Sensitive characterization of complex chemical reactions in black garlic preparation based on on-line extraction electrospray ionization mass spectrometry.

Changes in chemical composition during food processing and handling are crucial for the alteration of food flavor and function, and accurate characterization of key chemical reaction pathways in complex food matrices is one of the core challenges in food chemistry research. Here, this study attempts to establish a strategy for sensitive characterization of chemical reactions during food processing based on on-line extraction electrospray ionization mass spectrometry (oEESI-MS). The process of making garlic into black garlic, a traditional global flavor food, was chosen as an exemplary research template.

BioTRY: A Comprehensive Knowledge Base for Titer, Rate, and Yield of Biosynthesis.

Synthetic biology is rapidly evolving into a data-intensive science that increasingly relies on massive data sets; one of its applications is the evaluation of the economic viability of fermentation processes. However, the key economic indicators, namely titer, rate, and yield (TRY), which respectively reflect the downstream processing, reactor size, and raw material costs, are not well captured in bioinformatics databases. In this paper, we present BioTRY, an intuitive and user-friendly tool that contains >5,000 biochemicals and >3,800 strains, along with over 52,000 corresponding TRY entries with original references.

Mechanism of apoptosis in oral squamous cell carcinoma promoted by cardamonin through PI3K/AKT signaling pathway.

Currently, surgical resection remains the primary approach for treating oral squamous cell carcinoma (OSCC), with limited options for effective drug therapy. Cardamonin, a principal compound derived from Myristica fragrans of the Zingiberaceae family, has garnered attention for its potential to suppress the onset and progression of various malignancies encompassing breast cancer, hepatocellular carcinoma, and ovarian cancers. Nevertheless, the involvement of cardamonin in the treatment of OSCC and its underlying mechanisms are yet to be elucidated.

Reciprocal inhibition of autophagy and Botrytis cinerea-induced programmed cell death in 'Shine Muscat' grapes.

Botrytis cinerea causes gray mold, decreasing the quality of table grapes. The berry response to B. cinerea infection was explored in present study, focusing on the relationship between presence of autophagy and programmed cell death (PCD).

Light-responsive transcription factors VvHYH and VvGATA24 mediate wax terpenoid biosynthesis in Vitis vinifera.

The cuticular wax that covers the surfaces of plants is the first barrier against environmental stresses and increasingly accumulates with light exposure. However, the molecular basis of light-responsive wax biosynthesis remains elusive. In grape (Vitis vinifera), light exposure resulted in higher wax terpenoid content and lower decay and abscission rates than controls kept in darkness.

[Analysis of chemical compositions in different parts of Isodon japonicus using UPLC-Q-TOF-MS technique combined with chemometrics].

In order to analyze the similarities and differences of chemical compositions between the roots and stems and leaves of Isodon japonicus(IJ), this study utilized UPLC-Q-TOF-MS technology to systematically characterize its chemical compositions, analyzed and identified the structure of its main compounds, and established a method for simultaneous determination of its content by refe-rence substance. A total of 34 major compounds in IJ, including 14 reference compounds, were identified or predicted online. Moreover, an UPLC-UV content determination method was developed for 11 compounds [danshensu, caffeic acid, vicenin-2,(1S,2S)-globoidnan B, rutin,(+)-rabdosiin,(-)-rabdosiin,(1S,2S)-rabdosiin, shimobashiric acid C, rosmarinic acid, and pedalitin].

Exploring the bi-directional relationship between periodontitis and dyslipidemia: a comprehensive systematic review and meta-analysis.

Aim: As periodontitis and dyslipidemia are diseases that occur with high incidence, the relationship between them has attracted much attention. Previous studies on these diseases have tended to focus on lipid parameters and periodontitis, we aimed to investigate the relationship between dyslipidemia and periodontitis.

Materials And Methods: A comprehensive search to identify the studies investigating the relationship between dyslipidemia and periodontitis was performed on PubMed, Web of Science and Cochrane Library before the date of August, 2023.

High-throughput prediction of enzyme promiscuity based on substrate-product pairs.

The screening of enzymes for catalyzing specific substrate-product pairs is often constrained in the realms of metabolic engineering and synthetic biology. Existing tools based on substrate and reaction similarity predominantly rely on prior knowledge, demonstrating limited extrapolative capabilities and an inability to incorporate custom candidate-enzyme libraries. Addressing these limitations, we have developed the Substrate-product Pair-based Enzyme Promiscuity Prediction (SPEPP) model.

RCN1 deficiency inhibits oral squamous cell carcinoma progression and THP-1 macrophage M2 polarization.

Reticulocalbin 1 (RCN1), a calcium-binding protein located in the endoplasmic reticulum (ER) lumen, contains six conserved regions. Its main functions include maintaining intracellular homeostasis and regulating cell proliferation and apoptosis, and it plays an important role in the development of various tumours. However, the exact function of RCN1 in oral squamous cell carcinoma (OSCC) is not fully understood.

MCF2Chem: A manually curated knowledge base of biosynthetic compound production.

Background: Microbes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced via these cell factories have also grown substantially. However, no database is available that provides detailed information on the microbial cell factories and the synthesized compounds.

RDBridge: a knowledge graph of rare diseases based on large-scale text mining.

Motivation: Despite low prevalence, rare diseases affect 300 million people worldwide. Research on pathogenesis and drug development lags due to limited commercial potential, insufficient epidemiological data, and a dearth of publications. The unique characteristics of rare diseases, including limited annotated data, intricate processes for extracting pertinent entity relationships, and difficulties in standardizing data, represent challenges for text mining.

CCIBP: a comprehensive cosmetic ingredients bioinformatics platform.

Summary: Cosmetics form an important part of our daily lives, and it is therefore important to understand the basic physicochemical properties, metabolic pathways, and toxicological and safe concentrations of these cosmetics molecules. Therefore, comprehensive cosmetic ingredients bioinformatics platform (CCIBP) was developed here, which is a unique comprehensive cosmetic database providing information on regulations, physicochemical properties, and human metabolic pathways for cosmetic molecules from major regions of the world, whilst also correlating plant information in natural products. CCIBP supports formulation analysis, efficacy component analysis, and also combines knowledge of synthetic biology to facilitate access to natural molecules and biosynthetic production.

Factors impacting the behavior of phytoremediation in pesticide-contaminated environment: A meta-analysis.

Phytoremediation provides substantial advantages, including eco-friendliness, cost-effectiveness, efficiency, and visual appeal. However, the current knowledge of the factors influencing phytoremediation in pesticide-contaminated environments remains limited. It is critical to understand phytoremediation and the factors affecting the variation in removal efficiency.

Data-Driven Prediction of Molecular Biotransformations in Food Fermentation.

Fermentation products, together with food components, determine the sense, nutrition, and safety of fermented foods. Traditional methods of fermentation product identification are time-consuming and cumbersome, which cannot meet the increasing need for the identification of the extensive bioactive metabolites produced during food fermentation. Hence, we propose a data-driven integrated platform (FFExplorer, http://www.

Porphyromonas gingivalis Gingipains Destroy the Vascular Barrier and Reduce CD99 and CD99L2 Expression To Regulate Transendothelial Migration.

Porphyromonas gingivalis is an important periodontal pathogen that can cause vascular injury and invade local tissues through the blood circulation, and its ability to evade leukocyte killing is critical to its distal colonization and survival. Transendothelial migration (TEM) is a series of that enable leukocytes to squeeze through endothelial barriers and migrate into local tissues to perform immune functions. Several studies have shown that P.

SynBioTools: a one-stop facility for searching and selecting synthetic biology tools.

Background: The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology.

Results: We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools.

Proteomic investigation and biomarker identification of lung and spleen deficiency syndrome in HIV/AIDS immunological nonresponders.

Background: Human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS) immunological nonresponders (HIV/AIDS-INRs) whose CD4 cell counts do not rebound after highly active antiretroviral therapy (HAART) treatment usually experience severely impaired immune function and high mortality. Traditional Chinese medicine (TCM) has many advantages in the field of AIDS, especially its promotion of patients' immune reconstitution. Accurate differentiation of TCM syndromes is a prerequisite for guiding an effective TCM prescription.

Plant species shape the bacterial communities on the phyllosphere in a hyper-arid desert.

Microorganisms are an important component of global biodiversity. However, they are vulnerable to hyper-arid climates in desert regions. Xerophytes are desert vegetation with unique biodiversity.

Oxidative Damage in Roots of Rice (Oryza sativa L.) Seedlings Exposed to Microplastics or Combined with Cadmium.

This study aimed to investigate the effect of 10-40 mg L polystyrene microplastics (PS-MPs), 0.05 mg L cadmium (Cd) and their combination on the growth and related physiological and toxicological responses in Oryza sativa L. seedling roots.

Genome-wide identification, characterization, and expression analysis of UDP-glycosyltransferase genes associated with secondary metabolism in alfalfa ( L.).

Uridine diphosphate glycosyltransferases (UGTs) are enzymes that catalyze glycosylation modifications and play an essential role in regulating plant metabolism. Alfalfa ( L.) is the most important legume in the world due to its high yields and protein content; however, the genes in alfalfa have not yet been studied.

Species identity and combinations differ in their overall benefits to plants inoculated with single or multiple endophytic fungi under drought conditions.

Although desert plants often establish multiple simultaneous symbiotic associations with various endophytic fungi in their roots, most studies focus on single fungus inoculation. Therefore, combined inoculation of multiple fungi should be applied to simulate natural habitats with the presence of a local microbiome. Here, a pot experiment was conducted to test the synergistic effects between three extremely arid habitat-adapted root endophytes (, and sp.

BioBulkFoundary: a customized webserver for exploring biosynthetic potentials of bulk chemicals.

Summary: Advances in metabolic engineering have boosted the production of bulk chemicals, resulting in tons of production volumes of some bulk chemicals with very low prices. A decrease in the production cost and overproduction of bulk chemicals makes it necessary and desirable to explore the potential to synthesize higher-value products from them. It is also useful and important for society to explore the use of design methods involving synthetic biology to increase the economic value of these bulk chemicals.

The interaction of CD300lf and ceramide reduces the development of periodontitis by inhibiting osteoclast differentiation.

Aim: The regulation of osteoclasts (OCs) by inhibitory immunoreceptors maintains bone homeostasis and is considered an important determinant of the extent of periodontal pathology. The aim of this study was to investigate the role of the inhibitory immunoreceptor CD300lf and its ligand ceramide in osteoclastogenesis in periodontitis.

Materials And Methods: The expression of CD300lf was measured in vitro and in a ligature-induced periodontitis model.

AddictedChem: A Data-Driven Integrated Platform for New Psychoactive Substance Identification.

The mechanisms underlying drug addiction remain nebulous. Furthermore, new psychoactive substances (NPS) are being developed to circumvent legal control; hence, rapid NPS identification is urgently needed. Here, we present the construction of the comprehensive database of controlled substances, AddictedChem.