Sweet cherry (Prunus avium L.) is a popular fruit tree grown for its juicy fruit and pleasing appearance. The fruit pf the sweet cherry contains active antioxidants and other chemical compounds ...essential for human health. For this study, we performed the transcriptomics and metabolomics analysis using young Green Peel (GP) and mature Red Peel (RP) from sweet cherries to understand the underlying genetic mechanism regulating fruit development and ripening. Using high-throughput RNA sequencing and ultra-performance liquid chromatography, with quadrupole time-of-flight tandem mass spectrometry, respectively, metabolic and transcript profiling was obtained. Relative to GP, there were equal quantities of pronouncedly varied metabolites in RP (n = 3564). Differentially expressed genes (DEGs, n = 3564), containing 45 transcription factor (TF) families, were recorded in RP. Meanwhile, 182 differentially expressed TF (DETF) members of 37 TF families, were displayed in abundance in RP compared to GP sweet cherries. The largest quantities of DETFs were members of the ERF (25) and basic helix–loop–helix (bHLH) (19) families, followed by the MYB (18), WRKY (18), and C2H2 (12) families. Interestingly, most ERF genes were down-regulated, whereas CCCH genes were mainly up-regulated in RP. Other DETFs exhibited significant variations. In addition, RT-QPCR results and metabolomics data together with transcriptomic data revealed that the abundance of catechin, epicatechin, rhoifolin, myricetin, keracyanin, and the other six glycosyltransferase genes was highly increased in RP when compared to GP sweet cherries. The relatively higher expression of DETFs, metabolite, and flavonoid biosynthesis in RP sweet cherries suggests the accumulation of distinct metabolites that cause red coloring during fruit development and ripening. Thus, the metabolomics and transcriptomic analysis of the current study are powerful tools for providing more valuable information for the metabolic engineering of flavonoids biosynthesis in sweet cherries. They are also helpful in understanding the relationship between genotype and phenotype.
Deep Neural Network (DNN) models are widely used for image classification. While they offer high performance in terms of accuracy, researchers are concerned about if these models inappropriately make ...inferences using features irrelevant to the target object in a given image. To address this concern, we propose a metamorphic testing approach that assesses if a given inference is made based on irrelevant features. Specifically, we propose two metamorphic relations (MRs) to detect such unreliable inferences. These relations expect (a) the classification results with different labels or the same labels but less certainty from models after corrupting the relevant features of images, and (b) the classification results with the same labels after corrupting irrelevant features. The inferences that violate the metamorphic relations are regarded as unreliable inferences. Our evaluation demonstrated that our approach can effectively identify unreliable inferences for single-label classification models with an average precision of 64.1% and 96.4% for the two MRs, respectively. As for multi-label classification models, the corresponding precision for MR-1 and MR-2 is 78.2% and 86.5%, respectively. Further, we conducted an empirical study to understand the problem of unreliable inferences in practice. Specifically, we applied our approach to 18 pre-trained single-label image classification models and 3 multi-label classification models, and then examined their inferences on the ImageNet and COCO datasets. We found that unreliable inferences are pervasive. Specifically, for each model, more than thousands of correct classifications are actually made using irrelevant features. Next, we investigated the effect of such pervasive unreliable inferences, and found that they can cause significant degradation of a model’s overall accuracy. After including these unreliable inferences from the test set, the model’s accuracy can be significantly changed. Therefore, we recommend that developers should pay more attention to these unreliable inferences during the model evaluations. We also explored the correlation between model accuracy and the size of unreliable inferences. We found the inferences of the input with smaller objects are easier to be unreliable. Lastly, we found that the current model training methodologies can guide the models to learn object-relevant features to certain extent, but may not necessarily prevent the model from making unreliable inferences. We encourage the community to propose more effective training methodologies to address this issue.
The major active constituents from Amaryllidaceae family were reported to be Amaryllidaceae alkaloids (AAs), which exhibited a wide spectrum of biological activities, such as anti-tumor, anti-viral, ...and acetyl-cholinesterase-inhibitory activities. In order to better understand their potential as a source of bioactive AAs and the phytochemical variations among three different species of Lycoris herbs, the HPLC fingerprint profiles of Lycoris aurea (L. aurea), L. radiata, and L. guangxiensis were firstly determined and compared using LC-UV and LC-MS/MS. As a result, 39 peaks were resolved and identified as AAs, of which nine peaks were found in common for all these three species, while the other 30 peaks could be revealed as characteristic AAs for L. aurea, L. radiata and L. guangxiensis, respectively. Thus, these AAs can be used as chemical markers for the identification and quality control of these plant species. To further reveal correlations between chemical components and their pharmaceutical activities of these species at the molecular level, the bioactivities of the total AAs from the three plant species were also tested against HepG2 cells with the inhibitory rate at 78.02%, 84.91% and 66.81% for L. aurea, L. radiata and L. guangxiensis, respectively. This study firstly revealed that the three species under investigation were different not only in the types of AAs, but also in their contents, and both contributed to their pharmacological distinctions. To the best of our knowledge, the current research provides the most detailed phytochemical profiles of AAs in these species, and offers valuable information for future valuation and exploitation of these medicinal plants.
Introduction The Sanxingdui Site in Guanghan City, Sichuan Province, China, is one of the precious heritage sites of the ancient Chinese civilization. Archaeological work at Sanxingdui is of great ...significance in clarifying the origins and main contents of the ancient Shu culture and the Yangtze River civilization. Since the 1920s, archaeologists have conducted extensive excavations and research at the site, with particular attention given to the large number of ivory artifacts unearthed. However, the buried ivory is influenced by soil pH, temperature, humidity, and other physical and chemical factors, along with the potential impact of microbial activities that may lead to the corrosion and decomposition of ivory. By understanding the types and activities of microorganisms, appropriate measures can be taken to protect and preserve cultural relics. Methods Multi-point sampling of soil samples around the ivory of the three sacrificial pits at the Sanxingdui site was carried out, and strict aseptic operation was carried out during the sampling process. Subsequently, the microbial community structure and diversity in the buried ivory soil of Sanxingdui site were identified and analyzed by Illumina high-throughput sequencing technology. Results 16S rRNA and internal transcribed spacer sequence analysis revealed significant differences in the soil microbial community structure among different sacrificial pits. The dominant bacterial phyla were the Proteobacteria, GAL15, Actinobacteriota, Bacteroidota, and Methylomirabilota. The dominant fungal phyla were Ascomycota, Mortierellomhcota, and Basidiomycota. Most dominant bacterial and fungal communities play an indispensable role in the ivory corrosion mechanism, promoting the decay and decomposition process through various means such as decomposing organic matter and producing acidic substances. Discussion It is particularly important to take a series of measures to control microbial activity to effectively protect ivory. Our preliminary study of the mechanism of action of microorganisms on ivory in a buried environment provides a scientific basis to prevent and protect against microbial degradation in ancient ivory unearthed in Sanxingdui. Following the research results, suitable antibacterial agents tailored to the preservation environment and microbial characteristics of ancient ivory can be prepared. Ensure that the selected antibacterial agents meet safety and effectiveness requirements to maximize protection against microbial degradation of ancient ivory.
Facing the increasingly severe Cr(VI) pollution, bioreduction has proved to be an eco-friendly remediation method. An isolated strain identified as
Lysinibacillus
can relatively reduce Cr(VI) well. ...Even if the concentration of Cr(VI) increased to 250mg/L, the strain HST-98 could also grow and remove Cr(VI) well. After optimization of reaction conditions, the optimal pH, temperature, and electron donor are 8~9, 36°C, and sodium lactate, respectively. Coexisting metal ions such as Cu
2+
, Co
2+
, and Mn
2+
are beneficial to reduce Cr(VI), while Zn
2+
, Ni
2+
, and Cd
2+
are just the opposite. What is more, the mechanism of the reduction by the strain HST-98 is chiefly mediated by intracellular enzymes. After gene sequence homology blast and analysis, the genes and enzymes related to chromium metabolism in strain HST-98 have been annotated, which helps us to further understand the reduction mechanism of the strain HST-98. In general,
Lysinibacillus
sp. HST-98 is a potential candidate to repair the Cr(VI)-contaminated sites.
A consortium composed of many different bacterial species is required to efficiently degrade polycyclic aromatic hydrocarbons (PAH) in oil-contaminated soil. We obtained six PAH-degrading microbial ...consortia from three oil-contaminated soils using two different isolation culture media. Denaturing gradient gel electrophoresis (DGGE) and sequence analyses of amplified 16s rRNA genes confirmed the bacterial community was greatly affected by both the culture medium and the soil from which the consortia were enriched. Three bacterial consortia enriched using malt yeast extract (MYE) medium showed higher degradation rates of PAHs than consortia enriched using Luria broth (LB) medium. Consortia obtained from a soil and then added back to that same soil was more effective in degrading PAHs than adding, to the same soil, consortia isolated from other, unrelated soils. This suggests that inoculum used for bioremediation should be from the same, or very similar nearby soils, as the soil that is actually being bioremediated.
•Six PAH-degrading microbial consortia were isolated from three oil-contaminated soils.•The bacterial community by 16s rRNA genes was affected by culture media and source soil.•Inoculum should be from the same or similar soil as the soil being bioremediated.
Bioremediation of oil-contaminated soils was most effective when using inoculum of microbial consortia from the same or similar soil as the soil being bioremediated.
A novel Gram-stain-negative, moderately halotolerant, rod-shaped bacterium, designated strain L3
T
, was isolated from a wetsalted hide in Chengdu, China. The organism grew optimally at 30 °C, at pH ...8 and with 5–10% (w/v) NaCl. The major cellular fatty acids were C
16:0
, C
16:1
ω
7c, C
18:1
ω
7c and C
19:0
cyclo
ω
8c; the predominant respiratory quinone was Q-9; the phospholipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and three unidentified phospholipids. Phylogenetic trees based on the 16S rRNA,
gyrB
and
rpoD
genes’ sequences, obtained using three different algorithms, clearly revealed the isolate belonged to the genus
Salinicola
, and was found to be closely related to
Salinicola acroporae
JCM 30412
T
,
Salinicola socius
CGMCC 1.12383
T
and
Salinicola lusitanus
CR50
T
. The draft genome was approximately 4.5 Mb in size with 4486 predicted coding sequences, and the G+C content was 62.6 mol%. The maximum values of ANI and dDDH between strain L3
T
and the three above-mentioned type species were 89.2% and 63.8%, respectively. Differential phenotypic properties, together with the genome analysis, support the view that strain L3
T
represents a novel species,
Salinicola corii
sp. nov., with the type strain L3
T
(=CGMCC 1.17272
T
=KCTC 72572
T
).
Root-knot nematodes (RKNs) pose a worldwide threat to agriculture of many crops including cucumber. Genetic transformation (GT) has emerged as a powerful tool for exploration of plant-RKN ...interactions and genetic improvement of RKN resistance. However, it is usually difficult to achieve a highly efficient and stable GT protocol for most crops due to the complexity of this process.
Here we firstly applied the hairy root transformation system in exploring root-RKN interactions in cucumber plants and developed a rapid and efficient tool transformation using Rhizobium rhizogenes strain K599. A solid-medium-based hypocotyl-cutting infection (SHI) method, a rockwool-based hypocotyl-cutting infection (RHI) method, and a peat-based cotyledon-node injection (PCI) method was evaluated for their ability to induce transgenic roots in cucumber plants. The PCI method generally outperformed the SHI and RHI methods for stimulating more transgenic roots and evaluating the phenotype of roots during nematode parasitism. Using the PCI method, we generated the CRISPR/Cas9-mediated malate synthase (MS) gene (involved in biotic stress responses) knockout plant and the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16, a potential host susceptibility gene for RKN) promoter-driven GUS expressing plant. Knockout of MS in hairy roots resulted in effective resistance against RKNs, while nematode infection induced a strong expression of LBD16-driven GUS in root galls. This is the first report of a direct link between these genes and RKN performance in cucumber.
Taken together, the present study demonstrates that the PCI method allows fast, easy and efficient in vivo studies of potential genes related to root-knot nematode parasitism and host response.
Nitrogen (N) is a macronutrient that plays a crucial role in plant growth and development. Nitrate (
) is the most abundant N source in aerobic soils. Plants have evolved two adaptive mechanisms such ...as up-regulation of the high-affinity transport system (HATS) and alteration of the root system architecture (RSA), allowing them to cope with the temporal and spatial variation of
. However, little information is available regarding the nitrate transporter in cucumber, one of the most important fruit vegetables in the world. In this study we isolated a nitrate transporter named
from cucumber. Analysis of the expression profile of the
showed that
is a high affinity nitrate transporter which mainly located in mature roots. Subcellular localization analysis revealed that CsNRT2.1 is a plasma membrane transporter. In N-starved
knock-down plants, both of the constitutive HATS (cHATS) and inducible HATS (iHATS) were impaired under low external
concentration. Furthermore, the
knock-down plants showed reduced root length and lateral root numbers. Together, our results demonstrated that CsNRT2.1 played a dual role in regulating the HATS and RSA to acquire
effectively under N limitation.
Microbial transglutaminases (MTGs) are widely used in the food industry. In this study, the MTG gene of
sp. TYQ1024 was cloned and expressed in a food-grade bacterial strain,
SCK6. Extracellular ...activity of the MTG after codon and signal peptide (SP Ync M) optimization was 20 times that of the pre-optimized enzyme. After purification, the molecular weight of the MTG was 38 kDa and the specific activity was 63.75 U/mg. The optimal temperature and pH for the recombinant MTG activity were 50°C and 8.0, respectively. MTG activity increased 1.42- fold in the presence of β-ME and 1.6-fold in the presence of DTT. Moreover, 18% sodium chloride still resulted in 83% enzyme activity, which showed good salt tolerance. Cross-linking gelatin with the MTG increased the strength of gelatin 1.67 times and increased the thermal denaturation temperature from 61.8 to 75.8°C. The MTG also significantly increased the strength and thermal stability of gelatin. These characteristics demonstrated the huge commercial potential of MTG, such as for applications in salted protein foods.
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