bluuebunny/crossref_metadata_2025 huggingface dataset:
Progressive heterogeneity of enlarged and irregularly shaped apicoplasts inP. falciparumpersister blood stages after drug treatment
Authors: Micchelli Chiara E. , Percopo Caroline , Traver Maria , Brzostowski Joseph , Amin Shuchi N. , Prigge Sean T. , Sá Juliana M. , Wellems Thomas E.
Published: January 2024

Morphological modifications and shifts in organelle relationships are hallmarks of dormancy in eukaryotic cells. Communications between altered mitochondria and nuclei are associated with metabolic quiescence of cancer cells that can survive chemotherapy. In plants, changes in the pathways between nuclei, mitochondria, and chloroplasts are associated with cold stress and bud dormancy.Plasmodium falciparumparasites, the deadliest agent of malaria in humans, contain a chloroplast-like organelle (apicoplast) derived from an ancient photosynthetic symbiont. Antimalarial treatments can fail because a small fraction of the blood stage parasites enter dormancy and recrudesce after drug exposure. Altered mitochondrial-nuclear interactions in these persisters have been described forP. falciparum, but interactions of the apicoplast remained to be characterized. In the present study, we examined the apicoplasts of persisters obtained after exposure to dihydroartemisinin (a first-line antimalarial drug) followed by sorbitol treatment, or after exposure to sorbitol treatment alone. As previously observed, the mitochondrion of persisters was consistently enlarged and in close association with the nucleus. In contrast, the apicoplast varied from compact and oblate, like those of active ring stage parasites, to enlarged and irregularly shaped. Enlarged apicoplasts became more prevalent later in dormancy, but regular size apicoplasts subsequently predominated in actively replicating recrudescent parasites. All three organelles, nucleus, mitochondrion, and apicoplast, became closer during dormancy. Understanding their relationships in erythrocytic-stage persisters may lead to new strategies to prevent recrudescences and protect the future of malaria chemotherapy.

Significance Statement

Dormancy of blood-stage malaria parasites (as persister forms) frequently undermines treatment and may facilitate the evolution of drug resistance. Here, we examine changes that occur in dormancy with twoP. falciparumorganelles relative to the nucleus: the mitochondrion and the plastid-like apicoplast. As previously reported, the mitochondrion of persisters is consistently enlarged, irregularly shaped, and shifted into close apposition with the nucleus. However, apicoplasts exhibit a greater variety of shapes, volumes, and relative positioning during dormancy: some persisters maintain a regular appearing apicoplast, while others show dramatically altered apicoplasts, reminiscent of the chloroplast swelling and degradation that occurs with death from reactive oxygen species in various plant cells. Improved understanding of these processes will support new approaches in antimalarial chemotherapy.
Accuracy of phylogenetic reconstructions from continuous characters analyzed under parsimony and its parametric correlates
Authors: Tagliacollo Victor A , de Pinna Mario , Chuctaya Junior , Datovo Alessio
Published: January 2024

Quantitative traits are a source of evolutionary information often difficult to handle in cladistics. Tools exist to analyze this kind of data without subjective discretization, avoiding biases in the delimitation of categorical states. Nonetheless, the ability of continuous characters to accurately infer relationships is incompletely understood, particularly under parsimony analysis. This study evaluates the accuracy of phylogenetic reconstructions from simulated matrices of continuous characters evolving under alternative evolutionary processes and analyzed by parsimony. We generated 100 trees to simulate 9,000 matrices containing 26 terminals and 100 continuous characters evolving under: Brownian-Motion (BM), Ornstein-Uhlenbeck (OU) and Early-Burst (EB) processes assuming variable parametrizations. Our comparisons of cladograms revealed that matrices analyzed by parsimony carry phylogenetic signals to infer relationships, but the accuracy is higher for matrices simulated under BM, regardless of the parameterization schemes. Implementation of equal or implied weighting with multiple penalization strengths against homoplasies did not affect cladogram inferences. Accuracy of continuous characters in resolving relationships is skewed toward apical nodes of the trees. Our simulations provide controlled tests of the usefulness of quantitative traits in phylogenetics, specifically under neutral evolution, and demonstrate their effectiveness in estimating shallower nodes among recently diverged species, regardless of parameters and weighting schemes.
Streamlining the alignment of UAV and TLS forest point clouds: an approach based on ground and tree stems
Authors: Puletti Nicola , Innocenti Simone , Guasti Matteo
Published: January 2024

Accurate co-registration of terrestrial and aerial point clouds may provide a high-resolution description of tree components for large forest areas. However, an automated approach for co-registering point clouds is still needed, given the challenges in geospatial data processing, particularly in complex topographical conditions. The main objective of this study is to present the application of a novel procedure for the co-registration of point clouds obtained from terrestrial and UAV surveys in Mediter-ranean forests.
How much warming can mosquito vectors tolerate?
Authors: Couper Lisa , Desire Uwera Nalukwago Desire , Lyberger Kelsey , Farner Johannah , Mordecai Erin A
Published: January 2024

Climate warming is expected to substantially impact the global landscape of mosquito-borne disease, but these impacts will vary across disease systems and regions. Understanding which diseases, and where within their distributions, these impacts are most likely to occur is critical for preparing public health interventions. While research has centered on potential warming-driven expansions in vector transmission, less is known about the potential for vectors to experience warming-driven stress or even local extirpations. In conservation biology, species risk from climate warming is often quantified through vulnerability indices such as thermal safety margins — the difference between an organism's upper thermal limit and its habitat temperature. Here, we estimated thermal safety margins for 8 mosquito species (includingAedes aegyptiandAnopheles gambiae) that are the vectors of malaria, dengue, chikungunya, Zika, West Nile and other major arboviruses, across their known ranges to investigate which mosquitoes and regions are most and least vulnerable to climate warming. We find that several of the most globally important mosquito vector species have positive thermal safety margins across the majority of their ranges when realistic assumptions of mosquito behavioral thermoregulation are incorporated. On average, the lowest climate vulnerability, in terms of both the magnitude and duration of thermal safety, was just south of the equator and at northern temperate range edges, and the highest climate vulnerability was in the subtropics. Mosquitoes living in regions largely comprised of desert and xeric shrubland biomes, including the Middle East, the western Sahara, and southeastern Australia have the highest climate vulnerability across vector species.
Tractography-based automated identification of the retinogeniculate visual pathway with novel microstructure-informed supervised contrastive learning
Authors: Li Sipei , Zhang Wei , Yao Shun , He Jianzhong , Zhu Ce , Gao Jingjing , Xue Tengfei , Xie Guoqiang , Chen Yuqian , Torio Erickson F. , Feng Yuanjing , Bastos Dhiego CA , Rathi Yogesh , Makris Nikos , Kikinis Ron , Bi Wenya Linda , Golby Alexandra J , O’Donnell Lauren J , Zhang Fan
Published: January 2024

The retinogeniculate visual pathway (RGVP) is responsible for carrying visual information from the retina to the lateral geniculate nucleus. Identification and visualization of the RGVP are important in studying the anatomy of the visual system and can inform the treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced imaging method that uniquely enablesin vivomapping of the 3D trajectory of the RGVP. Currently, identification of the RGVP from tractography data relies on expert (manual) selection of tractography streamlines, which is time-consuming, has high clinical and expert labor costs, and is affected by inter-observer variability. In this paper, we present a novel deep learning framework,DeepRGVP, to enable fast and accurate identification of the RGVP from dMRI tractography data. We design a novel microstructure-informed supervised contrastive learning method that leverages both streamline label and tissue microstructure information to determine positive and negative pairs. We propose a simple and successful streamline-level data augmentation method to address highly imbalanced training data, where the number of RGVP streamlines is much lower than that of non-RGVP streamlines. We perform comparisons with several state-of-the-art deep learning methods that were designed for tractography parcellation, and we show superior RGVP identification results using DeepRGVP. In addition, we demonstrate a good generalizability of DeepRGVP to dMRI tractography data from neurosurgical patients with pituitary tumors and we show DeepRGVP can successfully identify RGVPs despite the effect of lesions affecting the RGVPs. Overall, our study shows the high potential of using deep learning to automatically identify the RGVP.
Climate and urbanization drive changes in the habitat suitability ofSchistosoma mansonicompetent snails in Brazil
Authors: Glidden Caroline K. , Singleton Alyson L. , Chamberlin Andrew , Tuan Roseli , Palasio Raquel G.S. , Caldeira Roberta Lima , Monteiro Antônio Miguel V. , Lwiza Kamazima M. M. , Liu Ping , Silva Vivian , Athni Tejas S. , Sokolow Susanne H. , Mordecai Erin A. , De Leo Giulio A.
Published: January 2024

Schistosomiasis is a neglected tropical disease caused bySchistosomaparasites.Schistosomaare obligate parasites of freshwaterBiomphalariasnails, so controlling snail populations is critical to reducing transmission risk. As snails are sensitive to environmental conditions, we expect their distribution is significantly impacted by global change. Here, we leveraged machine learning, remote sensing, and 30 years of snail occurrence records to map the historical and current distribution of competentBiomphalariathroughout Brazil. We identified key features influencing the distribution of suitable habitat and determined howBiomphalariahabitat has changed with climate and urbanization over the last three decades. Our models show that climate change has driven broad shifts in snail host range, whereas expansion of urban and peri-urban areas has driven localized increases in habitat suitability. Elucidating change inBiomphalariadistribution – while accounting for non-linearities that are difficult to detect from local case studies – can help inform schistosomiasis control strategies.
Fascin structural plasticity mediates flexible actin bundle construction
Authors: Gong Rui , Reynolds Matthew J. , Carney Keith R. , Hamilton Keith , Bidone Tamara C. , Alushin Gregory M.
Published: January 2024

Fascin crosslinks actin filaments (F-actin) into bundles that support tubular membrane protrusions including filopodia and stereocilia. Fascin dysregulation drives aberrant cell migration during metastasis, and fascin inhibitors are under development as cancer therapeutics. Here, we use cryo-electron microscopy, cryo-electron tomography coupled with custom denoising, and computational modeling to probe fascin’s F-actin crosslinking mechanisms across spatial scales. Our fascin crossbridge structure reveals an asymmetric F-actin binding conformation that is allosterically blocked by the inhibitor G2. Reconstructions of seven-filament hexagonal bundle elements, variability analysis, and simulations show how structural plasticity enables fascin to bridge varied inter-filament orientations, accommodating mismatches between F-actin’s helical symmetry and bundle hexagonal packing. Tomography of many-filament bundles and modeling uncovers geometric rules underlying emergent fascin binding patterns, as well as the accumulation of unfavorable crosslinks that limit bundle size. Collectively, this work shows how fascin harnesses fine-tuned nanoscale structural dynamics to build and regulate micron-scale F-actin bundles.
Improving the application of Important Plant Areas to conserve threatened habitats: a case study of Uganda
Authors: Richards Sophie L. , Kalema James , Ojelel Samuel , Williams Jenny , Darbyshire Iain
Published: January 2024

Important Plant Areas (IPAs) are a successful method of identifying priority areas for plant conservation. Assessment of IPAs, however, often relies on criteria related to species, while incorporation of habitats has been less consistent. Using Uganda as a case study, we test the application of the threatened habitat criterion – criterion C. We identified nationally threatened habitats using Red List of Ecosystems criteria and assess, for the first time, how differing application of thresholds under criterion C can influence IPA network outcomes. Eleven threatened habitats were identified, with declines switching from predominantly forest to savanna after the mid-20thcentury. Significantly, we found current IPA guidance on use of Criterion C needlessly limits the number of sites that qualify as IPAs. The “five best sites” threshold is reserved for countries where quantitative data is unavailable, however, the application of the relevant thresholds to quantitative data largely generated fewer than five IPAs, comparably limiting conservation opportunities identified. We recommend, therefore, that the “five best” threshold is available for application on both qualitative and quantitative data. This will bolster the value of IPAs in conserving and restoring threatened and ecologically important habitats under the Kunming-Montreal Global Biodiversity Framework.
Vascular damage and excessive proliferation compromise liver function after extended hepatectomy in mice
Authors: Rudder Maxime De , Manco Rita , Coubeau Laurent , Fontaine Alix , Bertrand Claude , Leclercq Isabelle A. , Dili Alexandra
Published: January 2024

Surgical resection remains the gold standard for liver tumor treatment, yet the emergence of post-operative liver failure, known as the small for size syndrome (SFSS), poses a substantial challenge. The activation of hypoxia sensors in a SFSS liver remnant initiated early angiogenesis, improving vascular architecture, safeguarding against liver failure and reducing mortality. The study aimed to elucidate vascular remodeling mechanisms in SFSS, its impact on hepatocyte function and subsequent liver failure. Mice underwent extended partial hepatectomy to induce SFSS, a subset were exposed to hypoxia immediately after surgery. Hypoxia bolstered post- hepatectomy survival rates. Early proliferation of liver sinusoidal cells coupled with augmented recruitment of endothelial progenitor cells (EPC) via the VEGF/SDF-1α pathway resulted in heightened vascular density, improved lobular perfusion, and limited hemorrhagic events in the regenerating liver under hypoxia. The administration of G-CSF mimicked the effects of hypoxia on vascular remodeling and EPC recruitment, though it failed to rescue survival. Compared to normoxia, hypoxia restrained hepatocyte proliferation yet improved the function of the regenerating remnant, favoring functional preservation in the liver remnant. Injection of AAV8- TBG-HNF4α virus for hepatocyte-specific overexpression of HNF4α, the master regulator of hepatocyte function, enforced functionality in proliferating hepatocytes. The combination, only, of HNF4α overexpression and G-CSF treatment rescued survival post-SFSS-setting hepatectomy. In summary, SFSS arises due to imbalance and desynchronized interplay between functional regeneration and vascular restructuring. To enhance survival following SFSS-hepatectomy, a two- pronged strategy is essential, addressing the preservation of function in the proliferating parenchymal cells alongside the simultaneous mitigation of vascular harm.

One Sentence Summary

Combined treatment with G-CSF and HNF4α overexpression rescues vascular damage and function to improve survival after extended hepatectomy in mice.
The neurodevelopmental trajectory of beta band oscillations: an OPM-MEG study
Authors: Rier Lukas , Rhodes Natalie , Pakenham Daisie , Boto Elena , Holmes Niall , Hill Ryan M , Reina Rivero Gonzalo , Shah Vishal , Doyle Cody , Osborne James , Bowtell Richard W , Taylor Margot , Brookes Matthew J
Published: January 2024

Neural oscillations mediate the coordination of activity within and between brain networks, supporting cognition and behaviour. How these processes develop throughout childhood is not only an important neuroscientific question but could also shed light on the mechanisms underlying neurological and psychiatric disorders. However, measuring the neurodevelopmental trajectory of oscillations has been hampered by confounds from instrumentation. In this paper, we investigate the suitability of a disruptive new imaging platform - Optically Pumped Magnetometer-based magnetoencephalography (OPM-MEG) - to study oscillations during brain development. We show how a unique 192-channel OPM-MEG device, which is adaptable to head size and robust to participant movement, can be used to collect high-fidelity electrophysiological data in individuals aged between 2 and 34 years. Data were collected during a somatosensory task, and we measured both stimulus-induced modulation of beta oscillations in sensory cortex, and whole-brain connectivity, showing that both modulate significantly with age. Moreover, we show that pan-spectral bursts of electrophysiological activity drive task-induced beta modulation, and that their probability of occurrence and spectral content change with age. Our results offer new insights into the developmental trajectory of beta oscillations and provide clear evidence that OPM-MEG is an ideal platform for studying electrophysiology in neurodevelopment.
Armed Macrophages as Hunters for Photodynamic Therapy of Systemic Bacterial Infections by Bathing in the Sunshine
Authors: Wang Zehui , Wang Lai , Zhou Lin , Zhang Xinfu , Xiao Yi
Published: January 2024

There has been a vision to conduct therapy using sunlight since ancient Greece, Egypt, and India. In modern medicine, photodynamic therapy is one popular form of therapy that uses light to excite photosensitizers to eliminate malignant and other diseased cells. It offers highly effective and broad-spectrum therapeutic efficacy. Yet, there are several hindrances to a real treatment of disease through photodynamic therapy, such as the limitation on the irradiation depth and areas, the regulation of side effects, etc. Usually, the patients should be kept in a dark environment during and after the therapeutic process for days to avoid side effects induced by light in daily life, not mention to conduct the phototherapy through sunbathing. Based on the above consideration, we propose an innovative idea to bring photodynamic therapy back to the origin of phototherapy-bathing in the sunshine. Namely, we designed a “live drug”, as a smart hunter, named A-RAWs, by loading an “off-on” type of photosensitizer in macrophages to solve two technical problems. Firstly, to find and capture bacteria accurately, and then transport these bacteria to the epidermis through the blood capillary, where sunlight is reachable. Secondly, to minimize the potential side effects and maximize the therapeutic time windows and efficacy by using bacteria as the trigger of the photodynamic effect. Specifically, we first designed and synthesized a lysosome-targeted and inflammation-activated NIR photosensitizer (Lyso710A), and loaded it in the lysosomes of macrophages. These “armed” macrophages were transferred into the infected host to capture deep-tissue bacteria through innate immunity and transport the captured bacteria through the bloodstream to superficial skin. Finally, the pathogenic bacteria are killed by the photodynamic effect when transported to the epidermis and receive sunbathing. In vivo experiment demonstrates a 100% therapeutic efficiency on systemic bacterial infection model. We also demonstrated the working mechanism of this “live drug” using a lung infection model. This hunter demonstrates high intelligence to break the limitations of current photodynamic therapy and executes photodynamic therapy of deep-tissue bacterial infection simply by bathing in the sunshine.

Abstract Figure
Identifying the genetic and epigenetic basis for asymmetric bZIP expression in temperature-stressed bread wheat
Authors: Kaur Raminder , Singh Dalwinder , Kumar Pankaj , Kaur Gazaldeep , Shah Koushik , Pandey Harshita , Devi Shamjetsabam Gangarani , Pandey Ajay Kumar , Rishi Vikas
Published: January 2024

Asymmetric expression in the bread wheat (Triticum aestivum) genome refers to the differential expression of genes from A, B, and D parental genomes. Bread wheat is a hexaploid crop with six copies of each chromosome. This complexity can result in unequal expression of genes from each parental genome, leading to asymmetry in gene expression. In other polyploid crops like cotton, transcription factors (TF) exhibit genome-biased expression; however, there are no comparable studies for bread wheat. One of the most prominent TFs families in plants is the basic Leucine Zippers (bZIP) which are eukaryote-specific proteins and regulate various biological processes, including stress-related responses. bZIP proteins are dimeric and several heptads long. They exhibit typical coiled-coil structures with strategically placed amino acids in each heptad, responsible for their stability and specificity. Here, we aim to decipher the structural basis of the asymmetric expression of the bZIP TFs in wheat under low and high-temperature conditions. Furthermore, 19 highly expressed stress-related TabZIP TFs were analysed for their asymmetric expression profiles as plants were exposed to temperature-stress conditions. Two benchmarks were used to analyse the asymmetric gene expression of bZIPs, i.e., a) the promoter’s occupancy by the epigenetic marker histones, namely, H3K4me3, H3k9ac (active) and H3K27me3 (repressive), b) density and diversity of cis-regulatory elements in the promoters. Notably, the genetic basis of the differences in protein sequences of bZIP triads was explored, which may impart structural stability to a specific homeolog enabling the plant to endure the stress conditions better.
The topography of DNA replication origins in Eukarya: GGN clusters, landmark nucleosomes, CDC6 and G4 structures
Authors: Bastolla Ugo , Gómez-Pinto Irene , Vergara Zaida , Gómez María , González Carlos , Gutiérrez Crisanto
Published: January 2024

Background

We recently identified tandem repeats of GGN triplets as a sequence motif strongly enriched in the DNA replication origins (ORIs) of theArabidopsis thalianagenome, where it correlates with the ORI strength quantified through short nascent strands sequencing.

Results

Here we show that clusters of four or more GGN repeats separated by short tracts (<7 nucleotides) are present in more than 65% ORIs of six model eukaryotic organisms:Leishmania major,Arabidopsis thaliana,Caenorhabditis elegans,Drosophila melanogaster,Mus musculusandHomo sapiens. The measured percentages vary with the experimental technique adopted for ORI determination. For all studied techniques and organisms, ORIs are significantly prone to be located within or near strong GGN clusters, although these are neither necessary nor sufficient for ORI activation. Interestingly, for same experimental technique, the association between ORIs and GGN clusters was stronger al later developmental stages for all organisms for which we could perform this comparison.

In accordance with a biophysical model of nucleosome positioning, the GGN clusters strongly favor nucleosome occupancy. At the same time, both GGN clusters and ORIs occur frequently within 1kb from nucleosome-depleted regions (NDR). We propose a structural model based on chromatin secondary structure in which the NDR and the well-positioned nucleosome at the GGN are close in space, which may favor functional interactions. We hypothesize that the presence of GGN at ORIs arose in part for promoting the above nucleosome organization Moreover, at least inArabidopsis, the replication protein CDC6 is very strongly associated with GGN clusters.

NMR experiments showed that clusters of at least four GGN can form G-quadruplex (G4)in vitro.Our data support the view that GGN clusters are formed through the interplay of mutational processes (GC skew at ORIs plus triplet expansion), and that similar mutational processes, i.e. AT skew at transcription start sites (TSS) and ORIs, might facilitate the formation of the NDR, thus favoring the evolvability of chromatin.

Conclusions

GGN clusters are easily evolvable sequence motifs enriched at ORIs of eukaryotic genomes. They favor G4 secondary structure and a nucleosome organization that may unify the apparent discrepancy between ORIs of higher eukaryotes and yeast.
AMAPEC: accurate antimicrobial activity prediction for fungal effector proteins
Authors: Mesny Fantin , Thomma Bart PHJ
Published: January 2024

Fungi typically occur in environments where numerous and diverse other microbes occur as well, often resulting in fierce competition for nutrients and habitat. To support fungal fitness in these environments, they evolved various mechanisms that mediate direct antagonism towards niche competitors. Among these, the secretion of proteins with antimicrobial activities has been reported in fungi with diverse lifestyles. Recently, several plant-associated fungi were shown to rely on the secretion of antimicrobial effector proteins to antagonize certain members of plant hosts’ microbiota and to successfully colonize plant tissues. Some of these effectors do not share homology with known antimicrobials and represent novel antibiotics. Accordingly, the occurrence and conservation of proteinaceous antimicrobials throughout the fungal tree of life remains enigmatic. Here we present a computational approach to annotate candidate antimicrobial effectors in fungal secretomes based on protein physicochemical properties. After curating a set of proteins that were experimentally verified to display antimicrobial activity and a set of proteins that lack such activity, we trained a machine learning classifier on properties of protein sequences and predicted structures. This predictor performs particularly well on fungal proteins (R2=0.89) according to our validations and is delivered as a software package named AMAPEC, dedicated toantimicrobialactivityprediction foreffectorcandidates. We subsequently used this novel software to predict antimicrobial effector catalogs in three phylogenetically distant fungi with distinct lifestyles, revealing relatively large catalogs of candidate antimicrobials for each of the three fungi, and suggesting a broad occurrence of such proteins throughout the fungal kingdom. Thus, AMAPEC is a unique method to uncover antimicrobials in fungal secretomes that are often sparsely functionally annotated, and may assist biological interpretations during omic analyses. It is freely available athttps://github.com/fantin-mesny/amapec.
Single-cell RNA sequencing of peripheral blood mononuclear cells reveals complex cellular signalling signatures of metformin treatment type 2 diabetes mellitus
Authors: Zhao Jin-Dong , Fang Zhao-Hui
Published: January 2024

Objective

Type 2 diabetes mellitus (T2DM) is a complex polygenic disease. The onset of the disease is related to autoimmunity. However, how immune cells function in the peripheral blood remains to be elucidated. Metformin is the first-line treatment. Exploring biomarkers of T2DM based on single-cell sequencing technology can provide new insights for the discovery of metformin treatment T2DM in molecular mechanisms.

Methods

We profiled 43,971 cells and 20,228 genes from peripheral blood mononuclear cells (PBMCs) of T2DM patients and healthy controls by single-nucleotide RNA sequencing.

Results

B cells, T cells, monocytes/macrophages, platelets, neutrophils, NK cells and cDC2s were grouped into 7 subclusters. Furthermore, T cells and monocytes/macrophages might be significantly correlated with the clinical characteristics of T2DM patients. RPL27 and AC018755.4 expression were strongly negative correlated with HbA1c. CD4+ T cells are mainly in the memory activation stage, and CD8+ T cells are effectors. The 50 genes whose expression varied with developmental time were associated with cytoplasmic translation, cell‒cell adhesion mediated by integrin, and the regulation of the inflammatory response. Monocytes/macrophages include classic monocytes and nonclassical monocytes. The GSEA results showed that the marker genes were enriched in the HALLMARK_INTERFERON_GAMMA_RESPONSE and HALLMARK_TNFA_SIGNALING_VIA_NFKB. The WGCNA results showed 14 modules. Meanwhile, TNFRSF1A is the most core genes in network interaction. Further analysis revealed ligand‒receptor pairs, including MIF-(CD74 + CD44), MIF-(CD74 + CXCR4), ANXA1-FPR1 and LGALS9-CD45.

Conclusions

Our study revealed that the transcriptional map of immune cells from PBMCs provided a framework for understanding the immune status of T2DM patients with metformin treatment via scRNA-seq analysis.
Antiviral action of different molecules obtained from invertebrates against coronavirus
Authors: Mendonca Ronaldo Z , Nascimento Roberto M , Fernandes Ana C.O , de Almeida Maria I.P , Junior Pedro I.S
Published: January 2024

The few availability of antivirals for new strains of highly pathogenic viruses has become a serious public health problem that leads to the death of thousands of people annually. For this reason, the search for new products against these agents has become an urgent need. Many studies have been carried out with this aim. Among the multiple sources of research for new antibiotics and antivirals, bioprospecting for molecules obtained from invertebrates, or their products, has become an increasingly frequent option. Arthropods appeared on the planet around 350 million years ago and have been one of the beings with the greatest adaptability and resistance. Invertebrates have been found in all known ecosystems. Their survival for so long, in such different environments, is an indication that they have a very efficient protection system against environmental infections, despite not having a developed immune system like mammals. Historically, products obtained mainly from bees, such as honey and propolis, have been shown to be of great pharmacological importance, being used as antimicrobials, anti-inflammatory, antitumor, healing and several other functions. However, these molecules have also been obtained from other invertebrates, such as caterpillars and spiders. Previous studies by our group have demonstrated an intense antiviral and antimicrobial activity of these materials. In this study, we identified, isolated and characterized compounds with potent antiviral effect against avian Coronavirus in propolis from Scaptotrigona aff postica, hemolymph of Lonomia obliqua and from mygalin, an acylpolyamine, isolated from hemocytes of spider Acanthoscurria gomesiana. The antiviral assay was carried out by reducing infectious foci in cultures of infected cells and treated with these differents substances obtained from invertebrates. Propolis and crude hemolymph reduced avian coronavirus by an average of 256 x when used at a concentration of 5% v/v and an average reduction of 8x when 160 uM of Mygalin was used. Propolis purified and sinthetic hemolymph reduced the virus titer by an average 64 fold. The virus reduction with synthetic mygalin, at a concentration of 26 uM, was average of 16 times. The antiviral responses of the 3 substances were dose dependent. By the other hand, the virus titer reduction was 2 times more intense when the substances were added 1 hour before cell infection with the virus. The chemical characterization of the elements present in the extracts was carried out by liquid chromatography.
The Interpretable Multimodal Machine Learning (IMML) framework reveals pathological signatures of distal sensorimotor polyneuropathy
Authors: Nguyen Phong BH , Garger Daniel , Maalmi Haifa , Prokisch Holger , Thorand Barbara , Adamski Jerzy , Kastenmüller Gabi , Waldenberger Melanie , Gieger Christian , Peters Annette , Suhre Karsten , Bönhof Gidon J , Rathmann Wolfgang , Roden Michael , Grallert Harald , Ziegler Dan , Herder Christian , Menden Michael P
Published: January 2024

Distal sensorimotor polyneuropathy (DSPN) is a common neurological disorder in elderly adults and people with obesity, prediabetes and diabetes and is associated with high morbidity and premature mortality. DSPN is a multifactorial disease and not fully understood yet. Here, we developed the Interpretable Multimodal Machine Learning (IMML) framework for predicting DSPN prevalence and incidence based on sparse multimodal data. Exploiting IMMLs interpretability further empowered biomarker identification. We leveraged the population-based KORA F4/FF4 cohort including 1,091 participants and their deep multimodal characterisation, i.e. clinical data, genomics, methylomics, transcriptomics, proteomics, inflammatory proteins and metabolomics. Clinical data alone is sufficient to stratify individuals with and without DSPN (AUROC = 0.752), whilst predicting DSPN incidence 6.5±0.2 years later strongly benefits from clinical data complemented with two or more molecular modalities (improved ΔAUROC >0.1, achieved AUROC of 0.714). Important and interpretable features of incident DSPN prediction include up-regulation of proinflammatory cytokines, down-regulation of SUMOylation pathway and essential fatty acids, thus yielding novel insights in the disease pathophysiology. These may become biomarkers for incident DSPN, guide prevention strategies and serve as proof of concept for the utility of IMML in studying complex diseases.
A split crRNA with CRISPR-Cas12a enables highly sensitive, selective, and multiplexed detection of RNA and DNA
Authors: Qiao Jie , Chen Yichuan , Wang Xinping , He Baoxia , Yin Wenhao , Liu Yi
Published: January 2024

The complete 40-nt CRISPR RNA (crRNA) of Cas12a can be artificially divided into two parts, including the 20-nt scaffold RNA with fixed sequences and the 20-nt spacer RNA with variable sequences, respectively. Herein, we found that Cas12a protein, scaffold RNA, and spacer RNA can be reassembled into an active ribonucleoprotein (RNP) which has atrans-cleavage activity comparable to that of wild-type Cas12a RNP. By leveraging such split CRISPR-Cas12a system (SCas12a), we devised fast fluorescence and lateral flow assays for highly sensitive, selective, and multiplexed detection of miRNAs without the need for reverse transcription and pre-amplification, achieving a limit of detection (LoD) of 10 fM. Additionally, our SCas12a assay enables detecting long-stranded RNA without secondary structure, as well as distinguishing mature miRNA from its precursor (pre-miRNA) that comprises the same sequence of miRNA. Beyond RNA detection, SCas12a outperforms wild-type Cas12a in specificity towards DNA point mutations. In combination with recombinase polymerase amplification (RPA), we set up a one-pot assay to detect attomolar concentrations of human papillomavirus (HPV) in patient samples. In conclusion, this work provides a simple, cost-effective, yet powerful SCas12a-based rapid nucleic acid detection platform in various diagnostic settings.

Significance Statement

Conventional Cas12a-based diagnostic methods cannot directly detect RNA targets. Here, we develop rapid fluorescence and lateral flow assays based on a split Cas12a system (called SCas12a), achieving amplification-free detection of RNA with high sensitivity and specificity. By supplying pooled activators, our method enables multiplexed detection of miRNA and DNA targets. In addition, SCas12a can discriminate mature miRNA from its pre-miRNA, which was achieved for the first time with CRISPR detection technology. Moreover, SCas12a outperforms wild-type Cas12a in specificity towards point mutation and can be combined with RPA to detect attomolar concentration of HPV in patient samples. Overall, this work offers a generic “split crRNA-activator” strategy for developing new CRISPR diagnostic tools.
Plural molecular and cellular mechanisms of pore domainKCNQ2encephalopathy
Authors: Abreo Timothy J. , Thompson Emma C. , Madabushi Anuraag , Soh Heun , Varghese Nissi , Vanoye Carlos G. , Springer Kristen , Park Kristen L. , Johnson Jim , Sims Scotty , Ji Zhigang , Chavez Ana G. , Jankovic Miranda J. , Habte Bereket , Zuberi Aamir R. , Lutz Cathleen , Wang Zhao , Krishnan Vaishnav , Dudler Lisa , Einsele-Scholz Stephanie , Noebels Jeffrey L. , George Alfred L. , Maheshwari Atul , Tzingounis Anastasios V. , Cooper Edward C.
Published: January 2024

KCNQ2variants in children with neurodevelopmental impairment are difficult to assess due to their heterogeneity and unclear pathogenic mechanisms. We describe a child with neonatal-onset epilepsy, developmental impairment of intermediate severity, andKCNQ2G256W heterozygosity. Analyzing prior KCNQ2 channel cryoelectron microscopy models revealed G256 as a node of an arch-shaped non-covalent bond network linking S5, the pore turret, and the ion path. Co-expression with G256W dominantly suppressed conduction by wild-type subunits in heterologous cells. Ezogabine partly reversed this suppression. G256W/+ mice have epilepsy leading to premature deaths. Hippocampal CA1 pyramidal cells from G256W/+ brain slices showed hyperexcitability. G256W/+ pyramidal cell KCNQ2 and KCNQ3 immunolabeling was significantly shifted from axon initial segments to neuronal somata. Despite normal mRNA levels, G256W/+ mouse KCNQ2 protein levels were reduced by about 50%. Our findings indicate that G256W pathogenicity results from multiplicative effects, including reductions in intrinsic conduction, subcellular targeting, and protein stability. These studies provide evidence for an unexpected and novel role for the KCNQ2 pore turret and introduce a valid animal model ofKCNQ2encephalopathy. Our results, spanning structure to behavior, may be broadly applicable because the majority ofKCNQ2encephalopathy patients share variants near the selectivity filter.
Understanding the Energy Landscape of Intrinsically Disordered Protein Ensembles
Authors: Viegas Rafael G. , Martins Ingrid B. S. , Leite Vitor B.P.
Published: January 2024

A substantial portion of various organisms’ proteomes comprises intrinsically dis-ordered proteins (IDPs) that lack a defined three-dimensional structure. These IDPs exhibit a diverse array of conformations, displaying remarkable spatio-temporal het-erogeneity and exceptional conformational flexibility. Characterizing the structure or structural ensemble of IDPs presents significant conceptual and methodological challenges owing to the absence of a well-defined native structure. While databases such as the Protein Ensemble Database (PED) provide IDP ensembles obtained through a combination of experimental data and molecular modeling, the absence of reaction coordinates poses challenges in comprehensively understanding pertinent aspects of the system. In this study, we leverage the Energy Landscape Visualization Method (JCTC, 6482, 2019) to scrutinize four IDP ensembles sourced from PED. ELViM, a methodology that circumvents the need fora priorireaction coordinates, aids in analyzing the ensembles. The specific IDP ensembles investigated are as follows: two fragments of Nucleoporin (NUL: 884-993 and NUS: 1313-1390), Yeast Sic 1 N-terminal (1-90), and the N-terminal SH3 domain of Drk (1-59). Utilizing ELViM enables comprehensive validation of ensembles, facilitating the detection of potential inconsistencies in the sampling process. Additionally, it allows for identifying and characterizing the most prevalent conformations within an ensemble. Moreover, ELViM facilitates the comparative analysis of ensembles obtained under diverse conditions, thereby providing a powerful tool for investigating the functional mechanisms of IDPs.
Unveiling the Impact of Vernalization on Seed Oil Content and Fatty Acid Composition in Rapeseed Through Simulated Shorter Winters
Authors: Çağlı İrem , Kıvrak Büşra Elif , Altunbaş Osman , Sönmez Çağla
Published: January 2024

Climate change is leading to warmer winters world-wide with an increasing number of extreme events every year. Plants are majorly impacted by the escalating effects of global warming. In this study, we set up an experimental model to simulate warmer and shorter winters under laboratory conditions. Winter and spring varieties of rapeseed (Brassica napusL.) were subjected to diverse vernalization scenarios including three and four weeks-long vernalization as well as vernalization interruptions by one week-long devernalization at warm temperatures. The aim of the study was to assess the effects of the ‘vernalization models’ onBnaFLC(BnaFLCA02,BnaFLCA10andBnaFLCC02) expression, some yield related traits, a set of genes involved in fatty acid synthesis and seed oil content and fatty acid composition. A notable difference in vernalization responsiveness was observed inBnaFLCA02,BnaFLCA10, andBnaFLCC02between the late-flowering winter variety, Darmor, the early-flowering winter variety Bristol and the spring variety, Helios, after a three-week vernalization period. Our findings unveil a robust correlation between vernalization and seed oil content, as well as fatty acid composition in rapeseed. While the expression levels of fatty acid synthesis-related genes, includingBnaFAD2,BnaFAD5,BnaFATB,BnaMCOA(AAE13), andBnaWD40, exhibited significant changes under cold conditions in leaves, the expression levels of the same genes in developing seeds did not exhibit a strong correlation with vernalization, flowering time, or oil and fatty acid contents in seeds. Our results suggest that vernalization plays a role in seed oil biosynthesis beyond its impact on flowering time.
Genomic and transcriptomic characteristics of type VI secretion system inKlebsiella pneumoniae
Authors: Li Wanzhen , Huang Xiaolan , Li Dan , Liu Xiaofen , Jiang Xiaoying , Bian Xingchen , Li Xin , Zhang Jing
Published: January 2024

The Type VI secretion system (T6SS) serves as a crucial molecular weapon in interbacterial competition and significantly influences cell-cell interactions. Various bacterial species utilize their T6SSs to execute a multitude of functions, dictated by their ecological niche. However, the characteristics of T6SS in clinicalKlebsiella pneumoniae, a common opportunistic nosocomial pathogen, have not been fully elucidated. Here, we conducted a genomic analysis of 65 clinicalK. pneumoniaeisolates obtained from patients with varying infections. Genes encoding a T6SS cluster were present in all analyzed strains ofK. pneumoniae. Strains of identical sequence type (ST) carried structurally and numerically identical T6SS. Our study also highlights the importance of selecting conserved regions in key T6SS genes for effective primer design in PCR identification. We then utilized the predominant ST11K. pneumoniaeHS11286 to investigate the effect of knocking out T6SS marker geneshcporvgrG. Transcriptome analysis identified a total of 1,298 co-upregulated and 1,752 co-downregulated differentially expressed genes. Additionally, the absence ofhcporvgrGgene suppressed the expression of other T6SS-related genes within the locus I cluster. Pathway analysis showed that the Δhcpmutant exhibited alterations in transport, establishment of localization, localization and cell processes. Furthermore, interbacterial competition experiments showed thathcpandvgrGare essential for competitive ability of ST11K. pneumoniaeHS11286. This study furthers our understanding of the genomic characteristics of T6SS inK. pneumoniaeand suggested that the involvement of multiple genes in T6SS of strain HS11286.

Importance

Gram-negative bacteria use T6SS to deliver effectors that interact with neighboring cells for niche advantage.K. pneumoniaeis an opportunistic nosocomial pathogen that often carriers multiple T6SS loci, the function of which has not yet been elucidated. We performed a genomic analysis of 65 clinicalK. pneumoniaestrains isolated from various sources, confirming that all strains contained T6SS. We then used transcriptomics to further study changes in gene expression and effect upon interbacterial competition following knockout of key T6SS genes in ST11K. pneumoniaeHS11286. Our findings revealed the distribution and genomic characteristics of T6SS in clinicalK. pneumoniae. This study also described the overall transcriptional changes in the predominant Chinese ST11 strain HS11286 upon deletion of crucial T6SS genes. Additionally, this work provides a reference for future research on the identification of T6SS in bacteria.
How Older Adults Maintain Lateral Balance While Walking on Narrowing Paths
Authors: Kazanski Meghan E. , Cusumano Joseph P. , Dingwell Jonathan B.
Published: January 2024

Background

Older adults have difficulty maintaining side-to-side balance while navigating daily environments. Losing balance in such circumstances can lead to falls. We need to better understand how older adults adapt lateral balance to navigate environment-imposed task constraints.

Research Question

How do older adults adjust mediolateral balance while walking along continually-narrowing paths, and what are the stability implications of these adjustments?

Methods

Eighteen older (71.6±6.0 years) and twenty younger (21.7±2.6 years) healthy adults traversed 25m-long paths that gradually narrowed from 45cm to 5cm. Participants switched onto an adjacent path when they chose. We quantified participants’ lateral center-of-mass dynamics and lateral Margins of Stability (MoSL) as paths narrowed. We quantified lateral Probability of Instability (PoIL) as the cumulative probability that participants would take a laterally unstable (MoSL<0) step as they walked. We also extracted these outcomes where participants switched paths.

Results

As paths narrowed, all participants exhibited progressively smaller averageMoSLand increasingly largerPoIL. However, theirMoSLvariability was largest at both the narrowest and widest path sections. Older adults exhibited consistently both larger average and more variableMoSLacross path widths. Taken into account together, these resulted in either comparable or somewhat largerPoILas paths narrowed. Older adults left the narrowing paths sooner, on average, than younger. As they did so, older adults exhibited significantly larger average and more variableMoSL, but somewhat smallerPoILthan younger.

Significance

Our results directly challenge the predominant interpretation that larger averageMoSLas indicating “greater stability”, which we argue isinconsistentwith the principles underlying its derivation. In contrast, analyzing step-to-step gait dynamics, together with estimatingPoILallows one to properly quantify instability risk. Furthermore, the adaptive strategies uncovered using these methods suggest potential targets for future interventions to reduce falls in older adults.