Mutation breeding of high-stress resistant strains for succinic acid production from corn straw

The production of succinic acid from corn stover is a promising and sustainable route; however, during the pretreatment stage, byproducts such as organic acids, furan-based compounds, and phenolic compounds generated from corn stover inhibit the microbial fermentation process. Selecting strains that are resistant to stress and utilizing nondetoxified corn stover hydrolysate as a feedstock for succinic acid production could be effective. In this study, A. succinogenes CICC11014 was selected as the original strain, and the stress-resistant strain A. succinogenes M4 was obtained by atmospheric and room temperature plasma (ARTP) mutagenesis and further screening. Compared to the original strain, A. succinogenes M4 exhibited a twofold increase in stress resistance and a 113% increase in succinic acid production when hydrolysate was used as the substrate. By conducting whole-genome resequencing of A. succinogenes M4 and comparing it with the original strain, four nonsynonymous gene mutations and two upstream regions with base losses were identified. KEY POINTS: • A high-stress-resistant strain A. succinogenes M4 was obtained by ARTP mutation •  The production of succinic acid increased by 113% • The mutated genes of A. succinogenes M4 were detected and analyzed.

Altered neurophysiological responses during empathy for pain in insomnia: evidence from an EEG study in non-clinical samples

BACKGROUND

This study aims to investigate the behavioral and neurophysiological changes accompanying the empathy for pain among individuals with insomnia in nonclinical samples, which has been scarcely explored in the existing literature despite the deleterious effects of sleep disturbance on social behavior, and interactions had been well-documented.

METHODS

Twenty-one individuals with insomnia in nonclinical samples and 20 healthy individuals as normal controls participated in the study. Electroencephalograph (EEG) was continuously recorded, while the participants underwent an empathy for pain task.

RESULTS

Subjective ratings of pain for painful and non-painful images revealed no statistically significant differences between the insomnia and control groups. The painful images induced a smaller P2 compared to non-painful images in the insomnia group, whereas no such difference was revealed for the controls. Moreover, a higher power density of the alpha and theta2 bands in the posterior brain regions was found in the insomnia group compared to the control group.

CONCLUSION

These findings suggest that individuals with insomnia exhibit altered neurophysiological responses to pain stimuli and a lower capacity to share empathy for pain. These alterations may be associated with changes in attentional mechanisms.

A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat

BACKGROUND

Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments.

RESULTS

We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection.

CONCLUSION

Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.

The drivers of collaborative innovation of the comprehensive utilization technologies of coal fly ash in China: a network analysis

Coal consumption brings a lot of coal fly ash (CFA). It requires interdisciplinary efforts in research, policy, and practice to improve the utilization of CFA. Although there have been a lot of achievements in technological innovation, the utilization of CFA is still difficult to match its output. So, it is urgent to explore how to guide its effective innovation. This paper uses social network analysis to discuss the characteristics of the collaborative innovation network of CFA comprehensive utilization technology in China. Then, this paper uses regression analysis to explore the differences in innovation performance under different research and development (R&D) backgrounds. The results show that (1) based on the network-level indicators, the collaborative innovation scale has an obvious trend of expanding. Partnerships increased from 20 to 574. Meanwhile, the network shows obvious scale-free and "small-world" characteristics, indicating that innovation resources are concentrated in a few organizations. (2) Based on the node-level indicators, the major contributor has shifted from universities and research institutions to enterprises. Enterprises account for the highest proportion (73%) and have the highest centrality (8.3). The betweenness centrality of the universities is 265, and only 14% of the organizations are universities which means universities play an important role in connecting different organizations in the network, but their participation in the collaborative innovation is insufficient. (3) Based on the collaborative relationship-level indicators, the cooperation is lack of depth. Only a small number of organizations, especially enterprises, have stable partners, showing the characteristic of "low cooperation width and high cooperation depth," which means fewer partners but more frequently collaborative innovation. (4) Based on the innovation performance, the innovation performance under the category of cooperative R&D, especially industry-academy cooperation, is better than that of independent R&D. But, industry-academy cooperation only occupied 43% of collaborative relationships in the network. Finally, this paper puts forward suggestions for governments from five aspects: decentralization, defining roles of enterprise and university, encouraging collaboration, changing the idea of the patent application, and promoting deeper cooperation.

Precipitation projection over Daqing River Basin (North China) considering the evolution of dependence structures

Understanding dynamic future changes in precipitation can provide prior information for nonpoint source pollution simulations under global warming. However, the evolution of the dependence structure and the unevenness characteristics of precipitation are rarely considered. This study applied a two-stage bias correction to daily precipitation and max/min temperature data in the Daqing River Basin (DQRB) with the HadGEM3-RA climate model. Validated from 1981 to 2015, future scenarios under two emission paths covering 2031-2065 and 2066-2100 were projected to assess variations in both the amount and unevenness of precipitation. The results suggested that, overall, the two-stage bias correction could reproduce the marginal distributions of variables and the evolution process of the dependence structure. In the future, the amount of precipitation in the plains is expected to increase more than that in the mountains, while precipitation unevenness, as measured by relative entropy, shows a slight increase in the mountains and a decrease in the plains, with enhanced seasonality. Conditioned on rising temperatures, high-/low-intensity precipitation tends to intensify/weaken precipitation unevenness. Additionally, the potential application of the bias correction method used herein and the possible impacts of uneven precipitation on nonpoint source pollution are given for further analyses. This study can provide useful information for future nonpoint source pollution simulations in the DQRB.

Integrative analysis of metabolome and transcriptome profiles provides insight into the fruit pericarp pigmentation disorder caused by 'Candidatus Liberibacter asiaticus' infection

BACKGROUND

Mandarin 'Shatangju' is susceptible to Huanglongbing (HLB) and the HLB-infected fruits are small, off-flavor, and stay-green at the maturity period. To understand the relationship between pericarp color and HLB pathogen and the effect mechanism of HLB on fruit pericarp coloration, quantitative analyses of HLB bacterial pathogens and carotenoids and also the integrative analysis of metabolome and transcriptome profiles were performed in the mandarin 'Shatangju' variety with four different color fruits, whole green fruits (WGF), top-yellow and base-green fruits (TYBGF), whole light-yellow fruits (WLYF), and whole dark-yellow fruits (WDYF) that were infected with HLB.

RESULTS

the HLB bacterial population followed the order WGF > TYBGF > WLYF > WDYF. And there were significant differences between each group of samples. Regarding the accumulation of chlorophyll and carotenoid, the chlorophyll-a content in WGF was the highest and in WDYF was the lowest. The content of chlorophyll-b in WGF was significantly higher than that in other three pericarps. There were significant differences in the total content of carotenoid between each group. WGF and TYBGF pericarps were low in phytoene, γ-carotene, β-cryptoxanthin and apocarotenal, while other kinds of carotenoids were significantly higher than those in WDYF. And WLYF was only short of apocarotenal. We comprehensively compared the transcriptome and metabolite profiles of abnormal (WGF, TYBGF and WLYF) and normal (WDYF, control) pericarps. In total, 2,880, 2,782 and 1,053 differentially expressed genes (DEGs), including 121, 117 and 43 transcription factors were identified in the three comparisons, respectively. The qRT-PCR confirmed the expression levels of genes selected from transcriptome. Additionally, a total of 77 flavonoids and other phenylpropanoid-derived metabolites were identified in the three comparisons. Most (76.65 %) showed markedly lower abundances in the three comparisons. The phenylpropanoid biosynthesis pathway was the major enrichment pathway in the integrative analysis of metabolome and transcriptome profiles.

CONCLUSIONS

Synthesizing the above analytical results, this study indicated that different color pericarps were associated with the reduced levels of some carotenoids and phenylpropanoids derivatives products and the down-regulation of proteins in flavonoids, phenylpropanoids derivatives biosynthesis pathway and the photosynthesis-antenna proteins.

Cell subtypes and immune dysfunction in peritoneal fluid of endometriosis revealed by single-cell RNA-sequencing

BACKGROUND

Endometriosis is a refractory and recurrent disease and it affects nearly 10% of reproductive-aged women and 40% of infertile patients. The commonly accepted theory for endometriosis is retrograde menstruation where endometrial tissues invade into peritoneal cavity and fail to be cleared due to immune dysfunction. Therefore, the comprehensive understanding of immunologic microenvironment of peritoneal cavity deserves further investigation for the previous studies mainly focus on one or several immune cells.

RESULTS

High-quality transcriptomes were from peritoneal fluid samples of patients with endometriosis and control, and firstly subjected to 10 × genomics single-cell RNA-sequencing. We acquired the single-cell transcriptomes of 10,280 cells from endometriosis sample and 7250 cells from control sample with an average of approximately 63,000 reads per cell. A comprehensive map of overall cells in peritoneal fluid was first exhibited. We unveiled the heterogeneity of immune cells and discovered new cell subtypes including T cell receptor positive (TCR+) macrophages, proliferating macrophages and natural killer dendritic cells in peritoneal fluid, which was further verified by double immunofluorescence staining and flow cytometry. Pseudo-time analysis showed that the response of macrophages to the menstrual debris might follow the certain differentiation trajectory after endometrial tissues invaded into the peritoneal cavity, that is, from antigen presentation to pro-inflammation, then to chemotaxis and phagocytosis. Our analyses also mirrored the dysfunctions of immune cells including decreased phagocytosis and cytotoxic activity and elevated pro-inflammatory and chemotactic effects in endometriosis.

CONCLUSION

TCR+ macrophages, proliferating macrophages and natural killer dendritic cells are firstly reported in human peritoneal fluid. Our results also revealed that immune dysfunction happens in peritoneal fluid of endometriosis, which may be responsible for the residues of invaded menstrual debris. It provided a large-scale and high-dimensional characterization of peritoneal microenvironment and offered a useful resource for future development of immunotherapy.

A network-based model to explore the role of testing in the epidemiological control of the COVID-19 pandemic

BACKGROUND

Testing is one of the most effective means to manage the COVID-19 pandemic. However, there is an upper bound on daily testing volume because of limited healthcare staff and working hours, as well as different testing methods, such as random testing and contact-tracking testing. In this study, a network-based epidemic transmission model combined with a testing mechanism was proposed to study the role of testing in epidemic control. The aim of this study was to determine how testing affects the spread of epidemics and the daily testing volume needed to control infectious diseases.

METHODS

We simulated the epidemic spread process on complex networks and introduced testing preferences to describe different testing strategies. Different networks were generated to represent social contact between individuals. An extended susceptible-exposed-infected-recovered (SEIR) epidemic model was adopted to simulate the spread of epidemics in these networks. The model establishes a testing preference of between 0 and 1; the larger the testing preference, the higher the testing priority for people in close contact with confirmed cases.

RESULTS

The numerical simulations revealed that the higher the priority for testing individuals in close contact with confirmed cases, the smaller the infection scale. In addition, the infection peak decreased with an increase in daily testing volume and increased as the testing start time was delayed. We also discovered that when testing and other measures were adopted, the daily testing volume required to keep the infection scale below 5% was reduced by more than 40% even if other measures only reduced individuals' infection probability by 10%. The proposed model was validated using COVID-19 testing data.

CONCLUSIONS

Although testing could effectively inhibit the spread of infectious diseases and epidemics, our results indicated that it requires a huge daily testing volume. Thus, it is highly recommended that testing be adopted in combination with measures such as wearing masks and social distancing to better manage infectious diseases. Our research contributes to understanding the role of testing in epidemic control and provides useful suggestions for the government and individuals in responding to epidemics.

A meta-analysis of the reproducibility of food frequency questionnaires in nutritional epidemiological studies

BACKGROUND

Reproducibility of FFQs measures the consistency of the same subject at different time points. We performed a meta-analysis to explore the reproducibility of FFQs and factors related to reproducibility of FFQs.

METHODS AND FINDINGS

A systematic literature review was performed before July 2020 using PubMed and Web of Science databases. Pooled intraclass and Spearman correlation coefficients (95% confidence interval) were calculated to assess the reproducibility of FFQs. Subgroup analyses based on characteristics of study populations, FFQs, or study design were performed to investigate factors related to the reproducibility of FFQs. A total of 123 studies comprising 20,542 participants were eligible for the meta-analysis. The pooled crude intraclass correlation coefficients ranged from 0.499 to 0.803 and 0.499 to 0.723 for macronutrients and micronutrients, respectively. Energy-adjusted intraclass correlation coefficients ranged from 0.420 to 0.803 and 0.507 to 0.712 for macronutrients and micronutrients, respectively. The pooled crude and energy-adjusted Spearman correlation coefficients ranged from 0.548 to 0.851 and 0.441 to 0.793, respectively, for macronutrients; and from 0.573 to 0.828 and 0.510 to 0.744, respectively, for micronutrients. FFQs with more food items, 12 months as dietary recall interval (compared to less than 12 months), and a shorter time period between repeated FFQs resulted in superior FFQ reproducibility.

CONCLUSIONS

In conclusion, FFQs with correlation coefficients greater than 0.5 for most nutrients may be considered a reliable tool to measure dietary intake. To develop FFQs with higher reproducibility, the number of food items and dietary recall interval should be taken into consideration.

Involvement of the Nervous System in SARS-CoV-2 Infection

As a severe and highly contagious infectious disease, coronavirus disease 2019 (COVID-19) has caused a global pandemic. Several case reports have demonstrated that the respiratory system is the main target in patients with COVID-19, but the disease is not limited to the respiratory system. Case analysis indicated that the nervous system can be invaded by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and that 36.4% of COVID-19 patients had neurological symptoms. Importantly, the involvement of the CNS may be associated with poor prognosis and disease worsening. Here, we discussed the symptoms and evidence of nervous system involvement (directly and indirectly) caused by SARS-CoV-2 infection and possible mechanisms. CNS symptoms could be a potential indicator of poor prognosis; therefore, the prevention and treatment of CNS symptoms are also crucial for the recovery of COVID-19 patients.

Mapping and identification of CsUp, a gene encoding an Auxilin-like protein, as a putative candidate gene for the upward-pedicel mutation (up) in cucumber

BACKGROUND

Pedicel orientation can affect the female flower orientation and seed yield in cucumber. A spontaneous mutant possessing upward growth of pedicels was identified in the wild type inbred strain 9930 and named upward-pedicel (up). The morphological and genetic analyses of up were performed in this study. In order to clone the up gene, 933 F₂ individuals and 524 BC₁ individuals derived from C-8-6 (WT) and up were used for map-based cloning.

RESULTS

up was mapped to a 35.2 kb physical interval on chromosome 1, which contains three predicted genes. Sequencing analysis revealed that a 5-bp deletion was found in the second exon of Csa1G535800, and it led to a frameshift mutation resulting in a premature stop codon. The candidate gene of CsUp (Csa1G535800) was further confirmed via genomic and cDNA sequencing in biparental and natural cucumber populations. Sequencing data showed that a 4-bp deletion was found in the sixth exon of Csa1G535800 in CGN19839, another inbred line, and there was also a mutation of an amino acid in Csa1G535800 that could contribute to the upward growth of pedicels in CGN19839. Moreover, it was found that Csa1G535800 exhibited strong expression in the pedicel of WT, suggesting its important role in development of pedicel orientation. Thus, Csa1G535800 was considered to be the candidate gene of CsUp.

CONCLUSIONS

CsUp encodes an Auxilin-like protein and controls pedicel orientation in cucumber. The identification of CsUp may help us to understand the mechanism of pedicel orientation development and allow for investigation of novel functions of Auxilin-like proteins in cucumber.

Theoretical Analysis of InGaAs/InAlAs Single-Photon Avalanche Photodiodes

Theoretical analysis and two-dimensional simulation of InGaAs/InAlAs avalanche photodiodes (APDs) and single-photon APDs (SPADs) are reported. The electric-field distribution and tunneling effect of InGaAs/InAlAs APDs and SPADs are studied. When the InGaAs/InAlAs SPADs are operated under the Geiger mode, the electric field increases linearly in the absorption layer and deviate down from its linear relations in the multiplication layer. Considering the tunneling threshold electric field in multiplication layer, the thickness of the multiplication layer should be larger than 300 nm. Moreover, SPADs can work under a large bias voltage to avoid tunneling in absorption layer with high doping concentrations in the charge layer.