bluuebunny/crossref_metadata_2025 huggingface dataset:
Scalable Risk Stratification for Heart Failure Using Artificial Intelligence applied to 12-lead Electrocardiographic Images: A Multinational Study
Authors: Dhingra Lovedeep S , Aminorroaya Arya , Sangha Veer , Camargos Aline Pedroso , Asselbergs Folkert W , Brant Luisa CC , Barreto Sandhi M , Ribeiro Antonio Luiz P , Krumholz Harlan M , Oikonomou Evangelos K , Khera Rohan
Published: April 2024

Background

Current risk stratification strategies for heart failure (HF) risk require either specific blood-based biomarkers or comprehensive clinical evaluation. In this study, we evaluated the use of artificial intelligence (AI) applied to images of electrocardiograms (ECGs) to predict HF risk.

Methods

Across multinational longitudinal cohorts in the integrated Yale New Haven Health System (YNHHS) and in population-based UK Biobank (UKB) and Brazilian Longitudinal Study of Adult Health (ELSA-Brasil), we identified individuals without HF at baseline. Incident HF was defined based on the first occurrence of an HF hospitalization. We evaluated an AI-ECG model that defines the cross-sectional probability of left ventricular dysfunction from a single image of a 12-lead ECG and its association with incident HF. We accounted for the competing risk of death using the Fine-Gray subdistribution model and evaluated the discrimination using Harrel’s c-statistic. The pooled cohort equations to prevent HF (PCP-HF) were used as a comparator for estimating incident HF risk.

Results

Among 231,285 individuals at YNHHS, 4472 had a primary HF hospitalization over 4.5 years (IQR 2.5-6.6) of follow-up. In UKB and ELSA-Brasil, among 42,741 and 13,454 people, 46 and 31 developed HF over a follow-up of 3.1 (2.1-4.5) and 4.2 (3.7-4.5) years, respectively. A positive AI-ECG screen portended a 4-fold higher risk of incident HF among YNHHS patients (age-, sex-adjusted HR [aHR] 3.88 [95% CI, 3.63-4.14]). In UKB and ELSA-Brasil, a positive-screen ECG portended 13- and 24-fold higher hazard of incident HF, respectively (aHR: UKBB, 12.85 [6.87-24.02]; ELSA-Brasil, 23.50 [11.09-49.81]). The association was consistent after accounting for comorbidities and the competing risk of death. Higher model output probabilities were progressively associated with a higher risk for HF. The model’s discrimination for incident HF was 0.718 in YNHHS, 0.769 in UKB, and 0.810 in ELSA-Brasil. Across cohorts, incorporating model probability with PCP-HF yielded a significant improvement in discrimination over PCP-HF alone.

Conclusions

An AI model applied to images of 12-lead ECGs can identify those at elevated risk of HF across multinational cohorts. As a digital biomarker of HF risk that requires just an ECG image, this AI-ECG approach can enable scalable and efficient screening for HF risk.
Cryo-EM insight into hydrogen positions and water networks in photosystem II
Authors: Hussein Rana , Graça André , Forsman Jack , Aydin A. Orkun , Hall Michael , Gaetcke Julia , Chernev Petko , Wendler Petra , Dobbek Holger , Messinger Johannes , Zouni Athina , Schröder Wolfgang P.
Published: April 2024

Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thereby sustains life on Earth. It catalyzes two chemical reactions, plastoquinone reduction and water oxidation to molecular oxygen, which both are performed at sequestered sites. While it is known that proton-coupled electron transfer is crucial for these processes, the molecular details have remained speculative due to incomplete structural data. Thus, we collected high-resolution cryo-EM data of photosystem II fromThermosynechococcus vestitus. The advanced structure (1.71 Å) reveals several previously unditected occupied water binding sites and more than half of the hydrogen and proton positions of the protein. This unprecedented insight into the structure of photosystem II significantly enhances our understanding of its intricate protein-water-cofactor interactions enabling solar-driven catalysis.

One sentence summary

Cryo-EM structure of PSII at 1.71 Å resolution reveals over 50% of hydrogen and proton sites and additional water binding sites, aiding catalytic insight.
Functional recruitment and connectivity of the cerebellum supports the emergence of Theory of Mind in early childhood
Authors: Manoli Aikaterina , Van Overwalle Frank , Grosse Wiesmann Charlotte , Valk Sofie L.
Published: April 2024

There is accumulating evidence that the human cerebellum is heavily implicated in adult social cognition. Yet, its involvement in the development of Theory of Mind (ToM), a hallmark of social cognition, remains elusive. In a functional MRI study involving children with emerging ToM abilities (N=41, age range: 3-12 years) and adults (N=78), we showed that children with ToM abilities activated cerebellar Crus I-II in response to ToM events during a movie-watching task, similar to adults. This activation was absent in children lacking ToM abilities. Functional connectivity profiles between cerebellar and cerebral ToM regions differed as a function of children’s ToM abilities. Notably, task-driven connectivity shifted from upstream to downstream connections between cerebellar and cerebral ToM regions from childhood to adulthood. Greater dependence on connections emerging from the cerebellum early in life suggests an important role of the cerebellum in establishing the cognitive processes underlying ToM in childhood and thus for the undisrupted development of social cognition.
Potassium rhythms couple the circadian clock to the cell cycle
Authors: Gil Rodríguez Sergio , Crosby Priya , Hansen Louise L. , Grünewald Ellen , Beale Andrew D. , Spangler Rebecca K. , Rabbitts Beverley M. , Partch Carrie L. , Stangherlin Alessandra , O’Neill John S. , van Ooijen Gerben
Published: April 2024

Circadian (∼24 h) rhythms are a fundamental feature of life, and their disruption increases the risk of infectious diseases, metabolic disorders, and cancer1–6. Circadian rhythms couple to the cell cycle across eukaryotes7,8but the underlying mechanism is unknown. We previously identified an evolutionarily conserved circadian oscillation in intracellular potassium concentration, [K+]i9,10. As critical events in the cell cycle are regulated by intracellular potassium11,12, an enticing hypothesis is that circadian rhythms in [K+]iform the basis of this coupling. We used a minimal model cell, the algaOstreococcus tauri,to uncover the role of potassium in linking these two cycles. We found direct reciprocal feedback between [K+]iand circadian gene expression. Inhibition of proliferation by manipulating potassium rhythms was dependent on the phase of the circadian cycle. Furthermore, we observed a total inhibition of cell proliferation when circadian gene expression is inhibited. Strikingly, under these conditions a sudden enforced gradient of extracellular potassium was sufficient to induce a round of cell division. Finally, we provide evidence that interactions between potassium and circadian rhythms also influence proliferation in mammalian cells. These results establish circadian regulation of intracellular potassium levels as a primary factor coupling the cell- and circadian cycles across diverse organisms.
LASSO Based Analysis for Prediction of Prognostic Signature Genes Associated with Breast Cancer
Authors: Guha Souvik
Published: April 2024

Background

Cancer is a genetic disease, where gene alterations play a significant role in the disease onset and pathogenesis. Analysis of the underlying gene interaction pathways could reveal new biomarkers and could also potentially help in the development of targeted drugs for therapeutics. Microarray techniques have emerged as powerful tools capable of simultaneously measuring the expression levels of thousands of genes, making them invaluable in cancer biology research. However, the processing of the resultant datasets poses significant challenges due to their high dimensionality. Also, feature extraction becomes essential to discern the crucial features within these extensive datasets. To mitigate these difficulties advanced computational techniques like Machine Learning (ML) could be instrumental. LASSO-regression-based classification is an advanced ML technique that can help in feature selection by evaluating individual parameters like genes.

Methods

This study focuses on uncovering key prognostic genes for breast cancer using a combination of LASSO regression-based classifier and statistical bioinformatics models. Differentially expressed genes (DEGs) were identified using the “Limma” package in R, and significant genes were further filtered using the LASSO-based classifier significance coefficient. Genes common to both methods were considered as the focus of this study. Additionally, Protein-Protein Interaction (PPI) networks of these key genes were constructed using STRING, and hub genes, significant modules, and associated genes were identified using Cytoscape.

Results

This study identified CCR8, CXCL11, CCL23, CCL24, CCL28, and CCL21 as signature prognostic genes for breast cancer, revealing a strong association between chemokines and breast cancer pathogenesis. Extensive literature searches were conducted to validate and confirm their prognostic significance in the disease.

Conclusion

These findings are pivotal for enhancing our comprehension of the pathways involved in breast cancer. Additionally, they hold promise as novel biomarkers for diagnostic purposes and may also reveal significant therapeutic targets for the management of breast cancer.
BEAN and HABAS: Polyphyletic insertions in RNAP that point to deep-time evolutionary divergence of bacteria
Authors: Alvarez-Carreño Claudia , Huynh Angela T. , Petrov Anton S. , Orengo Christine , Williams Loren Dean
Published: April 2024

The β and β’ subunits of the RNA polymerase (RNAP) are large proteins with complex multi-domain architectures that include several insertional domains. Here, we analyze the multi-domain organizations of bacterial RNAP-β and RNAP-β’ using sequence, experimentally determined structures and AlphaFold structure predictions. We observe that bacterial lineage-specific domains in RNAP-β belong to a group of domains that we call BEAN (Broadly Embedded ANnex) and that in RNAP-β’, bacterial lineage-specific domains are HAmmerhead/BArrel-Sandwich Hybrid (HABAS) domains. The BEAN domain has a characteristic three-dimensional structure composed of two square bracket-like elements that are antiparallel relative to each other. The HABAS domain contains a four-stranded open β-sheet with a GD-box-like motif in one of the β-strands and the adjoining loop. The BEAN domain is identified not only in the bacterial RNAP-β’, but also in the archaeal version of universal ribosomal protein L10. The HABAS domain is observed as an insertional domain in several metabolic proteins. The phylogenetic distributions of bacterial lineage-specific insertional domains of β and β’ subunits of RNAP follow the Tree of Life. The presence of insertional domains can help establish a relative timeline of events in the evolution of a protein because insertion is inferred to post-date the base domain. We discuss mechanisms that might account for the discovery of homologous insertional domains in non-equivalent locations in bacteria and archaea.
Proteomic Assessment of SKBR3/HER2+ Breast Cancer Cellular Response to Lapatinib and Investigational Ipatasertib Kinase Inhibitors
Authors: Karcini Arba , Mercier Nicole R. , Lazar Iulia M.
Published: April 2024

Modern cancer treatment approaches aim at achieving cancer remission by using targeted and personalized therapies, as well as harnessing the power of the immune system to recognize and eliminate the cancer cells. To overcome a relatively short-lived response due to the development of resistance to the administered drugs, combination therapies have been pursued, as well. To expand the outlook of combination therapies, the objective of this study was to use high-throughput data generation technologies such as mass spectrometry and proteomics to investigate the response of HER2+ breast cancer cells to a mixture of two kinase inhibitors that has not been adopted yet as a standard treatment regime. The broader landscape of biological processes that are affected by inhibiting two major pathways that sustain the growth and survival of cancer cells, i.e., EGFR and PI3K/AKT, was investigated by treating SKBR3/HER2+ breast cancer cells with Lapatinib or a mixture of Lapatinib/Ipatasertib small molecule drugs. Changes in protein expression and/or activity in response to the drug treatments were assessed by using two complementary quantitative proteomic approaches based on peak area and peptide spectrum match measurements. Over 900 proteins matched by three unique peptide sequences (FDR<0.05) were affected by the exposure of cells to the drugs. The work corroborated the anti-proliferative activity of Lapatinib and Ipatasertib, and, in addition to cell cycle and growth arrest processes enabled the identification of several multi-functional proteins with roles in cancer-supportive hallmark processes. Among these, immune response, adhesion and migration emerged as particularly relevant to the ability to effectively suppress the proliferation and dissemination of cancer cells. The supplementation of Lapatinib with Ipatasertib further affected the expression or activity of additional transcription factors and proteins involved in gene expression, trafficking, DNA repair, and development of multidrug resistance. Furthermore, over fifty of the affected proteins represented approved or investigational targets in the DrugBank database, which through their protein-protein interaction networks can inform the selection of effective therapeutic partners. Altogether, our findings exposed a broad plethora of yet untapped opportunities that can be further explored for enhancing the anti-cancer effects of each drug as well as of many other multi-drug therapies that target the EGFR/ERBB2 and PI3K/AKT pathways. The data are available via ProteomeXchange with identifier PXD051094.
Molecular Identification ofEchinococcusspp. and other Taeniid Tapeworms Using Next Generation Sequence Analysis of PCR Amplified 18s rRNA gene
Authors: Abu-Helu Rasmi , Kokaly George , Nojoum Sajeda , Matouk Imad , Ibrahim Murad , Abbasi Ibrahim
Published: April 2024

Cystic echinococcosis (CE) is a prevalent zoonotic disease caused by Echinococcus granulosus, with cosmopolitan distribution. The parasite is transmitted cyclically between canines and numerous intermediate herbivorous livestock animals. Also other taeniid tapeworm could infect domestic dogs and they pose significant veterinary and public health concerns worldwide. This study aimed to develop a sensitive molecular method for detecting Echinococcus spp. DNA in dog fecal samples using next-generation sequencing (NGS). A set of PCR primers targeting conserved regions of Taeniid tapeworms’ 18s rRNA genes was designed and tested for amplifying genomic DNA from various tapeworm species. The PCR system demonstrated high sensitivity, amplifying DNA from all tested tapeworm species, with differences observed in amplified band sizes. The primers were adapted for NGS analysis by adding forward and reverse adapters, enabling sequencing of amplified DNA fragments. Application of the developed PCR system to dog fecal samples collected from Yatta town, Palestine, revealed the presence ofE. granulosusDNA in five out of 50 samples. NGS analysis confirmed the specificity of the amplified DNA fragments, showing 98-99% similarity with the 18s rDNA gene ofE. granulosus. This study demonstrates the utility of NGS-based molecular methods for accurate and sensitive detection of Echinococcus spp. in dog fecal samples, providing valuable insights for epidemiological surveillance and control programs of echinococcosis in endemic regions.

Author Summary

Cystic echinococcosis, or hydatidosis, is a serious and chronic zoonotic disease in humans caused by the dog tapewormEchinococcus granulosus. The disease is transmitted cyclically between canines and numerous herbivorous livestock animals. DeterminingE. granulosusinfection in dogs is crucial for assessing infection risk and identifying new foci of active infections. The infection rate in dogs is also necessary for evaluating transmission dynamics and assessing the efficacy of control programs. In this study, we present a PCR system based on amplification of the 18S rDNA. New primers were designed following an alignment of various taeniid tapeworms’ 18S rDNA sequences. The current PCR system was adapted to be used in amplicon sequencing utilizing next-generation sequencing technology. This strategy enables accurate detection of tapeworm DNA extracted from dogs’ fecal samples and provides quantitative measurement of taeniid infection in dogs.
A large-scale and long-term experiment to identify effectiveness of ecosystem restoration
Authors: Elo Merja , Kareksela Santtu , Ovaskainen Otso , Abrego Nerea , Niku Jenni , Taskinen Sara , Aapala Kaisu , Kotiaho Janne S.
Published: April 2024

Ecosystem restoration will increase following the ambitious international targets, which calls for a rigorous evaluation of restoration effectiveness. Studies addressing restoration effectiveness across ecosystems have thus far shown varying and unpredictable patterns. A rigorous assessment of the factors influencing restoration effectiveness is best done with large-scale and long-term experimental data. Here, we present results from a well replicated long-term before-after control-impact experiment on restoration of forestry-drained boreal peatland ecosystems. Our data comprise 151 sites, representing six ecosystem types. Vegetation sampling has been conducted to the species level before restoration and two, five and ten years after restoration. We show that, on average, restoration stops and reverses the trend of further degradation. The variation in restoration outcomes largely arises from ecosystem types: restoration of nutrient-poor ecosystems has higher probability of failure. Our experiment provides clear evidence that restoration can be effective in halting the biodiversity loss of degraded ecosystems, although ecosystem attributes can affect the restoration outcome. These findings underlie the need for evidence-based prioritization of restoration efforts across ecosystems.
Time-based shifts in xylem vulnerability curves of angiosperms based on the flow-centrifuge method
Authors: Silva Luciano M. , Pfaff Jonas , Pereira Luciano , Miranda Marcela T. , Jansen Steven
Published: April 2024

Centrifuges provide a fast and standard approach to quantify embolism resistance of xylem in vulnerability curves (VCs). Traditionally, embolism formation in centrifuge experiments is assumingly driven by centrifuge speed, and thus pressure, but unaffected by spin time. Here, we explore to what extent embolism resistance is not only pressure but also spin time dependent, and hypothesise that time-stable hydraulic conductivity (Kh) values could shift VCs. We quantified time-based shifts in flow- centrifuge VCs and their parameter estimations for six angiosperm species by measuring Khat regular intervals over 15 minutes of spinning at a particular speed before a higher speed was applied to the same sample. We compared various VCs per sample based on cumulative spin time, and modelled the relationship between Kh, xylem water potential (Ψ), and spin time. Time-based changes of Khshowed considerable increases and decreases at low and high centrifuge speeds, respectively, which generally shifted VCs towards more positive Ψ values. Values corresponding to 50% loss of hydraulic conductivity (P50) increased up to 0.72 MPa inAcer pseudoplatanus, and on average by 8.5% for all six species compared to VCs that did not consider spin time. By employing an asymptotic exponential model, we estimated time-stable Kh, which improved the statistical significance of VCs in 5 of the 6 species studied. This model also revealed the instability of VCs at short spin times, and showed that embolism formation in flow-centrifuges followed a saturating exponential growth curve. Although pressure remains the major determinant of embolism formation, spin time should be considered in flow- centrifuge VCs to avoid overestimation of embolism resistance. This spin-time artefact is species- specific, and likely based on relatively slow gas diffusion associated with embolism spreading. It can be minimized by determining time-stable Khvalues for each centrifuge speed, without considerably extending the experimental time to construct VCs.
Mid-infrared photoacoustic brain imaging enabled by cascaded gas-filled hollow-core fiber lasers
Authors: Zhang Cuiling , Sui Kunyang , Meneghetti Marcello , Antonio-Lopez Jose Enrique , Dasa Manoj K. , Berg Rune W. , Amezcua-Correa Rodrigo , Wang Yazhou , Markos Christos
Published: April 2024

Significance

Extending the photoacoustic microscopy (PAM) into the mid-infrared (MIR) molecular fingerprint region constitutes a promising route towards label-free imaging of biological molecular structures. Realizing this objective requires a high-energy nano-second MIR laser source. However, existing MIR laser technologies are limited to either low pulse energy or free-space structure which is sensitive to environmental conditions. Fiber lasers are promising technologies for PAM for their potential of offering both high pulse energy and robust performance against environmental conditions. However, MIR high energy fiber laser has not yet been used for PAM because it is still at the infant research stage.

Aim

We aim to employ the emerging gas-filled anti-resonant hollow-core fiber (ARHCF) laser technology for MIR-PAM for the purpose of imaging myelin-rich regions in a mouse brain.

Approach

This laser source is developed with a ∼2.75 μJ high-pulse-energy nano-second laser at 3.4 μm, targeting the main absorption band of myelin sheaths, the primary chemical component of axons in the central nervous system. The laser mechanism relies on two-orders gas-induced vibrational stimulated Raman scattering (SRS) for nonlinear wavelength conversion, starting from a 1060 nm pump laser to 1409 nm through the 1storder Stokes generation in the nitrogen-filled 1ststage ARHCF, then, from 1409 nm to 3.4 μm through the 2ndstage hydrogen-filled ARHCF.

Results

The developed Raman laser was used for the first time for transmission-mode MIR-PAM of mouse brain regions containing rich myelin structures.

Conclusions

This work pioneers the potential use of high-energy and nano-second gas-filled ARHCF laser source to MIR-PAM, with a first attempt to report this kind of fiber laser source for PAM of lipid-rich myelin regions in a mouse brain. The proposed ARHCF laser technology is also expected to generate high-energy pulses at the ultraviolet (UV) region, which can significantly improve the lateral resolution of the PAM.
Recombinant Human TSH Fails to Induce the Proliferation and Migration of Papillary Thyroid Carcinoma Cell Lines
Authors: Kalampounias Georgios , Varemmenou Athina , Aronis Christos , Mamali Irene , Shaukat Athanasios-Nasir , Chartoumpekis Dionysios V , Katsoris Panagiotis , Michalaki Marina
Published: April 2024

Thyrotropin (TSH) suppression is required in the management of patients with papillary thyroid carcinoma (PTC) to improve their outcomes, inevitably causing iatrogenic thyrotoxicosis. Nevertheless, the evidence supporting this practice remains limited and weak, andin vitrostudies examining the mitogenic effects of TSH in cancerous cells used supraphysiological doses of bovine TSH, which produced conflicting results. Our study explores for the first time the impact of human recombinant thyrotropin (rh-TSH) on human PTC cell lines (K1 and TPC-1) that were transformed to overexpress the thyrotropin receptor (TSHR). The cells were treated with escalating doses of rh-TSH under various conditions, such as the presence or absence of insulin. The expression levels ofTSHRandthyroglobulin(Tg) were determined, and subsequently, the proliferation and migration of both transformed and non-transformed cells were assessed. Under the conditions employed, rh-TSH was not adequate to induce either the proliferation or the migration rate of the cells, whileTgexpression was increased. Our experiments indicate that clinically relevant concentrations of rh-TSH cannot induce proliferation and migration in PTC cell lines, even after overexpression of TSHR. Further research is warranted to dissect the underlying molecular mechanisms, and these results could translate into better management of PTC patients.
Chromosome-scale genome assembly the tropical abalone (Haliotis asinina)
Authors: Barkan Roy , Cooke Ira R , Watson Sue-Ann , Lau Sally C. Y. , Strugnell Jan M
Published: April 2024

Abalone (family Haliotidae) are an ecologically and economically significant group of marine gastropods that can be found in tropical and temperate waters. To date, only a fewHaliotisgenomes are available, all belonging to temperate species. Here, we provide the first reference genome of the tropical abaloneHaliotis asinina. The combination of PacBio long-read HiFi sequencing and Dovetail Omni-C sequencing allowed the chromosome-level assembly of this genome, while PacBio Isoform sequencing across five tissue types enabled the construction of high-quality gene models. This assembly resulted in 16 pseudo-chromosomes spanning over 1.12 Gb (98.1% of total scaffolds length), N50 of 67.09 Mb, the longest scaffold length of 105.96 Mb, and a BUSCO completeness score of 97.6%. This study identified 25,422 protein-coding genes and 61,149 transcripts. In an era of climate change and ocean warming, this genome of a heat-tolerant species can be used for comparative genomics with a focus on thermal resistance. This high-quality reference genome ofH. asininais a valuable resource for aquaculture, fisheries, and ecological studies.
Rat Anterior Insula Symmetrically Represents Tickling-Induced Playful Emotions
Authors: Dagher Sarah , Ishiyama Shimpei
Published: April 2024

Social play, an integral aspect of animal behavior, is inherently associated with positive emotions, yet the neuronal underpinnings of these playful states remain inadequately explored. We examined the anterior insula’s involvement in processing tickle-induced playful emotions in rats. Our findings revealed diverse patterns of insular activity during tickling, with 20% of the recorded units displaying strong activation, and another 20% exhibiting inhibition. These units responded similarly to other playful contexts, such as gentle touch and hand chase, but not to neutral locomotion. Tickle-activated units demonstrated a positive correlation of firing rates with appetitive vocalization rates, whereas tickle-inhibited units showed a negative correlation. Distinct spike waveforms were associated with the tickle response patterns, suggesting potential cell-type dependencies. However, pharmacological manipulation of the global anterior insula did not yield observable effects on play behavior in rats. Anterograde tracing revealed extensive insular projections to areas including the amygdala and nucleus accumbens. Taken together, our findings suggest that the anterior insula symmetrically represents tickle-induced playful emotional states.
Dynamic Tracking of Native Precursors in Adult Mice
Authors: Liu Suying , Adams Sarah E. , Zheng Haotian , Ehnot Juliana , Jung Seul K. , Jeffrey Greer , Menna Theresa , Purton Louise E. , Lee Hongzhe , Kurre Peter
Published: April 2024

Hematopoietic dysfunction has been associated with a reduction in the number of active precursors. However, precursor quantification at homeostasis and under diseased conditions is constrained by the scarcity of available methods. To address this issue, we optimized a method for quantifying a wide range of hematopoietic precursors. Assuming the random induction of a stable label in precursors following a binomial distribution, estimates depend on the inverse correlation between precursor numbers and the variance of precursor labeling among independent samples. Experimentally validated to cover the full dynamic range of hematopoietic precursors in mice (1 to 105), we utilized this approach to demonstrate that thousands of precursors, which emerge after modest expansion during fetal-to-adult transition, contribute to native and perturbed hematopoiesis. We further estimated the number of precursors in a mouse model of Fanconi Anemia, showcasing how repopulation deficits can be classified as autologous (cell proliferation) and non-autologous (lack of precursor). Our results support an accessible and reliable approach for precursor quantification, emphasizing the contemporary perspective that native hematopoiesis is highly polyclonal.
Biomaterial Scaffold Stiffness Influences the Foreign Body Reaction, Tissue Stiffness, Angiogenesis and Neuroregeneration in Spinal Cord Injury
Authors: Zheng Yifeng , Nützl Maximilian , Schackel Thomas , Chen Jing , Weidner Norbert , Müller Rainer , Puttagunta Radhika
Published: April 2024

Biomaterial scaffold engineering presents great potential in promoting axonal regrowth after spinal cord injury (SCI), yet persistent challenges remain, including the surrounding host foreign body reaction and improper host-implant integration. Recent advances in mechanobiology spark interest in optimizing the mechanical properties of biomaterial scaffolds to alleviate the foreign body reaction and facilitate seamless integration. The impact of scaffold stiffness on injured spinal cords has not been thoroughly investigated. Herein, we introduce stiffness-varied alginate anisotropic capillary hydrogel scaffolds implanted into adult rat C5 spinal cords post-lateral hemisection. Four weeks post-implantation, scaffolds with a stiffness approaching that of the spinal cord effectively minimize the host foreign body reaction via yes-associated protein (YAP) nuclear translocation. Concurrently, the softest scaffolds maximize cell infiltration and angiogenesis, fostering significant axonal regrowth but limiting the rostral-caudal linear growth. Furthermore, as measured by atomic force microscopy (AFM), the surrounding spinal cord softens when in contact with the stiffest scaffold while maintaining a natural level in contact with the softest one. In conclusion, our findings underscore the pivotal role of stiffness in scaffold engineering for SCIin vivo, paving the way for the optimal development of efficacious biomaterial scaffolds for tissue engineering in the central nervous system.
Tiny amphibious insects use tripod gait for seamless transition across land, water, and duckweed
Authors: O’Neil Johnathan N. , Yung Kai Lauren , Difini Gaetano , Walker Holden , Bhamla M. Saad
Published: April 2024

Insects exhibit remarkable adaptability in their locomotive strategies across diverse environments, a crucial trait for foraging, survival, and predator avoidance.Microvelia, tiny 2-3 mm insects that adeptly walk on water surfaces, exemplify this adaptability by using the alternating tripod gait in both aquatic and terrestrial terrains. These insects commonly inhabit low-flow ponds and streams cluttered with natural debris like leaves, twigs, and duckweed. Using high-speed imaging and pose-estimation software, we analyzeMicrovelia spp.’smovement across water, sandpaper (simulating land), and varying duckweed densities (10%, 25%, and 50% coverage). Our results revealMicroveliamaintain consistent joint angles and strides of their upper and hind legs across all duckweed coverages, mirroring those seen on sandpaper.Microveliaadjust the stride length of their middle legs based on the amount of duckweed present, decreasing with increased duckweed coverage and at 50% duckweed coverage, their middle legs’ strides closely mimic their strides on sandpaper. Notably,Microveliaachieve speeds up to 56 body lengths per second on water, nearly double those observed on sandpaper and duckweed (both rough, frictional surfaces), highlighting their higher speeds on low friction surfaces such as the water’s surface. This study highlightsMicrovelia’s ecological adaptability, setting the stage for advancements in amphibious robotics that emulate their unique tripod gait for navigating complex terrains.
DTX3L ubiquitin ligase ubiquitinates single-stranded nucleic acids
Authors: Dearlove Emily L. , Chatrin Chatrin , Buetow Lori , Ahmed Syed F. , Schmidt Tobias , Bushell Martin , Smith Brian O. , Huang Danny T.
Published: April 2024

Ubiquitination typically involves covalent linking of ubiquitin (Ub) to a lysine residue on a protein substrate. Recently, new facets of this process have emerged, including Ub modification of non-proteinaceous substrates like ADP-ribose by the DELTEX E3 ligase family. Here we show that the DELTEX family member DTX3L expands this non-proteinaceous substrate repertoire to include single-stranded DNA and RNA. Although the N-terminal region of DTX3L contains single-stranded nucleic acid binding domains and motifs, the minimal catalytically competent fragment comprises the C-terminal RING and DTC domains (RD). DTX3L-RD catalyses ubiquitination of the 3’-end of single-stranded DNA and RNA, as well as double-stranded DNA with a 3’ overhang of two or more nucleotides. This modification is reversibly cleaved by deubiquitinases. NMR and biochemical analyses reveal that the DTC domain binds single-stranded DNA and facilitates the catalysis of Ub transfer from RING-bound E2-conjugated Ub. Our study unveils the direct ubiquitination of nucleic acids by DTX3L, laying the groundwork for understanding its functional implications.
Negative regulation of APC/C activation by MAPK-mediated attenuation of Cdc20Slp1under stress
Authors: Sun Li , Chen Xuejin , Song Chunlin , Shi Wenjing , Liu Libo , Bai Shuang , Wang Xi , Chen Jiali , Jiang Chengyu , Wang Shuang-min , Luo Zhou-qing , Wang Ruiwen , Wang Yamei , Jin Quan-wen
Published: April 2024

Mitotic anaphase onset is a key cellular process tightly regulated by multiple kinases. The involvement of mitogen-activated protein kinases (MAPKs) in this process has been established inXenopusegg extracts. However, the detailed regulatory cascade remains elusive, and also it is unknown whether the MAPKs-dependent mitotic regulation is evolutionarily conserved in the single cell eukaryotic organism such as fission yeast (Schizosaccharomyces pombe). Here we show that two MAPKs inS. pombeindeed act in concert to restrain anaphase-promoting complex/cyclosome (APC/C) activity upon activation of the spindle assembly checkpoint (SAC). One MAPK, Pmk1, binds and phosphorylates Slp1Cdc20, the co-activator of APC/C. Phosphorylation of Slp1Cdc20by Pmk1, but not by Cdk1, promotes its subsequent ubiquitylation and degradation. Intriguingly, Pmk1-mediated phosphorylation event is also required to sustain SAC under environmental stress. Thus, our study establishes a new underlying molecular mechanism of negative regulation of APC/C by MAPK upon stress stimuli, and provides an unappreciated framework for regulation of anaphase entry in eukaryotic cells.

One-sentence summary

Inhibitory effect on the activation of anaphase promoting complex/cyclosome (APC/C) by MAPK Pmk1
HOIL1 mediates MDA5 activation through ubiquitination of LGP2
Authors: Cheng Deion , Zhu Junji , Liu GuanQun , Gack Michaela U. , MacDuff Donna A.
Published: April 2024

The RIG-I-like receptors (RLRs), RIG-I and MDA5, are innate sensors of RNA virus infections that are critical for mounting a robust antiviral immune response. We have shown previously that HOIL1, a component of the Linear Ubiquitin Chain Assembly Complex (LUBAC), is essential for interferon (IFN) induction in response to viruses sensed by MDA5, but not for viruses sensed by RIG-I. LUBAC contains two unusual E3 ubiquitin ligases, HOIL1 and HOIP. HOIP generates methionine-1-linked polyubiquitin chains, whereas HOIL1 has recently been shown to conjugate ubiquitin onto serine and threonine residues. Here, we examined the differential requirement for HOIL1 and HOIP E3 ligase activities in RLR-mediated IFN induction. We determined that HOIL1 E3 ligase activity was critical for MDA5-dependent IFN induction, while HOIP E3 ligase activity played only a modest role in promoting IFN induction. HOIL1 E3 ligase promoted MDA5 oligomerization, its translocation to mitochondrial-associated membranes, and the formation of MAVS aggregates. We identified that HOIL1 can interact with and facilitate the ubiquitination of LGP2, a positive regulator of MDA5 oligomerization. In summary, our work identifies LGP2 ubiquitination by HOIL1 in facilitating the activation of MDA5 and the induction of a robust IFN response.
Downregulation of Semaphorin 4A in keratinocytes reflects the features of non-lesional psoriasis
Authors: Kume Miki , Koguchi-Yoshioka Hanako , Nakai Shuichi , Matsumura Yutaka , Tanemura Atsushi , Yokoi Kazunori , Matsuda Shoichi , Nakamura Yuumi , Otani Naoya , Taminato Mifue , Tomita Koichi , Kubo Tateki , Wataya-Kaneda Mari , Kumanogoh Atsushi , Fujimoto Manabu , Watanabe Rei
Published: April 2024

Abstract

Psoriasis is a multifactorial disorder mediated by IL-17-producing T cells, involving immune cells and skin-constituting cells. Semaphorin 4A (Sema4A), an immune semaphorin, is known to take part in T helper type 1/17 differentiation and activation. However, Sema4A is also crucial for maintaining peripheral tissue homeostasis and its involvement in skin remains unknown. Here, we revealed that while Sema4A expression was pronounced in psoriatic blood lymphocytes and monocytes, it was downregulated in the keratinocytes of both psoriatic lesions and non-lesions compared to controls. Imiquimod application induced more severe dermatitis in Sema4A knockout (KO) mice compared to wild-type (WT) mice. The naïve skin of Sema4AKO mice showed increased T cell infiltration and IL-17A expression along with thicker epidermis and distinct cytokeratin expression compared to WT mice, which are hallmarks of psoriatic non-lesions. Analysis of bone marrow chimeric mice suggested that Sema4A expression in keratinocytes plays a regulatory role in imiquimod-induced dermatitis. The epidermis of psoriatic non-lesion and Sema4AKO mice demonstrated mTOR complex 1 upregulation, and the application of mTOR inhibitors reversed the skewed expression of cytokeratins in Sema4AKO mice. Conclusively, Sema4A- mediated signaling cascades can be triggers for psoriasis and targets in the treatment and prevention of psoriasis.
Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies
Authors: Greshnova Aleksandra , Pál Karol , Martinez Juan Francisco Iturralde , Canzar Stefan , Makova Kateryna D.
Published: April 2024

Ychromosomes of great apes harborAmpliconicGenes (YAGs)—multi-copy gene families (BPY2,CDY,DAZ,HSFY,PRY,RBMY,TSPY,VCY, andXKRY) that encode proteins important for spermatogenesis. Previous work assembled YAG transcripts based on their targeted sequencing but not using reference genome assemblies, potentially resulting in an incomplete transcript repertoire. Here we used the recently produced gapless telomere-to-telomere (T2T) Y chromosome assemblies of great ape species (bonobo, chimpanzee, human, gorilla, Bornean orangutan, and Sumatran orangutan) and analyzed RNA data from whole-testis samples for the same species. We generated hybrid transcriptome assemblies by combining targeted long reads (Pacific Biosciences), untargeted long reads (Pacific Biosciences) and untargeted short reads (Illumina)and mapping them to the T2T reference genomes. Compared to the results from the reference-free approach, average transcript length was more than two times higher, and the total number of transcripts decreased three times, improving the quality of the assembled transcriptome. The reference-based transcriptome assemblies allowed us to differentiate transcripts originating from different Y chromosome gene copies and from their non-Y chromosome homologs. We identified two sources of transcriptome diversity—alternative splicing and gene duplication with subsequent diversification of gene copies. For each gene family, we detected transcribed pseudogenes along with protein-coding gene copies. We revealed previously unannotated gene copies of YAGs as compared to currently available NCBI annotations, as well as novel isoforms for annotated gene copies. This analysis paves the way for better understanding Y chromosome gene functions, which is important given their role in spermatogenesis.
High intracellular calcium amounts inhibit activation-induced proliferation of mouse T cells
Authors: Joseph Joel P , Kumar Tanisha , Chatterjee Kaushik , Nandi Dipankar
Published: April 2024

Optimal T cell activation is critical to orchestrate adaptive immune responses. Calcium is critical for T cell activation and integrates signaling pathways necessary to activate key transcription factors. In fact, patients with calcium channelopathies are immunodeficient. Here, we investigated the effects of different concentrations of intracellular calcium on activation of mouse T cells. High intracellular calcium amounts inhibitedin vitroT cell proliferation as evidenced by a decreased cell cycling-to-hypodiploidy ratio in two models of activation: the combination of phorbol 12-myristate 13-acetate (PMA) and Ionomycin (an ionophore)/Thapsigargin (a SERCA inhibitor) or plate bound anti-CD3 and anti-CD28. High intracellular calcium amounts increased the production of reactive oxygen species (ROS) in T cells activated with PMA and Ionomycin and scavenging excess ROS using N-acetyl cysteine (NAC) or PEGylated superoxide dismutase (PEG-SOD) rescued the decrease in cycling-to-hypodiploidy ratio. To test the universality of our observations, we studied the effects of tert-Butylhydroquinone (tBHQ), a SERCA inhibitor and Nrf2 activator. tBHQ alone did not increase intracellular calcium amounts but increase was observed along with PMA. Also, tBHQ inhibited T cell activation in a dose-dependent manner in bothin vitromodels of T cell activation. Importantly, intraperitoneal injection of tBHQ ameliorated Dextran Sodium Sulfate (DSS)-induced colitis in mice as evidenced by rescue of colon length shortening and lower disease activity index. Overall, this study identifies high calcium amounts as a potential target to lower T cell activation. The implications of these observations are discussed as this strategy may be important in treatment of some autoimmune diseases.
A disease-associated PPP2R3C-MAP3K1 phospho-regulatory module controls centrosome function
Authors: Ganga Anil Kumar , Sweeney Lauren K. , Rubio Ramos Armando , Bishop Cassandra S. , Hamel Virginie , Guichard Paul , Breslow David K.
Published: April 2024

Centrosomes have critical roles in microtubule organization and in cell signaling.1–8However, the mechanisms that regulate centrosome function are not fully defined, and thus how defects in centrosomal regulation contribute to disease is incompletely understood. From functional genomic analyses, we find here that PPP2R3C, a PP2A phosphatase subunit, is a distal centriole protein and functional partner of centriolar proteins CEP350 and FOP. We further show that a key function of PPP2R3C is to counteract the kinase activity of MAP3K1. In support of this model,MAP3K1knockout suppresses growth defects caused byPPP2R3Cinactivation, and MAP3K1 and PPP2R3C have opposing effects on basal and microtubule stress-induced JNK signaling. Illustrating the importance of balanced MAP3K1 and PPP2R3C activities, acute overexpression of MAP3K1 severely inhibits centrosome function and triggers rapid centriole disintegration. Additionally, inactivatingPPP2R3Cmutations and activatingMAP3K1mutations both cause congenital syndromes characterized by gonadal dysgenesis.9–15As a syndromicPPP2R3Cvariant is defective in centriolar localization and binding to centriolar protein FOP, we propose that imbalanced activity of this centrosomal kinase-phosphatase pair is the shared cause of these disorders. Thus, our findings reveal a new centrosomal phospho-regulatory module, shed light on disorders of gonadal development, and illustrate the power of systems genetics to identify previously unrecognized gene functions.
Structure and function of an intermediate GPCR-Gαβγ complex
Authors: Bi Maxine , Wang Xudong , Wang Jinan , Xu Jun , Sun Wenkai , Adediwura Victor Ayo , Miao Yinglong , Cheng Yifan , Ye Libin
Published: April 2024

Unraveling the signaling roles of intermediate complexes is pivotal for G protein-coupled receptor (GPCR) drug development. Despite hundreds of GPCR-Gαβγ structures, these snapshots primarily capture the fully activated end-state complex. Consequently, a comprehensive understanding of the conformational transitions during GPCR activation and the roles of intermediate GPCR-G protein complexes in signaling remain elusive. Guided by a conformational landscape profiled by19F quantitative NMR (19F-qNMR) and Molecular Dynamics (MD) simulations, we resolved the structure of an unliganded GPCR-G protein intermediate complex by blocking its transition to the fully activated end-state complex. More importantly, we presented direct evidence that the intermediate GPCR-Gαsβγ complex initiates a rate-limited nucleotide exchange without progressing to the fully activated end-state complex, thereby bridging a significant gap in our understanding the complexity of GPCR signaling. Understanding the roles of individual conformational states and their complexes in signaling efficacy and bias will help us to design drugs that discriminately target a disease-related conformation.
ARID1A-BAF coordinates ZIC2 genomic occupancy for epithelial to mesenchymal transition in cranial neural crest lineage commitment
Authors: Barnada Samantha M. , de Gracia Aida Giner , Morenilla-Palao Cruz , López-Cascales María Teresa , Scopa Chiara , Waltrich Francis J. , Mikkers Harald M.M. , Cicardi Maria Elena , Karlin Jonathan , Trotti Davide , Peterson Kevin A. , Brugmann Samantha A. , Santen Gijs W. E. , McMahon Steven B. , Herrera Eloísa , Trizzino Marco
Published: April 2024

The BAF chromatin remodeler regulates lineage commitment including cranial neural crest cell (CNCC) specification. Variants in BAF subunits cause Coffin-Siris Syndrome (CSS), a congenital disorder characterized by coarse craniofacial features and intellectual disability. Approximately 50% of CSS patients carry variants in one of the mutually exclusive BAF subunits,ARID1A/ARID1B. WhileArid1adeletion in mouse neural crest causes severe craniofacial phenotypes, little is known about the role of ARID1A in CNCC specification. Using CSS patient-derivedARID1A+/-iPSCs to model CNCC specification, we discoveredARID1A-haploinsufficiency impairs epithelial to mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from the neural tube. Furthermore, wild-type ARID1A-BAF regulates enhancers associated with EMT genes. ARID1A-BAF binding at these enhancers is impaired in heterozygotes while binding at promoters is unaffected. At the sequence level, these EMT enhancers contain binding motifs for ZIC2, and ZIC2 binding at these sites is ARID1A-dependent. When excluded from EMT enhancers, ZIC2 relocates to neuronal enhancers, triggering aberrant neuronal gene activation. In mice, deletion ofZic2impairs NCC delamination, whileZIC2overexpression in chick embryos at pre-migratory neural crest stages elicits ectopic delamination from the neural tube. These findings reveal a novel ARID1A-ZIC2 axis essential for EMT and CNCC delamination.