancer
Authors: Raunkilde L , Andersen RF , Timm S , Jørgensen M , Lindebjerg J , Rafaelsen SR , Hansen TF , Jensen LH
Published: December 2024

Background

Pathological lymph node involvement (pN+) is an indicator of poor prognosis in localized colon cancer. Currently, the preoperative risk classification fails to accurately identify pN+, which could be instrumental in the selection of patients for neoadjuvant chemotherapy (NAC). This study aimed to develop an assay for preoperative methylated circulating tumor DNA (meth-ctDNA) as a predictive marker of pN+ and as a biomarker for initiating NAC in patients with localized colon cancer.

Materials and methods

203 patients operated for colon cancer stage I-III at Vejle Hospital were randomly assigned (1:1) to a discovery and a validation cohort. A multiplex assay of a tumor-specific (NPY) and two organ-specific (GAL3ST3, KANK1) meth-ctDNAs was designed and methylation analysis was performed using droplet digital PCR. The ability of preoperative meth-ctDNA to predict pN+ was assessed using receiver operating characteristics (ROC) analysis.

Results

ROC analyses of meth-ctDNA (negative/positive) to predict pN+ had an area under the curve of 52% and 57% in the discovery and validation cohort, respectively. Survival analysis in the validation cohort confirmed a higher rate of 48 months disease-free survival in meth-ctDNA negative compared to positive patients (HR=2.31, 95% CI 1.01-5.2). The difference also applied to 4-year overall survival (HR=3.62, 95% CI 1.15-11.4). In a multivariate analysis, meth-ctDNA remained the strongest prognostic factor of DFS (HR 2.46, 95% CI 1.03-5.88) and OS (HR 4.54, 95% CI 1.32-15.6) in relation to clinical T- or N-category, gender and age.

Conclusion

The preoperative meth-ctDNA multiplex assay did not predict pN+. The findings suggest meth-ctDNA as a more powerful marker than N-category in identifying high-risk patients who would potentially benefit from NAC.
Systematic review and meta-analysis of protocols and yield of direct from sputum sequencing ofMycobacterium tuberculosis
Authors: Mann B.C. , Loubser J. , Omar S. , Glanz C. , Ektefaie Y. , Jacobson K.R. , Warren R.M. , Farhat M.R.
Published: December 2024

Direct sputum whole genome sequencing (dsWGS) can revolutionizeMycobacterium tuberculosis(Mtb) diagnosis by enabling rapid detection of drug resistance and strain diversity without the biohazard of culture. We searched PubMed, Web of Science and Google scholar, and identified 8 studies that met inclusion criteria for testing protocols for dsWGS. Utilising meta-regression we identify several key factors positively associated with dsWGS success, including higherMtbbacillary load, mechanical disruption, and enzymatic/chemical lysis. Specifically, smear grades of 3+ (OR = 14.7, 95% CI: 3.5, 62.1; p = 0.0005) were strongly associated with improved outcomes, whereas decontamination with sodium hydroxide (NaOH) was negatively associated (OR = 0.005, 95% CI: 0.001, 0.03; p = 7e-06), likely due to its harsh effects onMtbcells. Furthermore, mechanical lysis (OR = 193.3, 95% CI: 11.7, 3197.8; p = 0.008) and enzymatic/chemical lysis (OR = 18.5, 95% CI: 1.9, 183.1; p = 0.02) were also strongly associated with improved dsWGS. Across the studies, we observed a high degree of variability in approaches to sputum pre-processing prior to dsWGS highlighting the need for standardized best practices. In particular we conclude that optimizing pre-processing steps including decontamination with the exploration of alternatives to NaOH to better preserve Mtb cells and DNA, and best practices for cell lysis during DNA extraction as priorities. Further and considering the strong association betweenMtbload and successful dsWGS, protocol improvements for optimal sputum sample collection, handling, and storage could also further enhance the success rate of dsWGS.
Non-shivering thermogenesis is intact upon brown-adipocyte specific loss of ATGL and HSL due to white adipose tissue browning
Authors: Manandhar Yelina , Pirchheim Anita , Hofer Peter , Vujic Nemanja , Kolb Dagmar , Hoefler Gerald , Kratky Dagmar , Schweiger Martina , Taschler Ulrike , Zimmermann Robert , Zechner Rudolf , Schreiber Renate
Published: December 2024

Intracellular fatty acids (FAs) activate and fuel non-shivering thermogenesis (NST) mediated via uncoupling protein 1 (UCP1). Adipose triglyceride lipase (ATGL) and hormone-sensitive lipase (HSL) are the two main triacylglycerol lipases in adipocytes that control FA availability. We showed previously that a brown adipocyte-specific loss of ATGL does not affect cold-induced thermogenesis in brown adipose tissue (BAT) and NST, raising the question whether HSL-mediated FA release is sufficient to allow NST. Here, we show that a brown adipocyte-specific loss of both ATGL and HSL in mice leads to impaired BAT thermogenic capacity in cold, but still allows normal NST. The BAT defect is attributed to an impaired abundance of mitochondria as well as reduced oxidative capacity despite increased adipocyte numbers in BAT. Notably, the reduced thermogenesis in BAT of BAT-iDAKO mice leads to a concomitant upregulation of UCP1 expression (browning) in white adipose tissue (WAT) indicating that thermogenesis partially shifts from BAT towards WAT. In accordance with this assumption, genetic loss of ATGL and HSL in both BAT and WAT leads to dysfunctional BAT thermogenesis and defective browning in WAT resulting in blunted NST. Our study highlights the metabolic adaptability of adipose tissue and the critical role of intracellular lipolysis in the regulation of thermogenesis.
Structure of the human taurine transporter TauT reveals substrate recognition and mechanisms of inhibition
Authors: Lu Yishuo , Ding Dian , Chen Hongyi , Jiang Peijun , Yin Yuxin
Published: December 2024

Taurine, a sulfur-containing amino acid, plays a crucial role in human health due to its antioxidant, anti-inflammatory, osmoregulatory properties1,2. Taurine levels are primarily regulated by the sodium-/chloride-dependent taurine transporter (TauT)3. Inhibitors of TauT have potential in the treatment of certain diseases, including neurological disorders and cancer4,5. Here, we present five structures of TauT: in the substrate-free apo state, in complex with taurine and in complex with taurine-mimetic inhibitors β-alanine, GABA and guanidinoethyl sulfonate (GES), each with varying length of linear structure, in both inward-facing and occluded conformations. The taurine-, β-alanine- and GABA-bound hTauT structures, in the presence of NaCl, adopt an occluded conformation, with ligands binding in the central pocket. In the presence of KCl, GES-bound hTauT adopts an inward-facing conformation, with two molecules positioned along the substrate translocation pathway with one into the deep central cavity and the other precluded conformational change from inward-facing to occluded state. Combined with function analysis, our structures provided insights into the overall architecture, substrate coordination and inhibitor recognition mechanisms of TauT.
HIV-1 protein coding sequences are present in relevant bacteria
Authors: Pelaez-Prestel Hector F. , Mozas-Gutierrez Juan , Lafuente Esther M. , Reche Pedro A.
Published: December 2024

Human Immunodeficiency Virus (HIV) is a retrovirus that attacks the immune system, causing acquired immunodeficiency syndrome (AIDS). Early diagnosis and treatment of HIV infected individuals are considered key to reduce HIV transmission and developing AIDS. Therefore, HIV diagnostics play an important role in the battle against AIDS. HIV tests are regarded as reliable and very specific. However, false-positive results are known to occur, usually caused by infections with unrelated pathogens leading to cross-reactive antibodies. In this work, we found through TBLASTN searches that the genome of several bacterial species, most frequentlyKlebsiella pneumoniae and Escherichia coli, contain segments matching HIV-1 proteins, including p24 and other proteins relevant for HIV testing, with a high degree of similarity (sequence identity > 95 %). The presence of HIV-1 in these bacteria of the human microbiota does not appear to be an artifact, since HIV-1 proteins were detected in different isolates of the same species. The proteome of other common viruses, particularly Influenza A virus and Hepatitis B virus, was also detected in bacterial genomes, but to a much lesser extent. Overall, our findings support that some bacteria can acquire HIV-1 genetic material and could interfere with HIV testing, causing false-positives.
Experimental monkeypox virus infection in rats
Authors: Rockx Barry , van Keulen Lucien , van der Poel Wim H.M. , Ariën Kevin K. , Vercauteren Koen , van de Water Sandra , Harders-Westerveen José , Schreur Paul J. Wichgers , van der Giessen Joke , Maas Miriam , Stockhofe Norbert , Liesenborghs Laurens
Published: December 2024

The global spread of Monkeypox virus (MPXV) clade IIb in 2022/2023 raised concerns about spillback into new animal reservoirs. Experimental inoculation of rats with MPXV resulted in skin lesions and viral shedding in the respiratory tract and skin. These findings suggest a potential role for rats in MPXV transmission.
Loss of Pigment Epithelium Derived Factor Sensitizes C57BL/6J Mice to Light-Induced Retinal Damage
Authors: Shelton Debresha A. , Papania Jack T. , Getz Tatiana E. , Sellers Jana T. , Giradot Preston E. , Chrenek Micah A. , Grossniklaus Hans E. , Boatright Jeffrey H. , Nickerson John M.
Published: December 2024

5.1

Purpose

Pigment epithelium-derived factor (PEDF) is a neurotrophic glycoprotein secreted by the retinal pigment epithelium (RPE) that supports retinal photoreceptor health. Deficits in PEDF are associated with increased inflammation and retinal degeneration in aging and diabetic retinopathy. We hypothesized that light-induced stress in C57BL/6J mice deficient in PEDF would lead to increased retinal neuronal and RPE defects, impaired expression of neurotrophic factor Insulin-like growth factor 1 (IGF-1), and overactivation of Galectin-3-mediated inflammatory signaling.

Methods

C57BL/6J mice expressing the RPE65 M450/M450 allele were crossed to PEDFKO/KOand wildtype (PEDF+/+) littermates. Mice were exposed to 50,000 lux light for 5 hours to initiate acute damage. Changes in visual function outcomes were tracked via electroretinogram (ERG), confocal scanning laser ophthalmoscopy(cSLO), and spectral domain optical coherence tomography (SD-OCT) on days 3, 5, and 7 post-light exposure. Gene and protein expression of Galectin-3 were measured by digital drop PCR (ddPCR) and western blot. To further investigate the role of galectin-3 on visual outcomes and PEDF expression after damage, we also used a small-molecule inhibitor to reduce its activity.

Results

Following light damage, PEDFKO/KOmice showed more severe retinal thinning, impaired visual function (reduced a-, b-, and c-wave amplitudes), and increased Galectin-3 expressing immune cell infiltration compared to PEDF+/+. PEDFKO/KOmice had suppressed damage-associated increases in IGF-1 expression. Additionally, baseline Galectin-3 mRNA and protein expression were reduced in PEDFKO/KOmice compared to PEDF+/+. However, after light damage, Galectin-3 expression decreases in PEDF+/+mice but increases in PEDF KO/KO mice without reaching PEDF+/+levels. Galectin-3 inhibition worsens retinal degeneration, reduces PEDF expression in PEDF+/+mice, and mimics the effects seen in PEDF knockouts.

Conclusions

Loss of PEDF alone does not elicit functional defects in C57BL/6J mice. However, under light stress, PEDF deficiency significantly increases severe retinal degeneration, visual deficits, Galectin-3 expression, and suppression of IGF-1 than PEDF+/+. PEDF deficiency reduced baseline expression of Galectin-3, and pharmacological inhibition of Galectin-3 worsens outcomes and suppresses PEDF expression in PEDF+/+,suggesting a novel co-regulatory relationship between the two proteins in mitigating light-induced retinal damage.
Structural analysis of tilvestamab in complex with AXL
Authors: Christakou Eleni , Lopez Andrea J. , Muruganandam Gopinath , Micklem David , Lorens James B. , Kursula Petri
Published: December 2024

AXL is a receptor tyrosine kinase with a significant role in various biological processes and important medical implications, particularly in cancer. AXL transduces signals from the extracellular environment into the cytoplasm by binding to its ligand, growth arrest-specific protein 6 (GAS6). Activation of AXL leads to autophosphorylation of its intracellular domain and subsequent activation of downstream signaling pathways involved in cell proliferation, migration, differentiation, and survival. Tilvestamab (also known as BGB149) is a first-in-class, humanized, therapeutic anti-AXL function-blocking monoclonal antibody. We carried out a structural characterization of the AXL-tilvestamab complex, using both negative-stain and cryogenic transmission electron microscopy as well as synchrotron small-angle X-ray scattering. While AXL-Fc was highly elongated and formed large, heterogeneous complexes with the full antibody, homogeneous samples for structural studies could be made using the monomeric soluble AXL extracellular domain, the Fab fragment of tilvestamab, and an anti-Fab nanobody. Both SAXS and cryo-EM confirmed successful complex formation between the three proteins, and a low-resolution 3D model for the tilvestamab-AXL complex is presented. The data allow for sample optimization for high-resolution structural biology as well as designing mutations that could alter binding affinity and specificity.
MEMO: A Micro Memo Sensor Detecting microRNA-RISC using an Accurate Cell-Free Expression Platform
Authors: Copeland Caroline E. , Heitmeier Chloe J. , Kim Jeehye , Kwon Yong-Chan
Published: December 2024

Circulating microRNAs have emerged as potential prognostic biomarkers of various diseases. They serve as micro memos sent out by cells, which scientists can intercept to gain real-time insights into cellular and disease status. However, establishing a standardized microRNA detection platform remains a challenge. Here, we integrate the RNA-induced silencing complex (RISC), which occupies mature microRNAs, into a complex cell-free synthetic genetic circuit using three different RNA polymerases, creating an innovative microRNA biosensor that is sensitive, precise, and cost-effective. The RISC protects the microRNA degradation during isolation and ensures the elimination of false target interactions, enhancing the detection robustness. With a limit of detection of 81 pM, affordability, and the possibility for on-demand use, this system proves to be a strong miRNA sensing tool.
Temporal and Hemispheric Dynamics in Neural Processing of Auditory and Speech Stimuli Across Linguistic Complexity: A MEG Source Space Study
Authors: Krauss Patrick , Kölbl Nikola , Müller-Voggel Nadia , Rampp Stefan , Kaltenhäuser Martin , Tzirdis Konstantin , Schilling Achim
Published: December 2024

In this study we investigated the neural processing of auditory stimuli of varying complexity: a non-linguistic (pure tone), a simple linguistic (phoneme) and a complex linguistic (word) stimulus. We recorded brain activity of 30 healthy, righthanded participants using magnetoencephalography (MEG), and compared the resulting evoked fields (ERFs) in source space in three different time intervals, i.e. early (0-250ms), mid (250-500ms) and late (500-750ms) responses. Our results reveal a bilateral activation during early response and rightlateralized activation in the mid-phase for all stimuli. Hoewever, the late response exhibited lateralization variations. The pure tone predominantly activated the right hemisphere, consistent with pitch processing theories. The phoneme primarily engaged the left hemisphere, supporting its role in phonemic processing. Notably, the word elicited activation in both hemispheres, reflecting phonemic processing on the left and stress patterns on the right. These findings highlight the intricate interplay between temporal processing and hemispheric lateralization in speech perception, emphasizing the importance of stimulus complexity and temporal dynamics in understanding auditory and speech processing.
Wisteria floribundaagglutinin enhancesZaire ebolavirusentry through interactions at specific N-linked glycosylation sites on the virus glycoprotein complex
Authors: Duncan Joshua D. , Pathak Monika , King Barnabas J. , Bamber Holly , Radford Paul , Dey Jayasree , Richardson Charlotte , Astbury Stuart , McClure C. Patrick , Ball Jonathan K. , Urbanowicz Richard A. , Tarr Alexander W.
Published: December 2024

Entry ofZaireebolavirus(EBOV) into a host cell is a complex process requiring interactions between the viral glycoproteins (GP) and cellular factors. These entry factors are cell-specific and can include cell surface lectins and phosphatidylserine receptors. NPC1 is critical to the late stage of the entry process. Entry has been demonstrated to be enhanced by interactions between the virion and surface-expressed lectins, which interact with carbohydrate moieties attached to the GP. In addition, soluble lectins, including mannose binding lectin (MBL), can enhance entryin vitro. However, the mechanism of lectin-mediated enhancement remains to be defined.

This study investigated the potential of three plant lectins,Wisteria floribundaagglutinin (WFA), soybean agglutinin (SBA) andGalanthus nivalisagglutinin (GNA), which possess different carbohydrate binding specificities, to enhance EBOV entry by binding to the GP. WFA was observed to potently enhance entry of lentiviral pseudotype viruses (PVs) expressing the GP of threeEbolavirusspecies (Zaire, Sudan [SUDV] and Reston [RESTV]), with the greatest impact on EBOV. SBA had a modest enhancing effect on entry that was specific to EBOV, while GNA had no impact on entry of any of theEbolavirusspecies. None of the lectins enhanced entry of control PVs expressing the surface proteins of other RNA viruses tested. WFA was demonstrated to bind directly with the EBOV-GP via the glycans, and mutational analysis implicated N238as contributing to the interaction. Furthermore, enhancement was observed in both human and bat cell lines indicating a highly conserved mechanism of action. We conclude that binding of WFA to EBOV GP through interactions including the glycan at N238results in GP alterations that enhance entry, providing evidence of a mechanism for lectin-mediated virus entry enhancement. Targeting lectin-ligand interactions presents a potential strategy for restrictingEbolavirusentry.
CENcyclopedia: Dynamic Landscape of Kinetochore Architecture Throughout the Cell Cycle
Authors: Chen Yu-Chia , Kilic Ece , Wang Evelyn , Rossman Will , Suzuki Aussie
Published: December 2024

The kinetochore, an intricate macromolecular protein complex located on chromosomes, plays a pivotal role in orchestrating chromosome segregation. It functions as a versatile platform for microtubule assembly, diligently monitors microtubule binding fidelity, and acts as a force coupler. Comprising over 100 distinct proteins, many of which exist in multiple copies, the kinetochore’s composition dynamically changes throughout the cell cycle, responding to specific timing and conditions. This dynamicity is important for establishing functional kinetochores, yet the regulatory mechanisms of these dynamics have largely remained elusive. In this study, we employed advanced quantitative immunofluorescence techniques to meticulously chart the dynamics of kinetochore protein levels across the cell cycle. These findings offer a comprehensive view of the dynamic landscape of kinetochore architecture, shedding light on the detailed mechanisms of microtubule interaction and the nuanced characteristics of kinetochore proteins. This study significantly advances our understanding of the molecular coordination underlying chromosome segregation.
“Undruggable KRAS”: druggable after all
Authors: Cox Adrienne D. , Der Channing J.
Published: December 2024

The threeRASgenes (HRAS,KRAS, andNRAS) comprise the most frequently mutated oncogene family in cancer.KRASis the predominant isoform mutated in cancer and is most prevalently mutated in major causes of cancer deaths including lung, colorectal, and pancreatic cancers. Despite extensive academic and industry efforts to target KRAS, it would take nearly four decades before approval of the first clinically effective KRAS inhibitors for the treatment of KRAS mutant lung cancer. We revisit past anti-KRAS strategies and painful lessons learned and then focus on the rapidly evolving landscape of direct RAS inhibitors, resistance mechanisms, and potential combination treatments.
An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
Authors: Li Chong , Bonder Marc Jan , Syed Sabriya , Jensen Matthew ,   Human Genome Structural Variation Consortium (HGSVC),   HGSVC Functional Analysis Working Group, Gerstein Mark B. , Zody Michael C. , Chaisson Mark J.P. , Talkowski Michael E. , Marschall Tobias , Korbel Jan O. , Eichler Evan E. , Lee Charles , Shi Xinghua
Published: December 2024

The human genome is packaged within a three-dimensional (3D) nucleus and organized into structural units known as compartments, topologically associating domains (TADs), and loops. TAD boundaries, separating adjacent TADs, have been found to be well conserved across mammalian species and more evolutionarily constrained than TADs themselves. Recent studies show that structural variants (SVs) can modify 3D genomes through the disruption of TADs, which play an essential role in insulating genes from outside regulatory elements’ aberrant regulation. However, how SV affects the 3D genome structure and their association among different aspects of gene regulation and candidatecis-regulatory elements (cCREs) have rarely been studied systematically. Here, we assess the impact of SVs intersecting with TAD boundaries by developing an integrative Hi-C analysis pipeline, which enables the generation of an in-depth catalog of TADs and TAD boundaries in human lymphoblastoid cell lines (LCLs) to fill the gap of limited resources. Our catalog contains 18,865 TADs, including 4596 sub-TADs, with 185 SVs (TAD–SVs) that alter chromatin architecture. By leveraging the ENCODE registry of cCREs in humans, we determine that 34 of 185 TAD–SVs intersect with cCREs and observe significant enrichment of TAD–SVs within cCREs. This study provides a database of TADs and TAD–SVs in the human genome that will facilitate future investigations of the impact of SVs on chromatin structure and gene regulation in health and disease.
Exact survival probability of a time-dependent open Ising chain at zero temperature
Authors: Suzuki Takayuki
Published: December 2024

In this study, we rigorously derived the survival probability in a time-dependent Ising chain coupled with a bosonic system at zero temperature. We found that nonadiabatic transitions can occur in finite systems due to effects of the external environment, even in parameter regions that are adiabatic in isolated systems. This phenomenon is attributed to cooperative effects similar to those in the Dicke model, becoming particularly pronounced under strong-coupling conditions. Furthermore, considering a continuous-mode boson bath, this cooperative effect can potentially enhance the accuracy of estimating the coupling strength with the environment. These findings may provide new insights and serve as a criterion for evaluating existing and future simulation methods of open many-body quantum systems.

Published by the American Physical Society
2024
Lean healthcare applied in emergency services: an empirical evaluation
Authors: Bonamigo Andrei , Santos Gabriel Nascimento , Chaves Sandra Maria do Amaral , Calado Robisom Damasceno
Published: December 2024

Purpose

This study aims to analyse the setup time management using the single-minute exchange of die (SMED) method in 24 h Emergency Care Units (ECUs).

Design/methodology/approach

A total of 1,098 reports in A3 form format were analysed and grouped into analysis categories to evaluate the implications of SMED in managing setup time in the 24 h ECUs. The content analysis was based on Bardin (2011). The findings were grouped into three categories.

Findings

The findings demonstrate the contributions of the Lean Healthcare approach in the 24 h ECUs through SMED analysis to reduce setup time in activities characterised as waste in 24 h UPAs.

Research limitations/implications

In this study, data were collected directly from the Good Practices Application, from a specific project conducted in ECUs, which could generate selection bias. Finally, the datas were categorised according to the categories defined a posteriori, which may lead to interpretation bias.

Practical implications

The implications listed from the SMED perspective for setup time management allow us to guide managers, consultants, researchers, and health professionals to provide continuous improvement in 24 h ECUs. The findings can serve as a basis for reducing configuration time in other public and private healthcare service organisations.

Social implications

SMED applied in 24 h ECUs makes it possible to improve emergency services provided to society and increase the capacity to care for patients and society in general. In addition, reducing costs for health service financiers, such as government and private institutions.

Originality/value

To the best of the authors’ knowledge, this is the first study that correlates the setup time management of the SMED method in crucial areas of 24 h ECUs, demonstrating opportunities for its application in reducing time in patient journeys. The findings show the benefits of Lean in these environments and highlight several opportunities for applying SMED to reduce setup in activities characterised as waste in 24 h UPA. SMED allows for improved operational excellence in emergency units and enables target opportunities to increase user satisfaction and service capacity.
Biodiversity of key soil phylotypes is associated with increased plant richness and productivity following agricultural abandonment and afforestation
Authors: Wang Jianyu , Li Yuyu , Ji Yongbiao , He Jia , Zhang Junhong , Dong Zhenghong , Zhang Zhangxing , Xu Ran , Hu Wenhui , Fan Miaochun , Chen Wenqing
Published: December 2024

Anthropogenic land use modifications are causing severe degradation of terrestrial ecosystems, and multiple revegetation strategies are emerging globally to counteract the loss of plant richness and productivity. While soil microorganisms are essential for plant community dynamics, the role of soil microbial biodiversity in regulating changes in plant richness and productivity under different revegetation strategies remains unknown.

We used multitrophic co‐occurrence networks to identify soil network modules of strongly co‐occurring phylotypes along a 50‐year revegetation chronosequence of agricultural abandonment and afforestation. Soil biodiversity within these modules was related to soil nutrient cycling functions, plant richness and productivity (understorey layer in afforestation), elucidating how these network modules are associated with changes in plant richness and productivity.

Plant richness and productivity increased simultaneously following both agricultural abandonment and afforestation. However, the biodiversity of key soil taxa within distinct network modules was associated with these coupled increases through the regulation of different nutrient cycling functions. Key soil phylotypes within the network modules involved in nitrogen (N) cycling correlated with the simultaneous increase in plant richness and productivity following agricultural abandonment. In contrast, those involved in phosphorus (P) and sulphur (S) cycling were linked to the coupled responses of both plant richness and productivity under afforestation. This reflects the divergent microbial mechanisms associated with the coupled increase in plant richness and productivity along the revegetation chronosequence for both agricultural abandonment and afforestation.

Synthesis. Our findings provide correlative evidence that the biodiversity of key phylotypes within soil network modules is closely associated with the simultaneous increase in plant richness and productivity following the cessation of agricultural management. We identify key soil taxa, specific to each revegetation strategy, that could serve as potential targets for genomic and cultivation‐based approaches to counteract plant community degradation. Revegetation efforts to enhance plant richness and productivity should focus on soil phylotypes associated with N cycling after agricultural abandonment and those involved in P and S cycling during afforestation.
The Efficacy of Anlotinib Plus Whole Brain Radiotherapy in Advanced Non‐Small Cell Lung Cancer With Multiple Brain Metastases: A Retrospective Study
Authors: Liu Lipin , Xu Yonggang , Gao Hong , Zhao Ting , Chen Dazhi , Jin Jingyi , Gao Cui , Li Gaofeng , Zhong Qiuzi
Published: December 2024

Purpose

This study aimed to compare the efficacy of anlotinib plus whole‐brain radiotherapy (WBRT) with that of WBRT alone in non‐small cell lung cancer (NSCLC) patients with multiple brain metastases (BMs).

Methods

The clinical data of patients with NSCLC and multiple BMs who received WBRT between 2019 and 2022 were collected. The patients were assigned to anlotinib plus WBRT group and WBRT group according to the treatment used.

Results

A total of 64 patients were eligible for analysis; 21 were treated with anlotinib plus WBRT, and 43 were treated with WBRT. The anlotinib plus WBRT group had a greater proportion of patients who were young and had a better performance status and adenocarcinoma histology than did the WBRT group. The median follow‐up time was 18.0 months. The median intracranial progression‐free survival (iPFS) was significantly longer in the anlotinib plus WBRT group than in the WBRT group (12.9 months vs. 7.4 months, p = 0.004). The median overall survival (OS) was 14.6 months in the anlotinib plus WBRT group and 9.4 months in the WBRT group (p = 0.039). Considering death as a competing risk to intracranial progression, the 1‐year cumulative incidence of intracranial progression in the anlotinib plus WBRT group (26.7%) was significantly lower than that in the WBRT group (64.3%) (p = 0.021). There was no significant difference in treatment‐related toxicity between the anlotinib plus WBRT group and the WBRT group.

Conclusion

Compared with WBRT alone, anlotinib plus WBRT might confer superior intracranial PFS for NSCLC patients with multiple BMs without increasing treatment‐related toxicity.