bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sodium lignosulfonate improves shoot growth of Oryza sativa via enhancement of photosynthetic activity and reduced accumulation of reactive oxygen species
Authors: Kok Andrew De-Xian , Wan Abdullah Wan Muhamad Asrul Nizam , Tang Chu-Nie , Low Lee-Yoon , Yuswan Mohd Hafis , Ong-Abdullah Janna , Tan Ngai-Paing , Lai Kok-Song 
Published: June 2021

AbstractLignosulfonate (LS) is a by-product obtained during sulfite pulping process and is commonly used as a growth enhancer in plant growth. However, the underlying growth promoting mechanism of LS on shoot growth remains largely unknown. Hence, this study was undertaken to determine the potential application of eco-friendly ion-chelated LS complex [sodium LS (NaLS) and calcium LS (CaLS)] to enhance recalcitrant indica rice MR 219 shoot growth and to elucidate its underlying growth promoting mechanisms. In this study, the shoot apex of MR 219 rice was grown on Murashige and Skoog medium supplemented with different ion chelated LS complex (NaLS and CaLS) at 100, 200, 300 and 400 mg/L The NaLS was shown to be a better shoot growth enhancer as compared to CaLS, with optimum concentration of 300 mg/L. Subsequent comparative proteomic analysis revealed an increase of photosynthesis-related proteins [photosystem II (PSII) CP43 reaction center protein, photosystem I (PSI) iron-sulfur center, PSII CP47 reaction center protein, PSII protein D1], ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), carbohydrate metabolism-related proteins (glyceraldehyde-3-phosphate dehydrogenase 3, fructose-bisphosphate aldolase) and stress regulator proteins (peptide methionine sulfoxide reductase A4, delta-1-pyrroline-5-carboxylate synthase 1) abundance in NaLS-treated rice as compared to the control (MSO). Consistent with proteins detected, a significant increase in biochemical analyses involved in photosynthetic activities, carbohydrate metabolism and protein biosynthesis such as total chlorophyll, rubisco activity, total sugar and total protein contents were observed in NaLS-treated rice. This implies that NaLS plays a role in empowering photosynthesis activities that led to plant growth enhancement. In addition, the increased in abundance of stress regulator proteins were consistent with low levels of peroxidase activity, malondialdehyde content and phenylalanine ammonia lyase activity observed in NaLS-treated rice. These results suggest that NaLS plays a role in modulating cellular homeostasis to provide a conducive cellular environment for plant growth. Taken together, NaLS improved shoot growth of recalcitrant MR 219 rice by upregulation of photosynthetic activities and reduction of ROS accumulation leading to better plant growth.
Molecular characterization of sequence-driven peptide glycation
Authors: Berger Michelle T. , Hemmler Daniel , Walker Alesia , Rychlik Michael , Marshall James W. , Schmitt-Kopplin Philippe 
Published: June 2021

AbstractPeptide glycation is an important, yet poorly understood reaction not only found in food but also in biological systems. The enormous heterogeneity of peptides and the complexity of glycation reactions impeded large-scale analysis of peptide derived glycation products and to understand both the contributing factors and how this affects the biological activity of peptides. Analyzing time-resolved Amadori product formation, we here explored site-specific glycation for 264 peptides. Intensity profiling together with in-depth computational sequence deconvolution resolved differences in peptide glycation based on microheterogeneity and revealed particularly reactive peptide collectives. These peptides feature potentially important sequence patterns that appear in several established bio- and sensory-active peptides from independent sources, which suggests that our approach serves system-wide applicability. We generated a pattern peptide map and propose that in peptide glycation the herein identified molecular checkpoints can be used as indication of sequence reactivity.
Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19
Authors: Redhead Martin A. , Owen C. David , Brewitz Lennart , Collette Amelia H. , Lukacik Petra , Strain-Damerell Claire , Robinson Sean W. , Collins Patrick M. , Schäfer Philipp , Swindells Mark , Radoux Chris J. , Hopkins Iva Navratilova , Fearon Daren , Douangamath Alice , von Delft Frank , Malla Tika R. , Vangeel Laura , Vercruysse Thomas , Thibaut Jan , Leyssen Pieter , Nguyen Tu-Trinh , Hull Mitchell , Tumber Anthony , Hallett David J. , Schofield Christopher J. , Stuart David I. , Hopkins Andrew L. , Walsh Martin A. 
Published: June 2021

AbstractEffective agents to treat coronavirus infection are urgently required, not only to treat COVID-19, but to prepare for future outbreaks. Repurposed anti-virals such as remdesivir and human anti-inflammatories such as barcitinib have received emergency approval but their overall benefits remain unclear. Vaccines are the most promising prospect for COVID-19, but will need to be redeveloped for any future coronavirus outbreak. Protecting against future outbreaks requires the identification of targets that are conserved between coronavirus strains and amenable to drug discovery. Two such targets are the main protease (Mpro) and the papain-like protease (PLpro) which are essential for the coronavirus replication cycle. We describe the discovery of two non-antiviral therapeutic agents, the caspase-1 inhibitor SDZ 224015 and Tarloxotinib that target Mpro and PLpro, respectively. These were identified through extensive experimental screens of the drug repurposing ReFRAME library of 12,000 therapeutic agents. The caspase-1 inhibitor SDZ 224015, was found to be a potent irreversible inhibitor of Mpro (IC50 30 nM) while Tarloxotinib, a clinical stage epidermal growth factor receptor inhibitor, is a sub micromolar inhibitor of PLpro (IC50 300 nM, Ki 200 nM) and is the first reported PLpro inhibitor with drug-like properties. SDZ 224015 and Tarloxotinib have both undergone safety evaluation in humans and hence are candidates for COVID-19 clinical evaluation.
Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout
Authors: Cáceres Pablo , Barría Agustín , Christensen Kris A. , Bassini Liane N. , Correa Katharina , Garcia Baltasar , Lhorente Jean P. , Yáñez José M. 
Published: June 2021

AbstractSea lice (Caligus rogercresseyi) is an ectoparasite which causes major production losses in the salmon aquaculture industry worldwide. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two of the most susceptible salmonid species to sea lice infestation. The objectives of this study were to: (1) identify genomic regions associated with resistance toCaligus rogercresseyiin Atlantic salmon and rainbow trout by performing single-step Genome-Wide Association studies (ssGWAS), and (2) identify candidate genes related to trait variation based on exploring orthologous genes within the associated regions across species. A total of 2626 Atlantic salmon and 2643 rainbow trout were challenged and genotyped with 50 K and 57 K SNP panels, respectively. We ran two independent ssGWAS for sea lice resistance on each species and identified 7 and 13 regions explaining more than 1% of the genetic variance for the trait, with the most important regions explaining 3% and 2.7% for Atlantic salmon and rainbow trout, respectively. We identified genes associated with immune response, cytoskeleton function, and cell migration when focusing on important genomic regions for each species. Moreover, we found 15 common orthogroups which were present in more than one associated genomic region, within- or between-species; however, only one orthogroup showed a clear potential biological relevance in the response against sea lice. For instance,dual-specificity protein phosphatase 10-like(dusp10) anddual-specificity protein phosphatase 8(dusp8) were found in genomic regions associated with lice density in Atlantic salmon and rainbow trout, respectively.Dusp10anddusp8are modulators of the MAPK pathway and might be involved in the differences of the inflammation response between lice resistant and susceptible fish from both species. Our results provide further knowledge on candidate genes related to sea lice resistance and may help establish better control for sea lice in fish populations.
Transposon sequencing analysis of Bradyrhizobium diazoefficiens 110spc4
Authors: Baraquet Claudine , Dai Weijun , Mendiola Jose , Pechter Kieran , Harwood Caroline S. 
Published: June 2021

AbstractBradyrhizobium diazoefficiens USDA110 is one of the most effective nitrogen-fixing symbionts of soybeans. Here we carried out a large-scale transposon insertion sequencing (Tn-seq) analysis of strain Bd110spc4, which is derived from USDA110, with the goal of increasing available resources for identifying genes crucial for the survival of this plant symbiont under diverse conditions. We prepared two transposon (Tn) insertion libraries of Bd110spc4 with 155,042 unique Tn insertions when the libraries were combined, which is an average of one insertion every 58.7 bp of the reference USDA110 genome. Application of bioinformatic filtering steps to remove genes too small to be expected to have Tn insertions, resulted in a list of genes that were classified as putatively essential. Comparison of this gene set with genes putatively essential for the growth of the closely related alpha-proteobacterium, Rhodopseudomonas palustris, revealed a small set of five genes that may be collectively essential for closely related members of the family Bradyrhizobiaceae. This group includes bacteria with diverse lifestyles ranging from plant symbionts to animal-associated species to free-living species.
Fms-like tyrosine kinase 3-internal tandem duplications epigenetically activates checkpoint kinase 1 in acute myeloid leukemia cells
Authors: Zhang Yudong , Yuan Lingli 
Published: June 2021

AbstractIt is not clear how Fms-like tyrosine kinase 3-internal tandem duplications (FLT3-ITD) regulates checkpoint kinase 1 (CHK1) in acute myeloid leukemia (AML). In this study, we investigated the regulatory effect of FLT3-ITD on CHK1. Our results showed that CHK1 was highly expressed in FLT3-ITD positive AML. The overall survival rate and disease-free survival rate of AML patients with high CHK1 level were lower than those of patients with low CHK1 level. Mechanistically, FLT3-ITD recruited p300 to the CHK1 promoter and subsequently acetylated H3K27, thereby enhancing the transcription of CHK1. Interfering with the expression of CHK1 significantly inhibited the cell proliferation and induced cell apoptosis in FLT3-ITD positive MV4-11 cells. In addition, CHK1 knockdown promoted the sensitivity of MV4-11 cells to the epigenetic inhibitors JQ1 and C646. This study discovers a new therapeutic target for FLT3-ITD + AML and provided evidence for the combination of epigenetic inhibitors for AML treatment.
Analysis of the dark proteome of Chandipura virus reveals maximum propensity for intrinsic disorder in phosphoprotein
Authors: Sharma Nishi R. , Gadhave Kundlik , Kumar Prateek , Saif Mohammad , Khan Md. M. , Sarkar Debi P. , Uversky Vladimir N. , Giri Rajanish 
Published: June 2021

AbstractChandipura virus (CHPV, a member of the Rhabdoviridae family) is an emerging pathogen that causes rapidly progressing influenza-like illness and acute encephalitis often leading to coma and death of the human host. Given several CHPV outbreaks in Indian sub-continent, recurring sporadic cases, neurological manifestation, and high mortality rate of this infection, CHPV is gaining global attention. The ‘dark proteome’ includes the whole proteome with special emphasis on intrinsically disordered proteins (IDP) and IDP regions (IDPR), which are proteins or protein regions that lack unique (or ordered) three-dimensional structures within the cellular milieu. These proteins/regions, however, play a number of vital roles in various biological processes, such as cell cycle regulation, control of signaling pathways, etc. and, therefore, are implicated in many human diseases. IDPs and IPPRs are also abundantly found in many viral proteins enabling their multifunctional roles in the viral life cycles and their capability to highjack various host systems. The unknown abundance of IDP and IDPR in CHPV, therefore, prompted us to analyze the dark proteome of this virus. Our analysis revealed a varying degree of disorder in all five CHPV proteins, with the maximum level of intrinsic disorder propensity being found in Phosphoprotein (P). We have also shown the flexibility of P protein using extensive molecular dynamics simulations up to 500 ns (ns). Furthermore, our analysis also showed the abundant presence of the disorder-based binding regions (also known as molecular recognition features, MoRFs) in CHPV proteins. The identification of IDPs/IDPRs in CHPV proteins suggests that their disordered regions may function as potential interacting domains and may also serve as novel targets for disorder-based drug designs.
Determining the burden of fungal infections in Zimbabwe
Authors: Pfavayi Lorraine T. , Denning David W. , Baker Stephen , Sibanda Elopy N. , Mutapi Francisca 
Published: June 2021

AbstractZimbabwe currently faces several healthcare challenges, most notably HIV and associated infections including tuberculosis (TB), malaria and recently outbreaks of cholera, typhoid fever and COVID-19. Fungal infections, which are also a major public health threat, receive considerably less attention. Consequently, there is dearth of data regarding the burden of fungal diseases in the country. We estimated the burden of fungal diseases in Zimbabwe based on published literature and ‘at-risk’ populations (HIV/AIDS patients, survivors of pulmonary TB, cancer, chronic obstructive pulmonary disease, asthma and patients receiving critical care) using previously described methods. Where there was no data for Zimbabwe, regional, or international data was used. Our study revealed that approximately 14.9% of Zimbabweans suffer from fungal infections annually, with 80% having tinea capitis. The annual incidence of cryptococcal meningitis andPneumocystis jiroveciipneumonia in HIV/AIDS were estimated at 41/100,000 and 63/100,000, respectively. The estimated prevalence of recurrent vulvovaginal candidiasis (RVVC) was 2,739/100,000. The estimated burden of fungal diseases in Zimbabwe is high in comparison to other African countries, highlighting the urgent need for increased awareness and surveillance to improve diagnosis and management.
Cell-fate decision of mesenchymal stem cells toward osteocyte differentiation is committed by spheroid culture
Authors: Kim Jeonghyun , Adachi Taiji 
Published: June 2021

AbstractOsteocytes are mechanosensory commander cells to regulate bone remodeling throughout the lifespan. While the osteocytes are known as terminally differentiated cells derived from mesenchymal stem cells, the detailed mechanisms of osteocyte differentiation remain unclear. In this study, we fabricated 3D self-organized spheroids using human mesenchymal stem cells (MSCs). Under the osteogenesis induction medium, the spheroid culture model exerted the osteocyte-likeness within 2 days compared to a conventional 2D monolayer model. Moreover, we showed that an inhibition of actin polymerization in the spheroid further up-regulated the osteocyte gene expressions. Notably, we represented that the cell condensed condition acquired in the 3D spheroid culture model determined a differentiation fate of MSCs to osteocytes. Taken together, we suggest that our self-organized spheroid model can be utilized as a new in vitro model to represent the osteocyte and to recapitulate an in vitro ossification process.
Trends in use of e-cigarette device types and heated tobacco products from 2016 to 2020 in England
Authors: Tattan-Birch Harry , Brown Jamie , Shahab Lion , Jackson Sarah E. 
Published: June 2021

AbstractThis study examined use trends of e-cigarette devices types, heated tobacco products (HTPs) and e-liquid nicotine concentrations in England from 2016 to 2020. Data were from a representative repeat cross-sectional survey of adults aged 16 or older. Bayesian logistic regression was used to estimate proportions and 95% credible intervals (CrIs). Of 75,355 participants, 5.3% (weighted = 5.5%) were currently using e-cigarettes or HTPs, with the majority (98.7%) using e-cigarettes. Among e-cigarette users, 53.7% (CrI 52.0–55.1%) used tank devices, 23.7% (22.4–25.1%) mods, 17.3% (16.1–18.4%) pods, and 5.4% (4.7–6.2%) disposables. Tanks were the most widely used device type throughout 2016–2020. Mods were second until 2020, when pods overtook them. Among all e-cigarette/HTP users, prevalence of HTP use remains rare (3.4% in 2016 versus 4.2% in 2020), whereas JUUL use has risen from 3.4% in 2018 to 11.8% in 2020. Across all years, nicotine concentrations of ≤ 6 mg/ml were most widely (41.0%; 39.4–42.4%) and ≥ 20 mg/ml least widely used (4.1%; 3.4–4.9%). Among e-cigarette/HTP users, ex-smokers were more likely than current smokers to use mod and tank e-cigarettes, but less likely to use pods, disposables, JUUL and HTPs. In conclusion, despite growing popularity of pods and HTPs worldwide, refillable tank e-cigarettes remain the most widely used device type in England.
Fabrication of 2D-MoSe2 incorporated NiO Nanorods modified electrode for selective detection of glucose in serum samples
Authors: Jeevanandham Gayathri , Vediappan Kumaran , ALOthman Zeid A. , Altalhi Tariq , Sundramoorthy Ashok K. 
Published: June 2021

AbstractLayered molybdenum diselenide (MoSe2) nanosheets were formed by the weak Van der Waals forces of attraction between Se and Mo atoms. MoSe2has a larger space between the adjacent layers and smaller band gaps in the range of 0.85 to ~ 1.6 eV. In this study, MoSe2nanosheets decorated nickel oxide (NiO) nanorods have been synthesized by hydrothermal method using sodium molybdate and selenium metal powder. NiO/MoSe2composite formation was confirmed by powder X-ray diffraction analysis. In addition, the presence of MoSe2nanosheets on NiO nanorods were confirmed by field emission scanning electron microscopy, high-resolution transmission electron microscopy and X-ray photoelectron spectroscopy. The Nyquist plots of NiO/MoSe2coated glassy carbon electrode (GCE) was indicated that it had lower charge transfer resistance compared to NiO/GCE and MoSe2/GCE. Furthermore, as-prepared NiO/MoSe2/GCE was used to detect glucose in alkaline solution by cyclic voltammetry and amperometry techniques. The NiO/MoSe2/GCE was exhibited a linear response for the oxidation of glucose from 50 µM to 15.5 mM (R2 = 0.9842) at 0.5 V by amperometry. The sensor response time and the limit of detection were found to be 2 s and 0.6 µM for glucose. Moreover, selectivity of the NiO/MoSe2sensor was tested in the presence of common interferent molecules such as hydrogen peroxide, fructose, lactose, ascorbic acid, uric acid, and dopamine. It was found that NiO/MoSe2/GCE did not respond to these interfering biomolecules. In addition, NiO/MoSe2/GCE had shown high stability, reproducibility and repeatability. Finally, the practical application of the sensor was demonstrated by detecting glucose in human blood serum with the acceptable recovery.
Interactions of nasal epithelium with macrophages and dendritic cells variously alter urban PM-induced inflammation in healthy, asthma and COPD
Authors: Paplinska-Goryca Magdalena , Misiukiewicz-Stepien Paulina , Proboszcz Malgorzata , Nejman-Gryz Patrycja , Gorska Katarzyna , Zajusz-Zubek Elwira , Krenke Rafal 
Published: June 2021

AbstractUrban particulate matter (UPM) is an important trigger of airway inflammation. The cross-talk between the external and internal matrix in the respiratory tract occurs due to the transepithelial network of macrophages/dendritic cells. This study characterized the immune processes induced by the epithelium after UPM exposure in special regard to interactions with monocyte-derived dendritic cells (moDCs) and monocyte-derived macrophages (moMφs) in obstructive lung diseases. A triple-cell co-culture model (8 controls, 10 asthma, and 8 patients with COPD) utilized nasal epithelial cells, along with moMφs, and moDCs was exposed to UPM for 24 h. The inflammatory response of nasal epithelial cells to UPM stimulation is affected differently by cell–cell interactions in healthy people, asthma or COPD patients of which the interactions with DCs had the strongest impact on the inflammatory reaction of epithelial cells after UPM exposure. The epithelial remodeling and DCs dysfunction might accelerate the inflammation after air pollution exposure in asthma and COPD.
Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP
Authors: Singh Abhijeet , Müller Bettina , Schnürer Anna 
Published: June 2021

AbstractAcetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.
GREB1L overexpression correlates with prognosis and immune cell infiltration in lung adenocarcinoma
Authors: Yu Yilin , Wang Zhiping , Zheng Qunhao , Li Jiancheng 
Published: June 2021

AbstractGREB1L is a protein-coding gene that is an important paralog of GREB1. However, its effects in lung adenocarcinoma (LUAD) have not been determined. Thus, we evaluated the prognostic value of GREB1L in LUAD using bioinformatics approaches. In particular, we evaluated the relationship between GREB1L and LUAD using a wide range of databases and analysis tools, including TCGA, GEO, HPA, TIMER, cBioPortal, and MethSurv. Compared with its expression in normal lung tissues, GREB1L expression was significantly increased in LUAD tissues. A univariate Cox analysis showed that high GREB1L expression levels were correlated with a poor OS in LUAD. Additionally, GREB1L expression was independently associated with OS through a multivariate Cox analysis. GSEA analysis revealed enrichment in cell cycle, immune regulation, and methylation. Moreover, high GREB1L expression was associated with poor survival. We also found that the methylation and genetic alteration level was associated with prognosis in patients with LUAD. Finally, an analysis of immune infiltration showed that GREB1L is correlated with immune cell infiltration, PD-1, and PD-L1. In summary, these results indicate that GREB1L is a potential molecular marker for poor prognosis in LUAD and provide additional insight for the development of therapies and prognostic markers.