Recycling selectable markers via Cre/loxP system for constructing Komagataella phaffii strains co-expressing multiple proteins

OBJECTIVE

A convenient strategy was developed to recycle selectable markers using Cre/loxP system for constructing Komagataella phaffii strains co-expressing multiple proteins.

RESULTS

A plasmid in this strategy was generated from pPICZαA with integration of lox71-Sh ble-lox66. Firstly, the plasmid was inserted with one target protein gene and then transformed into K. phaffii KM71. Secondly, the auxiliary plasmid pPICZαA/cre/his4 containing CRE recombinase gene was further chromosomally inserted to Sh ble gene therein. Finally, methanol induction was conducted to produce CRE for Cre/loxP-mediated recombination, and consequently, the sequence between lox71 and lox66 was deleted, leading to recycling of ZeoR and His- markers. Then the resulted strain expressing the one target protein was used as the host to which another target protein gene could be inserted by the same procedures.

CONCLUSIONS

With easy manipulation, the method was effective in recycling of the selectable markers, and consequently two protein genes were sequential integrated chromosomally and successfully co-expressed in the yeast.

Molecular Phylogenetics and the Evolution of Morphological Complexity in Aytoniaceae (Marchantiophyta)

Aytoniaceae are one of the largest families of complex thalloid liverworts (Marchantiopsida), consisting of about 70 species, with most species being distributed in temperate areas. However, the phylogeny and evolution of the morphological character of Aytoniaceae are still poorly understood. Here, we employed two chloroplast loci, specifically, rbcL and trnL-F, along with a 26S nuclear ribosomal sequence to reconstruct the phylogeny and track the morphological evolution of Aytoniaceae. Our results reveal that Aytoniaceae are monophyletic, and five monophyletic clades were recovered (i.e., Asterellopsis-Cryptomitrium, Calasterella, Mannia, Reboulia-Plagiochasma, and Asterella). Asterella was divided into five clades (i.e., Asterella lindenbergiana, subg. Saccatae, subg. Phragmoblepharis, subg. Wallichianae, and subg. Asterella), except for Asterella palmeri, which is the sister of Asterellopsis grollei. Bayesian molecular clock dating indicates that the five primary clades within Aytoniaceae underwent divergence events in the Cretaceous period. Asterellopsis differentiated during the early Upper Cretaceous (c. 84.2 Ma), and Calasterella originated from the late Lower Cretaceous (c. 143.0 Ma). The ancestral Aytoniaceae plant is reconstructed as the absence of a pseudoperianth, lacking equatorial apertures, and having both male and female reproductive organs on the main thallus. At present, Asterellopsis consists of two species known in Asia and America with the new transfer of Asterella palmeri to Asterellopsis. A new subgenus, Asterella subg. Lindenbergianae, is proposed.

Implicit weight bias: shared neural substrates for overweight and angry facial expressions revealed by cross-adaptation

The perception of facial expression plays a crucial role in social communication, and it is known to be influenced by various facial cues. Previous studies have reported both positive and negative biases toward overweight individuals. It is unclear whether facial cues, such as facial weight, bias facial expression perception. Combining psychophysics and event-related potential technology, the current study adopted a cross-adaptation paradigm to examine this issue. The psychophysical results of Experiments 1A and 1B revealed a bidirectional cross-adaptation effect between overweight and angry faces. Adapting to overweight faces decreased the likelihood of perceiving ambiguous emotional expressions as angry compared to adapting to normal-weight faces. Likewise, exposure to angry faces subsequently caused normal-weight faces to appear thinner. These findings were corroborated by bidirectional event-related potential results, showing that adaptation to overweight faces relative to normal-weight faces modulated the event-related potential responses of emotionally ambiguous facial expression (Experiment 2A); vice versa, adaptation to angry faces relative to neutral faces modulated the event-related potential responses of ambiguous faces in facial weight (Experiment 2B). Our study provides direct evidence associating overweight faces with facial expression, suggesting at least partly common neural substrates for the perception of overweight and angry faces.

Probiotic Roles of Clostridium butyricum in Piglets: Considering Aspects of Intestinal Barrier Function

China, as the global leader in pork production and consumption, is faced with challenges in ensuring sustainable and wholesome growth of the pig industry while also guaranteeing meat food safety amidst the ban on antibiotics usage in animal feed. The focus of the pig industry lies in guaranteeing piglet health and enhancing overall production performance through nutrition regulation. Clostridium butyricum (C. butyricum), a new type of probiotic, possesses characteristics such as heat resistance, acid resistance, and bile-salt tolerance, meaning it has potential as a feed additive. Previous studies have demonstrated that C. butyricum has a probiotic effect on piglets and can serve as a substitute for antibiotics. The objective of this study was to review the probiotic role of C. butyricum in the production of piglets, specifically focusing on intestinal barrier function. Through this review, we explored the probiotic effects of C. butyricum on piglets from the perspective of intestinal health. That is, C. butyricum promotes intestinal health by regulating the functions of the mechanical barrier, chemical barrier, immune barrier, and microbial barrier of piglets, thereby improving the growth of piglets. This review can provide a reference for the rational utilization and application of C. butyricum in swine production.

The nuclear receptor gene E75 plays a key role in regulating the molting process of the spider mite, Tetranychus urticae

The nuclear receptor gene Ecdysone-induced protein 75 (E75), as the component of ecdysone response genes in the ecdysone signaling pathway, has important regulatory function for insect molting. However, the regulatory function of E75 during the molting process of spider mites is not yet clear. In this study, the expression pattern of E75 in the molting process of the spider mite Tetranychus urticae was analyzed. The results showed that there was a peak at 8 h post-molting, followed by a decline 8 h after entering each respective quiescent stage across various developmental stages. During the deutonymph stage, the expression dynamics of E75, observed at 4-h intervals, indicated that the transcript levels of TuE75 peaked at 24 h, coinciding with the onset of molting in the mites. To investigate the function of TuE75 during the molting process, silencing TuE75 through dsRNA injection into deutonymph mites at the age of 8 h yielded a notable outcome: 78% of the deutonymph mites were unable to progress to the adult stage. Among these phenotypic mites, 37% were incapable of transitioning into the quiescent state and eventually succumbed after a certain period. An additional 41% of the mites successfully entered the quiescent state but encountered difficulties in shedding the old epidermis, leading to eventual mortality. In summary, these results suggested that TuE75 plays a key role in the molting process of T. urticae.

A parent-report measure of children's anxiety: psychometric properties of the Macquarie Anxiety Behavioural Scale (MABS) in a Chinese sample of preschool children

OBJECTIVE

The Macquarie Anxiety Behavioural Scale (MABS) is a newly developed scale to assess anxiety in children and teenagers. The present study aimed to evaluate the reliability and validity of the Chinese version of the MABS, as well as the measurement invariance across different age groups in a preschool-aged sample.

METHODS

A total of 1007 parents with children aged 3-6 years participated in the study. Internal consistency was assessed by calculating Cronbach's alpha, McDonald's omega and average inter-item correlation values. Confirmatory factor analysis (CFA) was conducted to examine the five-factor model. Multi-group CFA was conducted to test the measurement equivalence across different age groups (3- and 4-year-olds and 5- and 6-year-olds). Convergent, divergent, and criterion-related validity were assessed with Pearson correlation coefficients.

RESULTS

Internal consistency for the MABS total score was good and that of the subscales was acceptable. The CFA results showed that the five-factor structure of the MABS was supported in preschoolers (e.g., CFI = 0.929, TLI = 0.914, RMSEA = 0.050). In addition, scalar invariance of the MABS was supported across different age groups (e.g., ΔCFI = - 0.003, ΔTLI = 0, ΔRMSEA = 0). Furthermore, the MABS showed good convergent and divergent validity as well as criterion-related validity.

CONCLUSION

The Chinese version of the MABS demonstrated satisfactory psychometric properties and appeared to be a valid and reliable instrument for measuring anxiety in preschool children.

The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses

Hemiculterella wui is an endemic small freshwater fish, distributed in the Pearl River system and Qiantang River, China. In this study, we identified and annotated the complete mitochondrial genome sequence of H. wui. The mitochondrial genome was 16,619 bp in length and contained 13 protein coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. The nucleotide composition of the mitochondrial genome was 29.9% A, 25.3% T, 27.4% C, and 17.5% G, respectively. Most PCGs used the ATG start codon, except COI and ATPase 8 started with the GTG start codon. Five PCGs used the TAA termination codon and ATPase 8 ended with the TAG stop codon, and the remaining seven genes used two incomplete stop codons (T and TA). Most of the tRNA genes showed classical cloverleaf secondary structures, except that tRNASer(AGY) lacked the dihydrouracil loop. The average Ka/Ks value of the ATPase 8 gene was the highest, while the average Ka/Ks value of the COI gene was the lowest. Phylogenetic analyses showed that H. wui has a very close relationship with Pseudohemiculter dispar and H. sauvagei. This study will provide a valuable basis for further studies of taxonomy and phylogenetic analyses in H. wui and Xenocyprididae.

SAM protects against alveolar septal cell apoptosis in autoimmune emphysema rats

BACKGROUND

Hypomethylation of the perforin gene promoter in CD4 + T cells, inflammation and oxidative stress, might be involved in alveolar septal cell apoptosis associated with emphysema in rats. This study aimed to investigate the effects of S-adenosylmethionine (SAM) on this kind of apoptosis in rats with autoimmune emphysema.

METHODS

Twenty-four rats were randomly divided into three groups: a normal control group, a model group, and a SAM group. Pathological changes in lung tissues were observed, and the mean linear intercept (MLI) and mean alveolar number (MAN) were measured. The levels of anti-endothelial cell antibodies (AECA) in serum, alveolar septal cell apoptosis, perforin gene promotor methylation in CD4 + T cells in the spleen, and the levels of cytokines, malondialdehyde (MDA), and glutathione (GSH) and the activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in bronchoalveolar lavage fluid (BALF) were investigated.

RESULTS

The MLI, apoptosis index (AI) of alveolar septal cells, levels of AECA in serum, and levels of tumour necrosis factor-α (TNF-α), matrix metalloproteinase-9 (MMP-9) and MDA in BALF were increased, while the MAN, methylation levels, and the activities of GSH, SOD and GSH-Px in BALF were decreased in the model group compared with those in the normal control group and the SAM group (all P < 0.05). The levels of interleukin-8 (IL-8) in BALF were greater in the model group than in the normal control group (P < 0.05).

CONCLUSIONS

SAM protects against alveolar septal cell apoptosis, airway inflammation and oxidative stress in rats with autoimmune emphysema possibly by partly reversing the hypomethylation of the perforin gene promoter in CD4 + T cells.

Alterations in the balance of sex hormones may affect rat prostatic inflammation and fibrosis, and osteopontin might be involved in this process

OBJECTIVE

This study aimed to investigate the effects of sex hormone imbalance on rat prostatic inflammation and fibrosis and identify the key molecules involved.

METHODS

Castrated Sprague-Dawley (SD) rats were treated with a constant dose of oestradiol (E2) and different doses of dihydrotestosterone (DHT) to achieve different oestrogen/androgen ratios. After 8 weeks, serum E2 and DHT concentrations, relative seminal vesicle weights, histopathological changes and inflammation were measured, collagen fiber content and oestrogen receptor (ER) and androgen receptor (AR) expression were detected, mRNA sequencing and bioinformatics analysis were performed to identify differentially expressed genes (DEGs).

RESULTS

The severity of inflammation in the rat dorsolateral prostate (DLP) was higher, collagen fibre content and ER expression in the rat DLP and prostatic urethra were increased and AR expression in the rat DLP was decreased in the 1:1 E2/DHT-treated group than that in the 1:10 E2/DHT-treated group. RNA-seq analysis identified 487 DEGs, and striking increases in the expression of mRNAs encoding collagen, collagen synthesis and degradation enzymes, growth factors and binding proteins, cytokines and chemokines, and cell-surface molecules were confirmed in the 1:1 E2/DHT-treated group compared to the 1:10 E2/DHT-treated group. mRNA expression of secreted phosphoprotein 1 (Spp1) and protein expression of osteopontin (OPN, encoded by Spp1) were increased in the 1:1 E2/DHT-treated group compared to the 1:10 E2/DHT-treated group, and Spp1 expression correlated positively with Mmp7, Cxcl6 and Igfn1 expression.

CONCLUSIONS

The imbalance in the oestrogen/androgen ratio may affect rat prostatic inflammation and fibrosis, and OPN might be involved in this process.

Differences of oribatid mite community and trophic structure between karst caves and surface different moss habitats

In order to reveal the community characteristics and trophic structure of oribatid mites in different moss habitats in karst caves, the oribatid mites in the moss habitats of ground (GD), understory (US), cave wall (CW), surface shrub (SB) and farmland (FL) outside the cave were collected in October 2021. Through the identification and data analysis of oribatid mites, 2352 oribatid mites were found, belonging to 45 families and 72 genera, most of which were Gymnonota. The family number, genus number, individual number, individual density, dominant genus composition, community diversity, community similarity, MGP (Analysis methods for ecological groups of oribatid mites) ecological group of oribatid mites and trophic structure of oribatid mites in different moss were analyzed. The results showed that: (1) The number of families, genera, individuals, and individual density of SB and FL are higher than those of the other three habitats; (2) Platyliodes, Oppiella, Tectocepheus, Scutovertex, Scheloribates and Trichogalumna are the dominant genera of the oribatid mites in the cave moss habitat, among them, Tectocepheus and Trichogaluna have the most obvious advantages; (3) The diversity index of shrub (SB) was higher than that of other four habitats; Similarity between ground and cave wall, shrub and farmland is high; (4) The MGP ecological group of oribatid mites in different habitats is dominated by O type (Overall type belongs to MGP analysis results, 20%≤M,G,P≤50%), and a total of 42 genera of oribatid mites preliminarily constitute the trophic structure of oribatid mites in the cave moss habitat. Based on the above results, it can be concluded that there are differences in the community structure of oribatid mites in different moss habitats in the study area, and the use of dominant genera of mites can preliminarily indicate the environmental conditions of different moss habitats. This study enriches the study of mites in karst cave mosses, and can provide theoretical significance for the protection of cave biodiversity in karst areas.

The Underlying Mechanisms of Sleep Deprivation Exacerbating Neuropathic Pain

Pain disrupts sleep, and sleep deprivation or interference can alter pain perception in animals and humans, for example by increasing sensitivity to pain. However, the mechanism by which sleep affects neuropathic pain remains unclear. In this review, we discuss the available evidence from the epidemiologic, clinical, and human, as well as laboratory studies. In previous studies, we have found that sleep deprivation affects various injurious systems, including opioids, dopaminergic, immune, orexins, hypothalamic-pituitary-adrenal axis, and adenosine. At the same time, these systems play a crucial role in neuropathic pain regulation. In the complex interactions between these neurobiological systems, there may be potential regulatory pathways through which sleep deprivation amplifies neuropathic pain. Because of the impact sleep problems and neuropathic pain can have on the patients' quality of life, studying the link between sleep and neuropathic pain is important for neuropathic pain prevention and public health.

Perturbing BEAMs: EEG adversarial attack to deep learning models for epilepsy diagnosing

Deep learning models have been widely used in electroencephalogram (EEG) analysis and obtained excellent performance. But the adversarial attack and defense for them should be thoroughly studied before putting them into safety-sensitive use. This work exposes an important safety issue in deep-learning-based brain disease diagnostic systems by examining the vulnerability of deep learning models for diagnosing epilepsy with brain electrical activity mappings (BEAMs) to white-box attacks. It proposes two methods, Gradient Perturbations of BEAMs (GPBEAM), and Gradient Perturbations of BEAMs with Differential Evolution (GPBEAM-DE), which generate EEG adversarial samples, for the first time by perturbing BEAMs densely and sparsely respectively, and find that these BEAMs-based adversarial samples can easily mislead deep learning models. The experiments use the EEG data from CHB-MIT dataset and two types of victim models each of which has four different deep neural network (DNN) architectures. It is shown that: (1) these BEAM-based adversarial samples produced by the proposed methods in this paper are aggressive to BEAM-related victim models which use BEAMs as the input to internal DNN architectures, but unaggressive to EEG-related victim models which have raw EEG as the input to internal DNN architectures, with the top success rate of attacking BEAM-related models up to 0.8 while the top success rate of attacking EEG-related models only 0.01; (2) GPBEAM-DE outperforms GPBEAM when they are attacking the same victim model under a same distortion constraint, with the top attack success rate 0.8 for the former and 0.59 for the latter; (3) a simple modification to the GPBEAM/GPBEAM-DE will make it have aggressiveness to both BEAMs-related and EEG-related models (with top attack success rate 0.8 and 0.64), and this capacity enhancement is done without any cost of distortion increment. The goal of this study is not to attack any of EEG medical diagnostic systems, but to raise concerns about the safety of deep learning models and hope to lead to a safer design.

The association of cognition with protein energy wasting and synaptic transmission in chronic kidney disease

INTRODUCTION

In recent years, consciousness impairment in patients with end-stage renal disease (ESRD) has been paid more and more attention, but the cause and mechanism of consciousness state change is not clear.

METHODS

As the hippocampus played a crucial role in consciousness, we explored the pathological and electrophysiological changes in chronic kidney disease (CKD) mouse hippocampus.

RESULTS

Whole-cell recordings in hippocampal neurons showed that miniature excitatory postsynaptic current (mEPSC) frequency decreased, but the amplitude was unaltered in CKD_8w mice. In addition, α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor-mediated EPSCs (AMPAR-EPSCs) and N-methyl-D-aspartic acid receptor-mediated EPSCs (NMDAR-EPSCs) in hippocampal Schaffer collateral-CA1 synapses displayed a significant decline in CKD_8w mice. Although the ratio of AMPAR-/NMDAR-EPSCs did not change, the paired-pulse ratio (PPR) in CKD_8w mice increased. Intriguingly, the mEPSC frequency and AMPAR-/NMDAR-EPSCs amplitudes were positively associated with body weight, and the mEPSC frequency was negatively correlated with serum creatinine in CKD_8w mice, indicating a potential correlation between cognition and nutritional status in patients with CKD. To confirm the above hypothesis, we collected the clinical data from multiple hemodialysis centers to analyze the correlation between cognition and nutritional status.

CONCLUSION

Our analysis indicated that protein energy wasting (PEW) was a possible independent risk factor for consciousness dysfunction in maintenance hemodialysis (MHD) patients. Our results provided a more detailed mechanism underlying the cognitive impairment (CI) in ESRD patients at the synaptic level. Last but not least, our results showed that PEW was a probable new independent risk factor for CI in cases with ESRD.

Phylogenetic Analysis of Two New Mitochondrial Genomes of Singapora shinshana and Seriana bacilla from the Karst Region of Southwest China

Leafhoppers have been identified as a serious threat to different plants. To explore the characteristics of mitogenomes and reveal the phylogenetic positions of two species in the Typhlocybinae, complete mitogenomes of Singapora shinshana and Seriana bacilla were sequenced and annotated for the first time with lengths of 15,402 bp and 15,383 bp, respectively. The two mitogenomes contained 13 PCGs, 22 tRNA genes and 2 rRNA genes. The genome content, gene order, nucleotide composition, codon usage and amino acid composition are similar to those of other typical mitogenomes of Typhlocybinae. All 13 PCGs started with ATN codons, except for atp8 (TTA) and nad5 (TTG). All tRNAs were folded into a typical cloverleaf secondary structure, except for tRNA-Ser1 and tRNA-Val. Moreover, phylogenetic trees were constructed and analyzed based on all the PCGs from 42 mitogenomes using maximum likelihood (ML) and Bayesian inference (BI) methods. The results supported that eleven subfamilies are all monophyletic groups, S. shinshana and S. bacilla are members of Erythroneurini, but S. shinshana and the genus Empoascanara have a very close relationship with ((((Empoascanara sipra+ Empoascanara wengangensis) + Empoascanara dwalata) + Empoascanara gracilis) + S. shinshana), and S. bacilla is closely related to the genus Mitjaevia ((Mitjaevia dworakowskae + Mitjaevia shibingensis) + S. bacilla). These results provide valuable information for future study of evolutionary relationships in Typhlocybinae.

Assessment of combined algal toxicity of TiO2 nanoparticles and organochlorines in karst surface waters

The widespread use of nanoparticles (NPs) and organic pollutants increases the risk of their coexistence in the aquatic environments. It is uncertain how the combined toxicities of NPs and OCs affect aquatic organisms in surface waters. In this study, the binary combined toxicities of TiO₂ NPs with three different organochlorines (OCs)-pentachlorobenzene (PeCB), 3,3,4,4-tetrachlorobiphenyl (PCB-77), and atrazine on Chlorella pyrenoidosa in three karst surface water bodies were investigated. The correlation analysis results indicated that the toxicities of TiO₂ NPs and OCs to algae were mainly related to the total organic carbon (TOC) and ionic strength of surface water. Surface water relieved the growth inhibition of the pollutants on algae as compared with ultrapure water (UW). The combined toxic effect caused by the co-exposure of TiO₂ NPs-atrazine was synergistic and had an antagonistic effect for TiO₂ NPs-PCB-77 in four types of water bodies. However, the co-exposure of TiO₂ NPs-PeCB had an additive effect in the Huaxi Reservoir (HX) and synergistic effects in Baihua Lake (BH), Hongfeng Lake (HF), and UW. TiO₂ NPs increased the bioaccumulation of OCs by algae. Both PeCB and atrazine significantly increased the bioaccumulation of TiO₂ NPs by algae, except for PeCB in HX; however, PCB-77 reduced the bioaccumulation of TiO₂ NPs by algae. The toxic effects of TiO₂ NPs and OCs on algae in different water bodies were the result of the nature of the pollutants, bioaccumulation, hydrochemical properties, and other factors.

The Symptoms of Benign Prostatic Hyperplasia Patients with Stromal-Dominated Hyperplasia Nodules May Be Associated with Prostate Fibrosis

Objective

The aim of the present study was to observe the effect of the stroma proportion in hyperplasia nodules on the clinical symptoms of benign prostatic hyperplasia (BPH) patients and to identify the different genes and pathways in prostatic hyperplasia nodules between patients with epithelial-dominated hyperplasia (EDH) and stromal-dominated hyperplasia (SDH) nodules.

Methods

Sixty-seven BPH patient samples underwent transurethral resection of the prostate (TURP) were collected and retrospectively analyzed. The differences in clinical parameters between the EDH and SDH groups were investigated. Collagen fiber percentage was assessed, and the correlation with clinical parameters was evaluated. mRNA sequencing in hyperplasia nodules of 8 BPH patients was performed, and differentially expressed genes (DEGs) between the EDH and SDH groups were screened. These DEGs were analyzed using GO, KEGG and PPI analysis.

Results

The results showed the IPSS was significantly higher in the SDH group than in the EDH group (p < 0.01). The collagen fiber percentage of BPH nodules was higher in the SDH group than in the EDH group (p < 0.05), and the collagen fiber percentage was positively correlated with the IPSS (r = 0.4058, p = 0.0007). A total of 172 DEGs were obtained, including 63 up-regulated genes and 109 down-regulated genes. GO and KEGG pathway enrichment analyses showed DEGs were mainly enriched in extracellular matrix structural constituents. The top 10 hub genes were associated to the components of extracellular matrix and fibrosis.

Conclusion

These results suggested that the symptoms of BPH patients with SDH nodules may be associated with prostate fibrosis and fibrosis may be a significant contributing factor in BPH/LUTS patients with SDH nodules.

Effect of Corn Straw Blending on Phosphorus Specification and Bioavailability of Incinerated Sludge Ash

Phosphorus is a depletable resource, and the consumption of phosphorus fertilizer increases with the growing population size. Phosphorus recycled from incinerated sludge ash can be a complement to phosphatic fertilizers in districts suffering from phosphorus resource shortages (e.g., Germany, Japan, and Sweden). The apatite inorganic phosphorus (AP) content in incinerated sludge ash is a key factor influencing the recoverability and bioavailability. Biomass straw is rich in calcium and magnesium minerals and can be used as an additive to be blended with sludge to increase the AP content. However, most of the current studies added excessive amounts of calcium-based or biomass additives, and the bioavailability of various Ca-Mg-P minerals generated after the addition of biomass has not been systematically discussed. In this study, the changes of the phosphorus form in the mixed sludge and biomass with Ca/P in the range of 1.0-2.5 are studied, and the influence of temperature and additives on the phosphorus form and the bioavailability of phosphorus in the ash samples are discussed by combining X-ray diffraction and citric acid (CA) leaching experiments. The AP content is very low in the residue of the sludge or corn straw (CS) that has been burned individually. The sludge and the blended sludge and CS were incinerated at various temperatures. As the incineration temperature increased, the conversion of non-apatite inorganic phosphorus (NAIP) to AP was promoted, but the bioavailability did not change until 1050 °C for samples with a Ca/P of 2.5. In the range from 750 to 950 °C, higher temperature promotes the formation of Ca₂P₂O₇ and CaP₂O₆. CaP₂O₆ is insoluble in CA; thus, the bioavailability changes little from 750 to 950 °C, although the AP content increases. With the increase of Ca/P, the conversion of NAIP to AP and the bioavailability of phosphorus were promoted. For the blended sludge and CS ash, Ca₇Mg₂P₆O₂₄ appears at 950 and 1050 °C and the bioavailability also increases.

Complete chloroplast genome features of the model heavy metal hyperaccumulator Arabis paniculata Franch and its phylogenetic relationships with other Brassicaceae species

Arabis paniculata Franch (Brassicaceae) has been widely used for the phytoremediation of heavy mental, owing to its hyper tolerance of extreme Pb, Zn, and Cd concentrations. However, studies on its genome or plastid genome are scarce. In the present study, we obtained the complete chloroplast (cp) genome of A. paniculata via de novo assembly through the integration of Illumina reads and PacBio subreads. The cp genome presents a typical quadripartite cycle with a length of 153,541 bp, and contains 111 unigenes, with 79 protein-coding genes, 28 tRNAs and 4 rRNAs. Codon usage analysis showed that the codons for leucine were the most frequent codons and preferentially ended with A/U. Synonymous (Ks) and non-synonymous (Ka) substitution rate analysis indicated that the unigenes, ndhF and rpoC2, related to "NADH-dehydrogenase" and "RNA polymerase" respectively, underwent the lowest purifying selection pressure. Phylogenetic analysis demonstrated that Arabis flagellosa and A. hirsuta are more similar to each other than to A. paniculata, and Arabis is the closest relative of Draba among all Brassicaceae genera. These findings provide valuable information for the optimal exploitation of this model species as a heavy-metal hyperaccumulator.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01151-1.

Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species

Moricandia arvensis, a plant species originating from the Mediterranean, has been classified as a rare C3-C4 intermediate species, and it is a possible bridge during the evolutionary process from C3 to C4 plant photosynthesis in the family Brassicaceae. Understanding the genomic structure, gene order, and gene content of chloroplasts (cp) of such species can provide a glimpse into the evolution of photosynthesis. In the present study, we obtained a well-annotated cp genome of M. arvensis using long PacBio and short Illumina reads with a de novo assembly strategy. The M. arvensis cp genome was a quadripartite circular molecule with the length of 153,312 bp, including two inverted repeats (IR) regions of 26,196 bp, divided by a small single copy (SSC) region of 17,786 bp and a large single copy (LSC) region of 83,134 bp. We detected 112 unigenes in this genome, comprising 79 protein-coding genes, 29 tRNAs, and four rRNAs. Forty-nine long repeat sequences and 51 simple sequence repeat (SSR) loci of 15 repeat types were identified. The analysis of Ks (synonymous) and Ka (non-synonymous) substitution rates indicated that the genes associated with “subunits of ATP synthase” (atpB), “subunits of NADH-dehydrogenase” (ndhG and ndhE), and “self-replication” (rps12 and rpl16) showed relatively higher Ka/Ks values than those of the other genes. The gene content, gene order, and LSC/IR/SSC boundaries and adjacent genes of the M. arvensis cp genome were highly conserved compared to those in related C3 species. Our phylogenetic analysis demonstrated that M. arvensis was clustered into a subclade with cultivated Brassica species and Raphanus sativus, indicating that M. arvensis was not involved in an independent evolutionary origin event. These results will open the way for further studies on the evolutionary process from C3 to C4 photosynthesis and hopefully provide guidance for utilizing M. arvensis as a resource for improvinng photosynthesis efficiency in cultivated Brassica species.

Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae)

Eruca sativa Mill. (Brassicaceae) is an important edible vegetable and a potential medicinal plant due to the antibacterial activity of its seed oil. Here, the complete chloroplast (cp) genome of E. sativa was de novo assembled with a combination of long PacBio reads and short Illumina reads. The E. sativa cp genome had a quadripartite structure that was 153,522 bp in size, consisting of one large single-copy region of 83,320 bp and one small single-copy region of 17,786 bp which were separated by two inverted repeat (IRa and IRb) regions of 26,208 bp. This complete cp genome harbored 113 unique genes: 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Forty-nine long repetitive sequences and 69 simple sequence repeats were identified in the E. sativa cp genome. A codon usage analysis of the E. sativa cp genome showed a bias toward codons ending in A/T. The E. sativa cp genome was similar in size, gene composition, and linearity of the structural region when compared with other Brassicaceae cp genomes. Moreover, the analysis of the synonymous (Ks) and non-synonymous (Ka) substitution rates demonstrated that protein-coding genes generally underwent purifying selection pressure, expect ycf1, ycf2, and rps12. A phylogenetic analysis determined that E. sativa is evolutionarily close to important Brassica species, indicating that it may be possible to transfer favorable E. sativa alleles into other Brassica species. Our results will be helpful to advance genetic improvement and breeding of E. sativa, and will provide valuable information for utilizing E. sativa as an important resource to improve other Brassica species.