-
PLoS Computational Biology Aug 2023Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize...
Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is critical to understand the mechanisms behind the interactions that structure microbial consortia and determine their functions. Constraint-based reconstruction and analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as the state-of-the-art tool to simulate the behavior of microbial communities from their constituent genomes. In the last decade, many tools have been developed that use COBRA approaches to simulate multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these tools have not been systematically evaluated regarding their software quality, most suitable application, and predictive power. Hence, it is uncertain which tools users should apply to their system and what are the most urgent directions that developers should take in the future to improve existing capacities. This study conducted a systematic evaluation of COBRA-based tools for microbial communities using datasets from two-member communities as test cases. First, we performed a qualitative assessment in which we evaluated 24 published tools based on a list of FAIR (Findability, Accessibility, Interoperability, and Reusability) features essential for software quality. Next, we quantitatively tested the predictions in a subset of 14 of these tools against experimental data from three different case studies: a) syngas fermentation by C. autoethanogenum and C. kluyveri for the static tools, b) glucose/xylose fermentation with engineered E. coli and S. cerevisiae for the dynamic tools, and c) a Petri dish of E. coli and S. enterica for tools incorporating spatiotemporal variation. Our results show varying performance levels of the best qualitatively assessed tools when examining the different categories of tools. The differences in the mathematical formulation of the approaches and their relation to the results were also discussed. Ultimately, we provide recommendations for refining future GEM microbial modeling tools.
Topics: Microbial Consortia; Escherichia coli; Saccharomyces cerevisiae; Genome; Software
PubMed: 37578975
DOI: 10.1371/journal.pcbi.1011363 -
Plants (Basel, Switzerland) Jul 2023Salinization is a global agricultural problem with many negative effects on crops, including delaying germination, inhibiting growth, and reducing crop yield and...
Salinization is a global agricultural problem with many negative effects on crops, including delaying germination, inhibiting growth, and reducing crop yield and quality. This study compared the salt tolerance of 20 soybean varieties at the germination stage to identify soybean germplasm with a high salt tolerance. Germination tests were conducted in Petri dishes containing 0, 50, 100, 150, and 200 mmol L NaCl. Each Petri dish contained 20 soybean seeds, and each treatment was repeated five times. The indicators of germination potential, germination rate, hypocotyl length, and radicle length were measured. The salt tolerance of 20 soybean varieties was graded, and the theoretical identification concentration was determined by cluster analysis, the membership function method, one-way analysis of variance, and quadratic equation analysis. The relative germination rate, relative germination potential, relative root length, and relative bud length of the 20 soybean germplasms decreased when the salt concentration was >50 mmol L, compared with that of the Ctrl. The half-lethal salt concentration of soybean was 164.50 mmol L, and the coefficient of variation was 18.90%. Twenty soybean varieties were divided into three salt tolerance levels following cluster analysis: Dongnong 254, Heike 123, Heike 58, Heihe 49, and Heike 68 were salt-tolerant varieties, and Xihai 2, Suinong 94, Kenfeng 16, and Heinong 84 were salt-sensitive varieties, respectively. This study identified suitable soybean varieties for planting in areas severely affected by salt and provided materials for screening and extracting parents or genes to breed salt-tolerant varieties in areas where direct planting is impossible. It assists crop breeding at the molecular level to cope with increasingly serious salt stress.
PubMed: 37570942
DOI: 10.3390/plants12152789 -
Gut and Liver Jul 2023Among several methods used to prevent endoscopic submucosal dissection (ESD) bleeding, the recently developed hemostatic powder (HP) has few technical limitations and is...
BACKGROUND/AIMS
Among several methods used to prevent endoscopic submucosal dissection (ESD) bleeding, the recently developed hemostatic powder (HP) has few technical limitations and is relatively easy-to-use. This study aimed to analyze the hemostatic effects and mechanisms of two HPs using a porcine upper gastrointestinal hemorrhage model.
METHODS
We evaluated HPs (Endospray and epidermal growth factor [EGF]-endospray) for adhesion, waterproofing ability, permeability, and absorption . ESD was performed to induce bleeding ulcers in the porcine stomachs. In a total of three pigs, three bleeding ulcers per animal were generated. Hemostasis and rebleeding were evaluated endoscopically. After 72 hours, the animals were sacrificed, and histologically analyzed.
RESULTS
The water absorption of HPs was over 20 times the initial value within 30 minutes. The gelated HPs completely blocked water penetration into the applied site within 5 minutes and strongly adhered to the Petri-dish surface for up to 6 hours. The initial hemostasis rates within 5 minutes were 33.3%, 100.0%, and 66.7%, and the rebleeding rates at 6 to 72 hours after HP application were 33.3%, 16.7%, and 33.3% (control, Endospray, and EGF-endospray groups, respectively). Histological analysis revealed the thickness of the regenerated mucosa (522.1, 514.5, and 680.3 μm) and the submucosal layer (1,510.3, 2,848.2, and 3,062.3 μm) and the number of newly formed blood vessels (15.3, 17.9, and 20.5) in the control, Endospray, and EGF-endospray groups, respectively.
CONCLUSIONS
The endoscopic HPs demonstrated the ability to elicit effective initial hemostasis and the histological ulcer-healing effect of EGF in an animal model of hemorrhagic gastric ulcers.
Topics: Swine; Animals; Hemostatics; Epidermal Growth Factor; Powders; Endoscopic Mucosal Resection; Ulcer; Gastric Mucosa; Hemostasis
PubMed: 36510773
DOI: 10.5009/gnl220149 -
Environmental Pollution (Barking, Essex... Aug 2023Microplastics (MPs) in soil undergo different aging processes such as photoaging, mechanical abrasion and biodegradation, leading to alterations in the surface...
Microplastics (MPs) in soil undergo different aging processes such as photoaging, mechanical abrasion and biodegradation, leading to alterations in the surface properties of MPs. In this study, we investigated the adsorption-desorption of chlorpyrifos (CPF) on pristine and UV light-aged low-density polyethylene (LDPE) and biodegradable (Bio) MPs that were derived from plastic mulch films. We also tested the bioconcentration of pristine and aged MPs (LDPE- and Bio-MPs aged under UV light and LDPE-MPs aged in three different soils) associated with CPF by earthworms (Lumbricus terrestris). The results showed that UV-aged MPs showed higher CPF adsorption capacities than pristine MPs, with the adsorption capacities at 184.9 ± 5.3, 200.5 ± 1.8, 193.0 ± 8.7, and 215.9 ± 1.1 μg g for pristine LDPE-, UV-aged LDPE-, pristine Bio- and UV-aged Bio-MPs, respectively. The desorption rate of CPF from UV-aged LDPE-MPs within 48 h was lower than the desorption from pristine ones (28.8 ± 7.7% vs. 40.0 ± 3.9%), while both pristine and UV-aged Bio-MPs showed very low CPF desorption rates. A 4-day Petri dish experiment showed that UV-aged MPs were significantly less concentrated in earthworm casts than pristine counterparts (52% and 36% lower for UV-aged LDPE- and Bio-MPs), while UV-aged MPs with adsorbed CPF were concentrated significantly more than UV-aged MPs without CPF. Interestingly, LDPE-MPs aged in soil with a high carbon, nitrogen, and carbon-to-nitrogen ratio were significantly more concentrated in earthworm casts than pristine LDPE-MPs. In conclusion, UV-aged MPs acted as stronger vectors for CPF than pristine MPs. The bioconcentration of MPs differed significantly due to microplastic aging, as well as the combined effect with CPF. Moreover, LDPE-MPs aged in soil with enriched carbon and nitrogen were significantly concentrated in earthworm casts. Further studies on the environmental behaviours of aged MPs associated with other pollutants in soil, especially soils high in carbon and nitrogen, are needed.
Topics: Animals; Microplastics; Plastics; Chlorpyrifos; Polyethylene; Adsorption; Bioaccumulation; Soil; Oligochaeta
PubMed: 37247767
DOI: 10.1016/j.envpol.2023.121910 -
Journal of Visualized Experiments : JoVE Jul 2023The mustard aphid (L. erysimi) is a pest that infests various cruciferous crops and transmits plant viruses. To achieve eco-friendly pest management, entomopathogenic...
The mustard aphid (L. erysimi) is a pest that infests various cruciferous crops and transmits plant viruses. To achieve eco-friendly pest management, entomopathogenic fungi (EPF) are potential microbial control agents for controlling this pest. Therefore, virulence screening of EPF isolates under Petri dish conditions is necessary before field application. However, the mustard aphid is a parthenogenetic insect, making it difficult to record data during Petri dish experiments. A modified system for detached-leaf bioassays was developed to address this issue, using a micro-sprayer to inoculate conidia onto aphids and prevent drowning by facilitating air-drying after spore suspension. The system maintained high relative humidity throughout the observation period, and the leaf disc remained fresh for over ten days, allowing parthenogenetic reproduction of the aphids. To prevent offspring buildup, a process of daily removal using a painting brush was implemented. This protocol demonstrates a stable system for evaluating the virulence of EPF isolates against mustard aphids or other aphids, enabling the selection of potential isolates for aphid control.
Topics: Animals; Aphids; Mustard Plant; Fungi; Spores, Fungal; Insecta
PubMed: 37677031
DOI: 10.3791/65312 -
Polymers Sep 2023The diverse applications of metal oxide-biopolymer matrix as a nanocomposite heterogenous catalyst have caused many researches to scrutinize the potential of this...
The diverse applications of metal oxide-biopolymer matrix as a nanocomposite heterogenous catalyst have caused many researches to scrutinize the potential of this framework. In this study, a novel hybrid barium oxide-chitosan nanocomposite was synthesized through a facile and cost-effective co-precipitation method by doping barium oxide nanoparticles within the chitosan matrix at a weight percentage of 20 wt.% BaO-chitosan. A thin film of the novel hybrid material was produced by casting the nanocomposite solution in a petri dish. Several instrumental methods, including Fourier-transform infrared (FTIR), scanning electron microscope (SEM), energy dispersive spectroscopy (EDS), and X-ray diffraction (XRD), were used to analyze and characterize the structure of the BaO-CS nanocomposite. The chemical interaction with barium oxide molecules resulted in a noticeable displacement of the most significant chitosan-specific peaks in the FTIR spectra. When the surface morphology of SEM graphs was analyzed, a dramatic morphological change in the chitosan surface was also discovered; this morphological change can be attributed to the surface adsorption of BaO molecules. Additionally, the patterns of the XRD demonstrated that the crystallinity of the material, chitosan, appears to be enhanced upon interaction with barium oxide molecules with the active sites, OH and NH groups, along the chitosan backbone. The prepared BaO-CS nanocomposite can be used successfully as an effective heterogenous recyclable catalyst for the reaction of ,-(alkane-diyl)bis(2-chloroacetamide) with 2-(arylidinehydrazine)-1-carbothioamide as a novel synthetic approach to prepare 2-hydrazonothiazol-4(5)-ones. This new method provides a number of benefits, including quick and permissive reaction conditions, better reaction yields, and sustainable catalysts for multiple uses.
PubMed: 37765671
DOI: 10.3390/polym15183817 -
Plant Disease Oct 2023Pseudostellaria heterophylla is one of the traditional medicines in China. From 2020 to 2022, postharvest wet root rot disease was observed with an incidence of 2~5% on...
Pseudostellaria heterophylla is one of the traditional medicines in China. From 2020 to 2022, postharvest wet root rot disease was observed with an incidence of 2~5% on the tuberous roots of the harvested P. heterophylla in Zherong county, Fujian province, China, which usually occurs under damp and unventilated conditions. The symptoms of the disease were as follows: white mycelia grew on the surface of tuberous root initially and gradually wrapped around the roots, the internal root tissue turned yellow and became wet decay finally. To identify the causal agent, a total of 20 samples with symptomatic tuberous roots were collected. Small pieces (3 mm2) were treated by surface disinfection with 75% ethanol and 1% NaOCl, then rinsed 3 times with sterile water. These treated pieces were transferred onto potato dextrose agar (PDA) and incubated at 25°C in the dark for 7 d. Ten pure cultures were obtained using single-spore isolation method. The fungus colonies initially produced white aerial mycelium, subsequently exhibited yellow pigmentation. Mycelia were consisted of smooth, hyaline, branched, and septate hyphae. The conidia were solitary or clustered, brown or dark brown, smooth, ellipsoidal to spherical, 6.66 (5.50-7.81)×5.65 (4.17-7.22) µm (n=50) in size. The conidiophores were hyaline or pale brown and produced conidiogenous cells, which were pale brown, smooth, ampulliform, and 10.14 (8.82-15.30) um long (n=50). Based on these morphological characteristics, the fungus was identified as the genus Apiospora (Arthrinium). The rDNA-ITS region and partial β-tubulin gene (BenA) were amplified using the primers ITS1/ITS4 (White et al. 1990) and Bt2a/Bt2b (Glass and Donaldson 1995), respectively. The sequences of isolates FJAT-32563 and FJAT-32564 were deposited in GenBank (ITS, OM920984 and OM920985; BenA, OM953823 and OM953824). All sequences had more than 99% similarity with those of A. arundinis strain CBS:106.12 (ITS, KF144883; BenA, KF144973). In the multilocus phylogenetic analysis (ITS + BenA), the two isolates clustered together with other strains of A. arundinis with 100% bootstrap support. The isolates were therefore identified as A. arundinis based on both morphological and molecular characteristics. To confirm the pathogenicity, fresh tuberous roots were selected and surface disinfected, then the roots were immersed with a quarter length in the conidial suspension (106/mL) for 30 min, whereas the control roots were immersed with sterile water (n=30). They were placed in petri dish with wet filter paper at 25±2℃, maintaining 80% relative humidity in the dark. The white aerial mycelium appeared at 5 days after inoculation, and wet root rot decaying occurred after inoculation for 21 days. The symptoms were similar to those described above, whereas the control roots were asymptomatic. The same fungus was re-isolated from the infected roots, showing similar morphological characteristics and molecular traits. Koch's postulates were completed and the pathogenicity test for the isolates has been repeated thrice. Previously, A. arundinis was reported to infect peach and sugarcane (Ji et al. 2020; Liao et al. 2022). To our knowledge, this is the first report of A. arundinis causing wet root rot of P. heterophylla in China. The disease would be a potentially new threat to this medicinal plant.
PubMed: 37883638
DOI: 10.1094/PDIS-05-23-0911-PDN -
Biomaterials Sep 2024The gel microsphere culture system (GMCS) showed various advantages for mesenchymal stem cell (MSC) expansion and delivery, such as high specific surface area, small and...
The gel microsphere culture system (GMCS) showed various advantages for mesenchymal stem cell (MSC) expansion and delivery, such as high specific surface area, small and regular shape, extensive adjustability, and biomimetic properties. Although various technologies and materials have been developed to promote the development of gel microspheres, the differences in the biological status of MSCs between the GMCS and the traditional Petri dish culture system (PDCS) are still unknown, hindering gel microspheres from becoming a culture system as widely used as petri dishes. In the previous study, an excellent "all-in-one" GMCS has been established for the expansion of human adipose-derived MSCs (hADSCs), which showed convenient cell culture operation. Here, we performed transcriptome and proteome sequencing on hADSCs cultured on the "all-in-one" GMCS and the PDCS. We found that hADSCs cultured in the GMCS kept in an undifferentiation status with a high stemness index, whose transcriptome profile is closer to the adipose progenitor cells (APCs) in vivo than those cultured in the PDCS. Further, the high stemness status of hADSCs in the GMCS was maintained through regulating cell-ECM interaction. For application, bilayer scaffolds were constructed by osteo- and chondro-differentiation of hADSCs cultured in the GMCS and the PDCS. The effect of osteochondral regeneration of the bilayer scaffolds in the GMCS group was better than that in the PDCS group. This study revealed the high stemness and excellent functionality of MSCs cultured in the GMCS, which promoted the application of gel microspheres in cell culture and tissue regeneration.
Topics: Microspheres; Humans; Mesenchymal Stem Cells; Adipose Tissue; Cell Differentiation; Animals; Extracellular Matrix; Cells, Cultured; Tissue Scaffolds; Gels; Chondrogenesis; Osteogenesis; Cell Culture Techniques
PubMed: 38776592
DOI: 10.1016/j.biomaterials.2024.122616 -
Development (Cambridge, England) Dec 2023In recent years, there have been notable advancements in the ability to programme human cell identity, enabling us to design and manipulate cell function in a Petri...
In recent years, there have been notable advancements in the ability to programme human cell identity, enabling us to design and manipulate cell function in a Petri dish. However, current protocols for generating target cell types often lack efficiency and precision, resulting in engineered cells that do not fully replicate the desired identity or functional output. This applies to different methods of cell programming, which face similar challenges that hinder progress and delay the achievement of a more favourable outcome. However, recent technological and analytical breakthroughs have provided us with unprecedented opportunities to advance the way we programme cell fate. The Company of Biologists' 2023 workshop on 'Novel Technologies for Programming Human Cell Fate' brought together experts in human cell fate engineering and experts in single-cell genomics, manipulation and characterisation of cells on a single (sub)cellular level. Here, we summarise the main points that emerged during the workshop's themed discussions. Furthermore, we provide specific examples highlighting the current state of the field as well as its trajectory, offering insights into the potential outcomes resulting from the application of these breakthrough technologies in precisely engineering the identity and function of clinically valuable human cells.
Topics: Humans; Cellular Reprogramming; Cell Differentiation
PubMed: 38078653
DOI: 10.1242/dev.202300 -
Plant Disease Aug 2023Sunflower broomrape (Orobanche cumana Wallr.) is a holoparasitic plant species which mainly parasitizes a few species of the Asteraceae in the wild and is exclusively...
Sunflower broomrape (Orobanche cumana Wallr.) is a holoparasitic plant species which mainly parasitizes a few species of the Asteraceae in the wild and is exclusively found growing on sunflower in agricultural fields (Fernández-Martínez et al. 2015). O. cumana is a serious threat to sunflower production in Xinjiang and Inner Mongolia (Shi et al. 2015). Karelinia caspia (Pall.) Less. (Asteraceae) is an ecologically important plant species occurring across the desert ecosystems of Russia, Central Asia, and northwest China. It plays an important role in reducing wind erosion and desertification (Xu et al. 2018). During the 2018 and 2019 growing seasons, sunflower broomrape was observed parasitizing K. caspia in non-cultivated areas adjacent to sunflower fields near Beitun city (87°51'E, 47°15'N) in Xinjiang, China. Sunflower broomrape plants were identified morphologically as O. cumana according to Pujadas-Salvà and Velasco (2000). The host plants were identified morphologically as K. caspia according to Lin et al (1979). The ribosomal DNA internal transcribed spacer (ITS) and the trnL-F region of the parasite were amplified by PCR using primer pairs ITS1/ITS4 and trnL-FF/trnL-FR, respectively (Taberlet et al. 1991; Anderson et al. 2004). The ITS sequence of the parasite (Accession No. MT795725.1) showed 100% identity (675bp out of 689bp) to that of O. cernua var. cumana (KC811228.1). The trnl-F sequence of the parasite (Accession No. ON843707) showed 98% identity (675 of 689 bp) to O.cernua var. cumana (KT387722.1). Multi-locus phylogenetic analysis of the two sequences showed clustering with sunflower broomrape. The ITS region of the parasite and host was were amplified by PCR using the primer pair ITS1F/ITS4R (Taberlet et al.1991), and the ITS sequences of the host (Accession No. MT791995.1) showed 99.86% identity (728bp of 802bp) to that of K. caspia (LN607483.1). Rhizotron and pot experiments were carried out to assess the parasitic relationship between O. cumana and K. caspia. In the rhizotron experiment, 2-week-old seedlings of K. caspia were inoculated with sterilized 400 O. cumana seeds in a 15-cm petri dish filled with a sponge overlaid with glass fiber filter paper. The parasitic state of O. cumana was observed 9 days after inoculation. In another trial, seeds of K. caspia were sowed in 2-L and 4-L pots containing sand-vermiculite-compost (1:1:1 v:v:v). These pots were artificially inoculated with 50 mg of O. cumana seeds per 1 kg of substrate. After 20 and 70 days, corresponding to the early parasitic and flowering stages, respectively, of O. cumana, K. caspia plants were uprooted from the media and washed carefully. The parasitic relationship was confirmed by the attachment position of the broomrape to the K. caspia root. To our knowledge, this is the first report of O. cumana parasitizing K. caspia in Xinjiang, China. This phenomenon means that sunflower broomrape can raise up seed on a newly recognized host. Weed eradication in and near sunflower fields is a key measure to control sunflower broomrape.
PubMed: 37555727
DOI: 10.1094/PDIS-05-23-0988-PDN