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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 -
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 -
Parasites & Vectors Jul 2023Numerous bioassay methods have been used to test the efficacy of repellents for ticks, but the comparability of results across different methods has only been evaluated...
BACKGROUND
Numerous bioassay methods have been used to test the efficacy of repellents for ticks, but the comparability of results across different methods has only been evaluated in a single study. Of particular interest are comparisons between bioassays that use artificial containers (in vitro) with those conducted on a human subject (in vivo) for efficacy testing of new potential unregistered active ingredients, which most commonly use in vitro methods.
METHODS
We compared four different bioassay methods and evaluated three ingredients (DEET [N,N-Diethyl-meta-toluamide], peppermint oil and rosemary oil) and a negative control (ethanol) over a 6-h period. Two of the methods tested were in vivo bioassay methods in which the active ingredient was applied to human skin (finger and forearm bioassays), and the other two methods were in vitro methods using artificial containers (jar and petri dish bioassays). All four bioassays were conducted using Ixodes scapularis nymphs. We compared the results using nymphs from two different tick colonies that were derived from I. scapularis collected in the US states of Connecticut and Rhode Island (northern origin) and Oklahoma (southern origin), expecting that ticks of different origin would display differences in host-seeking behavior.
RESULTS
The results between bioassay methods did not differ significantly, even when comparing those that provide the stimulus of human skin with those that do not. We also found that tick colony source can impact the outcome of repellency bioassays due to differences in movement speed; behavioral differences were incorporated into the assay screening. DEET effectively repelled nymphs for the full 6-h duration of the study. Peppermint oil showed a similar repellent efficacy to DEET during the first hour, but it decreased sharply afterwards. Rosemary oil did not effectively repel nymphs across any of the time points.
CONCLUSIONS
The repellency results did not differ significantly between the four bioassay methods tested. The results also highlight the need to consider the geographic origin of ticks used in repellency bioassays in addition to species and life stage. Finally, our results indicate a limited repellent efficacy of the two essential oils tested, which highlights the need for further studies on the duration of repellency for similar botanically derived active ingredients and for evaluation of formulated products.
Topics: Humans; Animals; Ixodes; DEET; Biological Assay; Connecticut; Ethanol; Insect Repellents; Nymph
PubMed: 37430360
DOI: 10.1186/s13071-023-05845-7 -
Scientific Reports Jul 2023The mechanisms governing chemotaxis in Chlamydomonas reinhardtii are largely unknown compared to those regulating phototaxis despite equal importance on the migratory...
The mechanisms governing chemotaxis in Chlamydomonas reinhardtii are largely unknown compared to those regulating phototaxis despite equal importance on the migratory response in the ciliated microalga. To study chemotaxis, we made a simple modification to a conventional Petri dish assay. Using the assay, a novel mechanism governing Chlamydomonas ammonium chemotaxis was revealed. First, we found that light exposure enhances the chemotactic response of wild-type Chlamydomonas strains, yet phototaxis-incompetent mutant strains, eye3-2 and ptx1, exhibit normal chemotaxis. This suggests that Chlamydomonas transduces the light signal pathway in chemotaxis differently from that in phototaxis. Second, we found that Chlamydomonas collectively migrate during chemotaxis but not phototaxis. Collective migration during chemotaxis is not clearly observed when the assay is conducted in the dark. Third, the Chlamydomonas strain CC-124 carrying agg1, the AGGREGATE1 gene (AGG1) null mutation, exhibited a more robust collective migratory response than strains carrying the wild-type AGG1 gene. The expression of a recombinant AGG1 protein in the CC-124 strain suppressed this collective migration during chemotaxis. Altogether, these findings suggest a unique mechanism; ammonium chemotaxis in Chlamydomonas is mainly driven by collective cell migration. Furthermore, it is proposed that collective migration is enhanced by light and suppressed by the AGG1 protein.
Topics: Chlamydomonas reinhardtii; Chemotaxis; Ammonium Compounds; Chlamydomonas; Cell Movement; Light
PubMed: 37402785
DOI: 10.1038/s41598-023-36818-6 -
Micromachines May 2023A new generation of nanoscale photosensitizer agents has improved photothermal capabilities, which has increased the impact of photothermal treatments (PTTs) in cancer...
A new generation of nanoscale photosensitizer agents has improved photothermal capabilities, which has increased the impact of photothermal treatments (PTTs) in cancer therapy. Gold nanostars (GNS) are promising for more efficient and less invasive PTTs than gold nanoparticles. However, the combination of GNS and visible pulsed lasers remains unexplored. This article reports the use of a 532 nm nanosecond pulse laser and polyvinylpyrrolidone (PVP)-capped GNS to kill cancer cells with location-specific exposure. Biocompatible GNS were synthesized via a simple method and were characterized under FESEM, UV-visible spectroscopy, XRD analysis, and particle size analysis. GNS were incubated over a layer of cancer cells that were grown in a glass Petri dish. A nanosecond pulsed laser was irradiated on the cell layer, and cell death was verified via propidium iodide (PI) staining. We assessed the effectiveness of single-pulse spot irradiation and multiple-pulse laser scanning irradiation in inducing cell death. Since the site of cell killing can be accurately chosen with a nanosecond pulse laser, this technique will help minimize damage to the cells around the target cells.
PubMed: 37374759
DOI: 10.3390/mi14061173 -
Insects Jun 2023Exposure of lepidopteran pests to () proteins has been shown to affect the behavior of larvae, including increased movement and avoidance of -expressing plants or diet....
Exposure of lepidopteran pests to () proteins has been shown to affect the behavior of larvae, including increased movement and avoidance of -expressing plants or diet. Therefore, we hypothesized that the behavior of western bean cutworm, (Smith) (Lepidoptera: Noctuidae), an important pest of maize, could be affected when exposed to plants. To test this hypothesis, we conducted a series of artificial arena and on-plant experiments to determine neonate behavior when exposed to and non- plant tissue. Video tracking experiments presented neonate larvae with the choice of or non- pollen in a Petri dish for 15 min while being video recorded for analysis with EthoVision software. This study showed an increase in mean velocity and total time spent moving for larvae in the presence of Cry1F vs. non- when compared with Vip3A vs. non- or Cry1F vs. Vip3A. However, there was no difference in total distance moved or time spent in the food zone for all scenarios. Maize tissue choice experiments allowed neonatal larvae the choice of feeding on or non- tassel or leaves for 9 h in Petri dish arenas. This experiment showed that larvae preferred tassel tissue over leaves but did not indicate that larvae could distinguish between and non- tissue. In contrast, on-plant experiments (including a whole plant neonate dispersal study under controlled conditions and an in-field silking behavior experiment) indicated that the presence of Cry1F and Vip3A toxins increased plant abandonment, suggesting that larvae are able to detect and avoid toxins. The discrepancy of these results is likely due to the on-plant studies providing more field-realistic environmental conditions and a longer duration of exposure to Bt toxins for the behavioral experiments. Our results represent the first steps in understanding the complex behavior of when exposed to plants. A better understanding of the response of larvae when exposed to traits can aid in the management of this pest, particularly for the design of resistance management strategies and refuge design.
PubMed: 37367340
DOI: 10.3390/insects14060524 -
Gels (Basel, Switzerland) May 2023Macroscopic spatial patterns were formed in calcium alginate gels when a drop of a calcium nitrate solution was placed on the center of a sodium alginate solution on a...
Macroscopic spatial patterns were formed in calcium alginate gels when a drop of a calcium nitrate solution was placed on the center of a sodium alginate solution on a petri dish. These patterns have been classified into two groups. One is multi-concentric rings consisting of alternating cloudy and transparent areas observed around the center of petri dishes. The other is streaks extending to the edge of the petri dish, which are formed to surround the concentric bands between the concentric bands and the petri dish edge. We have attempted to understand the origins of the pattern formations using the properties of phase separation and gelation. The distance between two adjacent concentric rings was roughly proportional to the distance from where the calcium nitrate solution was dropped. The proportional factor increased exponentially for the inverse of the absolute temperature of the preparation. The also depended on the concentration of alginate. The pattern characteristics in the concentric pattern agreed with those in the Liesegang pattern. The paths of radial streaks were disturbed at high temperatures. The length of these streaks shortened with increasing alginate concentration. The characteristics of the streaks were similar to those of crack patterns resulting from inhomogeneous shrinkage during drying.
PubMed: 37367115
DOI: 10.3390/gels9060444 -
Biochip Journal May 2023In vitro model systems have been advanced to recapitulate important physiological features of the target organ in vivo more closely than the conventional cell line... (Review)
Review
In vitro model systems have been advanced to recapitulate important physiological features of the target organ in vivo more closely than the conventional cell line cultures on a petri dish. The advanced organotypic model systems can be used as a complementary or alternative tool for various testing and screening. Numerous data from germ-free animal studies and genome sequencings of clinical samples indicate that human microbiota is an essential part of the human body, but current in vitro model systems rarely include them, which can be one of the reasons for the discrepancy in the tissue phenotypes and outcome of therapeutic intervention between in vivo and in vitro tissues. A coculture model system with appropriate microbes and host cells may have great potential to bridge the gap between the in vitro model and the in vivo counterpart. However, successfully integrating two species in one system introduces new variables to consider and poses new challenges to overcome. This review aims to provide perspectives on the important factors that should be considered for developing organotypic bacterial coculture models. Recent advances in various organotypic bacterial coculture models are highlighted. Finally, challenges and opportunities in developing organotypic microbial coculture models are also discussed.
PubMed: 37363268
DOI: 10.1007/s13206-023-00103-5 -
Frontiers in Endocrinology 2023Testicular Leydig cells (LCs) are the primary known source of testosterone, which is necessary for maintaining spermatogenesis and male fertility. However, the...
Testicular Leydig cells (LCs) are the primary known source of testosterone, which is necessary for maintaining spermatogenesis and male fertility. However, the isolation, identification, and functional analysis of testosterone in duck LCs are still ambiguous. The aim of the present study was to establish a feasible method for isolating highly purified primary duck LCs. The highly purified primary duck LCs were isolated from the fresh testes of 2-month-old ducks via the digestion of collagenase IV and Percoll density gradient centrifugation; hematoxylin and eosin (H&E), immunohistochemistry (IHC) staining, ELISA, and radioimmunoassay were performed. Results revealed that the LCs were prominently noticeable in the testicular interstitium of 2-month-old ducks as compared to 6-month-old and 1-year-old ducks. Furthermore, IHC demonstrated that the cultured LCs occupied 90% area of the petri dish and highly expressed 3β-HSD 24 h after culture (hac) as compared to 48 and 72 hac. Additionally, ELISA and radioimmunoassay indicate that the testosterone level in cellular supernatant was highly expressed in 24 and 48 hac, whereas the testosterone level gradually decreased in 72 and 96 hac, indicating the primary duck LCs secrete testosterone at an early stage. Based on the above results, the present study has effectively developed a technique for isolating highly purified primary duck LCs and identified its biological function in synthesizing testosterone.
Topics: Animals; Male; Leydig Cells; Ducks; Testosterone; Testis; Cells, Cultured
PubMed: 37347106
DOI: 10.3389/fendo.2023.1195618