bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractGenus 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

AbstractImmune 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

AbstractAutophagy, 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

AbstractTrehalose-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

AbstractThe 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

AbstractThe 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

AbstractStressful 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

AbstractThe 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

AbstractTIM29 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

AbstractSelf-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

AbstractKnowing 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

AbstractMelanoma 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

AbstractMicrobial 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

AbstractNevoid 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.