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1. Expression of mapk1 and egr1 genes in Onchidium reevesii under tidal stimulation

Author:
Rongyu Wu; Rongcheng Rao; Xiaoming Zhang; Heding Shen
Source:
Aquaculture and fisheries 2023 v.8 no.1 pp. 42-49
ISSN:
2468-550X
Subject:
bioinformatics,   etc   ; Biomphalaria glabrata; aquaculture; ganglia; genes; memory; nucleotide sequences; phylogeny;     Show all 8 Subjects
Abstract:
... Previous studies have speculated that tidal rhythm of Onchidium reevesii was linked to its memory ability, which has not been well explained. Mapk1 and egr1 genes are closely related to memory formation in the MAPK signaling pathway that have been extensively studied in vertebrates. These two genes are involved in Long-term potentiation (LTP), which is generally regarded as one of the main molecul ...
DOI:
10.1016/j.aaf.2021.06.005

2. Food quality 4.0: From traditional approaches to digitalized automated analysis

Author:
Abdo Hassoun; Sandeep Jagtap; Guillermo Garcia-Garcia; Hana Trollman; Mirian Pateiro; José M. Lorenzo; Monica Trif; Alexandru Vasile Rusu; Rana Muhammad Aadil; Vida Šimat; Janna Cropotova; José S. Câmara
Source:
Journal of food engineering 2023 v.337 pp. 111216
ISSN:
0260-8774
Subject:
bioinformatics,   etc   ; artificial intelligence; automation; food analysis; food industry; food quality;     Show all 6 Subjects
Abstract:
... Food quality has recently received considerable attention from governments, researchers, and consumers due to the increasing demand for healthier and more nutritious food products. Traditionally, food quality is determined using a range of destructive and time-consuming approaches with modest analytical performance, underscoring the urgent need to develop novel analytical techniques. The Fourth In ...
DOI:
10.1016/j.jfoodeng.2022.111216

3. Characterization of invertase inhibitors (InvInhs) in tea plant, and their potential roles in participating in growth, development and cold response

Author:
Shan He; Bo Li; Huan Wang; Shicai Liang; Zhaotang Ding; Yu Wang; Kai Fan; Jianhui Hu; Xinchao Wang; Wenjun Qian
Source:
Scientia horticulturae 2023 v.308 pp. 111580
ISSN:
0304-4238
Subject:
bioinformatics,   etc   ; acclimation; beta-fructofuranosidase; chromosomes; cold; cold stress; cultivars; genome; tea; water stress;     Show all 10 Subjects
Abstract:
... Invertase inhibitor (InvInh) represses acid invertase (AI) activity though interacting with AI at post-translation level, which plays important roles in vegetative and reproductive processes and stress responses of plant. Our previous studies revealed that CsAI genes were involved in regulating cold response of tea plant, while the post-translation regulation mechanism of AI and the roles of InvIn ...
DOI:
10.1016/j.scienta.2022.111580

4. Regulation of action sites for reducing the allergenicity of pea protein based on enzymatic hydrolysis with Alcalase

Author:
Jie Ding; Liu Dong; Pengfei Jiang; Yue Tang; Songyi Lin
Source:
Food chemistry 2023 v.398 pp. 133930
ISSN:
0308-8146
Subject:
bioinformatics,   etc   ; allergenicity; electrophoresis; enzymatic hydrolysis; epitopes; experimental design; food chemistry; hydrophobicity; models; pea protein; peptides; peptidomics; subtilisin; vicilin;     Show all 14 Subjects
Abstract:
... Enzymatic hydrolysis could reduce the allergenicity of pea protein. Box-Behnken model was used to extract vicilin with the lowest and highest allergenicity, and enzymatic hydrolysis, electrophoresis, spectroscopy, bioinformatics, and peptidomics of Nano-LC-MS/MS were utilized to explore the relationship between reduced allergenicity and structural changes. After enzymatic hydrolysis, the allergeni ...
DOI:
10.1016/j.foodchem.2022.133930

5. Design and experimental validation of an optimized microalgae-bacteria consortium for the bioremediation of glyphosate in continuous photobioreactors

Author:
Lisa Borella; Giulia Novello; Matteo Gasparotto; Giancarlo Renella; Marco Roverso; Sara Bogialli; Francesco Filippini; Eleonora Sforza
Source:
Journal of hazardous materials 2023 v.441 pp. 129921
ISSN:
0304-3894
Subject:
bioinformatics,   etc   ; Chlorella; Comamonas; Pseudomonas stutzeri; acclimation; bioaugmentation; glyphosate; glyphosate resistance; microalgae; oxygen; photobioreactors; wastewater; wastewater treatment; water pollution; Europe;     Show all 15 Subjects
Abstract:
... Glyphosate will be banned from Europe by the end of 2022, but its widespread use in the last decades and its persistence in the environment require the development of novel remediation processes. In this work, a bacterial consortium was designed de novo with the aim to remove glyphosate from polluted water, supported by the oxygen produced by a microalgal species. To this goal, bioinformatics tool ...
DOI:
10.1016/j.jhazmat.2022.129921

6. Identification of upregulated genes in glioblastoma and glioblastoma cancer stem cells using bioinformatics analysis

Author:
Hasan Onur Caglar; Zekeriya Duzgun
Source:
Gene 2023 v.848 pp. 146895
ISSN:
0378-1119
Subject:
bioinformatics,   etc   ; brain neoplasms; data collection; databases; fibroblast growth factor receptor 3; gene expression; genes; glioblastoma; protein-protein interactions; therapeutics;     Show all 10 Subjects
Abstract:
... Glioblastoma (GBM) is the most common malignant brain tumor among adults. Cancer stem cells (CSCs) are known to drive treatment resistance and recurrence. However, a few CSC markers have been identified as therapeutic targets for GBM. This study aimed to show highly coexpressed genes in GBM CSCs and TCGA GBM samples and to identify possible therapeutic targets for GBM. The gene expression profiles ...
DOI:
10.1016/j.gene.2022.146895

7. Combining LC-MS/MS profiles with network pharmacology to predict molecular mechanisms of the hyperlipidemic activity of Lagenaria siceraria stand

Author:
Subhadip Banerjee; Amrendra Tiwari; Amit Kar; Joydeb Chanda; Sayan Biswas; Gudrun Ulrich-Merzenich; Pulok K. Mukherjee
Source:
Journal of ethnopharmacology 2023 v.300 pp. 115633
ISSN:
0378-8741
Subject:
bioinformatics,   etc   ; Ayurvedic medicine; Lagenaria siceraria; albino; alcohols; animals; atorvastatin; computer simulation; ferulic acid; food plants; hesperidin; high fat diet; hyperlipidemia; hypertension; insulin; lipids; mechanism of action; metabolites; obesity; p-coumaric acid; pharmacology;     Show all 21 Subjects
Abstract:
... Lagenaria siceraria Stand. (Family: Cucurbitaceae), popularly known as bottle gourd, is traditionally used in Ayurvedic medicine as a food plant, especially in hypertension and obesity. Investigations were undertaken to assign novel lead combinations from this common food plant to multi-molecular modes of actions in the complex disease networks of obesity and hypertension. LC–MS/MS based metabolit ...
DOI:
10.1016/j.jep.2022.115633

8. DBDPE and ZnO NPs synergistically induce neurotoxicity of SK-N-SH cells and activate mitochondrial apoptosis signaling pathway and Nrf2-mediated antioxidant pathway

Author:
Liying Dong; Shutao Wang; Lin Zhang; Dongmei Liu; Hong You
Source:
Journal of hazardous materials 2023 v.441 pp. 129872
ISSN:
0304-3894
Subject:
bioinformatics,   etc   ; antioxidant enzymes; apoptosis; caspase-3; cytochrome c; cytotoxicity; decabromodiphenyl ethane; flame retardants; gene expression; homeostasis; humans; membrane potential; mitochondria; mitochondrial membrane; nanoparticles; neurotoxicity; oxidative stress; protein synthesis; risk perception; viability; zinc oxide;     Show all 21 Subjects
Abstract:
... Decabromodiphenyl ethane (DBDPE), a new brominated flame retardant, could negatively affect neurobehavior and pose health risks to humans. Humans are also exposed to widely used nanomaterials. This study investigated the combined toxic effects and action types of DBDPE and Zinc oxide nanoparticles (ZnO NPs) on human neuroblastoma SK-N-SH cells and the toxicity mechanisms. DBDPE inhibited the viabi ...
DOI:
10.1016/j.jhazmat.2022.129872

9. Richness estimation in microbiome data obtained from denoising pipelines

Author:
Sven Kleine Bardenhorst; Marius Vital; André Karch; Nicole Rübsamen
Source:
Computational and Structural Biotechnology Journal 2022 v.20 pp. 508-520
ISSN:
2001-0370
Subject:
bioinformatics,   etc   ; biotechnology; microbiome;     Show all 3 Subjects
Abstract:
... The quantification of richness within a sample—either measured as the number of observed species or approximated by estimation—is a common first step in microbiome studies and is known to be highly dependent on sequencing depth, which itself is highly variable between samples. Rarefaction curves serve as a tool to investigate this dependency and it is often argued that after rarefying data—sub-sam ...
DOI:
10.1016/j.csbj.2021.12.036

10. New Insights into Phase Separation Processes and Membraneless Condensates of EIN2

Author:
Jian Lu; Chi-Kuang Wen; Georg Groth
Source:
Plants 2022 v.11 no.16 pp. -
ISSN:
2223-7747
Subject:
bioinformatics,   etc   ; condensates; ethylene; separation;     Show all 4 Subjects
Abstract:
... Recent technological advances allow us to resolve molecular processes in living cells with high spatial and temporal resolution. Based on these technological advances, membraneless intracellular condensates formed by reversible functional aggregation and phase separation have been identified as important regulatory modules in diverse biological processes. Here, we present bioinformatic and cellula ...
DOI:
10.3390/plants11162149

11. Sustainability, resilience and complexity in supply networks: A literature review and a proposal for an integrated agent-based approach

Author:
Gustavo Larrea-Gallegos; Enrico Benetto; Antonino Marvuglia; Tomás Navarrete Gutiérrez
Source:
Sustainable Production and Consumption 2022 v.30 pp. 946-961
ISSN:
2352-5509
Subject:
bioinformatics,   etc   ; dissociation; model validation;     Show all 3 Subjects
Abstract:
... Supply Networks (SN) can be seriously affected by unplanned disruptions producing important consequences on system’s functioning. These alterations may have implications over dimensions of sustainability due to the re-adaptation of the network to cope with the disruptive event. In this sense, it is relevant to understand how sustainability can be measured while considering aspects like resilience ...
DOI:
10.1016/j.spc.2022.01.009

12. DREAM: Drug-drug interaction extraction with enhanced dependency graph and attention mechanism

Author:
Yong Shi; Pei Quan; Tianlin Zhang; Lingfeng Niu
Source:
Methods 2022 v.203 pp. 152-159
ISSN:
1046-2023
Subject:
bioinformatics,   etc   ; biomedical research; drug interactions;     Show all 3 Subjects
Abstract:
... Drug-drug interactions (DDIs) aim at describing the effect relations produced by a combination of two or more drugs. It is an important semantic processing task in the field of bioinformatics such as pharmacovigilance and clinical research. Recently, graph neural networks are applied on dependency graph to promote the performance of DDI extraction with better semantic representations. However, cur ...
DOI:
10.1016/j.ymeth.2022.02.002

13. Opportunities and Limitations of Molecular Methods for Studying Bat-Associated Pathogens

Author:
Silvia Zemanová; Ľuboš Korytár; Jana Tomčová; Marián Prokeš; Monika Drážovská; Łukasz Myczko; Piotr Tryjanowski; Gréta Nusová; Alicja Matysiak; Anna Ondrejková
Source:
Microorganisms 2022 v.10 no.9 pp. -
ISSN:
2076-2607
Subject:
bioinformatics,   etc   ; ecology; molecular biology; prediction;     Show all 4 Subjects
Abstract:
... Bats have been identified as reservoirs of zoonotic and potentially zoonotic pathogens. Significant progress was made in the field of molecular biology with regard to infectious diseases, especially those that infect more than one species. Molecular methods, sequencing and bioinformatics have recently become irreplaceable tools in emerging infectious diseases research and even outbreak prediction. ...
DOI:
10.3390/microorganisms10091875

14. Overview of tRNA Modifications in Chloroplasts

Author:
Maxime Fages-Lartaud; Martin Frank Hohmann-Marriott
Source:
Microorganisms 2022 v.10 no.2 pp. -
ISSN:
2076-2607
Subject:
bioinformatics,   etc   ; Chlamydomonas reinhardtii; aminoacylation; chloroplasts;     Show all 4 Subjects
Abstract:
... The chloroplast is a promising platform for biotechnological innovation due to its compact translation machinery. Nucleotide modifications within a minimal set of tRNAs modulate codon–anticodon interactions that are crucial for translation efficiency. However, a comprehensive assessment of these modifications does not presently exist in chloroplasts. Here, we synthesize all available information c ...
DOI:
10.3390/microorganisms10020226

15. BinMat: A molecular genetics tool for processing binary data obtained from fragment analysis in R

Author:
Clarke van Steenderen
Source:
Biodiversity data journal 2022 v.10 pp. e77875
ISSN:
1314-2828
Subject:
bioinformatics,   etc   ; biodiversity; molecular biology; statistics;     Show all 4 Subjects
Abstract:
... Processing and visualising trends in the binary data (presence or absence of electropherogram peaks), obtained from fragment analysis methods in molecular biology, can be a time-consuming and often cumbersome process. Scoring and analysing binary data (from methods, such as AFLPs, ISSRs and RFLPs) entail complex workflows that require a high level of computational and bioinformatic skills. The app ...
DOI:
10.3897/BDJ.10.e77875

16. OBI: A computational tool for the analysis and systematization of the positive selection in proteins

Author:
Julián H. Calvento; Franco Leonardo Bulgarelli; Ana Julia Velez Rueda
Source:
MethodsX 2022 v.9 pp. 101786
ISSN:
2215-0161
Subject:
bioinformatics,   etc   ; drug resistance; vaccine development;     Show all 3 Subjects
Abstract:
... There are multiple tools for positive selection analysis, including vaccine design and detection of variants of circulating drug-resistant pathogens in population selection. However, applying these tools to analyze a large number of protein families or as part of a comprehensive phylogenomics pipeline could be challenging. Since many standard bioinformatics tools are only available as executables, ...
DOI:
10.1016/j.mex.2022.101786

17. A fine-grained navigation network construction method for urban environments

Author:
Xiayin Lou; Min Sun; Shihao Yang
Source:
International journal of applied earth observation and geoinformation 2022 v.113 pp. 102994
ISSN:
1569-8432
Subject:
bioinformatics,   etc   ; computer software; spatial data;     Show all 3 Subjects
Abstract:
... Fine-grained navigation is becoming increasingly demanded in urban areas. However, current navigation software fails to provide accurate paths on grounds without roads (GWR) like residential communities, squares, parks, etc. In this work, a method for the construction of fine-grained navigation networks for urban environments is developed. Remote sensing images are used to estimate the traversabil ...
DOI:
10.1016/j.jag.2022.102994

18. A single evolutionarily divergent mutation determines the different FAD‐binding affinities of human and rat NQO1 due to site‐specific phosphorylation

Author:
Juan Luis Pacheco‐Garcia; Dmitry Loginov; Bruno Rizzuti; Pavla Vankova; Jose L. Neira; Daniel Kavan; Noel Mesa‐Torres; Rita Guzzi; Petr Man; Angel L. Pey
Source:
FEBS letters 2022 v.596 no.1 pp. 29-41
ISSN:
0014-5793
Subject:
bioinformatics,   etc   ; humans; mutation; phosphorylation; rats;     Show all 5 Subjects
Abstract:
... The phosphomimetic mutation S82D in the cancer‐associated, FAD‐dependent human NADP(H):quinone oxidoreductase 1 (hNQO1) causes a decrease in flavin‐adenine dinucleotide‐binding affinity and intracellular stability. We test in this work whether the evolutionarily recent neutral mutation R80H in the vicinity of S82 may alter the strong functional effects of S82 phosphorylation through electrostatic ...
DOI:
10.1002/1873-3468.14238

19. Diverse sesquiterpenoids from Litsea lancilimba Merr. with potential neuroprotective effects against H2O2-induced SH-SY5Y cell injury

Author:
Yi-Jie ZHANG; Ming BAI; Jia-Yi LI; Shu-Yan QIN; Yu-Yang LIU; Xiao-Xiao HUANG; Jiang ZHENG; Shao-Jiang SONG
Source:
Chinese journal of natural medicines 2022 v.20 no.9 pp. 701-711
ISSN:
1875-5364
Subject:
bioinformatics,   etc   ; Litsea; humans; sesquiterpenoids; spectroscopy;     Show all 5 Subjects
Abstract:
... Five undescribed sesquiterpenoids (1–5), and nine known sesquiterpenoids (6–14) were obtained from the fruits of Litsea lancilimba Merr. by LC-MS/MS molecular networking strategies. Litsemene A (1) possessed a unique 8-member ring through unexpected cyclization of the methyl group on C-10 of guaiane. Their structures were elucidated by spectroscopic techniques including IR, UV, NMR, HR-ESI-MS, and ...
DOI:
10.1016/S1875-5364(22)60199-7

20. Reconstruction of the rRNA Sequences of LUCA, with Bioinformatic Implication of the Local Similarities Shared by Them

Author:
Yu Men; Guoliang Lu; Yanhui Wang; Jinzhong Lin; Qiang Xie
Source:
Biology 2022 v.11 no.6 pp. -
ISSN:
2079-7737
Subject:
bioinformatics,   etc   ; ancestry; nucleotides; phylogeny; ribosomes;     Show all 5 Subjects
Abstract:
... The theory of the RNA world, especially with the catalytic capability of RNA, provides a reasonable framework explaining the evolution of molecular genetics system before the scenario of the central dogma. However, it remains a challenge to deduce the origin mechanism of rRNAs. Here we reconstructed the phylogenetic relationships of archaea and bacteria with bootstrap values of most nodes, especia ...
DOI:
10.3390/biology11060837