Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Fall Ethephon Application Enhances the Freezing Tolerance of Magnolia wufengensis During Overwintering

Magnolia wufengensis L.Y. Ma et L. R. Wang, a rare species which has been introduced and cultivated from southern China to northern China, frequently suffers from freezing injuries. To figure out the influence of ethephon (ETH) application on the cold tolerance during the natural overwintering of M. wufengensis, one-year shoots subjected to ethephon application at four concentrations (0, 700, 1000, and 1500 mg·L−1) were collected to measure the physiological and biochemical changes from September 2017 to 1 April 2018. The fall ETH application increased the freezing tolerance of M. wufengensis, and the optimum concentration for M. wufengensis was 1000 mg·L−1 (T2), which not only improved the shoot freezing tolerance by 1.4 times, but also led to a 25.0% faster cold acclimation rate and 13.7% slower de-acclimation rate. Moreover, 1000 mg·L−1 ETH delayed bud-burst in the spring by 10. 7 d, which was helpful for effectively avoiding cold spells in the spring, and improved the rates of bud survival by 47.1%. The improved freezing tolerance under exogenous ETH application was associated with an increased dehydration and accumulation of proline content. It seems that exogenous ETH application may be used on M. wufengensis grown in northern China to protect against freezing tolerance during the overwintering period

Histological, Morpho-Physiological, and Biochemical Changes during Adventitious Rooting Induced by Exogenous Auxin in Magnolia wufengensis Cuttings

Magnolia wufengensis, a rare ornamental tree species, is now in a huge gap between market demand and actual supply of seedlings. As cutting propagation is one of the most important means to solve the shortage of seedling supply, this study developed an efficient cutting propagation procedure of M. wufengensis, revealed the morphological and histological changes of adventitious root formation, and explored the rhythm correlation between rooting process and physiological and biochemical changes. Cuttings pre-treated with NAA:IBA (2:1) exhibited the best rooting performance. Anatomical analysis demonstrated that adventitious root primordia of M. wufengensis were initiated from cambial and parenchyma cells of xylem, with no relationship to the callus formed on the epidermis. The rooting process of M. wufengenis can be divided into four periods: induction phase (0–8 dap) (dap means days after planting), initiation phase (8–13 dap), expression phase (13–18 dap), and extension phase (18–28 dap). NAA:IBA (2:1) induced the accumulations of 3-indoleacetic-acid and increased the contents of peroxidase and polyphenol-oxidase near the wounding at induction phase. The initiation phase, with the first histological modifications to the formation of meristemoids, correspond to the increase of peroxidase, polyphenol-oxidase, and soluble protein contents. The synergistic reaction of low 3-indoleacetic-acid and high levels of gibberellins and zeatin also stimulates the initiation phase. In the expression and extension phase, high activities of polyphenol-oxidase, IAA-oxidase, and increased contents of soluble protein co-stimulate the emergence and outgrowth of adventitious roots. The present study not only provides optimized protocol by application of auxin combination but also presents insights in the histological, morpho-physiological, and biochemical changes in stem cuttings of M. wufengensis

Fine-Scale analysis of both wild and cultivated horned galls provides insight into their quality differentiation

Abstract Background Galla chinensis is a traditional Chinese medicine (TCM) produced due to the interaction between the Fordinae aphids and the Rhus plant species. Horned galls with high tannin content are the most widely cultivated gall type, and Wufeng county of Hubei province in China is the center of cultivation. However, long-term artificial cultivation and domestication of horned galls to meet the increasing production demand have led to quality degradation. Understanding the reasons underlying quality degradation is urgent for horned gall production and application. The present study used a combination of metabolic, genetic, and ecological analyses to investigate the quality and genetic differentiation of the horned galls under long-term domestication as well as the potential relationships between them. Results Analysis of gallic acid content and other three phenotypic traits (fresh weight, gall size, and wall thickness) revealed quality differentiation of horned galls collected from five locations in Wufeng, in which the cultivated samples from Wang Jiaping (WJP) showed the highest degradation. Genetic differentiation between the cultivated and wild Rhus chinensis trees in WJP, and between WJP and the other populations was detected based on SSR molecular markers, however, no significant difference in genetic structure was seen for the aphid populations. Among the various ecological factors examined, temperature was identified as the primary one affecting the quality of horned galls. Conclusions Both genetic and ecological factors caused quality differentiation of horned galls. The collection of diverse germplasm of host trees and aphids will help reduce the quality degradation of horned galls in Wufeng

mTOR inhibition reprograms cellular proteostasis by regulating eIF3D-mediated selective mRNA translation and promotes cell phenotype switching.

Cells maintain and dynamically change their proteomes according to the environment and their needs. Mechanistic target of rapamycin (mTOR) is a key regulator of proteostasis, homeostasis of the proteome. Thus, dysregulation of mTOR leads to changes in proteostasis and the consequent progression of diseases, including cancer. Based on the physiological and clinical importance of mTOR signaling, we investigated mTOR feedback signaling, proteostasis, and cell fate. Here, we reveal that mTOR targeting inhibits eIF4E-mediated cap-dependent translation, but feedback signaling activates a translation initiation factor, eukaryotic translation initiation factor 3D (eIF3D), to sustain alternative non-canonical translation mechanisms. Importantly, eIF3D-mediated protein synthesis enables cell phenotype switching from proliferative to more migratory. eIF3D cooperates with mRNA-binding proteins such as heterogeneous nuclear ribonucleoprotein F (hnRNPF), heterogeneous nuclear ribonucleoprotein K (hnRNPK), and Sjogren syndrome antigen B (SSB) to support selective mRNA translation following mTOR inhibition, which upregulates and activates proteins involved in insulin receptor (INSR)/insulin-like growth factor 1 receptor (IGF1R)/insulin receptor substrate (IRS) and interleukin 6 signal transducer (IL-6ST)/Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling. Our study highlights the mechanisms by which cells establish the dynamic change of proteostasis and the resulting phenotype switch

Motor Imagery Observed by fNIRS

Motor imagery (MI) is expected to activate brain areas related to motor functions, yet, the brain is constantly active to some extent leading to difficulties in differentiating MI from supposedly non-motor tasks. In this study, we use functional near-infrared spectroscopy (fNIRS) to offer an objective and spatially precise measurement of brain activity during MI. The fNIRS findings of this study using our MI-based exercise framework with 15 healthy subjects indicate that casual imagination and especially relaxation do not induce an intense motor brain activation compared to active MI performance. Furthermore, dynamic visual cues for MI appear to enhance brain activation around the motor brain areas of the majority of subjects and MI training helps some subjects to activate their motor cortex. Future research may refer to our framework to validate the competence of stroke patients in MI-based motor rehabilitation.</p

mTOR inhibition reprograms cellular proteostasis by regulating eIF3D-mediated selective mRNA translation and promotes cell phenotype switching

Summary: Cells maintain and dynamically change their proteomes according to the environment and their needs. Mechanistic target of rapamycin (mTOR) is a key regulator of proteostasis, homeostasis of the proteome. Thus, dysregulation of mTOR leads to changes in proteostasis and the consequent progression of diseases, including cancer. Based on the physiological and clinical importance of mTOR signaling, we investigated mTOR feedback signaling, proteostasis, and cell fate. Here, we reveal that mTOR targeting inhibits eIF4E-mediated cap-dependent translation, but feedback signaling activates a translation initiation factor, eukaryotic translation initiation factor 3D (eIF3D), to sustain alternative non-canonical translation mechanisms. Importantly, eIF3D-mediated protein synthesis enables cell phenotype switching from proliferative to more migratory. eIF3D cooperates with mRNA-binding proteins such as heterogeneous nuclear ribonucleoprotein F (hnRNPF), heterogeneous nuclear ribonucleoprotein K (hnRNPK), and Sjogren syndrome antigen B (SSB) to support selective mRNA translation following mTOR inhibition, which upregulates and activates proteins involved in insulin receptor (INSR)/insulin-like growth factor 1 receptor (IGF1R)/insulin receptor substrate (IRS) and interleukin 6 signal transducer (IL-6ST)/Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling. Our study highlights the mechanisms by which cells establish the dynamic change of proteostasis and the resulting phenotype switch

Wearable Safeguarding Leather Composite with Excellent Sensing, Thermal Management, and Electromagnetic Interference Shielding

Abstract This work illustrates a “soft‐toughness” coupling design method to integrate the shear stiffening gel (SSG), natural leather, and nonwoven fabrics (NWF) for preparing leather/MXene/SSG/NWF (LMSN) composite with high anti‐impact protecting, piezoresistive sensing, electromagnetic interference (EMI) shielding, and human thermal management performance. Owing to the porous fiber structure of the leather, the MXene nanosheets can penetrate leather to construct a stable 3D conductive network; thus both the LM and LMSN composites exhibit superior conductivity, high Joule heating temperature, and an efficient EMI shielding effectiveness. Due to the excellent energy absorption of the SSG, the LMSN composites possess a huge force‐buffering (about 65.5%), superior energy dissipation (above 50%), and a high limit penetration velocity of 91 m s−1, showing extraordinary anti‐impact performance. Interestingly, LMSN composites possess an unconventional opposite sensing behavior to piezoresistive sensing (resistance reduction) and impact stimulation (resistance growing), thus they can distinguish the low and high energy stimulus. Ultimately, a soft protective vest with thermal management and impact monitoring performance is further fabricated, and it shows a typical wireless impact‐sensing performance. This method is expected to have broad application potential in the next‐generation wearable electronic devices for human safeguarding

Additional file 1 of Fine-Scale analysis of both wild and cultivated horned galls provides insight into their quality differentiation

Additional file 1: Supplementary Figure 1. Different types of Galla Chinensis. (A) Horned gall. (B) Gallnut. (C) Flower-like gall. Supplementary Figure 2. Analysis of the key phenotypic traits. Comparative analysis of gallic acid (A), fresh weight (B), gall size (C), and wall thickness (D) between wild and cultivated horned galls. The fresh weight (E), gall size (G), wall thickness (I) of the horned galls from five locations. And the fresh weight (F), gall size (H), wall thickness (J) of wild and cultivated horned galls in each location. (*, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001). Supplementary Figure 3. Principal Component Analysis (PCA) analysis of Bai Nianguan (BNG) (A), Bai Luzhuang (BLZ) (B), Huang Liangping (HLP) (C), and Huo Shan (HS) (D) populations based on phenotypic traits. Supplementary Figure 4. Function annotation of Rhus chinensis unigenes on the basis of public database. (A) Summary of annotations of unigenes in six databases. (B) GO classification of annotated unigenes. (C) Functional classification of unigenes based on the KEGG pathway. (D) The COG functional distribution of annotated unigenes. Supplementary Figure 5. The genetic paraments of each R. chinensis and Schlechtendalia chinensis population (WJP, BNG, BLZ, HLP, and HS represent the population from Wang Jiaping, Bai Nianguan, Bai Luzhuang, Huang Liangping, and Huo Shan, respectively.). (A). The number of alleles (N). (B) The average number of alleles (NA). (C) The effective number of alleles (NE). (D) observed heterozygosity (HO). (E) expected heterozygosity (HE). (F) Shannon’s information index (I). (G) Nei’s gene diversity index (H). (H) Polymorphism information content (PIC). Supplementary Figure 6. STRUCTURE and PCA analysis of host trees and aphids based on SSR (Simple Sequence Repeat) loci. (A) Population structure of 102 R. chinensis accessions. (B) Population structure of 102 S. chinensis accessions. (C) Population structure of R. chinensis accessions in WJP and BLZ. (D) PCA analysis of R. chinensis accessions in WJP and BLZ. (E) Population structure of R. chinensis accessions in WJP. (F) PCA analysis of R. chinensis accessions in WJP. Supplementary Figure 7. Neighbour-Joining (NJ) analysis based on the SSR loci information of R. chinensis accessions. NJ tree of individuals from BNG (A), BLZ (B), HLP (C), and HS (D). The red stars represent the wild accessions and the blue stars represent the cultivated accessions. Supplementary Figure 8. Chromatograms of negative sample (A), gallic acid standard (B), and horned gall sample (C). Supplementary Table 1. Phenotypic data among 102 horned galls. Supplementary Table 2. Correlation analysis of phenotypic traits. Supplementary Table 3. Statistic of RNA-seq, ddRAD-seq data to R. chinensis and the reference genome data of S. chinensis. Supplementary Table 4. Genetic characterization of 23 pairs of R. chinensis SSR primers and 9 pairs of S. chinensis SSR primers. Supplementary Table 5. Analysis of molecular variance (AMOVA) for R. chinensis and S. chinensis populations. Supplementary Table 6. Sampling information. Supplementary Table 7. Method validation of the high-performance liquid chromatography (HPLC) analysis in horned galls