bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the detection ofA. cantonensisin brain tissues of mammalian hosts
Authors: Arango Micaela , Delgado-Serra Sofía , Haines Lee , Paredes-Esquivel Claudia
Published: December 2022

Angiostrongylus cantonensisis an invasive nematode parasite that can cause eosinophilic meningitis in many vertebrate hosts, including humans. This parasite is spreading rapidly through the six continents, with Europe being the final frontier. Sentinel surveillance may be a cost-effective surveillance strategy to monitor the arrival of this pathogen to new geographical regions as this can be easily expanded to incorporate symptomatic wildlife. Necropsy and tissue digestion techniques are often used to recover helminth parasites from vertebrate host tissues, however their application to detect brain parasites is poorly utilized. Here we show that employing these techniques in combination can 1) help resolve false positive and negative animals, 2) provide accurate parasitic load values and 3) establish an accurate prevalence ofA. cantonensis. Our adapted tissue digestion technique can be easily performed, especially in wildlife hospitals where animal infections often precede human cases. Early detection of the parasite increases the efficacy of prevention, treatment, and disease control strategies not only in humans, but also in susceptible animal populations.

Key Findings

Optimized brain digestion techniques can detect parasitic helminths (A. cantonensis) in mammalian hosts.

Accuracy identifying neurotropic parasitic infections can be increased if a standard digestion protocol is applied.

The technique presented here can be easily implemented to detect brain nematodes in wildlife hospitals.
Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
Authors: Andersson Axel , Behanova Andrea , Avenel Christophe , Windhager Jonas , Malmberg Filip , Wählby Carolina
Published: December 2022

Imaging-based spatial transcriptomics techniques generate image data that, once processed, results in a set of spatial points with categorical labels for different mRNA species. A crucial part of analyzing downstream data involves the analysis of these point patterns. Here, biologically interesting patterns can be explored at different spatial scales. Molecular patterns on a cellular level would correspond to cell types, whereas patterns on a millimeter scale would correspond to tissue-level structures. Often, clustering methods are employed to identify and segment regions with distinct point-patterns. Traditional clustering techniques for such data are constrained by reliance on complementary data or extensive machine learning, limiting their applicability to tasks on a particular scale. This paper introduces ‘Points2Regions’, a practical tool for clustering spatial points with categorical labels. Its flexible and computationally efficient clustering approach enables pattern discovery across multiple scales, making it a powerful tool for exploratory analysis. Points2Regions has demonstrated efficient performance in various datasets, adeptly defining biologically relevant regions similar to those found by scale-specific methods. As a Python package integrated into TissUUmaps and a Napari plugin, it offers interactive clustering and visualization, significantly enhancing user experience in data exploration. In essence, Points2Regions presents a user-friendly and simple tool for exploratory analysis of spatial points with categorical labels.
Symbiotic nutrient cycling enables the long-term survival of Aiptasia in the absence of heterotrophic food sources
Authors: Rädecker Nils , Meibom Anders
Published: December 2022

Phototrophic Cnidaria are mixotrophic organisms that can complement their heterotrophic diet with nutrients assimilated by their algal endosymbionts. Metabolic models suggest that the translocation of photosynthates and their derivatives from the algae may be sufficient to cover the metabolic energy demands of the host. However, the importance of heterotrophy to the nutritional budget of these holobionts remains unclear. Here, we report on the long-term survival of the photosymbiotic anemone Aiptasia in the absence of heterotrophic food sources. Following one year of heterotrophic starvation, these anemones remained fully viable but showed an 85 % reduction in biomass compared to their regularly fed counterparts. This shrinking was accompanied by a reduction in host protein content and algal density, indicative of severe nitrogen limitation. Nonetheless, isotopic labeling experiments combined with NanoSIMS imaging revealed that the contribution of algal-derived nutrients to the host metabolism remained unaffected due to an increase in algal photosynthesis and more efficient carbon translocation. Taken together, our results suggest that, on a one- year timescale, heterotrophic feeding is not essential to fulfilling the energy requirements of the holobiont. But, while symbiotic nutrient cycling effectively retains carbon in the holobiont over long time scales, our data suggest that heterotrophic feeding is a critical source of nitrogen required for holobiont growth under oligotrophic conditions.
On the origin and evolution of the mosquito male-determining factorNix
Authors: Biedler James K. , Aryan Azadeh , Qi Yumin , Wang Aihua , Martinson Ellen O. , Hartman Daniel A. , Yang Fan , Sharma Atashi , Morton Katherine S. , Potters Mark , Chen Chujia , Dobson Stephen L. , Ebel Gregory D. , Kading Rebekah C. , Paulson Sally , Xue Rui-De , Strand Michael R. , Tu Zhijian
Published: December 2022

The mosquito family Culicidae is divided into two subfamilies named the Culicinae and Anophelinae.Nix, the dominant male-determining factor, has only been found in the culicinesAedes aegyptiandAe. albopictus, two important arboviral vectors that belong to the subgenus Stegomyia. Here we performed sex-specific whole-genome sequencing and RNAseq of divergent mosquito species and explored additional male-inclusive datasets to investigate the distribution ofNix. Except for the Culex genus,Nixhomologs were found in all species surveyed from the Culicinae subfamily, including 12 additional species from three highly divergent tribes comprising 4 genera, suggestingNixoriginated at least 133-165 MYA. Heterologous expression of one of three divergentNixORFs inAe. aegyptiresulted in partial masculinization of genetic females as evidenced by morphology anddoublesexsplicing. It is not clear whether insufficient transgene expression or sequence divergence or both are responsible for the lack of phenotype for the other two. Phylogenetic analysis suggestsNixis related tofemaleless(fle), a recently described intermediate sex-determining factor found exclusively in anopheline mosquitoes.Nixfrom all species has a conserved structure, including three RNA-recognition motifs (RRMs), as doesfle. However,Nixhas evolved at a much faster rate thanfle. The RRM3 of bothNixandfleare related to the single RRM of a widely distributed and conserved splicing factortransformer-2(tra2). RRM3-based phylogenetic analysis suggests this domain inNixandflemay have evolved fromtra2in a common ancestor of mosquitoes. Our results provide insights into the evolution of sex-determination and homomorphic sex chromosomes in mosquitoes, and will inform broad applications of mosquito-control strategies based on manipulating sex ratios towards the non-biting males.
Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomics
Authors: Qiu Xiaojie , Zhu Daniel Y. , Yao Jiajun , Jing Zehua , Zuo Lulu , Wang Mingyue , Min Kyung Hoi (Joseph) , Pan Hailin , Wang Shuai , Liao Sha , Lai Yiwei , Hao Shijie , Lu Yuancheng Ryan , Hill Matthew , Martin-Rufino Jorge D. , Weng Chen , Riera-Escandell Anna Maria , Chen Mengnan , Wu Liang , Zhang Yong , Wei Xiaoyu , Li Mei , Huang Xin , Xiang Rong , Yang Zhuoxuan , Liu Chao , Xia Tianyi , Liang Yingxin , Xu Junqiang , Hu Qinan , Hu Yuhui , Zhu Hongmei , Li Yuxiang , Chen Ao , Esteban Miguel A. , Gu Ying , Lauffenburger Douglas A. , Xu Xun , Liu Longqi , Weissman Jonathan S. , Liu Shiping , Bai Yinqi
Published: December 2022

Cells do not live in a vacuum, but in a milieu defined by cell–cell communication that can be measured via emerging high-resolution spatial transcriptomics approaches. However, analytical tools that fully leverage such data for kinetic modeling remain lacking. Here we present Spateo (aristoteleo/spateo-release), a general framework for quantitative spatiotemporal modeling of single-cell resolution spatial transcriptomics. Spateo delivers novel methods for digitizing spatial layers/columns to identify spatially-polar genes, and develops a comprehensive framework of cell-cell interaction to reveal spatial effects of niche factors and cell type-specific ligand-receptor interactions. Furthermore, Spateo reconstructs 3D models of whole embryos, and performs 3D morphometric analyses. Lastly, Spateo introduces the concept of “morphometric vector field” of cell migrations, and integrates spatial differential geometry to unveil regulatory programs underlying various organogenesis patterns of Drosophila. Thus, Spateo enables the study of the ecology of organs at a molecular level in 3D space, beyond isolated single cells.
Aldo-Keto Reductase Family 1 Member A1 (AKR1A1) Deficiency Exacerbates Alcohol-Induced Hepatic Oxidative Stress, Inflammation, Steatosis, and Fibrosis
Authors: Lan Ying-Wei , Chen Wan-Ru , Yen Chih-Ching , Chong Kowit-Yu , Chen Ying-Cheng , Fan Hueng-Chuen , Chen Ming-Shan , Chen Chuan-Mu
Published: December 2022

Background

Alcohol-associated liver disease (ALD) covers a wide range of hepatic lesions that depend on the amount and duration of alcohol consumption, from early and reversible conditions to hepatic steatosis and severe lesions, including steatohepatitis and alcoholic fibrosis, to irreversible cirrhosis. AKR1A1, an aldo-keto reductase family member, participates in the detoxification of alcohol-derived acetaldehyde, but its role in ALD remains unclear. In this study, we studied the role of AKR1A1 in the development of ALD usingAkr1a1-/-knockout mice and palmitic acid/oleic acid (P/O) plus ethanol-treated AML12 hepatocyte cells.

Methods

Levels of AKR1A1 were measured in mice fed with the Lieber-DeCarli diet containing 5% alcohol (alcohol-fed, AF) or control liquid diet (pair-fed, PF). The effects of AKR1A1 on the liver function, inflammation, oxidative stress, lipid accumulation, and fibrosis were assessed in AF-inducedAkr1a1-/-and ICR control mice.

Results

Data showed thatAF-Akr1a1-/-mice exhibited an exacerbation of liver injury and increased gene and protein levels of inflammatory mediators, oxidative stress, lipid accumulation, and fibrosis, whilst decreased expression of antioxidant enzymes in their livers than the AF-ICR mice. Therefore, loss of AKR1A1 can activate 4-HNE/p53 signaling to modulate ROS and antioxidant balance, increase lipid peroxidation, fatty acid synthesis and lipid droplet formation, reduced fatty acid β-oxidation, and elevated proinflammatory and fibrotic mediator, eventually exacerbate the ALD. Inin vitrostudy, we further demonstrated that knockdown ofAkrlalaggravated the effects of alcohol plus P/O-induced oxidative stress and steatosis, LPS-stimulated inflammation, and TGF-β1-induced fibrosis in AML12 hepatocyte cells.

Conclusion

our results revealed that AKR1A1 exerts protective effects on alcohol-induced liver injury, steatosis, and fibrosis, possibly by regulating the 4-HNE-p53 signaling pathway.
Modelling metastasis in zebrafish unveils regulatory interactions of cancer-associated fibroblasts with circulating tumour cells
Authors: Hurtado Pablo , Martínez-Pena Inés , Yepes-Rodríguez Sabrina , Bascoy-Otero Miguel , Abuín Carmen , Fernández-Santiago Cristóbal , Sánchez Laura , López-López Rafael , Piñeiro Roberto
Published: December 2022

The dynamic intercommunication between tumour cells and cells from the microenvironment, such as cancer-associated fibroblast (CAFs), is a key factor driving breast cancer (BC) metastasis. Clusters of circulating tumour cells (CTCs), known to bare a higher efficiency at establishing metastases, are found in the blood of BC patients, often accompanied by CAFs in heterotypic CTC-clusters. Previously we have shown the utility of CTC-clusters models and the zebrafish embryo as a model of metastasis to understand the biology of breast cancer CTC-clusters. In this work, we use the zebrafish embryo to study the interactions between CTCs in homotypic clusters and CTC-CAFs in heterotypic CTC-clusters to identify potential pro-metastatic traits derived from CTC-CAF communication. We found that upon dissemination CAFs seem to exert a pro-survival and pro-proliferative effect on the CTCs, but only when CTCs and CAFs remain joined as cell clusters. Our data indicate that the clustering of CTC and CAF allows the establishment of physical interactions that when maintained over time favour the selection of CTCs with a higher capacity to survive and proliferate upon dissemination. Importantly, this effect seems to be dependent on the survival of disseminated CAFs and was not observed in the presence of normal fibroblasts. Moreover, we show that CAFs can exert regulatory effects on the CTCs without being involved in promoting tumour cell invasion, and these effects are differential based on the BC cell molecular phenotype, and the crosstalk between tumour cells and CAFs, i.e. paracrine or physical interaction. Lastly, we show that the physical communication between BC cells and CAFs leads to the production of soluble factors involved in BC cell survival and proliferation. These findings suggest the existence of a CAF-regulatory effect on CTC survival and proliferation sustained by cell-to-cell contacts and highlight the need to understand the molecular mechanisms that mediate the interaction between the CTCs and CAFs in clusters enhancing the metastatic capacity of CTCs.
Dalpiciclib Partially Abrogates ER Signaling Activation Induced by Pyrotinib In HER2+HR+Breast Cancer
Authors: Bu Jiawen , Zhang Yixiao , Niu Nan , Bi Kewei , Sun Lisha , Qiao Xinbo , Wang Yimin , Zhang Yinan , Jiang Xiaofan , Wang Dan , Ma Qingtian , Li Huajun , Liu Caigang
Published: December 2022

Background

Recent evidences from clinical trials (NCT04486911) revealed that the combination of pyrotinib, letrozole and dalpiciclib exerted optimistic therapeutic effect to treat HER2+HR+breast cancer, however, the underlying molecular mechanism remained further investigation.

Methods

Through the drug sensitivity test, the drug combination efficacy of pyrotinib, tamoxifen and dalpiciclib to BT474 cells were tested. The underlying molecular mechanisms were investigated using immunofluorescence, western blot analysis, immunohistochemical staining and cell cycle analysis. Potential risk factor which may indicate the responsiveness to drug treatment in HER2+/HR+breast cancer was selected out using RNA-sequence and tested using immunohistochemical staining and in vivo drug susceptibility test.

Results

We found that pyrotinib combined with dalpiciclib exerted better cytotoxic efficacy than pyrotinib combined with tamoxifen in BT474 cells. Degradation of HER2 could enhance ER nuclear transportation, activating ER signaling pathway in BT474 cells whereas dalpiciclib could partially abrogate this process. This may be the underlying mechanism by which combination of pyrotinib, tamoxifen and dalpiciclib exerted best cytotoxic effect. Furthermore, CALML5 was revealed to be a risk factor in the treatment of HER2+/HR+breast cancer and the usage of dalpiciclib might overcome this.

Conclusion

Our study provided evidence that the usage of dalpiciclib in the treatment of HER2+/HR+breast cancer could partially abrogate the estrogen signaling pathway activation caused by anti-HER2 therapy and revealed that CALML5 could serve as a risk factor in the treatment of HER2+/HR+breast cancer.

Funding

This study was supported by the National Natural Science Foundation of China (#U20A20381, #81872159)
Latitude influences stability via stabilizing mechanisms in naturally-assembled forest ecosystems at different spatial grains
Authors: Zhou Tianyang , Craven Dylan , Kreft Holger , Zhang Jiaxin , Wang Xugao , Lian Juyu , Ye Wanhui , Jin Guangze , Mi Xiangcheng , Yao Yujun , Ren Haibao , Yang Jie , Cao Min , Wang Congrong , Qin Yuanzhi , Zhou Gang , Fei Yanan , Xu Yaozhan , Qiao Xiujuan , Jiang Mingxi , Guerrero-Ramírez Nathaly R.
Published: December 2022

Ecosystem stability reveals how ecosystems respond to global change over time. Yet, the focus of past research on small spatial grains and extents overlooks scale dependence and how broad-scale environmental gradients shape stability. Here, we use forest inventory data covering a broad latitudinal gradient from the temperate to the tropical zone to examine cross-scale variation in stability of aboveground biomass and underlying stabilizing mechanisms. While stability did not shift systematically with latitude at either spatial grain, we found evidence that species asynchrony increased towards the tropics at the small spatial grain while species stability decreased at both spatial grains. Moreover, latitude stabilized forest communitiesviaits effects on both stabilizing mechanisms, which compensated for the weak and destabilizing effects of species richness. Yet, the trade-off in the relative importance of species stability and species asynchrony for stability was not mediated by latitude, suggesting that context-dependent factors - to a greater extent than macroecological ones - underlie large-scale patterns of stability. Our results highlight the crucial role of species asynchrony and species stability in determining ecosystem stability across broad-scale environmental gradients, suggesting that conserving biodiversity alone may not be sufficient for stabilizing naturally-assembled forest ecosystems.
Targeting the TR4-induced RCC cells-derived exosomally initiated signaling increases Sunitinib efficacy
Authors: Wang Zhenwei , Sun Yin , Xu Huiyang , Huang Chi-Ping , Cheng Bo , Chou Fuju , You Bosen , Qiu Xiaofu , Yang Guosheng , Chang Chawnshang
Published: December 2022

Sunitinib is the first-line therapy for metastatic clear cell renal cell carcinoma (RCC) via suppressing neoangiogenesis and tumor growth. The detailed mechanisms, especially whether and how RCC cells can impact endothelial cells sensitivity to Sunitinib, remain unclear. Here, we found that TR4 was commonly upregulated in RCC tissue and relative to tumor angiogenesis. Tube formation and Mouse aortic ring assay showed that the overexpression or knockdown of TR4 in RCC cells enhanced or reduced the angiogenesis of endothelial cells and their resistance to Sunitinib in vitro. Mechanistically, We found that TR4 transcriptionally increase ADAM15 expression, as a consequence, exosomes carrying relatively large amounts of ADAM15 secreted from RCC cell resulted in activating the EGFR phosphorylation and reducing the efficacy of Sunitinib in endothelial cells. Targeting the TR4-induced renal cancers-derived exosomelly initiated signaling with a small molecular, CRM197, increases sunitinib efficacy in vitro and xenograft tumor models. Taken together, our findings indicate a novel function of TR4 in RCC blunted the efficacy of sunitinib via exosomal ADAM15-induced activation of EGFR signaling pathway in endothelial cells.
Interplay of p53 and XIAP protein dynamics orchestrates cell fate in response to chemotherapy
Authors: Abukwaik Roba , Vera-Siguenza Elias , Tennant Daniel A. , Spill Fabian
Published: December 2022

Chemotherapeutic drugs are used to treat almost all types of cancer, but the intended response, i.e., elimination, is often incomplete, with a subset of cancer cells resisting treatment. Two critical factors play a role in chemoresistance: the p53 tumour suppressor gene and the X-linked inhibitor of apoptosis (XIAP). These proteins have been shown to act synergistically to elicit cellular responses upon DNA damage induced by chemotherapy, yet, the mechanism is poorly understood. This study introduces a mathematical model characterising the apoptosis pathway activation by p53 before and after mitochondrial outer membrane permeabilisation upon treatment with the chemotherapy Doxorubicin (Dox).“In-silico”simulations show that the p53 dynamics change dose-dependently. Under medium to high doses of Dox, p53 concentration ultimately stabilises to a high level regardless of XIAP concentrations. However, caspase-3 activation may be triggered or not depending on the XIAP induction rate, ultimately determining whether the cell will perish or resist. Consequently, the model predicts that failure to activate apoptosis in some cancer cells expressing wild-type p53 might be due to heterogeneity between cells in upregulating the XIAP protein, rather than due to the p53 protein concentration. Our model suggests that the interplay of the p53 dynamics and the XIAP induction rate is critical to determine the cancer cells’ therapeutic response.
Limits to evolutionary rescue by conjugative plasmids
Authors: Geoffroy Félix , Uecker Hildegard
Published: December 2022

Plasmids may carry genes coding for beneficial traits and thus contribute to adaptation of bacterial populations to environmental stress. Conjugative plasmids can horizontally transfer between cells, which a priori facilitates the spread of adaptive alleles. However, if the potential recipient cell is already colonized by another incompatible plasmid, successful transfer may be prevented. Competition between plasmids can thus limit horizontal transfer. Previous modeling has indeed shown that evolutionary rescue by a conjugative plasmid is hampered by incompatible resident plasmids in the population. If the rescue plasmid is a mutant variant of the resident plasmid, both plasmids transfer at the same rates. A high conjugation rate then has two, potentially opposing, effects – a direct positive effect on spread of the rescue plasmid and an increase in the fraction of resident plasmid cells. This raises the question whether a high conjugation rate always benefits evolutionary rescue. In this article, we systematically analyse three models of increasing complexity to disentangle the benefits and limits of increasing horizontal gene transfer in the presence of plasmid competition and plasmid costs. We find that the net effect can be positive or negative and that the optimal transfer rate is thus not always the highest one. These results can contribute to our understanding of the many facets of plasmid-driven adaptation and the wide range of transfer rates observed in nature.
B vitamin quantification in lentil seed tissues using ultra-performance liquid chromatography-selected reaction monitoring mass spectrometry
Authors: Marshall Jeremy , Vargas Ana , Bett Kirstin
Published: December 2022

Lentils are an important source of macronutrients, including protein and fiber, as well as micronutrients such as vitamins and minerals, especially in a plant-based diet. Quantifying variation among genotypes, including wild germplasm, is desirable to better understand the genetics of differential B vitamins content for breeding of this trait and to understand their potential contributions to the lentil crop. We analyzed thirty-four cultivated and three wild genotypes for vitamins B1, B2, B3, B5, B6, B7, and B9. Seeds were assayed whole, and separated into cotyledons only, or seed coats only. Variation for all B vitamins was observed across the cultivars. Overall, cotyledons had higher concentrations of B1 and B3, while seed coats had higher concentrations of B2, B5, B6, and B9. Wild accessions had the highest concentrations of vitamin B9 and were also among the highest for vitamin B2. These results demonstrate the differential distribution of B vitamins across seed tissues and lentil genotypes, and that dehulling prior to consumption results in the loss of B vitamins otherwise available in whole seeds. They also indicate there is genetic variability which could be used to increase B-vitamin levels in lentil via breeding.
Savory Signaling: T1R umami receptor modulates endoplasmic reticulum calcium store content and release dynamics in airway epithelial cells
Authors: McMahon Derek B , Jolivert Jennifer F. , Kuek Li Eon , Adappa Nithin D. , Palmer James N. , Lee Robert J
Published: December 2022

T1Rs are expressed in solitary chemosensory cells of the upper airway where they detect apical glucose levels and repress bitter taste receptor Ca2+ signaling pathways. Microbial growth leads to a decrease in apical glucose levels. T1Rs detect this change and liberate bitter taste receptor signaling, initiating an innate immune response to both kill and expel pathogens through releasing antimicrobial peptides and increasing nitric oxide production and ciliary beat frequency. However, chronic inflammation due to disease, smoking, or viral infections causes a remodeling of the airway epithelial. The resulting squamous metaplasia causes a loss of multi-ciliated cells and solitary chemosensory cells, replaced by basal epithelial cells. To understand how T1R function is altered during disease, we used basal epithelial cells as a model to study the function of T1R3 on Ca2+signaling dynamics. We found that both T1R1 and T1R3 detect amino acids and signal via cAMP, increasing the responsiveness of the cells to Ca2+signaling stimuli. Either knocking down T1R1/3 or treating wild-type cells with MEM amino acids caused a reduction in ER Ca2+content through a non-cAMP signaled pathway. Treatment with amino acids led to a reduction in downstream denatonium-induced Ca2+-signaled caspase activity. Thus, amino acids may be used to reduce unwanted apoptosis signaling in treatments containing bitter compounds.
Homeostasis in Networks with Multiple Inputs
Authors: de Oliveira Madeira João Luiz , Antoneli Fernando
Published: December 2022

Homeostasis, also known as adaptation, refers to the ability of a system to counteract persistent external disturbances and tightly control the output of a key observable. Existing studies on homeostasis in network dynamics have mainly focused on ‘perfect adaptation’ in deterministic single-input single-output networks where the disturbances are scalar and affect the network dynamics via a pre-specified input node. In this paper we provide a full classification of all possible network topologies capable of generating infinitesimal homeostasis in arbitrarily large and complex multiple-input parameter networks. Working in the framework of ‘infinitesimal homeostasis’ allows us to make no assumption about how the components are interconnected and the functional form of the associated differential equations, apart from being compatible with the network architecture. Remarkably, we show that there are just three distinct ‘mechanisms’ that generate infinitesimal homeostasis. Each of these three mechanisms generates a rich class of well-defined network topologies – calledhomeostasis subnetworks. Most importantly, we show that these classes of homeostasis subnetworks provides a topological basis for the classification of ‘homeostasis types’: the full set of all possible multiple-input parameter networks can be uniquely decomposed into these special homeostasis subnetworks. We build on previous work that treated the cases of single-input node and multiple-input node, both with a single scalar input parameter. Furthermore, we identify a new phenomenon that occurs in the multiparameter setting, that we callhomeostasis mode interaction, in analogy with the well-known characteristic of multiparameter bifurcation theory.
Target Recycling Amplification Process for Digital Detection of Exosomal MicroRNAs Through Photonic Resonator Absorption Microscopy
Authors: Wang Xiaojing , Shepherd Skye , Li Nantao , Che Congnyu , Song Tingjie , Xiong Yanyu , Palm Isabella Rose , Zhao Bin , Kohli Manish , Demirci Utkan , Lu Yi , Cunningham Brian T.
Published: December 2022

Exosomal microRNAs (miRNAs) have considerable potential as pivotal biomarkers to monitor cancer development, dis-ease progression, treatment effects and prognosis. Here, we report an efficient target recycling amplification process (TRAP) for the digital detection of exosomal miRNAs using photonic resonator absorption microscopy (PRAM). Through toehold-mediated DNA strand displacement reactions, we achieve multiplex digital detection with sub-attomolar sensitivity in 20 minutes, robust selectivity for single nucleotide variants, and a broad dynamic range from 1 aM to 1 pM. We then applied our TRAP system to quantify miRNA in exosomal total RNAs isolated from human cancer cell lines. Compared with traditional qRT-PCR methods, TRAP showed similar accuracy in profiling exosomal miRNAs derived from cancer cells, but also exhibited at least 31-fold and 61-fold enhancement in the limits of miRNA-375 and miRNA-21 detection, respectively. The TRAP approach is ideal for exosomal or circulating miRNA biomarker quantification, where the miRNAs are present in low concentrations or sample volume, with potentials for frequent, low-cost, and minimally invasive point-of-care testing.
A CXCR3-activating peptide increases Tear Break Up Time and corrects corneal haze in a rabbit model of environmental dry eye
Authors: Wells Alan , Wang Yadong , Shao Hanshuang , Sohnen Peri , Swamynathan Shivalingappa K.
Published: December 2022

Purpose

Environmentally-triggered dry eye disease (DED) or keratoconjunctivitis sicca (KCS), which constitutes the majority of DED cases, currently is palliatively treated with aqueous replacement solutions that do not target the dysfunction of the mucin and lipid components of tears. Herein, we tested whether a peptide that increased goblet cell numbers in a model of scleral chemical injury would also improve tear quality in environmental DED.

Methods

Environmental DED was established by exposing New Zealand white rabbits (8 per group, female) to 20% humidity with rapid air replacement and b.i.d. atropine sulfate eyedrops for 3 weeks prior to test article administration; this continued for the subsequent 3 weeks of testing. Animals were dosed by (A) saline, (B) b.i.d. eyedrop of peptide in saline, (C) b.i.d. eyedrop of peptide in coacervate, or (D) weekly subconjunctival injection of peptide.

Results

The environmental DED was established with both Schirmer and TBUT being reduced by from baseline at the start of test article; these levels were maintained as low through the testing period. All three treatment regimens increased TBUT approximately 3x to levels greater than prior to desiccation, with little effect on Schirmer. Corneal haze was present in all eyes after induction, and largely cleared up by all three treatments. End of study enucleation of the eye did not show any changes in goblet cells numbers, which remained high throughout the induction and treatment.

Conclusions

The treatment of environmental DED/KCS with a peptide that activates CXCR3 improved tear quality and reversed corneal pathology by promoting tear stability, while not affecting aqueous volume of the tears.
Zinc and laboratory emerge date impact honey bee gut microbiota and survival
Authors: Soares Kilmer Oliveira , Ricke Dylan , de Oliveira Celso José Bruno , Lima Marcos Venâncio , Mrofchak Ryan , Rodrigues Adriana Evangelista , Madden Christopher , Johnson Reed , Hale Vanessa L.
Published: December 2022

Honey bees (Apis mellifera) may be exposed to a wide variety of chemicals in the environment, including pesticides, antibiotics, and metals. Zinc, for example, is commonly included in fertilizers, pesticides, and feed additives, and is found in agricultural runoff. Honey bees can be exposed to zinc directly or indirectly by consuming zinc-contaminated nectar and pollen. However, there is a paucity of studies addressing the putative effects of zinc on honey bee’s health. In this study, we tested the effects of zinc on honey bee survivorship and gut microbiota. To evaluate survivorship, we exposed bees to six concentrations of zinc (0, 50, 100, 250, 500, or 1000 mg/L) and assessed survival daily for 10 days. To evaluate effects of zinc on gut microbiota, we exposed bees to 5 or 100 mg/L zinc. Bees were sampled before (day 0) and after zinc exposure (days 3, 6, and 9). Abdominal contents underwent DNA extraction and 16S rRNA sequencing (V3-V4) on an Illumina MiSeq. Sequences were filtered and processed through QIIME2 and DADA2. Zinc treatment had minimal effects on bacterial DNA concentrations and absolute cell counts while emerge date (the date a bee emerged from the brood comb) had a significant effect with decreased bacterial concentrations and cell counts observed at later emerge dates. Survival was only minimally impacted (>89% survival) at zinc concentrations up to 100 mg/L. Zinc had limited effects on overall gut microbial composition, diversity, and taxonomic abundances, with the greatest differences noted in the bee group exposed to the higher concentration of zinc (100 mg/L). In this group, several beneficial taxa (Lactobacillus, Rhizobiaceae,Gilliamella) were found at reduced abundances, whilePaenibacillus, a potentially pathogenic taxa, was found at increased abundances. This suggests that zinc exposure, even at relatively low levels, may negatively impact honey bee health, even if survivorship is not dramatically impacted. Notably, emerge date effects were also observed in microbial composition. These results demonstrate the need to include assessments of honey bee gut microbiota in addition to other metrics of honey bee health and survivorship when evaluating the potential effects of agrochemicals on honey bees
Bridging the gap between formal theory and scientific reform practices
Authors: Buzbas Erkan , Devezer Berna
Published: December 2022

A core problem that has been addressed in the scientific reform movement so far is the low rates of reproducibility of research results. Mainstream reform literature aimed at increasing reproducibility rates by implementing changes in research practice and scientific policy. At the sidelines of reform, theoreticians have worked on understanding the underlying causes of irreproducibility from ground up. Each approach faces its own challenges. While mainstream focus on swift practical changes has not been buttressed by sound theoretical arguments, theoretical work is slow and initially is only capable of answering questions in idealized setups, removed from real life constraints. In this article, we continue to develop theoretical foundations in understanding non-exact replications and meta-hypothesis tests in multi-lab replication studies, juxtapose these theoretical intuitions with practical reform examples, and expose challenges we face. In our estimation, a major challenge in the next generation of the reform movement is to bridge the gap between theoretical knowledge and practical advancements.
Understanding pediatric long COVID using a tree-based scan statistic approach: An EHR-based cohort study from the RECOVER Program
Authors: Lorman Vitaly , Rao Suchitra , Jhaveri Ravi , Case Abigail , Mejias Asuncion , Pajor Nathan M. , Patel Payal , Thacker Deepika , Bose-Brill Seuli , Block Jason , Hanley Patrick C. , Prahalad Priya , Chen Yong , Forrest Christopher B. , Bailey L. Charles , Lee Grace M. , Razzaghi Hanieh
Published: December 2022

STRUCTURED ABSTRACT

Objectives

Post-acute sequalae of SARS-CoV-2 infection (PASC) is not well defined in pediatrics given its heterogeneity of presentation and severity in this population. The aim of this study is to use novel methods that rely on data mining approaches rather than clinical experience to detect conditions and symptoms associated with pediatric PASC.

Materials and Methods

We used a propensity-matched cohort design comparing children identified using the new PASC ICD10CM diagnosis code (U09.9) (N=1309) to children with (N=6545) and without (N=6545) SARS-CoV-2 infection. We used a tree-based scan statistic to identify potential condition clusters co-occurring more frequently in cases than controls.

Results

We found significant enrichment among children with PASC in cardiac, respiratory, neurologic, psychological, endocrine, gastrointestinal, and musculoskeletal systems, the most significant related to circulatory and respiratory such as dyspnea, difficulty breathing, and fatigue and malaise.

Discussion

Our study addresses methodological limitations of prior studies that rely on pre-specified clusters of potential PASC-associated diagnoses driven by clinician experience. Future studies are needed to identify patterns of diagnoses and their associations to derive clinical phenotypes.

Conclusion

We identified multiple conditions and body systems associated with pediatric PASC. Because we rely on a data-driven approach, several new or under-reported conditions and symptoms were detected that warrant further investigation.

LAY SUMMARY

Pediatric long COVID in children does not currently have a precise clinical definition, in part due to its widely varying presentation in kids. By comparing children diagnosed with long COVID to children who had COVID-19 but were not diagnosed with long COVID, this study identified several groups of symptoms and conditions that are associated with pediatric long COVID. These findings can be used towards developing a precise definition of long COVID in children for use in future studies.
Reliable and generalizable brain-based predictions of cognitive functioning across common psychiatric illness
Authors: Chopra Sidhant , Dhamala Elvisha , Lawhead Connor , Ricard Jocelyn A. , Orchard Edwina R. , An Lijun , Chen Pansheng , Wulan Naren , Kumar Poornima , Rubenstein Arielle , Moses Julia , Chen Lia , Levi Priscila , Holmes Alexander , Aquino Kevin , Fornito Alex , Harpaz-Rotem Ilan , Germine Laura T. , Baker Justin T. , Yeo BT Thomas , Holmes Avram J.
Published: December 2022

A primary aim of precision psychiatry is the establishment of predictive models linking individual differences in brain functioning with clinical symptoms. In particular, cognitive impairments are transdiagnostic, treatment resistant, and contribute to poor clinical outcomes. Recent work suggests thousands of participants may be necessary for the accurate and reliable prediction of cognition, calling into question the utility of most patient collection efforts. Here, using a transfer-learning framework, we train a model on functional imaging data from the UK Biobank (n=36,848) to predict cognitive functioning in three transdiagnostic patient samples (n=101-224). The model generalizes across datasets, and brain features driving predictions are consistent between populations, with decreased functional connectivity within transmodal cortex and increased connectivity between unimodal and transmodal regions reflecting a transdiagnostic predictor of cognition. This work establishes that predictive models derived in large population-level datasets can be exploited to boost the prediction of cognitive function across clinical collection efforts.
Genomic, Functional and Structural Analyses Reveal Mechanisms of Evolutionary Innovation within the Sea Anemone 8 Toxin Family
Authors: Ashwood Lauren M. , Elnahriry Khaled A. , Stewart Zachary K. , Shafee Thomas , Naseem Muhammad Umair , Szanto Tibor G. , van der Burg Chloé A. , Smith Hayden L. , Surm Joachim M. , Undheim Eivind A.B. , Madio Bruno , Hamilton Brett R. , Guo Shaodong , Wai Dorothy C.C. , Coyne Victoria L. , Phillips Matthew J. , Dudley Kevin J. , Hurwood David A. , Panyi Gyorgy , King Glenn F. , Pavasovic Ana , Norton Raymond S. , Prentis Peter J.
Published: December 2022

ShK fromStichodactyla helianthushas established the therapeutic potential of sea anemone venom peptides, but many lineage-specific toxin families in actinarians remain uncharacterised. One such peptide family, sea anemone 8 (SA8), is present in all five sea anemone superfamilies. We explored the genomic arrangement and evolution of the SA8 gene family inActinia tenebrosaandTelmatactis stephensoni, characterised the expression patterns of SA8 sequences, and examined the structure and function of SA8 from the venom ofT.stephensoni. We identified ten SA8 genes in two clusters and six SA8 genes in five clusters forT. stephensoniandA. tenebrosa, respectively. Nine SA8T. stephensonigenes were found in a single cluster and an SA8 peptide encoded by an inverted SA8 gene from this cluster was recruited to venom. We show that SA8 genes in both species are expressed in a tissue-specific manner and the inverted SA8 gene has a unique tissue distribution. While functional activity of the SA8 putative toxin encoded by the inverted gene was inconclusive, its tissue localisation is similar to toxins used for predator deterrence. We demonstrate that, although mature SA8 putative toxins have similar cysteine spacing to ShK, SA8 peptides are distinct from ShK peptides based on structure and disulfide connectivity. Our results provide the first demonstration that SA8 is a unique gene family in actiniarians, evolving through a variety of structural changes including tandem and proximal gene duplication and an inversion event that together allowed SA8 to be recruited into the venom ofT.stephensoni.
SMRT-AgRenSeq-d in potato (Solanum tuberosum) identifies candidates for the nematode resistance Gpa5
Authors: Wang Yuhan , Brown Lynn H , Adams Thomas M , Cheung Yuk Woon , Li Jie , Young Vanessa , Todd Drummond T , Armstrong Miles R , Neugebauer Konrad , Kaur Amanpreet , Harrower Brian , Oome Stan , Wang Xiaodan , Bayer Micha , Hein Ingo
Published: December 2022

Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes.

To identify functional NLRs in established varieties, we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMRT-AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible potatoes that is translated into an F1 score. Using a SMRT-RenSeq based sequence representation of the NLRome from the cultivar Innovator, SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genesR1, R2-like, R3aandR3bin a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1 which indicates absolute linkage in the panel.

When applied to the elusive nematode disease resistance geneGpa5that controls the Potato Cyst Nematode (PCN) speciesGlobodera pallida(pathotypes Pa2/3), SMRT-AgRenSeq-d identified nine strong candidates. These map to the previously established position on potato chromosome 5 and are potential homologs of the late blight resistance geneR1.

Assuming that NLRs are involved in controlling many types of resistances, SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems. In potato, SMRT-AgRenSeq-d lends itself, for example, to further study the elusive PCN resistancesH1orH3for which phenotypic data exist.
Template-Directed RIG-I Agonist Assembly for Targeted Cancer Immunotherapy
Authors: Ghosh Subrata K. , Robertson Neil , Crosier Edward , Dudley Michael , Liu Qiyong P. , Medarova Zdravka
Published: December 2022

Recent developments in the use of pattern recognition receptors (PRRs) aim to harness the innate power of the immune system for cancer therapy. Understanding how to recruit PRRs, such as RIG-I, in a tumor-selective manner is critical for its adoption in the clinic. We describe the use of a tumor-selective template-based agonist of RIG-I to induce type-I IFN signaling and tumor cell apoptosis. The agonist, termed ss-ppp-miRNA-21, comprises a single stranded RNA oligonucleotide modified with a 5’-triphosphate and complementary to an endogenous miRNA enriched in tumor cells. We demonstrate the efficacy of the template-directed approach and detail mechanistic studies validating the hypothesis of a template-directed RIG-I agonist assembly using miRNA-21 as a target. The template-directed strategy described here moves us closer to making RIG-I a clinically relevant target in oncology because it achieves targeted activation of innate immunity in the tumor microenvironment in the context of systemic agonist injection.
Proximity labelling allows to study novel factors in chloroplast developmenta
Authors: Wurzinger Bernhard , Stael Simon , Leonardelli Manuela , Perolo Carlo , Melzer Michael , Chaturvedi Palak , Afjehi-Sadat Leila , Weckwerth Wolfram , Teige Markus
Published: December 2022

Chloroplast development is initiated by light-signals triggering the expression of nuclear encoded chloroplast genes in a first phase, followed by massive structural changes in the transition from proplastids to mature chloroplasts in the second phase. While the molecular players involved in the first phase are currently emerging, regulatory components of the second phase, demanding high plastid translational capacity and RNA processing, are still enigmatic. This is mostly due to the very limited amount of plant material at the early phases of development that makes biochemical studies such as identifying protein interaction networks very difficult. To overcome this problem, we developed a TurboID-based proximity labelling workflow that requires only very limited sample amounts to obtain mechanistic insights into protein interaction networks present in the early stages of plastid development. We used the CGL20a protein, a novel factor involved in chloroplast development, as bait forin vivoproximity labelling in developing seedlings 7 days after germination. We found that CGL20a resides in a nexus of RNA binding proteins mainly associated to ribosomal RNA (rRNA) including different ribosome-associated proteins.

One-sentence summary

The use of plastid-specific in vivo proximity labelling in Arabidopsis seedlings allows to identify novel components in chloroplast development in higher plants.
Antigen presentation by clonally diverse CXCR5+ B cells to CD4 and CD8 T cells is associated with durable response to immune checkpoint inhibitors
Authors: Ding Lizhong , Sun Lu , Bu Melissa T. , Zhang Yanjun , Scott Lauren N. , Prins Robert M. , Su Maureen A. , Lechner Melissa G. , Hugo Willy
Published: December 2022

The mechanism by which ICI (immune checkpoint inhibitor) induce durable antitumor T cell activity remains inadequately defined. Tumors from melanoma patients who responded to ICI or MAPK pathway inhibitors (MAPKi) therapy generally displayed increased T cell infiltration and interferon gamma (IFNγ) pathway activation. Yet, the rate of durable tumor control after ICI is almost twice that of MAPKi. Comparing the transcriptome of cohorts of melanoma patients treated with ICI or MAPKi therapy, we discovered that response to ICI is associated with CXCL13-driven recruitment of CXCR5+ B cells with higher clonal diversity than MAPKi. Higher B cell receptor (BCR) diversity allows presentation of diverse tumor antigens by B cells, resulting in robust increases of IFNγ pathway activity and CXCL13 expression in tumor reactive CD8 T cells after ICI therapy. Accordingly, ICI-treated melanoma patients, but not MAPKi, whose tumors displayed higher BCR diversity and IFNγ pathway score, survived significantly longer than those with either one or none. Thus, response to ICI, but not to MAPKi therapy, induces the recruitment of clonally diverse antigen presenting B cells that activate tumor specific, cytotoxic CD8 T cells to effect a durable antitumor immune response. Our result suggests that enhancing B cells’ tumor antigen presentation to intratumoral CD8 T cells can increase the rate of long-term response to ICI therapy.