bluuebunny/crossref_metadata_2025 huggingface dataset:
Real-world implementation of geriatric assessment in cancer care among older adults: the role of implementation science frameworks
Authors: Blackberry Irene , Boak Jennifer , Rasekaba Tshepo , Steer Christopher
Published: January 2025

Purpose of review

The evidence supporting geriatric assessment (GA) in cancer care is well established, and GA is recommended by the American Society of Clinical Oncology, the International Society of Geriatric Oncology, and other oncology bodies. However, effective implementation of GA remains inadequate. Using selected papers indexed in Medline from the most recent 18 months to July 2024, including two outstanding interest papers, this review aimed to describe enablers and barriers to GA implementation in oncology and contrasts implementation with and without an implementation science framework. Finally, we make recommendations on applying an implementation science framework to facilitate integrating GA in oncology.

Recent findings

Implementation science frameworks have been widely employed in health services research, but their use in geriatric oncology, particularly to guide GA implementation and evaluation, is limited. Lack of time in busy practices coupled with workforce shortages adds to the challenges of GA implementation and adoption. A variety of screening and assessment tools such as the G8, electronic rapid fitness assessment, and Eastern Cooperative Oncology Group are often used in lieu of geriatrician review and to streamline GA. When effectively implemented in oncology, GA informs care and treatment decisions for improved outcomes.

Despite the benefits for older adults, embedding GA into routine clinical practice is critical yet not common practice. The variety of available GA tools, logistics, and individual beliefs are some of the identified barriers to GA adoption in oncology. Enablers include organization readiness, adaptability, communication, and the use of multidisciplinary teams. Further research is needed to examine how implementation science frameworks could provide guidance and structure for successful GA implementation in oncology.
Buprenorphine: an old dog with new tricks
Authors: Ng Ai Deen , Dickman Andrew
Published: January 2025

Purpose of review

The survival rate of patients with a cancer or palliative care diagnosis has improved over the years although pain remains a debilitating symptom that many patients still require treatment with opioids. Compared to full mu-opioid receptor agonists such as morphine and oxycodone, buprenorphine continues to remain a second- or third-line choice in this group of patients.

We have reviewed the pharmacology and clinical utility of buprenorphine to stimulate debate around the first-line use of buprenorphine in the management of pain in cancer patients.

Recent findings

Buprenorphine has a pharmacological profile that is unique and unlike any other opioid. It is associated with many immediate and long-term benefits, with lower risks of adverse effects that make it an ideal first-line choice in the management of cancer pain.

Buprenorphine appears to be a promising choice of opioid for cancer patients. Studies have found that buprenorphine is a safe and effective choice for many patients, making it a suitable first-line option for the management of cancer pain.
Blood-based biomarkers of frailty in older patients with cancer
Authors: Akagunduz Baran , Ergün Yakup , Dog˘an Akagündüz Dig˘dem , Akbas¸ Nergis , Akagündüz Dilara , Karaog˘lu Aziz , Soysal Pinar
Published: January 2025

Purpose of review

This review aims to evaluate the current evidence on blood-based biomarkers for frailty detection in older cancer patients. It explores the potential of various biomarkers, including inflammatory markers and microRNAs (miRNAs), to serve as indicators of frailty and examines the limitations of existing studies. The review also highlights the need for further research to validate these biomarkers and improve their clinical applicability.

Recent findings

Recent studies have examined blood biomarkers associated with frailty in older cancer patients. Findings suggest that elevated granulocyte levels and lower macrophage-derived stem cells and regulatory T cells are linked to frailty. Inflammatory biomarkers such as interleukin-6 and specific miRNAs, as well as higher neutrophil-to-lymphocyte ratios, have also been identified as potential indicators of frailty. While these biomarkers show promise, no single marker has proven sufficient, and combining them may improve frailty detection. Further research is needed to validate their clinical usefulness in this population.

Blood-based biomarkers show potential for detecting frailty in older patients with cancer, but further research is needed, particularly beyond an inflammatory focus and with more robust study designs.
Effect of Social Restriction Due to the COVID-19 Pandemic on Activity of Daily Living and Disease Severity of Patients With Alzheimer Disease: Sub-analysis of a Double-blinded Noninferiority Study of Donepezil Patches and Donepezil Tablets
Authors: Nakamura Yu , Omori Takumi , Nishiyama Kenichi , Ishikawa Ichiro , Aoki Hiroshi , Nagakura Naoki
Published: January 2025

Background:

We previously reported that social restrictions due to the COVID-19 pandemic led to a decline in cognitive function in patients with Alzheimer disease (AD). Here, we assessed the effects of COVID-19 restrictions on the activities of daily living (ADL) and disease severity in patients by comparing them to a control group.

Methods:

We examined the impact on ADL, evaluated using disability assessment for dementia (DAD), and disease severity, evaluated using the ABC dementia scale, in patients with mild-to-moderate AD. We conducted a post hoc subgroup analysis of a double-blinded, noninferiority study of donepezil 27.5 mg patches and donepezil hydrochloride 5 mg tablets (JapicCTI-194582). After showing the noninferiority of both treatments, we combined the data from both groups for analysis.

Results:

The subpopulation of the per-protocol set grouped by completing the double-blinded evaluation before and on/after the mild lockdown was balanced (n=136 and n=120). Patient demographics were similar between the subgroups. The decline in the DAD and ABC dementia scale scores [least-squares mean (SE)] was ameliorated by social restriction [−3.810 (0.743) and −1.871 (0.697) and −1.147 (0.285) and −0.419 (0.267), respectively (not significant)].

Conclusion:

Normalcy and expectation biases can affect the evaluation of ADL and disease severity by caregivers under high stress and deterioration of mental conditions.
Sequestration of dead-end undecaprenyl phosphate-linked oligosaccharide intermediate
Authors: Hong Yaoqin , Qin Jilong , Doyle Matthew Thomas , Reeves Peter Richard
Published: January 2025

Most Gram-negative bacteria synthesize a plethora of cell surface polysaccharides that play key roles in immune evasion, cell envelope structural integrity and host–pathogen interactions. In the predominant polysaccharide Wzx/Wzy-dependent pathway, synthesis is divided between the cytoplasmic and periplasmic faces of the membrane. Initially, an oligosaccharide composed of 3–8 sugars is synthesized on a membrane-embedded lipid carrier, undecaprenyl pyrophosphate, within the cytoplasmic face of the membrane. This lipid-linked oligosaccharide is then translocated to the periplasmic face by the Wzx flippase, where it is polymerized into a repeat-unit polysaccharide. Structural alterations to the O-antigen repeating oligosaccharide significantly reduce polysaccharide yield and lead to cell death or morphological abnormalities. These effects are attributed to the substrate recognition function of the Wzx flippase, which we postulated to act as a gatekeeper to ensure that only complete substrates are translocated to the periplasmic face. Here, we labelled Salmonella enterica serovar Typhimurium group B1 with [14C] d-galactose. Our results showed that strains unable to synthesize the full O-antigen repeat unit accumulate significantly higher levels of Und-P-linked material (~10-fold). Importantly, this sequestration is alleviated by membrane disruption which opens the lipid-linked oligosaccharide at the cytosolic face to periplasmic ligation to support accumulation occurs at the cytosolic face of the membrane.
Fine-scale variation in pollen availability influencesBombus terrestriscolony behaviour, development and fitness
Authors: Lambert Harriet , Kopp Emanuel , Pashalidou Foteini , De Moraes Consuelo M. , Mescher Mark C.
Published: January 2025

Climate change threatens the long-established synchronization of seasonal pollinator activity and flowering time. Bumble bees are particularly vulnerable to these shifts, with resource availability playing a significant role in colony establishment and success. Recently, we documented a mechanism whereby pollen-deprived bumble bees deliberately damaged plant leaves, speeding up the production of flowers in two different species. However, it is unknown whether bumble bees obtain a benefit through this behaviour, both on a spatial and temporal scale. In the current study, we evaluate the effects of pollen availability on colony development, behaviour and reproductive fitness inBombus terrestrisusing semi-natural and laboratory experiments. We find that the close proximity of flowers has significant effects on reproductive investment and output ofB. terrestriscolonies in a small-scale rooftop experiment. Moreover, we find that small shifts in the timing of pollen availability (5 days) shape the behaviour and development of the first generation of offspring, with significant carry-over effects on reproductive fitness forB. terrestrismicrocolonies. This suggests that small changes in the distribution of food may have significant impacts on colony success that cannot be compensated for over the course of the season. Furthermore, our findings suggest bumble bee colonies can feasibly profit by altering the timing of pollen resources, even by a few days.
Endogenous recovery of hippocampal function following global cerebral ischemia in juvenile female mice is influenced by neuroinflammation and circulating sex hormones
Authors: Vigil Jose J. , Tiemeier Erika , Orfila James E. , Chalmers Nicholas E. , Chang Victoria N. , Mitchell Danae , Veitch Isobella , Falk Macy , Dietz Robert M. , Herson Paco S. , Quillinan Nidia
Published: January 2025

Cardiac arrest-induced global cerebral ischemia (GCI) in childhood often results in learning and memory deficits. We previously demonstrated in a murine cardiac arrest and cardiopulmonary resuscitation (CA/CPR) mouse model that a cellular mechanism of learning and memory, long-term potentiation (LTP), is acutely impaired in the hippocampus of juvenile males, correlating with deficits in memory tasks. However, little is known regarding plasticity impairments in juvenile females. We performed CA/CPR in juvenile (P21-25) female mice and used slice electrophysiology and hippocampal dependent behavior to assess hippocampal function. LTP was and contextual fear were impaired 7-days after GCI and endogenously recovered by 30-days. LTP remained impaired at 30 days in ovariectomized females, suggesting the surge in gonadal sex hormones during puberty mediates endogenous recovery. Unlike juvenile males, recovery of LTP in juvenile females was not associated with BDNF expression. NanoString transcriptional analysis revealed a potential role of neuroinflammatory processes, and specifically Cd68 pathways, in LTP impairment and hormone-dependent recovery. We were able to restore LTP in ovariectomized females with chronic and acute PPT administration, implicating estrogen receptor alpha in recovery mechanisms. This study supports a mechanism of endogenous LTP recovery after GCI in juvenile female mice which differs mechanistically from juvenile males and does not occur in adults of either sex.
Spatially-structured inflammatory response in the presence of a uniform stimulus
Authors: Jerison Elizabeth R. , Romeo Nicolas , Quake Stephen R.
Published: January 2025

Inflammatory responses occur within the complex spatial context of tissues and organs, and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here, we use a multiplexed RNA in situ hybridization approach, together with analytical tools, to study inflammatory gene expression in the larval zebrafish tailfin in response to a bath of lipopolysaccharide (LPS). We use this model system to address whether spatial structure emerges in the tissue response even absent the spatial variation introduced by a pathogen. We find that epithelial cells in the tailfin express several pro-inflammatory genes, and that across these genes, the uniform stimulus triggers a spatially non-uniform response. We use a graph-based spectral decomposition method to analyze its structure, and find that long modes dominate, creating zones of activation. Overall, these zones account for a majority of the variation in gene expression. Our results show that epithelial cells are important producers of pro-inflammatory effector molecules in this system, and that tissue induces spatial correlations even absent a structured input.
Small heat shock protein HSPB8 interacts with a pre-fibrillar TDP43 low complexity domain species to delay fibril formation
Authors: Jami Khaled M. , Farb Daniel C. , Osumi Kayla M. , Shafer Catelynn C. , Criscione Sophie , Murray Dylan T.
Published: January 2025

The loss of cellular proteostasis through aberrant stress granule formation is implicated in neurodegenerative diseases. Stress granules are formed by biomolecular condensation involving protein-protein and protein-RNA interactions. These assemblies are protective, but can rigidify, leading to amyloid-like fibril formation, a hallmark of the disease pathology. Key proteins dictating stress granule formation and disassembly, such as TDP43, contain low-complexity (LC) domains that drive fibril formation. HSPB8, a small heat shock protein, plays a critical role modulating stress granule fluidity, preventing aggregation and promoting degradation of misfolded proteins. We examined the interaction between HSPB8 and the TDP43 LC using thioflavin T (ThT) and fluorescence polarization (FP) aggregation assays, fluorescence microscopy and photobleaching experiments, and crosslinking mass spectrometry (XL-MS). Our results indicate that HSPB8 delays TDP43 LC aggregation through domain-specific interactions with fibril nucleating species, without affecting fibril elongation rates. These findings provide mechanistic insight into how ATP-independent chaperones mediate LC domain aggregation and provide a basis for investigating how the TDP43 LC subverts chaperone activity in neurodegenerative disease.

Significance Statement

ATP-independent chaperones facilitate clearance of aggregated proteins through autophagy. This study provides insight into the molecular mechanism by which small heat shock proteins interact with the aggregation-prone low complexity protein domains of RNA-binding proteins linked to neurodegenerative disease pathologies. The results provide a foundation for designing improved chaperones as therapeutics and illustrate a methodology to identify regions in low complexity domains for targeted drug development in the context of neurodegenerative disease.
Matrix stiffness induces heritable changes in chromosome numbers, consistent with solid tumor heterogeneity
Authors: Anlaş Alişya A. , Sprenger Markus T. , Wang Mai , Ontko Nick , Phan Steven , Discher Dennis E.
Published: January 2025

Solid tumors often have an abundance of collagen-I that stiffens the tissue, and they are invariably driven by mutations that include chromosome losses and gains. These observations are linked here by showing that 3D matrix stiffness induces heritable changes to a cell’s DNA. We use live-cell chromosome reporters (ChReporters) and hydrogels of tunable stiffness to show mitotic compression, micronuclei counts, ChReporter losses and heterogeneity all increase as functions of stiffness. Increased mistakes occur despite suppressed cell division in stiff matrix and minimal size variation between spheroids. Colonies of ChReporter-negative cells within cancer spheroids align with Luria-Delbruck’s seminal theory for heritable mutations, which predicts inter-spheroid variances that exceed Poisson statistics. Suppression of the contractility motor Myosin-II also increases chromosome loss in 3D but not 2D and does not affect spheroid growth – thus clarifying Myosin-II’s putative role as a tumor suppressor. Consistent with experiments, pan-cancer analyses of clinical data associates chromosome losses and gains with collagen-I levels and genetic variation. Stiff extracellular matrix thus drives mechano-evolution of solid tumors as a Darwin-Lamarck process with heterogeneity that complicates therapy.
Microscopic and structural observations of actin filament capping and severing by Cytochalasin D
Authors: Mitani Takahiro , Takeda Shuichi , Oda Toshiro , Narita Akihiro , Maéda Yuichiro , Honda Hajime , Fujiwara Ikuko
Published: January 2025

Cytochalasin D (CytoD) is widely used to inhibit actin polymerization, but the underlying regulatory mechanism is unclear. We addressed this using Total Internal Reflection Fluorescence (TIRF) microscopy. Our time course depolymerization assay of individual actin filaments showed that CytoD tightly caps the barbed end, with an estimated Kmvalue for inhibition of 4.1 nM and a duration time of ∼1 min. Consistently, in polymerization assays, CytoD at concentrations near the Kmvalue completely suppressed barbed end elongation. Interestingly, at lower concentrations, CytoD acted as a leaky capper, allowing actin monomer addition by rapidly binding to and dissociating from barbed ends. We interpreted this contradictory behavior as arising from differences in binding modes: capping one strand (fast dissociation) or both strands (slow dissociation). CytoD severs actin filaments at micromolar levels, a concentration range commonly used in cell biological studies. Although the severing rate is slower than cofilin, the frequency is higher, resulting in the fragmentation of filaments into shorter pieces. Severing activity was suppressed by inorganic phosphate or cofilin. We determined the crystal structure of CytoD bound to filamentous conformation (F-form) actin and found that CytoD fits better in the hydrophobic cleft of F-form actin than in the monomeric conformation actin, explaining the preferential binding towards barbed end subunits. The structure further indicates that CytoD prevents barbed end depolymerization by stabilizing the terminal subunits in the F-form, which is supported by our MD simulations. Collectively, our results demonstrate how CytoD regulates actin dynamics at the molecular level.
Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria
Authors: Ashraf Khuram U , Bunoro-Batista Mariana , Ansell T. Bertie , Punetha Ankita , Rosario-Garrido Stephannie , Firlar Emre , Kaelber Jason T. , Stansfeld Phillip J. , Petrou Vasileios I.
Published: January 2025

In Gram-negative bacteria, the enzymatic modification of Lipid A with aminoarabinose (L-Ara4N) leads to resistance against polymyxin antibiotics and cationic antimicrobial peptides. ArnC, an integral membrane glycosyltransferase, attaches a formylated form of aminoarabinose to the lipid undecaprenyl phosphate, enabling its association with the bacterial inner membrane. Here, we present cryo-electron microscopy structures of ArnC fromS. entericainapoand nucleotide-bound conformations. These structures reveal a conformational transition that takes place upon binding of the partial donor substrate. Using coarse-grained and atomistic simulations, we provide insights into substrate coordination before and during catalysis, and we propose a catalytic mechanism that may operate on all similar metal-dependent polyprenyl phosphate glycosyltransferases. The reported structures provide a new target for drug design aiming to combat polymyxin resistance.
High-Throughput Glycan Array Screening Reveals Rhamnogalacturonan-I as a Ligand for Arabidopsis Leucine-Rich Repeat Receptor Kinases
Authors: Lee Du-Hwa , Ruprecht Colin , Lee Jung-Min , Choi Min-Soo , Hrovat Tobias , Heo Geon , Edelbacher Natalie , Enugutti Balaji , Blaukopf Markus , Cho Chung Hyun , Lee Ho-Seok , Belkhadir Youssef , Smakowska-Luzan Elwira , Pfrengle Fabian
Published: January 2025

The plant cell wall not only serves as a physical barrier against pathogens but, when damaged, also functions as a source of cell wall-derived molecules that play crucial roles in plant immunity as damage-associated molecular patterns (DAMPs). While oligogalacturonides from homogalacturonan are well-studied DAMPs, the immune-signaling potential of other cell wall components remains largely unexplored. Conventional genetic and biochemical approaches aimed at identifying ligand-receptor pairs in plant immunity have been limited by the vast diversity of potential ligand molecules and functional redundancy of putative receptors. Here, we developed a high-throughput screening pipeline that simultaneously examines multiple interactions between plant cell wall-derived glycans and >350 extracellular domains (ECDs) of receptor kinases and receptor like proteins in Arabidopsis, resulting in the screening of >40,000 interactions. We discovered a group of leucine-rich repeat receptor kinases named ARMs (AWARENESS of RG-I MAINTENANCES) that interact with rhamnogalacturonan-I (RG-I), a major component of pectin. RG-I treatment induced pattern-triggered immunity responses, with distinct kinetics compared to oligogalacturonide responses. We identified RG-I oligosaccharide structures required for interaction with ARM receptors and immune activation, and found that ARM receptors are redundantly involved in plant immunity. Thus, our approach provides a powerful platform for discovering glycan-receptor pairs in plants.
Aging: an inevitable road toward gut microbiota pathoadaptation
Authors: Melo-Miranda Rita , Pinto Ana , Barreto Hugo C. , Jesus Catarina , Gordo Isabel , Duarte Iola , Sousa Ana
Published: January 2025

Laboratory-raised mice live approximately seven times longer and healthier lives compared to their wild counterparts, due to a standardized healthy diet and limited exposure to environmental stressors1.

Aging is associated with increased inflammation and microbial dysbiosis2–4. Collectively, these influence microbiota evolution and may contribute to the enrichment in pathobiont frequency observed in old age4. Alternatively, this increase could stem from a decline in colonization resistance5,6, creating favorable conditions for pathobiont invasion.

Here, we sought to test whether aging in healthy, controlled conditions, could prevent the selection of age-associated pathobionts.

We have followed the adaptive evolution of a commensal strain ofEscherichia coliin the guts of mice of advanced age and found that it acquired several mutations common to bacteria colonizing young mice, which were absent in old animals. This, together with the increase inAkkermansia muciniphilain mice of advanced age, suggest healthy aging7,8.

However, mutations acquired exclusively in the older were mainly pathoadaptive, tuning the metabolism to oxygen and iron availability, hypermotility, and biofilm formation.

In summary, while the evolutionary signature in the guts of very old mice shows youth-like features that may be associated with longevity, the selection of pathoadaptive traits is magnified in very old age.

While suggesting that a breach in colonization resistance is not needed to justify the abundance of age-associated pathobionts, our findings raise the question whether specialized bacteria, as opposing to generalists such asE. coli, will display the same ability to evolve pathoadaptive traits.

Highlights

Gut commensals face increasingly personalized selective pressures in the aging gut

Even healthy aging selects for pathoadaptive traits in the gut microbiota

E. coli‘s adaptive pattern better reflects the metabolome than microbiota composition

In Brief

Pathobionts are often enriched in the microbiota of the elderly. Melo-Miranda et al. showed that irrespectively of limiting the opportunity for gut invasion, the strength of selection for pathoadaptation increases with aging. Yet, the gut environment of extreme ages seems to converge, highlighting the discontinuity of the aging process.
High-Throughput Site-Specific N-Glycosylation Profiling of Human Fibrinogen in Atrial Fibrillation
Authors: Šoić Dinko , Kifer Domagoj , Szavits-Nossan Janko , Blivajs Aleksandar , Đerek Lovorka , Rudan Diana , Gornik Olga , Gudelj Ivan , Keser Toma
Published: January 2025

Fibrinogen is a major plasma glycoprotein involved in blood coagulation and inflammatory responses. Alterations in its glycosylation have been implicated in various pathological conditions, yet its site-specific N-glycosylation profile remains largely unexplored in a clinical context. Here, we present a high-throughput LC-MS workflow for site-specific analysis of fibrinogen N-glycosylation using a cost-effective ethanol precipitation enrichment method. The method demonstrated good intra- and inter-plate repeatability (CV: 5% and 12%, respectively) and was validated through the first assessment of intraindividual temporal stability in healthy individuals, revealing consistent glycosylation patterns within individuals. Application to 181 atrial fibrillation (AF) patients and 52 healthy controls identified three gamma chain glycoforms significantly associated with AF. Most notably, increased levels of the asialylated N4H5, known to enhance fibrin bundle thickness and promote clot formation, suggest a potential mechanism linking glycosylation changes to the prothrombotic state in AF. Furthermore, fibrinogen sialylation showed strong associations with cardiovascular risk factors, including triglycerides, BMI, and glucose levels. Longitudinal analysis of 108 AF patients six months post-catheter ablation showed stability in the AF-associated glycan profile. Our findings establish fibrinogen glycosylation as a potential biomarker for cardiovascular conditions and demonstrate the utility of site-specific glycosylation analysis for clinical applications.
Optimizing DNA origami assembly through selection of scaffold sequences that minimise off-target interactions
Authors: Shirt-Ediss Ben , Torelli Emanuela , Navarro Silvia Adriana , Khamis Hadeel , Kaplan Ariel , Trewby William , Elezgaray Juan , Moradzadeh-Esmaeili Nima , Haydell Michael , Keppner Daniel , Famulok Michael , Krasnogor Natalio
Published: January 2025

DNA origami is a mainstay of DNA nanotechnology and several efforts have been devoted to understanding how various factors of the self-assembly reaction affect the final yield of the target origami structure. This study analyses how base sequence affects origami yield through the generation of off-target side reactions during selfassembly. Off-target bindings are an under-explored phenomenon and can potentially introduce unwanted assembly barriers and kinetic traps in the origami folding pathway. We developed a multi-objective computational approach that takes a given origami design and scores different scaffold sequences (and their complementary staples) for the prevalence of four different types of off-target binding events. Using our method on DNA origami, we can select ‘bad’ regions of biological sequences (like lambda DNA phage) that, when used as origami scaffold sequences, have an excessive number of off-target side reactions for each shape. We show, using high-resolution atomic force microscopy (AFM), that these scaffold sequences largely fail to fold into the target triangle or rectangle structurein vitro, despite the scaffold sequence having a fully complementary staple set present. Conversely, using our method we can also select ‘good’ regions of biological sequences. These sequences are deficient in off-target reactions and when used as origami scaffolds, fold more successfully into their target structures as characterised by AFM.

These results have been validated in “blind” folding experiments at two different laboratories in which the experimenters did not know which scaffolds were good or bad folders. To further investigate assembly behaviour, optical tweezers experiments revealed distinct mechanical response profiles, correlating with scaffold-specific off-target interactions. While variants with higher GC content show a high mean unfolding force, variants with lower off-target binding demonstrated more uniform force-extension curves. Our analysis confirmed that high off-target binding leads to increased structural heterogeneity, as seen in the clustering behaviour of unfolding traces of OT experiments. Over-all, our work demonstrates how the off-target reactions implicit in base sequences can derail the origami self-assembly process if sufficiently prevalent, and we provide a software tool to select scaffold sequences that minimise off-target reactions for any DNA origami design.
Cracking Controls ATP Hydrolysis in the catalytic domain of a P-ATPase
Authors: Placenti M. Agueda , Martinez-Gache Santiago A. , González-Lebrero Rodolfo M. , Wolynes Peter G. , González Flecha F. Luis , Roman Ernesto A.
Published: January 2025

Membrane transporters are essential for cell homeostasis. Among them P-type ATPases, which couple ATP hydrolysis to solute transport, play a key role. Despite extensive research, the fine mechanisms by which this coupling occurs are not completely understood. In this work, we analyzed the effect of substrate, temperature, and urea on the steady state ATPase activity, tryptophan fluorescence and far-UV ellipticity of the catalytic domain of a thermophilic Cu(I) transport ATPase. Through local frustration analysis in combination with AlphaFold2 prediction, we identified a novel conformation, enabling molecular dynamics simulations of an open/close transition. Our results revealed a “cracking” mechanism as a key step in the catalytic cycle. Furthermore, we developed a model that fully describes all the experimental observations. These findings reinforce the idea that local unfolding is involved in enzyme catalysis and suggest a key role in the regulation of enzyme activity.
A Cooperative Model for Symmetric Ligand Binding to Protein Fibrils
Authors: Smith Matthew S. , DeGrado William F. , Grabe Michael , Shoichet Brian K.
Published: January 2025

A hallmark of neurodegenerative diseases like Alzheimer’s Disease (AD) and chronic traumatic encephalopathy (CTE) is the presence of toxic protein aggregates in neurons. In AD and CTE specifically, the protein tau forms insoluble fibrils that are hundreds of nanometers in length. Intriguingly, recent experimental structures suggest that tau ligands like the disaggregator EGCG and positron emission tomography (PET) tracers like GTP-1 and MK-6240 bind to tau fibrils in long stacks reflecting the symmetry of the protein across many binding sites. In these stacks, each ligand makes more contact with its symmetry mates than it does with the protein. To interpret the binding of these molecules and new ligands, we must understand the effects of the cooperativity between sites and the entropy coming from the number of sites. Here, we investigate a nearest-neighbors model of cooperativity and use statistical mechanics to derive binding isotherms for saturation and competition experiments. This model allows us to relate measuredEC50soIC50and so values to the intrinsic binding affinity to a single site and to cooperativity across sites in ways resembling the Cheng-Prusoff Equation. Depending on the degree of cooperativity between molecular species, this model permits solutions that lack the steep binding curves expected from cooperative systems and even solutions resembling 2-site systems. We finally consider conditions for a fibril’s detection in a PET scan and practical matters of fitting this model’s parameters to data.
Microglial plasticity governed by state-specific enhancer landscapes
Authors: Hamagami Nicole , Kapadia Dvita , Abduljawad Nora , Cheng Zuolin , McLaughlin Liam , Singhania Darsh , Barclay Kia M. , Yang Jin , Sun Zhixin , Bayguinov Peter , Yu Guoqiang , Gabel Harrison W. , Li Qingyun
Published: January 2025

Single-cell transcriptomic studies have identified distinct microglial subpopulations with shared and divergent gene signatures across development, aging and disease. Whether these microglial subsets represent ontogenically separate lineages of cells, or they are manifestations of plastic changes of microglial states downstream of some converging signals is unknown. Furthermore, despite the well-established role of enhancer landscapes underlying the identity of microglia, to what extent histone modifications and DNA methylation regulate microglial state switches at enhancers have not been defined. Here, using genetic fate mapping, we demonstrate the common embryonic origin of proliferative-region-associated microglia (PAM) enriched in developing white matter, and track their dynamic transitions into disease-associated microglia (DAM) and white matter-associated microglia (WAM) states in disease and aging contexts, respectively. This study links spatiotemporally discrete microglial states through their transcriptomic and epigenomic plasticity, while revealing state-specific histone modification profiles that govern state switches in health and disease.
Do monkeys see the way we do? Qualitative similarities and differences between monkey and human perception
Authors: Cherian Thomas , Jacob Georgin , Arun S.P.
Published: January 2025

Monkeys are widely used as model organisms for human vision and cognition. While their anatomy and physiology strongly correspond to humans, it is unclear to what extent their perception matches with ours. Previous studies have evaluated specific aspects of perception, after extensive training on customized tasks that could have altered their perception. To resolve these issues, we trained monkeys to perform an oddball visual search task on natural images, tested them on carefully controlled images to detect a variety of perceptual phenomena, and compared them with humans. This revealed a number of qualitative similarities and differences. Like humans, monkeys showed similar object relations, Weber’s law and amodal completion. However, unlike humans, monkeys did not show mirror confusion or a global advantage. These findings represent a first comprehensive evaluation of visual perception in monkeys and humans, revealing the limitations of monkeys as a model organism for human vision.

SIGNIFICANCE STATEMENT

Monkeys are widely used to study for vision and cognition, but is their perception like ours? Most previous studies have tested only single aspects of perception in monkeys, often after extensive training which could have altered their perception. Here, we overcame these limitations by training monkeys on a highly general oddball visual search task, testing them on many perceptual phenomena and comparing them with humans on the same tasks. Our results show that monkeys do indeed see the way we do, but with important differences that highlight their limitations as a model for human vision.
An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance inM. tuberculosisusing a reproducible algorithmic approach
Authors: Adlard Dylan , Joseph Lavania , Webster Hermione , O’Reilly Ailva , Knaggs Jeffrey , Peto Tim EA , Crook Derrick W , Omar Shaheed V , Fowler Philip W
Published: January 2025

Bedaquiline (BDQ) has only been approved for use for a little over a decade yet is a key drug for treating multi-drug resistant tuberculosis, however rising levels of resistance threaten to reduce its effectiveness. Catalogues of mutations associated with resistance to bedaquiline are key to detecting resistance genetically for either diagnosis or surveillance. At present building catalogues requires considerable expert knowledge, often requires the use of complex grading rules, and is an irreproducible process. We developed an automated method, catomatic, that associates genetic variants with resistance (or susceptibility) using a two-tailed binomial test with a stated background rate and applied it to a dataset of 11,867Mycobacterium tuberculosissamples with whole genome and bedaquline susceptibility testing data. Using this framework we investigated how to best classify variants and the phenotypic significance of minor alleles. The genesmmpS5andmmpL5are not directly associated with bedaquline resistance, and our catalogue ofRv0678,atpE, andpepQvariants attains a cross-validated sensitivity and specificity of 79.4 ± 1.8 % and 98.5 ± 0.3%, respectively, for 94 ± 0.4% of samples. Identifying samples with subpopulations containingRv0678variants improves sensitivity, and detection thresholds in bioinformatic pipelines should therefore be lowered. By using a more permissive and deterministic algorithm trained on a sufficient number of resistant samples we have reproducibly constructed an AMR catalogue for BDQ resistance-associated variants that is comprehensive and accurate.

Impact Statement

Bedaquiline has recently received global endorsement for tuberculosis treatment, yet the genetic determinants of antimicrobial resistance remain incompletely understood. Existing gold-standard methods for building mutation catalogs lack public accessibility and reproducibility. We introduce catomatic, a reproducible and publicly available method that employs simpler statistics to increase sensitivity to resistance-associated variants. This approach has enabled investigations into mechanisms of resistance, the significance of genetic subpopulations, and key data attributes that influence the ease of classifying effects and the accuracy of BDQ resistance phenotype prediction in clinical samples. We strongly emphasise the utility in using reproducible statistics and sustainably developed software in genetics-focussed microbiology.
Characterization of conformational dynamics and allostery of the catalytic domain of human mitochondrial YME1L protease
Authors: Black Megan K. , Kim Angelina S. , Chen Ching Y. , Goncalves Monica M. , Waseem Simrah , Vahidi Siavash , Huang Rui
Published: January 2025

Mitochondrial proteostasis is essential to maintain cellular function and survival. YME1L protease is an important contributor to proteostasis which belongs to the AAA+ (ATPasesAssociated with diverse cellularActivities) protease family and is anchored to the inner mitochondrial membrane. YME1L plays a pivotal role in mitochondrial protein quality control by selectively degrading misfolded and native proteins. The precise mechanisms by which nucleotide binding and hydrolysis influence YME1L’s conformational dynamics, proteolytic activity, and stability remain unclear. Here we characterize the conformational dynamics and allosteric regulation of the YME1L catalytic domain. Using a hexameric soluble YME1L construct, we employ hydrogen/deuterium exchange mass spectrometry (HDX-MS) and nuclear magnetic resonance (NMR) spectroscopy to demonstrate that nucleotide binding reduces the backbone flexibility and modulates the side-chain dynamics of the AAA+ domain, while Zn²⁺ binding stabilizes the protease domain. We also reveal novel long-range allostery between the AAA+ and protease domains of YME1L, mediated by a critical salt bridge on the inter-domain interface. We show the importance of the salt bridge in facilitating ATP-dependent substrate degradation by YME1L. Additionally, we show that ATP binding stabilizes the structure of the catalytic domain of YME1L and protects it from chemical modification- and heat-induced aggregation. These findings explain the nucleotide-driven regulation of YME1L and provide novel insights into understanding its proteolytic activity and structural stability under physiological and stress conditions.
Microbial functional guilds respond cohesively to rapidly fluctuating environments
Authors: Crocker Kyle , Skwara Abigail , Kannan Rathi , Murugan Arvind , Kuehn Seppe
Published: January 2025

Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to long-term seasonal or climactic variations. Understanding how microbial populations respond to these changes is critical for predicting the impact of perturbations, interventions, and climate change on communities. Since communities typically harbor tens to hundreds of distinct taxa, the response of microbial abundances to perturbations is potentially complex. However, while taxonomic diversity is high, in many communities taxa can be grouped into functional guilds of strains with similar metabolic traits. These guilds effectively reduce the complexity of the system by providing a physiologically motivated coarse-graining. Here, using a combination of simulations, theory, and experiments, we show that the response of guilds to nutrient fluctuations depends on the timescale of those fluctuations. Rapid changes in nutrient levels drive cohesive, positively correlated abundance dynamics within guilds. For slower timescales of environmental variation, members within a guild begin to compete due to similar resource preferences, driving negative correlations in abundances between members of the same guild. Our results provide a route to understanding the relationship between functional guilds and community response to changing environments, as well as an experimental approach to discovering functional guilds via designed nutrient perturbations to communities.
IonBench: a benchmark of optimisation strategies for mathematical models of ion channel currents
Authors: Owen Matt J. , Mirams Gary R.
Published: January 2025

Ion channel models present many challenging optimisation problems. These include unidentifiable parame- ters, noisy data, unobserved states, and a combination of both fast and slow timescales. This can make it difficult to choose a suitable optimisation routinea priori. Nevertheless, many attempts have been made to design optimisation routines specifically for ion channel models, however, little work has been done to compare these optimisation approaches. We have developed ionBench, an open-source optimisation bench- marking framework, to evaluate and compare these approaches against a standard set of ion channel optimisation problems. We included implementations of thirty-four unique optimisation approaches that have been previously applied to ion channel models and evaluated them against the ionBench test suite, consisting of five parameter optimisation problems derived from the cardiac ion channel literature. Each optimisation approach was initiated from multiple starting parameters and tasked with reproducing a problem-specific simulated dataset. Through ionBench, we tracked and evaluated the performance of these optimisations, identifying the expected run time until a successful optimisation for each approach, which was used for comparisons. Finally, we used these results, in addition to other literature results, to identify a new efficient approach. Its use could reduce computation time by multiple orders of magnitude, while also improving the reliability of ion channel parameter optimisation.
Chaetognaths exhibit the most extensive repertoire of Hox genes among protostomes
Authors: Ordoñez June F. , Wollesen Tim
Published: January 2025

1.

The evolutionary origins and body plan diversification within bilaterians hinge on our understanding of conserved developmental gene networks across diverse taxa. While significant advances have been made in elucidating the anterior-posterior (AP) axis patterning across well-studied bilaterian lineages, our understanding of the conservation of AP-patterning gene expression in underexplored protostomes with a phylogenetically informative position remains limited. Chaetognaths, a group of marine invertebrates, form a clade with Gnathifera as a sister to the remaining Lophotrochozoa, occupying an early-diverging branch of the spiralian lineage. Their phylogenetic position provides potentially valuable evolutionary insights into whether the AP patterning reflects conserved bilaterian mechanisms or reveals distinct lineage-specific adaptations. Here, we investigate the expression patterns of anterior nervous system markers (otx,nk2.1,six3/6) and Hox genes in post-embryonic stages of the chaetognathSpadella cephalopterausing fluorescence whole-mountin situhybridization. We identify expression domains of anterior-patterning genes in the cerebral ganglion and head structures, consistent with their conserved role in anterior central nervous system (CNS) specification in bilaterians. Additionally, we describe a staggered expression pattern of Hox genes, including previously undescribed central (Sce-med6) and posterior class (Sce-postCandSce-postD), along the ventral nerve cord (VNC) and post-anal tail. Our results demonstrate that chaetognaths exhibit the most extensive repertoire of Hox genes among protostomes, within metazoans only surpassed by chordates. All AP patterning genes are expressed in a staggered manner, with Hox gene expression absent in the head region. This pattern resembles the conserved expression profile inferred for the last common bilaterian ancestor and is only rudimentarily visible in other spiralians, including annelids and mollusks. Posterior Hox genes including the newly discoveredpostCandpostDgenes are absent in the hitherto investigated gnathiferan sister groups such as rotifers. The absence of a postanal tail in rotifers and other gnathiferans, combined with the expression of posterior Hox genes in the elongated postanal tail region, suggests their involvement in the formation of this unique chaetognath structure. Posterior flexibility of Hox genes, as previously hypothesized for chordates, likely contributed to the formation of the chaetognath tail during the early Cambrian period.
Supersolidity in Rydberg tweezer arrays
Authors: Homeier Lukas , Hollerith Simon , Geier Sebastian , Chiu Neng-Chun , Browaeys Antoine , Pollet Lode
Published: January 2025

Rydberg tweezer arrays provide a versatile platform to explore quantum magnets with dipolar XY or van der Waals Ising ZZ interactions. Here, we propose a scheme combining dipolar and van der Waals interactions between two Rydberg states, where the amplitude of the latter can be greater than that of the former, realizing an extended Hubbard model with long-range tunnelings in optical tweezer arrays. On the triangular lattice with repulsive interactions, we predict the existence of a robust supersolid phase with a critical entropy per particle S/N≈0.19 accessible in current Rydberg tweezer experiments supported by large-scale quantum Monte Carlo simulations. We further demonstrate the experimental feasibility by identifying pairs of Rydberg states in Rb87 realizing the required interactions. Such a lattice supersolid is long lived, found over a wide parameter range in an isotropic and flat two-dimensional geometry, and can be realized for hundreds of particles allowing one to directly probe the defect-induced picture of supersolids. Its thermodynamical and dynamical properties can hence be studied at a far larger scale than hitherto possible.

Published by the American Physical Society
2025