bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-pronged approach to human mesenchymal stromal cells senescence quantification with a focus on label-free methods
Authors: Zhai Weichao , Tan Jerome , Russell Tobias , Chen Sixun , McGonagle Dennis , Win Naing May , Yong Derrick , Jones Elena
Published: January 2021

Human mesenchymal stromal cells (hMSCs) have demonstrated, in various preclinical settings, consistent ability in promoting tissue healing and improving outcomes in animal disease models. However, translation from the preclinical model into clinical practice has proven to be considerably more difficult. One key challenge being the inability to perform in situ assessment of the hMSCs in continuous culture, where the accumulation of the senescent cells impairs the culture’s viability, differentiation potential and ultimately leads to reduced therapeutic efficacies. Histochemical $$\upbeta $$
β
-galactosidase staining is the current standard for measuring hMSC senescence, but this method is destructive and not label-free. In this study, we have investigated alternatives in quantification of hMSCs senescence, which included flow cytometry methods that are based on a combination of cell size measurements and fluorescence detection of SA-$$\upbeta $$
β
-galactosidase activity using the fluorogenic substrate, C$${_{12}}$$

12

FDG; and autofluorescence methods that measure fluorescence output from endogenous fluorophores including lipopigments. For identification of senescent cells in the hMSC batches produced, the non-destructive and label-free methods could be a better way forward as they involve minimum manipulations of the cells of interest, increasing the final output of the therapeutic-grade hMSC cultures. In this work, we have grown hMSC cultures over a period of 7 months and compared early and senescent hMSC passages using the advanced flow cytometry and autofluorescence methods, which were benchmarked with the current standard in $$\upbeta $$
β
-galactosidase staining. Both the advanced methods demonstrated statistically significant values, (r = 0.76, p $$\le $$
≤
0.001 for the fluorogenic C$${_{12}}$$

12

FDG method, and r = 0.72, p $$\le $$
≤
0.05 for the forward scatter method), and good fold difference ranges (1.120–4.436 for total autofluorescence mean and 1.082–6.362 for lipopigment autofluorescence mean) between early and senescent passage hMSCs. Our autofluroescence imaging and spectra decomposition platform offers additional benefit in label-free characterisation of senescent hMSC cells and could be further developed for adoption for future in situ cellular senescence evaluation by the cell manufacturers.
Radiation-induced cell cycle perturbations: a computational tool validated with flow-cytometry data
Authors: Lonati Leonardo , Barbieri Sofia , Guardamagna Isabella , Ottolenghi Andrea , Baiocco Giorgio
Published: January 2021

Cell cycle progression can be studied with computational models that allow to describe and predict its perturbation by agents as ionizing radiation or drugs. Such models can then be integrated in tools for pre-clinical/clinical use, e.g. to optimize kinetically-based administration protocols of radiation therapy and chemotherapy. We present a deterministic compartmental model, specifically reproducing how cells that survive radiation exposure are distributed in the cell cycle as a function of dose and time after exposure. Model compartments represent the four cell-cycle phases, as a function of DNA content and time. A system of differential equations, whose parameters represent transition rates, division rate and DNA synthesis rate, describes the temporal evolution. Initial model inputs are data from unexposed cells in exponential growth. Perturbation is implemented as an alteration of model parameters that allows to best reproduce cell-cycle profiles post-irradiation. The model is validated with dedicated in vitro measurements on human lung fibroblasts (IMR90). Cells were irradiated with 2 and 5 Gy with a Varian 6 MV Clinac at IRCCS Maugeri. Flow cytometry analysis was performed at the RadBioPhys Laboratory (University of Pavia), obtaining cell percentages in each of the four phases in all studied conditions up to 72 h post-irradiation. Cells show early $${\text{G}}_{2}$$

G
2

-phase block (increasing in duration as dose increases) and later $${\text{G}}_{1}$$

G
1

-phase accumulation. For each condition, we identified the best sets of model parameters that lead to a good agreement between model and experimental data, varying transition rates from $${\text{G}}_{1}$$

G
1

- to S- and from $${\text{G}}_{2}$$

G
2

- to M-phase. This work offers a proof-of-concept validation of the new computational tool, opening to its future development and, in perspective, to its integration in a wider framework for clinical use.
Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract
Authors: Westfall Susan , Carracci Francesca , Estill Molly , Zhao Danyue , Wu Qing-li , Shen Li , Simon James , Pasinetti Giulio Maria
Published: January 2021

The gut microbiota’s metabolome is composed of bioactive metabolites that confer disease resilience. Probiotics’ therapeutic potential hinges on their metabolome altering ability; however, characterizing probiotics’ metabolic activity remains a formidable task. In order to solve this problem, an artificial model of the human gastrointestinal tract is introduced coined the ABIOME (A Bioreactor Imitation of the Microbiota Environment) and used to predict probiotic formulations’ metabolic activity and hence therapeutic potential with machine learning tools. The ABIOME is a modular yet dynamic system with real-time monitoring of gastrointestinal conditions that support complex cultures representative of the human microbiota and its metabolome. The fecal-inoculated ABIOME was supplemented with a polyphenol-rich prebiotic and combinations of novel probiotics that altered the output of bioactive metabolites previously shown to invoke anti-inflammatory effects. To dissect the synergistic interactions between exogenous probiotics and the autochthonous microbiota a multivariate adaptive regression splines (MARS) model was implemented towards the development of optimized probiotic combinations with therapeutic benefits. Using this algorithm, several probiotic combinations were identified that stimulated synergistic production of bioavailable metabolites, each with a different therapeutic capacity. Based on these results, the ABIOME in combination with the MARS algorithm could be used to create probiotic formulations with specific therapeutic applications based on their signature metabolic activity.
The behavioural preview effect with faces is susceptible to statistical regularities: Evidence for predictive processing across the saccade
Authors: Huber-Huber Christoph , Melcher David
Published: January 2021

The world around us appears stable and continuous despite saccadic eye movements. This apparent visual stability is achieved by trans-saccadic perception leading at the behavioural level to preview effects: performance in processing a foveal stimulus is better if the stimulus remained unchanged (valid) compared to when it changed (invalid) during the saccade that brought it into focus. Trans-saccadic perception is known to predictively adapt to the statistics of the environment. Here, we asked whether the behavioural preview effect shows the same characteristics, employing a between-participants training design. Participants made saccades to faces which could change their orientation (upright/inverted) during the saccade. In addition, the post-saccadic face was slightly tilted and participants reported this tilt upon fixation. In a training phase, one group of participants conducted only invalid trials whereas another group conducted only valid trials. In a subsequent test phase with 50% valid and 50% invalid trials, we measured the preview effect. Invalid training reduced the preview effect. With a mixed-model analysis, we could show how this training effect gradually declines in the course of the test phase. These results show that the behavioural preview effect adapts to the statistics of the environment suggesting that it results from predictive processes.
Liposome encapsulated surfactant abetted copper nanoparticles alleviates biofilm mediated virulence in pathogenic Pseudomonas aeruginosa and MRSA
Authors: Kannan Suganya , Solomon Anitta , Krishnamoorthy Govindan , Marudhamuthu Murugan
Published: January 2021

In the present study lipopeptide biosurfactant with high emulsification capacity produced by human skin bacterium Paenibacillus thiaminolyticus was purified and subjected to FTIR and NMR spectral analysis which gave evidence of the active characteristics of the surfactant. To augment the antivirulent potential further, the mixer of copper and copper oxide nanoparticles (CuNPs) was synthesized, and characterized by UV–Visible spectroscopy, SEM-EDAX, TEM, and Zeta analysis. Here, we attempted to enhance the antimicrobial and antibiofilm activity with the assistance of encapsulated preparation of lipopeptide and CuNPs in multilamellar liposomes. The proposed mechanism of action of lipopeptide and CuNPs liposomal preparation negatively influences the cell metabolism, secreted virulence such as staphyloxanthin, pyocyanin, and extracellular polysaccharides. The significant decline in the growth of MRSA and P. aeruginosa in both planktonic form and biofilm by lipopeptide and CuNPs treatment were visualized using scanning electron microscopy and High content screening imaging system. In vivo studies revealed that treatment with lipopeptide and CuNPs in multilamellar liposomes extended the lifespan of infected Caenorhabditis elegans by about 75%. Therefore, this study typifies lipopeptide and CuNPs could credibly be a substantial substitute over conventional antibiotics in averting the biofilm associated pathogenesis of MRSA and P. aeruginosa.
Arbuscular mycorrhizal enhancement of phosphorus uptake and yields of maize under high planting density in the black soil region of China
Authors: Hou Liyuan , Zhang Xiaofei , Feng Gu , Li Zheng , Zhang Yubin , Cao Ning
Published: January 2021

Arbuscular mycorrhizal (AM) symbioses are an attractive means of improving the efficiency of soil phosphorus (P) that difficult to be used by plants and may provide a sustainable way of maintaining high yields while reducing P applications. However, quantifying the contribution of indigenous AM fungi on phosphorus uptake and yields of maize (Zea mays L.) under field conditions is not particularly clear. Mesh-barrier compartments were applied to monitor the distribution of hyphal P uptake throughout the experimental period under different planting densities and soil depths, over two consecutive years. AM symbioses enhanced plant P-acquisition efficiency, especially during the silking stage, and hyphae of AM fungi was assessed to contribution 19.4% at most to total available P content of soil. Moreover, the pattern of AM depletion of soil P generally matched shoot nutrient demand under the high planting density, which resulted in significantly increased yield in 2014. Although the hyphal length density was significantly decreased with soil depth, AM fungi still had high potential for P supply in deeper soil. It demonstrates the great potential of indigenous AM fungi to maize productivity in the high-yield area of China, and it would further provide the possibility of elimination P fertilizer applications to maintain high yields.
A pilot study investigating anterior segment optical coherence tomography angiography as a non-invasive tool in evaluating corneal vascularisation
Authors: Ong Hon Shing , Tey Kai Yuan , Ke Mengyuan , Tan Bingyao , Chua Jacqueline , Schmetterer Leopold , Mehta Jodhbir S. , Ang Marcus
Published: January 2021

The current assessment of corneal vascularisation (CV) relies on slit-lamp examination, which may be subjective. Dye-based angiographies, like indocyanine green angiography (ICGA), allows for good visualisation of anterior segment blood vessels. However, ICGA is invasive and can be associated with systemic adverse effects. Anterior segment optical coherence tomography angiography (AS-OCTA) is a non-invasive tool that has been shown to successfully delineate CV. However, there are no previous studies that have reported if AS-OCTA can determine CV stage and activity. We used an established CV model in rabbits to examine serial AS-OCTA scans of CV development and regression following treatment with anti-vascular endothelial growth factor. We compared AS-OCTA derived vascular measurements to that of ICGA determined vessel leakage and CV staging. Our results showed that AS-OCTA vessel densities and vessel branch area significantly correlated with the severity of CV based on ICGA (all p ≤ 0.05). We also found that AS-OCTA vessel densities correlated with ICGA vessel leakage time, following an inverse linear relationship (r2 = − 0.726, p < 0.01). Changes in aqueous levels of CXCL-12 and PIGF cytokines significantly correlated with AS-OCTA vessel densities (r2 = 0.736 and r2 = 0.731 respectively, all p < 0.05). In summary, we found that AS-OCTA derived vessel parameters may be useful for assessing CV severity, while vessel density correlates with CV activity and leakage. Thus, our pilot animal model study suggests that AS-OCTA may be a useful non-invasive imaging tool to provide objective assessment of CV to examine progression or response in treatment, which requires confirmation in clinical studies.
The effect of water immersion on vection in virtual reality
Authors: Fauville Géraldine , Queiroz Anna C. M. , Woolsey Erika S. , Kelly Jonathan W. , Bailenson Jeremy N.
Published: January 2021

Research about vection (illusory self-motion) has investigated a wide range of sensory cues and employed various methods and equipment, including use of virtual reality (VR). However, there is currently no research in the field of vection on the impact of floating in water while experiencing VR. Aquatic immersion presents a new and interesting method to potentially enhance vection by reducing conflicting sensory information that is usually experienced when standing or sitting on a stable surface. This study compares vection, visually induced motion sickness, and presence among participants experiencing VR while standing on the ground or floating in water. Results show that vection was significantly enhanced for the participants in the Water condition, whose judgments of self-displacement were larger than those of participants in the Ground condition. No differences in visually induced motion sickness or presence were found between conditions. We discuss the implication of this new type of VR experience for the fields of VR and vection while also discussing future research questions that emerge from our findings.
Statins for the prevention of proliferative vitreoretinopathy: cellular responses in cultured cells and clinical statin concentrations in the vitreous
Authors: Mysore Yashavanthi , del Amo Eva M. , Loukovaara Sirpa , Hagström Marja , Urtti Arto , Kauppinen Anu
Published: January 2021

Proliferative vitreoretinopathy (PVR) with rhegmatogenous retinal detachment (RRD) is a complex inflammatory ocular disease. Statins are widely used cholesterol-lowering drugs with putative anti-inflammatory properties. In this study, we have explored their efficacy in controlling post-surgical PVR formation. Simvastatin (SIM), atorvastatin (ATV), or rosuvastatin (RSV) were added to cultures of human retinal pigment epithelial cells (ARPE-19) prior to exposure with the bacterial lipopolysaccharide (LPS), and the production of pro-inflammatory cytokines (IL-6, IL-8, MCP-1) was examined using an enzyme-linked immunosorbent assay. In addition, the concentrations of simvastatin, atorvastatin, rosuvastatin, and their metabolites were measured from the vitreal samples of 20 patients undergoing vitrectomy (16 of them receiving oral statin therapy) using an ultra-performance liquid chromatography-tandem mass spectrometer technique. All statins alleviated LPS-induced inflammation at 5 µM concentration in the ARPE-19 cell cultures. Statin levels in the vitreous samples ranged from 6 to 316 pg/mL (ca. 0.1–7 M−10). Vitreal statin concentrations were similar to the typical steady-state unbound statin concentrations in plasma, indicating that only the unbound drug distributes from the blood circulation into the vitreous. Pharmacokinetic simulations of the intravitreal delivery of statins indicate that the measured clinical statin concentrations could be maintained with existing drug delivery technologies for months. Our results suggest that intravitreal statin therapy may have the potential in alleviating the risk of post-surgical PVR.
Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan
Authors: Yang JiYoung , Chiang Yu-Chung , Hsu Tsai-Wen , Kim Seon-Hee , Pak Jae-Hong , Kim Seung-Chul
Published: January 2021

Genus Rubus represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera (Chamaebatus, Idaoeobatus, and Malochobatus). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the Rubus species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic Rubus species: subg. Idaeobatus (R. glandulosopunctatus, R. incanus, R. parviaraliifolius, R rubroangustifolius, R. taitoensis, and R. taiwanicolus) and subg. Malachobatus (R. kawakamii and R. laciniastostipulatus) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions (rps16/trnQ, petA/psbJ, rpl32/trnL-UAG, and trnT-UGU/trnL-UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within Rubus in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.
Divergent immune landscapes of primary and syngeneic Kras-driven mouse tumor models
Authors: Gutierrez Wade R. , Scherer Amanda , McGivney Gavin R. , Brockman Qierra R. , Knepper-Adrian Vickie , Laverty Emily A. , Roughton Grace A. , Dodd Rebecca D.
Published: January 2021

Immune cells play critical functions in cancer, and mice with intact immune systems are vital to understanding tumor immunology. Both genetically engineered mouse models (GEMMs) and syngeneic cell transplant approaches use immunocompetent mice to define immune-dependent events in tumor development and progression. Due to their rapid and reproducible nature, there is expanded interest in developing new syngeneic tools from established primary tumor models. However, few studies have examined the extent that syngeneic tumors reflect the immune profile of their originating primary models. Here, we describe comprehensive immunophenotyping of two well-established GEMMs and four new syngeneic models derived from these parental primary tumors. To our knowledge, this is the first systematic analysis comparing immune landscapes between primary and orthotopic syngeneic tumors. These models all use the same well-defined human-relevant driver mutations, arise at identical orthotopic locations, and are generated in mice of the same background strain. This allows for a direct and focused comparison of tumor immune landscapes in carefully controlled mouse models. We identify key differences between the immune infiltrate of GEMM models and their corresponding syngeneic tumors. Most notable is the divergence of T cell populations, with different proportions of CD8+ T cells and regulatory T cells across several models. We also observe immune variation across syngeneic tumors derived from the same primary model. These findings highlight the importance of immune variance across mouse modeling approaches, which has strong implications for the design of rigorous and reproducible translational studies.
Adenosine A2A receptor signaling promotes FoxO associated autophagy in chondrocytes
Authors: Friedman Benjamin , Corciulo Carmen , Castro Cristina M. , Cronstein Bruce N.
Published: January 2021

Autophagy, a homeostatic pathway upregulated during cellular stress, is decreased in osteoarthritic chondrocytes and this reduction in autophagy is thought to contribute to the development and progression of osteoarthritis (OA). The adenosine A2A receptor (A2AR) is a potent anti-inflammatory receptor and deficiency of this receptor leads to the development of OA in mice. Moreover, treatment using liposomally conjugated adenosine or a specific A2AR agonist improved joint scores significantly in both rats with post-traumatic OA (PTOA) and mice subjected to a high fat diet obesity induced OA. Importantly, A2AR ligation is beneficial for mitochondrial health and metabolism in vitro in primary and the TC28a2 human cell line. An additional set of metabolic, stress-responsive, and homeostatic mediators include the Forkhead box O transcription factors (FoxOs). Data has shown that mouse FoxO knockouts develop early OA with reduced cartilage autophagy, indicating that FoxO-induced homeostasis is important for articular cartilage. Given the apparent similarities between A2AR and FoxO signaling, we tested the hypothesis that A2AR stimulation improves cartilage function through activation of the FoxO proteins leading to increased autophagy in chondrocytes. We analyzed the signaling pathway in the human TC28a2 cell line and corroborated these findings in vivo in a metabolically relevant obesity-induced OA mouse model. We found that A2AR stimulation increases activation and nuclear localization of FoxO1 and FoxO3, promotes an increase in autophagic flux, improves metabolic function in chondrocytes, and reduces markers of apoptosis in vitro and reduced apoptosis by TUNEL assay in vivo. A2AR ligation additionally enhances in vivo activation of FoxO1 and FoxO3 with evidence of enhanced autophagic flux upon injection of the liposome-associated A2AR agonist in a mouse obesity-induced OA model. These findings offer further evidence that A2AR may be an excellent target for promoting chondrocyte and cartilage homeostasis.
RNA interference of trehalose-6-phosphate synthase and trehalase genes regulates chitin metabolism in two color morphs of Acyrthosiphon pisum Harris
Authors: Wang Guang , Gou Yuping , Guo Sufan , Zhou Jing-Jiang , Liu Changzhong
Published: January 2021

Trehalose-6-phosphate synthase (TPS) and trehalase (TRE) directly regulate trehalose metabolism and indirectly regulate chitin metabolism in insects. Real-time quantitative PCR (RT-qPCR) and RNA interference (RNAi) were used to detect the expressions and functions of the ApTPS and ApTRE genes. Abnormal phenotypes were found after RNAi of ApTRE in the Acyrthosiphon pisum. The molting deformities were observed in two color morphs, while wing deformities were only observed in the red morphs. The RNAi of ApTPS significantly down-regulated the expression of chitin metabolism-related genes, UDP-N-acetyglucosamine pyrophosphorylase (ApUAP), chitin synthase 2 (Apchs-2), Chitinase 2, 5 (ApCht2, 5), endo-beta-N-acetylglucosaminidase (ApENGase) and chitin deacetylase (ApCDA) genes at 24 h and 48 h; The RNAi of ApTRE significantly down-regulated the expression of ApUAP, ApCht1, 2, 8 and ApCDA at 24 h and 48 h, and up-regulated the expression of glucose-6-phosphate isomerase (ApGPI) and Knickkopf protein (ApKNK) genes at 48 h. The RNAi of ApTRE and ApTPS not only altered the expression of chitin metabolism-related genes but also decreased the content of chitin. These results demonstrated that ApTPS and ApTRE can regulate the chitin metabolism, deepen our understanding of the biological functions, and provide a foundation for better understanding the molecular mechanism of insect metamorphosis.
Study of the characteristics and properties of the SiO2/TiO2/Nb2O5 material obtained by the sol–gel process
Authors: da Fonseca Bruna Teixeira , D’Elia Eliane , Siqueira Júnior José Márcio , de Oliveira Sanair Massafra , dos Santos Castro Kelly Leite , Ribeiro Emerson Schwingel
Published: January 2021

The SiO2/TiO2/Nb2O5 material was set by the sol–gel method and was characterized by several techniques through thermogravimetric, spectroscopic, and textural analyzes. For the two synthesized materials, the specific surface area was 350.0 and 494.0 m2 g−1 (SiTiNb-A and SiTiNb-B, respectively). An enhance of the crystalline order with the temperature increase of the thermal treatment was observed. Through X-ray Photoelectron Spectroscopy analysis, the binding energy values for the Ti 2p and Nb 3d levels showed the insertion of Ti and Nb atoms in the silica matrix. The Electron Dispersive Spectroscopy analyses also confirmed the high dispersion of the metals presented on the materials surface. The Thermogravimetric Analysis showed weight loss for the of 37.6% (SiTiNb-A) and 29.7% (SiTiNb-B). The presence of the crystalline phases TiO2-anatase and monoclinic-Nb2O5 in the materials was confirmed through the data obtained by association of powder X-ray Diffraction and FT-Raman. Values obtained from optical band-gap aimed the dependence of the oxides concentration and the calcination temperature. Finally, the pyridine adsorption studies have indicated the presence of Lewis and Brønsted acid sites.
Biological performance and oviposition preference of tomato pinworm Tuta absoluta when offered a range of Solanaceous host plants
Authors: Silva Gerson A. , Queiroz Elenir A. , Arcanjo Lucas P. , Lopes Mayara C. , Araújo Tamiris A. , Galdino Tarcisio S. V. , Samuels Richard I. , Rodrigues-Silva Nilson , Picanço Marcelo C.
Published: January 2021

The tomato pinworm Tuta absoluta (Lepidoptera: Gelechuidae) is native to South America and has now become the main tomato pest in Europe, Africa and Asia. The wide range of host plants attacked by this pest has been reported as one of the main reasons for the success of this important insect species. However, the information currently available on the biological performance of T. absoluta on Solanaceae has been obtained from a limited number of host species. The Solanaceae family is composed of thousands of species, many of which are potential hosts for T. absoluta. Our results showed that the highest oviposition rates occurred on cultivated tomato plants, potato and wild tomato. The lowest rates occurred on “gilo”, “jurubeba”, green pepper and pepper. The highest survival rates of the immature stages occurred on potato and the lowest on pepper, green pepper and “jurubeba”. Female fertility, following infestation of the different plant species, was highest for insects that developed on tomato or potato and the lowest rates were seen on American black nightshade. The net reproductive rate and the intrinsic growth rate were highest on potato and tomato. Cluster analysis grouped tomato and potato as highly susceptible to attack, American black nightshade, juá, eggplant, gilo and wild tomato as moderately susceptible, whilst pepper, green pepper and jurubeba were categorized as resistant to T. absoluta. These results clearly demonstrate that the choice of solanaceous host plant species has a direct impact on the fitness parameters of the tomato pinworm as well as survival potential, dispersion and establishment at new sites. These results are important for the planning of integrated pest management strategies.
Effects of developmental exposure to pesticides in wax and pollen on honey bee (Apis mellifera) queen reproductive phenotypes
Authors: Milone Joseph P. , Tarpy David R.
Published: January 2021

Stressful conditions during development can have sub-lethal consequences on organisms aside from mortality. Using previously reported in-hive residues from commercial colonies, we examined how multi-pesticide exposure can influence honey bee (Apis mellifera) queen health. We reared queens in beeswax cups with or without a pesticide treatment within colonies exposed to treated or untreated pollen supplement. Following rearing, queens were open-mated and then placed into standard hive equipment in an “artificial swarm” to measure subsequent colony growth. Our treated wax had a pesticide Hazard Quotient comparable to the average in beeswax from commercial colonies, and it had no measurable effects on queen phenotype. Conversely, colonies exposed to pesticide-treated pollen had a reduced capacity for viable queen production, and among surviving queens from these colonies we observed lower sperm viability. We found no difference in queen mating number across treatments. Moreover, we measured lower brood viability in colonies later established by queens reared in treated-pollen colonies. Interestingly, royal jelly from colonies exposed to treated pollen contained negligible pesticide residues, suggesting the indirect social consequences of colony-level pesticide exposure on queen quality. These findings highlight how conditions during developmental can impact queens long into adulthood, and that colony-level pesticide exposure may do so indirectly.
d,l-Methadone causes leukemic cell apoptosis via an OPRM1-triggered increase in IP3R-mediated ER Ca2+ release and decrease in Ca2+ efflux, elevating [Ca2+]i
Authors: Lee JungKwon , Rosales Jesusa L. , Byun Hee-Guk , Lee Ki-Young
Published: January 2021

The search continues for improved therapy for acute lymphoblastic leukemia (aLL), the most common malignancy in children. Recently, d,l-methadone was put forth as sensitizer for aLL chemotherapy. However, the specific target of d,l-methadone in leukemic cells and the mechanism by which it induces leukemic cell apoptosis remain to be defined. Here, we demonstrate that d,l-methadone induces leukemic cell apoptosis through activation of the mu1 subtype of opioid receptors (OPRM1). d,l-Methadone evokes IP3R-mediated ER Ca2+ release that is inhibited by OPRM1 loss. In addition, the rate of Ca2+ extrusion following d,l-methadone treatment is reduced, but is accelerated by loss of OPRM1. These d,l-methadone effects cause a lethal rise in [Ca2+]i that is again inhibited by OPRM1 loss, which then prevents d,l-methadone-induced apoptosis that is associated with activation of calpain-1, truncation of Bid, cytochrome C release, and proteolysis of caspase-3/12. Chelating intracellular Ca2+ with BAPTA-AM reverses d,l-methadone-induced apoptosis, establishing a link between the rise in [Ca2+]i and d,l-methadone-induced apoptosis. Altogether, our findings point to OPRM1 as a specific target of d,l-methadone in leukemic cells, and that OPRM1 activation by d,l-methadone disrupts IP3R-mediated ER Ca2+ release and rate of Ca2+ efflux, causing a rise in [Ca2+]i that upregulates the calpain-1-Bid-cytochrome C-caspase-3/12 apoptotic pathway.
TIM29 is required for enhanced stem cell activity during regeneration in the flatworm Macrostomum lignano
Authors: Mouton Stijn , Ustyantsev Kirill , Beltman Frank , Glazenburg Lisa , Berezikov Eugene
Published: January 2021

TIM29 is a mitochondrial inner membrane protein that interacts with the protein import complex TIM22. TIM29 was shown to stabilize the TIM22 complex but its biological function remains largely unknown. Until recently, it was classified as one of the Domain of Unknown Function (DUF) genes, with a conserved protein domain DUF2366 of unclear function. Since characterizing DUF genes can provide novel biological insight, we used previously established transcriptional profiles of the germline and stem cells of the flatwormMacrostomum lignanoto probe conserved DUFs for their potential role in germline biology, stem cell function, regeneration, and development. Here, we demonstrate that DUF2366/TIM29 knockdown inM. lignanohas very limited effect during the normal homeostatic condition but prevents worms from adapting to a highly proliferative state required for regeneration.
Substrate wettability guided oriented self assembly of Janus particles
Authors: Banik Meneka , Sett Shaili , Bakli Chirodeep , Raychaudhuri Arup Kumar , Chakraborty Suman , Mukherjee Rabibrata
Published: January 2021

Self-assembly of Janus particles with spatial inhomogeneous properties is of fundamental importance in diverse areas of sciences and has been extensively observed as a favorably functionalized fluidic interface or in a dilute solution. Interestingly, the unique and non-trivial role of surface wettability on oriented self-assembly of Janus particles has remained largely unexplored. Here, the exclusive role of substrate wettability in directing the orientation of amphiphilic metal-polymer Bifacial spherical Janus particles, obtained by topo-selective metal deposition on colloidal Polymestyere (PS) particles, is explored by drop casting a dilute dispersion of the Janus colloids. While all particles orient with their polymeric (hydrophobic) and metallic (hydrophilic) sides facing upwards on hydrophilic and hydrophobic substrates respectively, they exhibit random orientation on a neutral substrate. The substrate wettability guided orientation of the Janus particles is captured using molecular dynamic simulation, which highlights that the arrangement of water molecules and their local densities near the substrate guide the specific orientation. Finally, it is shown that by spin coating it becomes possible to create a hexagonal close-packed array of the Janus colloids with specific orientation on differential wettability substrates. The results reported here open up new possibilities of substrate-wettability driven functional coatings of Janus particles, which has hitherto remained unexplored.
Embeddings from deep learning transfer GO annotations beyond homology
Authors: Littmann Maria , Heinzinger Michael , Dallago Christian , Olenyi Tobias , Rost Burkhard
Published: January 2021

Knowing protein function is crucial to advance molecular and medical biology, yet experimental function annotations through the Gene Ontology (GO) exist for fewer than 0.5% of all known proteins. Computational methods bridge this sequence-annotation gap typically through homology-based annotation transfer by identifying sequence-similar proteins with known function or through prediction methods using evolutionary information. Here, we propose predicting GO terms through annotation transfer based on proximity of proteins in the SeqVec embedding rather than in sequence space. These embeddings originate from deep learned language models (LMs) for protein sequences (SeqVec) transferring the knowledge gained from predicting the next amino acid in 33 million protein sequences. Replicating the conditions of CAFA3, our method reaches an Fmax of 37 ± 2%, 50 ± 3%, and 57 ± 2% for BPO, MFO, and CCO, respectively. Numerically, this appears close to the top ten CAFA3 methods. When restricting the annotation transfer to proteins with < 20% pairwise sequence identity to the query, performance drops (Fmax BPO 33 ± 2%, MFO 43 ± 3%, CCO 53 ± 2%); this still outperforms naïve sequence-based transfer. Preliminary results from CAFA4 appear to confirm these findings. Overall, this new concept is likely to change the annotation of proteins, in particular for proteins from smaller families or proteins with intrinsically disordered regions.
Development of an immune-related gene pairs index for the prognosis analysis of metastatic melanoma
Authors: Huang Rong-zhi , Mao Min , Zheng Jie , Liang Hai-qi , Liu Feng-ling , Zhou Gui-you , Huang Yao-qing , Zeng Fan-yue , Li Xu
Published: January 2021

Melanoma is a skin cancer with great metastatic potential, which is responsible for the major deaths in skin cancer. Although the prognosis of melanoma patients has been improved with the comprehensive treatment, for patients with metastasis, the complexity and heterogeneity of diffuse diseases make prognosis prediction and systematic treatment difficult and ineffective. Therefore, we established a novel personalized immune-related gene pairs index (IRGPI) to predict the prognosis of patients with metastatic melanoma, which was conducive to provide new insights into clinical decision-making and prognostic monitoring for metastatic melanoma. Through complex analysis and filtering, we identified 24 immune-related gene pairs to build the model and obtained the optimal cut-off value from receiver operating characteristic curves, which divided the patients into high and low immune-risk groups. Meantime, the Kaplan–Meier analysis, Cox regression analysis and subgroup analysis showed that IRGPI had excellent prognostic value. Furthermore, IRGPI was shown that was closely associated with immune system in the subsequent tumor microenvironment analysis and gene set enrichment analysis. In addition, we broken through the data processing limitations of traditional researches in different platforms through the application of gene pairs, which would provide great credibility for our model. We believe that our research would provide a new perspective for clinical decision-making and prognostic monitoring in metastatic melanoma.
Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer
Authors: Gopinath Divya , Menon Rohit Kunnath , Wie Chong Chun , Banerjee Moinak , Panda Swagatika , Mandal Deviprasad , Behera Paresh Kumar , Roychoudhury Susanta , Kheur Supriya , Botelho Michael George , Johnson Newell W.
Published: January 2021

Microbial dysbiosis has been implicated in the pathogenesis of oral cancer. We analyzed the compositional and metabolic profile of the bacteriome in three specific niches in oral cancer patients along with controls using 16SrRNA sequencing (Illumina Miseq) and DADA2 software. We found major differences between patients and control subjects. Bacterial communities associated with the tumor surface and deep paired tumor tissue differed significantly. Tumor surfaces carried elevated abundances of taxa belonging to genera Porphyromonas, Enterobacteriae, Neisseria, Streptococcus and Fusobacteria, whereas Prevotella, Treponema, Sphingomonas, Meiothermus and Mycoplasma genera were significantly more abundant in deep tissue. The most abundant microbial metabolic pathways were those related to fatty-acid biosynthesis, carbon metabolism and amino-acid metabolism on the tumor surface: carbohydrate metabolism and organic polymer degradation were elevated in tumor tissues. The bacteriome of saliva from patients with oral cancer differed significantly from paired tumor tissue in terms of community structure, however remained similar at taxonomic and metabolic levels except for elevated abundances of Streptococcus, Lactobacillus and Bacteroides, and acetoin-biosynthesis, respectively. These shifts to a pro-inflammatory profile are consistent with other studies suggesting oncogenic properties. Importantly, selection of the principal source of microbial DNA is key to ensure reliable, reproducible and comparable results in microbiome studies.
Clinical and genetic profiling of nevoid basal cell carcinoma syndrome in Korean patients by whole-exome sequencing
Authors: Kim Boram , Kim Man Jin , Hur Keunyoung , Jo Seong Jin , Ko Jung Min , Park Sung Sup , Seong Moon-Woo , Mun Je-Ho
Published: January 2021

Nevoid basal cell carcinoma syndrome (NBCCS) is mainly characterised by multiple basal cell carcinomas (BCCs) caused by PTCH1, PTCH2, and SUFU. However, clinical and genetic data on Asian NBCCS patients are limited. We aimed to analyse the clinical phenotypes and genetic spectrum of Korean patients with NBCCS. Fifteen patients with NBCCS at Seoul National University Hospital were included, and their clinical data were analysed. Whole-exome sequencing and/or multiplex ligation-dependent probe amplification using peripheral blood were performed to identify genetic causes. Genetic analysis revealed that 73.3% (11/15) of the patients carried 9 pathogenic variants, only in the PTCH1 gene. Variants of uncertain significance (VUS) and likely benign were also detected in 2 (13.3%) and 2 (13.3%) patients, respectively. BCCs were found in the majority of the cases (93.3%) and the number of BCCs increased with age (ρ = 0.595, P = 0.019). This study revealed that PTCH1 pathogenic variants were the main cause of NBCCS in Korean patients. As BCCs are commonly detected, a periodic dermatologic examination is recommended. Finally, our results support the addition of genetic screening to the existing criteria for NBCCS diagnosis.
Incidence of cardiovascular events and mortality in Korean patients with chronic kidney disease
Authors: Ryu Hyunjin , Kim Jayoun , Kang Eunjeong , Hong Yeji , Chae Dong-Wan , Choi Kyu Hun , Han Seung Hyeok , Yoo Tae Hyun , Lee Kyubeck , Kim Yong-Soo , Chung Wookyung , Oh Yun Kyu , Kim Soo Wan , Kim Yeong Hoon , Sung Su Ah , Lee Joongyub , Park Sue K. , Ahn Curie , Oh Kook-Hwan ,   Representing KNOW-CKD Study Group
Published: January 2021

Few studies have investigated the incidence of cardiovascular disease (CVD) in the Asian chronic kidney disease (CKD) population. This study assessed the incidence of CVD, death, and a composite outcome of CVD and death in a prospective Korean predialysis CKD cohort. From a total of 2179 patients, incidence rates were analyzed, and competing risk analyses were conducted according to CKD stage. Additionally, incidence was compared to the general population. During a median 4.1 years of follow-up, the incidence of CVD, all-cause death, and the composite outcome was 17.2, 9.6, and 24.5 per 1000 person-years, respectively. These values were higher in diabetic vs. non-diabetic subjects (P < 0.001). For all outcomes, incidence rates increased with increasing CKD stage (CVD, P = 0.001; death, P < 0.001; and composite, P < 0.001). Additionally, CKD stage G4 [hazard ratio (HR) 2.8, P = 0.008] and G5 (HR 5.0, P < 0.001) were significant risk factors for the composite outcome compared to stage G1 after adjustment. Compared to the general population, the total cohort population (stages G1–G5) showed significantly higher risk of CVD (HR 2.4, P < 0.001) and the composite outcome (HR 1.7, P < 0.001). The results clearly demonstrate that CKD is a risk factor for CVD in an Asian population.
Sphingolipids and physical function in the Atherosclerosis Risk in Communities (ARIC) study
Authors: Li Danni , Alam Aniqa B. , Yu Fang , Kucharska-Newton Anna , Windham B. Gwen , Alonso Alvaro
Published: January 2021

Long-chain sphingomyelins (SMs) may play an important role in the stability of myelin sheath underlying physical function. The objective of this study was to examine the cross-sectional and longitudinal associations of long-chain SMs [SM (41:1), SM (41:2), SM (43:1)] and ceramides [Cer (41:1) and Cer (43:1)] with physical function in the Atherosclerosis Risk in Communities (ARIC) study. Plasma concentrations of SM (41:1), SM (41:2), SM (43:1), Cer (41:1) and Cer (43:1) were measured in 389 ARIC participants in 2011–13. Physical function was assessed by grip strength, Short Physical Performance Battery (SPPB), 4-m walking speed at both 2011–13 and 2016–17, and the modified Rosow-Breslau questionnaire in 2016–2017. Multivariable linear and logistic regression analyses were performed, controlling for demographic and clinical confounders. In cross-sectional analyses, plasma concentrations of SM 41:1 were positively associated with SPPB score (β-coefficients [95% confidence internal]: 0.33 [0.02, 0.63] per 1 standard deviation [SD] increase in log-transformed concentration, p value 0.04), 4-m walking speed (0.042 m/s [0.01, 0.07], p value 0.003), and negatively with self-reported disability (odds ratio = 0.73 [0.65, 0.82], p value < 0.0001). Plasma concentrations of the five metabolites examined were not significantly associated with longitudinal changes in physical function or incidence of poor mobility. In older adults, plasma concentrations of long-chain SM 41:1 were cross-sectionally positively associated with physical function.
Differential organ-specific inflammatory response to progranulin in high-fat diet-fed mice
Authors: Murakoshi Maki , Gohda Tomohito , Adachi Eri , Ichikawa Saki , Hagiwara Shinji , Suzuki Yusuke
Published: January 2021

Progranulin (PGRN) has been reported to bind tumor necrosis factor (TNF) receptor and to inhibit TNFα signaling. We evaluated the effect of augmentation of TNFα signaling by PGRN deficiency on the progression of kidney injury. Eight-week-old PGRN knockout (KO) and wild-type (WT) mice were fed a standard diet or high-fat diet (HFD) for 12 weeks. Albuminuria, markers of tubular damage, and renal mRNA levels of inflammatory cytokines were higher in HFD-fed KO (KO-HFD) mice than in HFD-fed WT (WT-HFD) mice. Body weight, vacuolization in proximal tubules, and systemic and adipose tissue inflammatory markers were lower in the KO-HFD mice than in the WT-HFD mice. The renal megalin expression was lower in the KO mice than in the WT mice regardless of the diet type. The megalin expression was also reduced in mouse proximal tubule epithelial cells stimulated with TNFα and in those with PGRN knockdown by small interfering RNA in vitro. PGRN deficiency was associated with both exacerbated renal inflammation and decreased systemic inflammation, including that in the adipose tissue of mice with HFD-induced obesity. Improved tubular vacuolization in the KO-HFD mice might partially be explained by the decreased expression of megalin in proximal tubules.
Detectable chromosome X mosaicism in males is rarely tolerated in peripheral leukocytes
Authors: Zhou Weiyin , Lin Shu-Hong , Khan Sairah M. , Yeager Meredith , Chanock Stephen J. , Machiela Mitchell J.
Published: January 2021

Age-related male Y and female X chromosome mosaicism is commonly observed in large population-based studies. To investigate the frequency of male X chromosome mosaicism, we scanned for deviations in chromosome X genotyping array intensity data in a population-based survey of 196,219 UK Biobank men. We detected 12 (0.006%) men with mosaic chromosome X gains ≥ 2 Mb and found no evidence for mosaic chromosome X loss, a level of detection substantially lower than for autosomes or other sex chromosomes. The rarity of chromosome X mosaicism in males relative to females reflects the importance of chromosome X gene dosage for leukocyte function.
An in vitro study on Staphylococcus schweitzeri virulence
Authors: Grossmann Almut , Froböse Neele J. , Mellmann Alexander , Alabi Abraham S. , Schaumburg Frieder , Niemann Silke
Published: January 2021

Staphylococcus schweitzeri belongs to the Staphylococcus aureus-related complex and is mainly found in African wildlife; no infections in humans are reported yet. Hence, its medical importance is controversial. The aim of this work was to assess the virulence of S. schweitzeri in vitro. The capacity of African S. schweitzeri (n = 58) for invasion, intra- and extracellular cytotoxicity, phagolysosomal escape, coagulase activity, biofilm formation and host cell activation was compared with S. aureus representing the most common clonal complexes in Africa (CC15, CC121, CC152). Whole genome sequencing revealed that the S. schweitzeri isolates belonged to five geographical clusters. Isolates from humans were found in two different clades. S. schweitzeri and S. aureus showed a similar host cell invasion (0.9 vs. 1.2 CFU/Vero cell), host cell activation (i.e. expression of pro-inflammatory cytokines, 4.1 vs. 1.7 normalized fold change in gene expression of CCL5; 7.3 vs. 9.9 normalized fold change in gene expression of IL8, A549 cells) and intracellular cytotoxicity (31.5% vs. 25% cell death, A549 cells). The extracellular cytotoxicity (52.9% vs. 28.8% cell death, A549 cells) was higher for S. schweitzeri than for S. aureus. Nearly all tested S. schweitzeri (n = 18/20) were able to escape from phagolysosomes. In conclusion, some S. schweitzeri isolates display virulence phenotypes comparable to African S. aureus. S. schweitzeri might become an emerging zoonotic pathogen within the genus Staphylococcus.