bluuebunny/crossref_metadata_2025 huggingface dataset:
Dietary iron deficiency impairs effector function of memory T cells following influenza infection
Authors: Bradley Marissa C. , Gray Joshua , Carpia Francesca La , Idzikowski Emma , Guyer Rebecca , Pethe Kalpana , Hod Eldad A. , Connors Thomas J.
Published: July 2024

The establishment of memory T cell responses is critical to protection against pathogens and is influenced by the conditions under which memory formation occurs. Iron is an essential micronutrient for multiple immunologic processes and nutritional deficiency is a common problem worldwide. Despite its prevalence, the impact of nutritional iron deficiency on the establishment of memory T cell responses is not fully understood. In this study we investigate the impact of nutritional iron deficiency on the generation, phenotype, and function of memory T cell responses using a murine model of dietary iron modulation in the context of influenza infection. Iron deficient mice have decreased systemic iron levels and develop significant anemia. Increased T cell expression of the transferrin receptor (CD71) is seen in iron deficient mice at baseline. During primary influenza infection, iron deficient mice experience increased weight loss and phenotypic evidence of impairments in T cell activation. Following recovery from infection, iron deficient mice generate increased influenza specific memory T cells which exhibit impaired ability to produce IFNγ, most notably within the lung. Importantly, the ability to produce IFNγ and TNFα is not recovered by co-culture with iron replete dendritic cells, suggesting a T cell intrinsic alteration in functional memory formation. Altogether, these results isolate a critical effect of nutritional iron deficiency on T cell memory development and function.
FuncFetch: An LLM-assisted workflow enables mining thousands of enzyme-substrate interactions from published manuscripts
Authors: Smith Nathaniel , Yuan Xinyu , Melissinos Chesney , Moghe Gaurav
Published: July 2024

Motivation

Thousands of genomes are publicly available, however, most genes in those genomes have poorly defined functions. This is partly due to a gap between previously published, experimentally-characterized protein activities and activities deposited in databases. This activity deposition is bottlenecked by the time-consuming biocuration process. The emergence of large language models (LLMs) presents an opportunity to speed up text-mining of protein activities for biocuration.

Results

We developed FuncFetch — a workflow that integrates NCBI E-Utilities, OpenAI’s GPT-4 and Zotero — to screen thousands of manuscripts and extract enzyme activities. Extensive validation revealed high precision and recall of GPT-4 in determining whether the abstract of a given paper indicates presence of a characterized enzyme activity in that paper. Provided the manuscript, FuncFetch extracted data such as species information, enzyme names, sequence identifiers, substrates and products, which were subjected to extensive quality analyses. Comparison of this workflow against a manually curated dataset of BAHD acyltransferase activities demonstrated a precision/recall of 0.86/0.64 in extracting substrates. We further deployed FuncFetch on nine large plant enzyme families. Screening 27,120 papers, FuncFetch retrieved 32,605 entries from 5547 selected papers. We also identified multiple extraction errors including incorrect associations, non-target enzymes, and hallucinations, which highlight the need for further manual curation. The BAHD activities were verified, resulting in a comprehensive functional fingerprint of this family and revealing that ∼70% of the experimentally characterized enzymes are uncurated in the public domain. FuncFetch represents an advance in biocuration and lays the groundwork for predicting functions of uncharacterized enzymes.

Availability and Implementation

Code and minimally-curated activities available at:https://github.com/moghelab/funcfetchandhttps://tools.moghelab.org/funczymedb
Interplay of Light, Melatonin, and Circadian Genes in Skin Pigmentation Regulation
Authors: Bertolesi Gabriel E. , Debnath Nilakshi , Heshami Neda , Bui Ryan , Zadeh-Haghighi Hadi , Simon Christoph , McFarlane Sarah
Published: July 2024

Highlights

Circadian pigmentation of tadpoles in vivo is mainly driven by melatonin

Light and melatonin differentially regulate proliferation

Melatonin mimics the expression of circadian core genes in the dark phase

Deregulation of the circadian rhythm inhibits melanin synthesis

Circadian regulation of skin pigmentation is essential for thermoregulation, UV protection, and synchronization of skin cell renewal. This regulation involves both cell-autonomous photic responses and non-cell-autonomous hormonal control, particularly through melatonin produced in a light-sensitive manner. Photosensitive opsins, cryptochromes, and melatonin regulate circadian rhythms in skin pigment cells. We studied light/dark cycles and melatonin coordination in melanin synthesis and cell proliferation ofXenopus laevismelanophores.In vivo, tadpole pigmentation shows robust circadian regulation mainly hormone-driven, in that isolated melanophores respond strongly to melatonin but only slightly to light. Melanophore proliferation is faster in the dark and slower with melatonin compared to a 12/12 light/dark cycle. Expression of circadian core genes (clock, bmal1, per1, per2, per3, cry1, cry2, and cry4) in melatonin-treated cells during the light phase mimics dark phase expression. Individual Cry overexpression did not affect melanisation or cell proliferation, likely due to functional redundancy. Melanin synthesis was inhibited by circadian cycle deregulation through: a) pharmacological inhibition of Cry1 and Cry2 degradation with KL001, b) continuous light or dark conditions, and c) melatonin treatment. Our findings suggest that circadian cycle regulation, rather than proliferative capacity, alters melanisation of melanophores.

Significance

Circadian rhythms are a highly conserved phenomenon in nature. In vertebrates, the modification of skin pigmentation and epidermal cell renewal in response to the environmental light-dark cycle are crucial physiological adaptations that serve various purposes, including thermoregulation, reducing ultraviolet damage, and regulating skin stem cell proliferation. Our observations indicate that,in vivo, the circadian regulation of skin pigmentation is more influenced by cycling-melatonin levels than light/dark. The deregulation of the circadian cell cycle through various mechanisms all inhibited melanisation while cell proliferation was increased or reduced, suggesting that proliferation and melanisation are mechanistically dissociated responses.

Graphical Abstract
Genetic variants affect diurnal glucose levels throughout the day
Authors: Sinnott-Armstrong Nasa , Strausz Satu , Urpa Lea , Abner Erik , Valliere Jesse ,   Estonian Biobank Research Team, Palta Priit , Dashti Hassan S , Daly Mark , Pritchard Jonathan K , Saxena Richa , Jones Samuel E , Ollila Hanna M
Published: July 2024

Circadian rhythms not only coordinate the timing of wake and sleep but also regulate homeostasis within the body, including glucose metabolism. However, the genetic variants that contribute to temporal control of glucose levels have not been previously examined. Using data from 420,000 individuals from the UK Biobank and replicating our findings in 100,000 individuals from the Estonian Biobank, we show that diurnal serum glucose is under genetic control. We discover a robust temporal association of glucose levels at the Melatonin receptor 1B (MTNR1B)(rs10830963, P = 1e-22) and a canonical circadian pacemaker gene Cryptochrome 2 (CRY2)loci (rs12419690, P = 1e-16). Furthermore, we show that sleep modulates serum glucose levels and the genetic variants have a separate mechanism of diurnal control. Finally, we show that these variants independently modulate risk of type 2 diabetes. Our findings, together with earlier genetic and epidemiological evidence, show a clear connection between sleep and metabolism and highlight variation atMTNR1BandCRY2as temporal regulators for glucose levels.
Computationally designed mRNA-launched protein nanoparticle vaccines
Authors: Hendricks Grace G. , Grigoryan Lilit , Navarro Mary Jane , Catanzaro Nicholas J. , Hubbard Miranda L. , Powers John M. , Mattocks Melissa , Treichel Catherine , Walls Alexandra C. , Lee Jimin , Ellis Daniel , Wang Jing Yang (John) , Cheng Suna , Miranda Marcos C. , Valdez Adian , Chao Cara W. , Chan Sidney , Men Christine , Johnson Max R. , Hui Harold , Wu Sheng-Yang , Lujan Victor , Muramatsu Hiromi , Lin Paulo J.C. , Sung Molly M.H. , Tam Ying K. , Leaf Elizabeth M. , Pardi Norbert , Baric Ralph S. , Pulendran Bali , Veesler David , Schäfer Alexandra , King Neil P.
Published: July 2024

Both protein nanoparticle and mRNA vaccines were clinically de-risked during the COVID-19 pandemic. These vaccine modalities have complementary strengths: antigen display on protein nanoparticles can enhance the magnitude, quality, and durability of antibody responses, while mRNA vaccines can be rapidly manufactured and elicit antigen-specific CD4 and CD8 T cells. Here we leverage a computationally designed icosahedral protein nanoparticle that was redesigned for optimal secretion from eukaryotic cells to develop an mRNA-launched nanoparticle vaccine for SARS-CoV-2. The nanoparticle, which displays 60 copies of a stabilized variant of the Wuhan-Hu-1 Spike receptor binding domain (RBD), formed monodisperse, antigenically intact assemblies upon secretion from transfected cells. An mRNA vaccine encoding the secreted RBD nanoparticle elicited 5- to 28-fold higher levels of neutralizing antibodies than an mRNA vaccine encoding membrane-anchored Spike, induced higher levels of CD8 T cells than the same immunogen when delivered as an adjuvanted protein nanoparticle, and protected mice from vaccine-matched and -mismatched SARS-CoV-2 challenge. Our data establish that delivering protein nanoparticle immunogens via mRNA vaccines can combine the benefits of each modality and, more broadly, highlight the utility of computational protein design in genetic immunization strategies.
Operational lessons learned from simulating an elimination response to a transboundary animal disease in wild animals
Authors: Chalkowski K , Pepin KM , Lavelle MJ , Miller RS , Fischer J , Brown VR , Glow M , Smith B , Cook S , Kohen K , Sherburne S , Smith H , Leland B , VerCauteren KC , Snow NP
Published: July 2024

Transboundary animal disease (TAD) introductions can have myriad economic, ecological, and societal impacts. When TADs are introduced into wild species, rapid and intense control efforts to reduce wild animal host populations are sometimes needed to eliminate the disease and prevent endemicity and spillover to domestic animal populations. Yet, such intensive efforts are non-trivial, and the rarity of TAD introductions means that personnel rarely have direct experience with these types of operations. Thus, explicit assessments of operational challenges for these kinds of efforts can provide direction to build emergency response preparedness capacity. Here, we simulated a TAD control effort in response to initial detection of a hypothetical index case of a TAD in wild pigs (Sus scrofa) (e.g., African swine fever; ASF). We used three removal methods (aerial control, trapping, and an experimental toxic bait). Then, we conducted an after-action assessment to identify operational challenges for rapidly reducing a population of invasive wild pigs within a simulated outbreak zone. We also simulated carcass recoveries of dispatched pigs, similar to what might be conducted during a response to a TAD with carcass-based transmission (e.g., ASF virus). Here, we describe operational challenges identified during our effort, alongside technological development solutions anda prioristrategy needs to improve TAD response operation outcomes.
Toward improved uncertainty quantification in predictions of forest dynamics: A dynamical model of forest change
Authors: Itter Malcolm , Finley Andrew O.
Published: July 2024

Models of forest dynamics are an important tool to understand and predict forest responses to global change. Despite recent model development, predictions of forest dynamics under global change remain highly variable reflecting uncertainty in future conditions, forest demographic processes, and the data used to parameterize and validate models. Quantifying this uncertainty and accounting for it when making adaptive management decisions is critical to our ability to conserve forest ecosystems in the face of rapidly changing conditions. Dynamical spatiotemporal models (DSTMs) are a particularly powerful tool in this setting given they quantify and partition uncertainty in demographic models and noisy forest observations, propagate uncertainty to predictions of forest dynamics, and support refinement of predictions based on new data and improved ecological understanding. A major challenge to the application of DSTMs in applied forest ecology has been the lack of a scalable, theoretical model of forest dynamics that generates predictions at the stand level—the scale at which management decisions are made. We address this challenge by integrating a matrix projection model motivated by the well-known McKendrick-von Foerster partial differential equation for size-structured population dynamics within a Bayesian hierarchical DSTM informed by continuous forest inventory data. The model provides probabilistic predictions of species-specific demographic rates and changes in the size-species distribution over time. The model is applied to predict long-term dynamics (60+ years) within the Penobscot Experimental Forest in Maine, USA, quantifying and partitioning uncertainty in inventory observations, process-based predictions, and model parameters for nine Acadian Forest species. We find that uncertainty in inventory observations drives variability in predictions for most species and limits the inclusion of ecological detail within the DSTM. We conclude with a discussion of how DSTMs can be used to reduce uncertainty in predictions of forest dynamics under global change through informed model refinement and the assimilation of multiple forest data sources.
Off-the-shelf image analysis models outperform human visual assessment in identifying genes controlling seed color variation in sorghum
Authors: Shrestha Nikee , Mangal Harshita , Torres-Rodriguez J. Vladimir , Tross Michael C. , Lopez-Corona Lina , Linders Kyle , Sun Guangchao , Mural Ravi V. , Schnable James C.
Published: July 2024

Seed color is a complex phenotype linked to both the impact of grains on human health and consumer acceptance of new crop varieties. Today seed color is often quantified via either qualitative human assessment or biochemical assays for specific colored metabolites. Imaging-based approaches have the potential to be more quantitative than human scoring while lower cost than biochemical assays. We assessed the feasibility of employing image analysis tools trained on rice (Oryza sativa) or wheat (Triticum aestivum) seeds to quantify seed color in sorghum (Sorghum bicolor) using a dataset of > 1,500 images. Quantitative measurements of seed color from images were substantially more consistent across biological replicates than human assessment. Genome-wide association studies conducted using color phenotypes for 682 sorghum genotypes identified more signals near known seed color genes in sorghum with stronger support than manually scored seed color for the same experiment. Previously unreported genomic intervals linked to variation in seed color in our study co-localized with a gene encoding an enzyme in the biosynthetic pathway leading to anthocyanins, tannins, and phlobaphenes – colored metabolites in sorghum seeds – and with the sorghum ortholog of a transcription factor shown to regulate several enzymes in the same pathway in rice. The cross-species transferability of image analysis tools, without the retraining, may aid efforts to develop higher value and health-promoting crop varieties in sorghum and other specialty and orphan grain crops.
Sequence programmable nucleic acid coacervates
Authors: Majumder Sumit , Coupe Sebastian , Fakhri Nikta , Jain Ankur
Published: July 2024

Nature uses bottom-up self-assembly to build structures with remarkable complexity and functionality. Understanding how molecular-scale interactions translate to macroscopic properties remains a major challenge and requires systems that effectively bridge these two scales. Here, we generate DNA and RNA liquids with exquisite programmability in their material properties. Nucleic acids are negatively charged, and in the presence of polycations, they may condense to a liquid-like state. Within these liquids, DNA and RNA retain sequence-specific hybridization abilities. We show that intermolecular hybridization in the condensed phase cross-links molecules and slows down chain dynamics. This reduced chain mobility is mirrored in the macroscopic properties of the condensates. Molecular diffusivity and material viscosity scale with the intermolecular hybridization energy, enabling precise sequence-based modulation of condensate properties over orders of magnitude. Our work offers a robust platform to create self-assembling programmable fluids and may help advance our understanding of liquid-like compartments in cells.
Constructing Ensemble Gene Functional Networks Capturing Tissue/condition-specific Co-expression from Unlabled Transcriptomic Data with TEA-GCN
Authors: Lim Peng Ken , Wang Ruoxi , Velankanni Jenet Princy Antony , Mutwil Marek
Published: July 2024

Gene co-expression networks (GCNs) generated from public transcriptomic datasets can elucidate the co-regulatory and co-functional relationships between genes, making GCNs an important tool to predict gene functions. However, current GCN construction methods are sensitive to the quality of the data, and the interpretability of the identified relationships between genes is still difficult. To address this, we present a novel method — Two-Tier Ensemble Aggregation (TEA-) GCN. TEA-GCN utilizes unsupervised partitioning of big transcriptomic datasets and three correlation coefficients to generate ensemble GCNs in a two-step aggregation process. We show that TEA-GCN outperforms in finding correct functional relationships between genes over the current state-of-the-art across three model species, and is able to not only capture condition/tissue-specific gene co-expression but explain them through the use of natural language processing (NLP). In addition, we found TEA-GCN to be especially performant in identifying relationships between transcription factors and their activation targets, making it effective in inferring gene regulatory networks. TEA-GCN is available athttps://github.com/pengkenlim/TEA-GCN.
First Insights into microbial changes within an Inflammatory Bowel Disease Family Cohort study
Authors: Rausch Philipp , Ratjen Ilka , Tittmann Lukas , Enderle Janna , Wacker Eike Matthias , Jaeger Kathrin , Ruehlemann Malte Christoph , Ellul Pierre , Kruse Robert , Halfvarsson Jonas , Roggenbuck Dirk , Ellinghaus David , Jacobs Gunnar , Krawczak Michael , Schreiber Stefan , Bang Corinna , Lieb Wolfgang , Franke Andre
Published: July 2024

Background: The prospective Kiel Inflammatory Bowel Disease (IBD) Family Cohort Study (KINDRED cohort) was initiated in 2013 to systematically and extensively collect data and biosamples from index IBD patients and their relatives (e.g., blood, stool), a population at high risk for IBD development. Regular follow-ups were conducted to collect updated health and lifestyle information, to obtain new biosamples, and to capture the incidence of IBD during development. By combining taxonomic and imputed functional microbial data collected at successive time points with extensive anthropometric, medical, nutritional, and social information, this study aimed to characterize the factors influencing the microbiota in health and disease via detailed ecological analyses. Results: Using two dysbiosis metrics (MD-index, GMHI) trained on the German KINDRED cohort, we identified strong and generalizable gradients within and across different IBD cohorts, which correspond strongly with IBD pathologies, physiological manifestations of inflammation (e.g., Bristol stool score, ASCA IgA/IgG), genetic risk for IBD, and general risk of disease onset. Anthropometric and medical factors influencing transit time strongly modify bacterial communities. Various Enterobacteriaceae (e.g., Klebsiella sp.) and opportunistic Clostridia pathogens (e.g., C. XIVa clostridioforme), characterize in combination with ectopic oral taxa (e.g. Veillonella sp., Cand. Saccharibacteria sp., Fusobacterium nucleatum) the distinct and chaotic IBD-specific communities. Functionally, amino acid metabolism and flagellar assembly are beneficial, while mucolytic functions are associated with IBD. Conclusions: Our findings demonstrate broad-scale ecological patterns which indicate drastic state transitions of communities into characteristically chaotic communities in IBD patients. These patterns appear to be universal across cohorts and influence physiological signs of inflammation, display high resilience, but show only little heritability/intrafamily transmission.
Distinct Plasma Protein Profiles Distinguish Faster from Slower Disease Progression in HIV-1 and HIV-2 infections
Authors: Johansson Emil , Nazziwa Jamirah , Freyhult Eva , Hong Mun-Gwan , Neptin Malin , Karlson Sara , Rezeli Melinda , da Silva Zacarias J. , Biague Antonio J. , Lindman Jacob , Palm Angelica , Medstrand Patrik , Månsson Fredrik , Norrgren Hans , Jansson Marianne , Esbjörnsson Joakim ,   the SWEGUB CORE group
Published: July 2024

The asymptomatic disease stage in HIV-2 infection is approximately twice as long compared to in HIV-1 infection, still the majority of HIV-2 infected individuals progress to AIDS in the absence of antiretroviral treatment. In this study, we applied data-independent acquisition mass spectrometry analysis of blood plasma samples collected from HIV negative, and HIV-1 or HIV-2 infected individuals in Guinea-Bissau with an estimated date of HIV infection, to explore associations between plasma proteome alterations and HIV disease progression. In total, 609 proteins were quantified and mapped towards publicly available data on tissue-enhanced genes, to provide insight on the tissue-specific origin of the detected proteins. Here we identified ten proteins that could differentiate between faster and slower HIV disease progression. The analysis also suggested a larger leakage of proteins from the sigmoid colon in HIV-1 compared to HIV-2 infection. Moreover, the levels of sigmoid colon and spleen tissue proteins were associated with disease progression among all HIV infected individuals. In conclusion, these results encourage further research on the role of both target and bystander cells in HIV disease progression.
Sex differences in circulating metabolites across glycemic status and risk of coronary heart disease
Authors: Yoshida Yilin , Li Danting , Li Xiang , Fonseca Vivian A. , Qi Lu , Mauvais-Jarvis Franck
Published: July 2024

Background

Women with type 2 diabetes (T2D) have a 50% excess risk of coronary heart disease (CHD) than men with T2D. We compared circulating metabolites and their associations with CHD in men and women across glycemic status.

Methods

We used metabolomic data (lipoproteins, fatty acids, amino acids, glycolysis, ketones, inflammation, and fluid balance) for 87,326 CHD-free UK Biobank participants. We used linear regressions to examine the association of sex and metabolites (log) in newly diagnosed T2D (diagnosis<2 yrs from baseline), prediabetes (A1c 5.7-6.5%), and euglycemia, accounting for age, race, Deprivation Index, income, smoking, alcohol drinking, obesity, physical activity, medications for hypertension, hyperlipidemia, and diabetes. We used Cox models to evaluate the association of metabolites and CHD risk by sex, adjusting the same covariates and menopausal status (women). All analyses were FDR-adjusted.

Findings

We included 1250 individuals with new T2D, 12,706 with prediabetes, and 83,315 with euglycemia. In adjusted linear regressions, women showed a progressive increase in atherogenic lipid and lipoprotein markers and inflammatory marker, glycoprotein acetyls, compared to men as their glycemic status advanced. However, women had lower levels of albumin during this transition. Menopausal status did not alter these sex differences. In a 10-year follow-up, an SD higher total TG, TG in VLDL, LDL, and HDL, saturated fatty acids (SFA) were positively associated with a higher risk of CHD in women with T2D but not in men (p-interactions 0.03-0.15).

Interpretation

With advancing glycemic status, women exhibited higher levels of atherogenic lipids and lipoproteins, as well as inflammatory markers, but lower circulating albumin. Women with T2D appear to be at a higher risk of CHD associated with TG, VLDL-TG, LDL-TG, and HDL-TG, and SFA than men with T2D.
Towards Treatment Effect Interpretability: A Bayesian Re-analysis of 194,129 Patient Outcomes Across 230 Oncology Trials
Authors: Sherry Alexander D. , Msaouel Pavlos , Kupferman Gabrielle S. , Lin Timothy A. , Jaoude Joseph Abi , Kouzy Ramez , El-Alam Molly B. , Patel Roshal , Koong Alex , Lin Christine , Passy Adina H. , Miller Avital M. , Beck Esther J. , Fuller C. David , Meirson Tomer , McCaw Zachary R. , Ludmir Ethan B.
Published: July 2024

Most oncology trials define superiority of an experimental therapy compared to a control therapy according to frequentist significance thresholds, which are widely misinterpreted. Posterior probability distributions computed by Bayesian inference may be more intuitive measures of uncertainty, particularly for measures of clinical benefit such as the minimum clinically important difference (MCID). Here, we manually reconstructed 194,129 individual patient-level outcomes across 230 phase III, superiority-design, oncology trials. Posteriors were calculated by Markov Chain Monte Carlo sampling using standard priors. All trials interpreted as positive had probabilities > 90% for marginal benefits (HR < 1). However, 38% of positive trials had ≤ 90% probabilities of achieving the MCID (HR < 0.8), even under an enthusiastic prior. A subgroup analysis of 82 trials that led to regulatory approval showed 30% had ≤ 90% probability for meeting the MCID under an enthusiastic prior. Conversely, 24% of negative trials had > 90% probability of achieving marginal benefits, even under a skeptical prior, including 12 trials with a primary endpoint of overall survival. Lastly, a phase III oncology-specific prior from a previous work, which uses published summary statistics rather than reconstructed data to compute posteriors, validated the individual patient-level data findings. Taken together, these results suggest that Bayesian models add considerable unique interpretative value to phase III oncology trials and provide a robust solution for overcoming the discrepancies between refuting the null hypothesis and obtaining a MCID.

SIGNIFICANCE STATEMENT

The statistical analyses of oncology trials are usually performed by calculatingPvalues, although these are poorly understood. UsingPvalue cutoffs, such asP< 0.05, may lead to some treatments being accepted which have little benefit, and other therapies being rejected which have considerable benefit. A more intuitive and direct probability— that an experimental treatment is better than a standard treatment—can be calculated by Bayesian statistics. Here we used software to obtain the outcomes of 194,129 patients enrolled across 230 trials and then calculated probabilities of benefit. Interpretations based onPvalues disagreed with the probabilities of benefit in one-third of trials. This study suggests that probabilities of benefit would considerably enhance the interpretation of oncology trials.
Laue-DIALS: open-source software for polychromatic X-ray diffraction data
Authors: Hewitt Rick A. , Dalton Kevin M. , Mendez Derek , Wang Harrison K. , Klureza Margaret A. , Brookner Dennis E. , Greisman Jack B. , McDonagh David , Šrajer Vukica , Sauter Nicholas K. , Brewster Aaron S. , Hekstra Doeke R.
Published: July 2024

Most X-ray sources are inherently polychromatic. Polychromatic (“pink”) X-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during exposure—ideal conditions for time-resolved applications. Analysis of such data is complicated, however, causing most X-ray facilities to discard>99% of X-ray photons to obtain monochromatic data. Key challenges in analyzing polychromatic diffraction data include lattice searching, indexing and wavelength assignment, correction of measured intensities for wavelength-dependent effects, and deconvolution of harmonics. We recently described an algorithm, Careless, that can perform harmonic deconvolution and correct measured intensities for variation in wavelength when presented with integrated diffraction intensities and assigned wavelengths. Here, we present Laue-DIALS, an open-source software pipeline that indexes and integrates polychromatic diffraction data. Laue-DIALS is based on the dxtbx toolbox, which supports the DIALS software commonly used to process monochromatic data. As such, Laue-DIALS provides many of the same advantages: an open-source, modular, and extensible architecture, providing a robust basis for future development. We present benchmark results showing that Laue-DIALS, together with Careless, provides a suitable approach to the analysis of polychromatic diffraction data, including for time-resolved applications.
Flexible Control of Motor Units: Is the Multidimensionality of Motor Unit Manifolds a Sufficient Condition?
Authors: Dernoncourt François , Avrillon Simon , Logtens Tijn , Cattagni Thomas , Farina Dario , Hug François
Published: July 2024

Understanding flexibility in the neural control of movement requires identifying the distribution of common inputs to the motor units. In this study, we identified large samples of motor units from two lower limb muscles: the vastus lateralis (VL; up to 60 motor units/participant) and the gastrocnemius medialis (GM; up to 67 motor units/participant). First, we applied a linear dimensionality reduction method to assess the dimensionality of the manifolds underlying the motor unit activity. We subsequently investigated the flexibility in motor unit control under two conditions: sinusoidal contractions with torque feedback, and online control with visual feedback on motor unit firing rates. Overall, we found that the activity of GM motor units was effectively captured by a single latent factor defining a unidimensional manifold, whereas the VL motor units were better represented by three latent factors defining a multidimensional manifold. Despite this difference in dimensionality, the recruitment of motor units in the two muscles exhibited similarly low levels of flexibility. Using a spiking network model, we tested the hypothesis that dimensionality derived from factorization does not solely represent descending cortical commands but is also influenced by spinal circuitry. We demonstrated that a heterogeneous distribution of inputs to motor units, or specific configurations of recurrent inhibitory circuits, could produce a multidimensional manifold. This study clarifies an important debated issue, demonstrating that while motor unit firings of a non-compartmentalised muscle can lie in a multidimensional manifold, the central nervous system may still have limited capacity for flexible control of these units.

Key points

To generate movement, the central nervous system distributes both excitatory and inhibitory inputs to the motor units.

The level of flexibility in the neural control of these motor units remains a topic of debate with significant implications for identifying the smallest unit of movement control.

By combining experimental data and in silico models, we demonstrated that the activity of a large sample of motor units from a single muscle can be represented by a multidimensional linear manifold; however, these units show very limited flexibility in their recruitment.

The dimensionality of the linear manifold may not directly reflect the dimensionality of descending inputs but could instead relate to the organisation of local spinal circuits.
Chimerism and altruism
Authors: Hitchcock Thomas J. , Patten Manus M.
Published: July 2024

Chimerism spans the tree of life, from mammals and corals to plants and fungi. In such organisms, individuals contain within them cells and genomes from another once distinct member of the population. This chimeric genetic composition may subsequently alter patterns of relatedness not only between those individuals, but also within them. Consequently, we may expect unique patterns of social behaviour in such species. To explore the social evolutionary consequences of chimerism, here we develop a kin-selection model of a structured population. First, we show how somatic and germline chimerism influence patterns of relatedness and play an important role in modulating social behaviour. Specifically, we find that increased heterogeneity of the soma relative to the germline boosts the opportunity for altruism between individuals. We then explore how differences in chimerism levels within the body may generate within-organism differences in the valuation of social partners and thus foment internal conflicts between tissues and organs. Finally, we show how differences in the development of male and female germlines in chimeras provides a novel source of relatedness asymmetry between maternal-origin and paternal-origin genes. Overall, we find that chimerism introduces additional opportunities for internal conflicts over the development of behavioural phenotypes, most of which have been unexplored by empiricists.
Evolutionary Origins of Self-sustained Kai Protein Circadian Oscillators
Authors: Mukaiyama Atsushi , Furuike Yoshihiko , Ito-Miwa Kumiko , Onoue Yasuhiro , Horiuchi Kota , Yamashita Eiki , Akiyama Shuji
Published: July 2024

Light–dark cycles affect photosynthetic efficiency in autotrophic cyanobacteria; therefore, determining whether ancient cyanobacteria possessed a self-sustained circadian clock when oxygenic photosynthetic systems were established is an important issue in chronobiology. Here we examined the oscillation of the clock protein KaiC in modern cyanobacteria, as well as the function and structure of ancestral Kai proteins, to determine the evolutionary origin of the self-sustained Kai-protein oscillators. The results show that the oldest double-domain KaiC in ancestral bacteria lacked the factors functionally and structurally essential for rhythmicity. The ancestral Kai proteins had acquired these factors through molecular evolution that occurred around Global Oxidation and Snowball Earth events, and were eventually inherited as a self-sustained circadian oscillator by the most recent common ancestor of cyanobacteria capable of oxygenic photosynthesis. This autonomous Kai protein oscillator was further inherited by most freshwater and marine cyanobacteria present today as an autotrophic basis for time-optimal acquisition and consumption of energy from oxygenic photosynthesis.
Novel Approach for Refractive Index Matching in Calcified Tissues
Authors: Laudier Damien , Mora-Antionette Macy , Garcia-Ortiz Andi , Lewis Karl J.
Published: July 2024

Tissue-clearing techniques have become indispensable in biomedical research, especially for three-dimensional (3D) imaging. These techniques enable the visualization of complex biological structures by rendering tissues transparent while preserving their structural integrity. Calcified tissues, such as bone and cartilage, pose a unique challenge in imaging studies due to their inherent opacity and rigidity. In this work, we introduce a novel modification to the BABB clearing protocol aimed at enhancing the clearing efficacy specifically for calcified tissues. Through this work, we provide an enhanced tissue-clearing method that addresses the specific challenges associated with calcified tissues. This advancement has the potential to facilitate more precise and comprehensive studies in fields such as developmental biology, orthopedics, and regenerative medicine.
Molecular and Mechanical Signatures Contributing to Epidermal Differentiation and Barrier Formation
Authors: Prado-Mantilla Alexandra , Ning Wenxiu , Lechler Terry
Published: July 2024

Formation of the skin barrier requires rapid proliferation coupled with differentiation and stratification of the embryonic epidermis. Basal progenitors give rise to progeny throughout development – first to intermediate cells, a transient proliferative suprabasal cell population, and later to spinous cells. Neither the function nor the differentiation trajectory of intermediate cells has been documented. We generated transcriptomes of intermediate and spinous cells and identified specific markers that distinguish these two populations. Further, we found that intermediate cells express a subset of genes in common with granular cells of the epidermis – the terminal living cell type that helps establish the barrier. Lineage tracing revealed that most intermediate cells directly transition to granular cells without expressing markers specific to spinous cells, thus revealing a distinct lineage pathway leading to granular fate. In addition to their transcriptional similarities, intermediate and granular cells both had hallmarks of increased actomyosin contractility. We found that rather than simply lying downstream of cell fate pathways, contractility was sufficient to suppress spinous fate and promote granular gene expression. Together, these data establish the molecular and mechanical characteristics of the developing epidermis that allow this tissue to rapidly develop barrier activity.
scRNA-seq identifies unique macrophage population in murine model of ozone induced asthma exacerbation
Authors: Ray Jess L. , Walum Joshua , Jelic Daria , Barnes Ryelie , Bentley Ian D. , Britt Rodney D. , Englert Joshua A. , Ballinger Megan N.
Published: July 2024

Ozone (O3) inhalation triggers asthmatic airway hyperresponsiveness (AHR), but the mechanisms by which this occurs are unknown. Previously, we developed a murine model of dust mite, ragweed, andaspergillus(DRA)-induced allergic lung inflammation followed by O3exposure for mechanistic investigation. The present study used single cell RNA-sequencing for unbiased profiling of immune cells within the lungs of mice exposed to DRA, O3, or DRA+O3, to identify the components of the immune cell niche that contribute to AHR. Alveolar macrophages (AMs) had the greatest number of differentially expressed genes following DRA+O3, most of which were unique to the 2-hit exposure. Following DRA+O3, AMs activated transcriptional pathways related to cholesterol biosynthesis, degradation of the extracellular matrix, endosomal TLR processing, and various cytokine signals. We also identified AM and monocyte subset populations that were unique to the DRA+O3group. These unique AMs activated gene pathways related to inflammation, sphingolipid metabolism, and bronchial constriction. The unique monocyte population had a gene signature that suggested phospholipase activation and increased degradation of the extracellular matrix. Flow cytometry analysis of BAL immune cells showed recruited monocyte-derived AMs after DRA and DRA+O3, but not after O3exposure alone. O3alone increased BAL neutrophils but this response was attenuated in DRA+O3mice. DRA-induced changes in the airspace immune cell profile were reflected in elevated BAL cytokine/chemokine levels following DRA+O3compared to O3alone. The present work highlights the role of monocytes and AMs in the response to O3and suggests that the presence of distinct subpopulations following allergic inflammation may contribute to O3-induced AHR.
Site-specific metabolic labeling reveals proteome-wide phospho-dynamics
Authors: Alevra Mihai , Correa Marrero Miguel , Kluever Verena , Mandad Sunit , Hemandhar-Kumar Nisha , Pan Kuan-Ting , van Gerwen Julian , Glowacki Selda Kabatas , Wildhagen Hanna , Ischebeck Till , Liu Yansheng , Rizzoli Silvio O. , Urlaub Henning , Beltrao Pedro , Fornasiero Eugenio F.
Published: July 2024

Protein phosphorylation is a critical post-translational modification that orchestrates cellular signaling. Here, we introduce PulsPhos, a method combining metabolic labeling with phosphoproteomics, spectral analysis and modeling, to quantify site-specific phosphorylation lifetimes in living cells. Phosphosite lifetimes vary over multiple orders of magnitude and are influenced by factors such as amino acid composition and subcellular localization. PulsPhos was readily applied to pharmacological perturbations revealing fundamental mechanisms governing protein phosphorylation dynamics.
Evidence for biomolecular condensates of MatP in spatiotemporal regulation of the bacterial cell division cycle
Authors: Barros-Medina Inés , Robles-Ramos Miguel Ángel , Sobrinos-Sanguino Marta , Luque-Ortega Juan Román , Alfonso Carlos , Margolin William , Rivas Germán , Monterroso Begoña , Zorrilla Silvia
Published: July 2024

An increasing number of proteins involved in bacterial cell cycle events have been recently shown to undergo phase separation. The resulting biomolecular condensates play an important role in cell cycle protein function and may be involved in development of persister cells tolerant to antibiotics. Here we report that theE. colichromosomal Ter macrodomain organizer MatP, a division site selection protein implicated in the coordination of chromosome segregation with cell division, forms biomolecular condensates in cytomimetic systems. These condensates are favored by crowding and preferentially localize at the membrane of microfluidics droplets, a behavior probably mediated by MatP-lipid binding. Condensates are negatively regulated and partially dislodged from the membrane by DNA sequences recognized by MatP (matS), which partition into them. Unexpectedly, MatP condensation is enhanced by FtsZ, a core component of the division machinery previously described to undergo phase separation. Our biophysical analyses uncover a direct interaction between the two proteins, disrupted bymatSsequences. This binding might have implications for FtsZ ring positioning at mid-cell by the Ter linkage, which comprises MatP and two other proteins that bridge the canonical MatP/FtsZ interaction. FtsZ/MatP condensates interconvert with bundles in response to GTP addition, providing additional levels of regulation. Consistent with discrete foci reported in cells, MatP biomolecular condensates may facilitate MatP’s role in chromosome organization and spatiotemporal regulation of cytokinesis and DNA segregation. Moreover, sequestration of MatP in these membraneless compartments, with or without FtsZ, could promote cell entry into dormant states that are able to survive antibiotic treatments.
Xist RNA binds select autosomal genes and depends on Repeat B to regulate their expression
Authors: Yao Shengze , Jeon Yesu , Kesner Barry , Lee Jeannie T
Published: July 2024

Xist, a pivotal player in X chromosome inactivation (XCI), has long been perceived as a cis-acting long noncoding RNA that binds exclusively to the inactive X chromosome (Xi). However, Xists ability to diffuse under select circumstances has also been documented, leading us to suspect that Xist RNA may have targets and functions beyond the Xi. Here, using female mouse embryonic stem cells (ES) and mouse embryonic fibroblasts (MEF) as models, we demonstrate that Xist RNA indeed can localize beyond the Xi. However, its binding is limited to approximately 100 genes in cells undergoing XCI (ES cells) and in post-XCI cells (MEFs). The target genes are diverse in function but are unified by their active chromatin status. Xist binds discretely to promoters of target genes in neighborhoods relatively depleted for Polycomb marks, contrasting with the broad, Polycomb-enriched domains reported for human XIST RNA. We find that Xist binding is associated with down-modulation of autosomal gene expression. However, unlike on the Xi, Xist binding does not lead to full silencing and also does not spread beyond the target gene. Over-expressing Xist in transgenic ES cells similarly leads to autosomal gene suppression, while deleting Xists Repeat B motif reduces autosomal binding and perturbs autosomal down-regulation. Furthermore, treating female ES cells with the Xist inhibitor, X1, leads to loss of autosomal suppression. Altogether, our findings reveal that Xist targets ~100 genes beyond the Xi, identify Repeat B as a crucial domain for its in-trans function in mice, and indicate that autosomal targeting can be disrupted by a small molecule inhibitor.
Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings
Authors: Lei Chon Lok , Clark Alexander P. , Clerx Michael , Wei Siyu , Bloothooft Meye , de Boer Teun P. , Christini David J. , Krogh-Madsen Trine , Mirams Gary R.
Published: July 2024

Cellular electrophysiology is the foundation of many fields, from basic science in neurology, cardiology, oncology to safety critical applications for drug safety testing, clinical phenotyping, etc. Patch-clamp voltage clamp is the gold standard technique for studying cellular electrophysiology. Yet, the quality of these experiments is not always transparent, which may lead to erroneous conclusions for studies and applications. Here, we have developed a new computational approach that allows us to explain and predict the experimental artefacts in voltage-clamp experiments. The computational model captures the experimental procedure and its inadequacies, including: voltage offset, series resistance, membrane capacitance and (imperfect) amplifier compensations, such as series resistance compensation and supercharging. The computational model was validated through a series of electrical model cell experiments. Using this computational approach, the artefacts in voltage-clamp experiments of cardiac fast sodium current, one of the most challenging currents to voltage clamp, were able to be resolved and explained through coupling the observed current and the simulated membrane voltage, including some typically observed shifts and delays in the recorded currents. We further demonstrated that the typical way of averaging data for current-voltage relationships would lead to biases in the peak current and shifts in the peak voltage, and such biases can be in the same order of magnitude as those differences reported for disease-causing mutations. Therefore, the presented new computational pipeline will provide a new standard of assessing the voltage-clamp experiments and interpreting the experimental data, which may be able to rectify and provide a better understanding of ion channel mutations and other related applications.
The dynamic crosstalk between cytoskeletal filaments regulates the cytoplasmic mechanics across the apicobasal axis
Authors: Ray Dipanjan , Sinha Deepak Kumar
Published: July 2024

The cytoplasm exhibits viscoelastic properties, displaying both solid and liquid-like behavior, and can actively regulate its mechanical attributes. The cytoskeleton is a major regulator among the numerous factors influencing cytoplasmic mechanics. We explore the interdependence of various cytoskeletal filaments and the impact of their density on cytoplasmic viscoelasticity. The heterogeneous distribution of these filaments give rise to polarised mechanical properties of the cytoplasm along the apicobasal axis. Actin filament (F-actin) disassembly softens the basal cytoplasm while stiffening the mid-cytoplasm due to increased vimentin filament assembly. Disruption of microtubules (MT) or depletion of vimentin softens both the basal and mid-cytoplasm. Cyto D treatment results in localised increase of vimentin assembly in the mid cytoplasm which is dependent on the cytolinker plectin. Nocodazole treatment has a negligible effect on F-actin distribution but significantly alters vimentin’s spatial arrangement. We demonstrate that Cyto D treatment upregulates vimentin expression via ROS-mediated activation of NF-κΒ. This manuscript investigates how different cytoskeletal filaments influence the rheological characteristics of various cytoplasmic regions.