Food Pesticide Residues Monitoring and Health Risk Assessment.

This Special Issue presents a share of the work published in the journal Foods on pesticide residue monitoring and risk assessment in food [...].

Predictive model of chemotherapy-related toxicity in elderly Chinese cancer patients.

Purpose: Older cancer patients are more likely to develop and die from chemotherapy-related toxicity. However, evidence on drug safety and optimal effective doses is relatively limited in this group. The aim of this study was to develop a tool to identify elderly patients vulnerable to chemotherapy toxicity. Patients and methods: Elderly cancer patients ≥60 years old who visited the oncology department of Peking Union Medical College Hospital between 2008 and 2012 were included. Each round of chemotherapy was regarded as a separate case. Clinical factors included age, gender, physical status, chemotherapy regimen and laboratory tests results were recorded. Severe (grade ≥3) chemotherapy-related toxicity of each case was captured according to the National Cancer Institute Common Terminology Criteria for Adverse Events, version 5.0. Univariate analysis was performed by chi-square statistics to determine which factors were significantly associated with severe chemotherapy toxicity. Logistic regression was used to build the predictive model. The prediction model was validated by calculating the area under the curve of receiver operating characteristic (ROC). Results: A total of 253 patients and 1,770 cases were included. The average age of the patients was 68.9 years. The incidence of grade 3-5 adverse events was 24.17%. Cancer type (non-GI cancers), BMI<20 kg/m2, KPS<90%, severe comorbidity, polychemotherapy, standard dose chemotherapy, low white blood cells count, anemia, low platelet cells count, low creatine level and hypoalbuminemia were associated with severe chemotherapy-related toxicity. We used these factors to construct a chemotherapy toxicity prediction model and the area under the ROC curve was 0.723 (95% CI, 0.687-0.759). Risk of toxicity increased with higher risk score (11.98% low, 31.51% medium, 70.83% high risk; p < 0.001). Conclusion: We constructed a predictive model of chemotherapy toxicity in elderly cancer patients based on a Chinese population. The model can be used to guide clinicians to identify vulnerable population and adjust treatment regimens accordingly.

Mechanical strain treatment improves nuclear transfer reprogramming efficiency by enhancing chromatin accessibility.

Cellular mechanical properties are considered to be important factors affecting cell fate transitions, but the links between cellular mechanical properties and transition efficiency and chromatin structure remain elusive. Here, we predicted that mechanical strain treatment could induce signatures of cellular dedifferentiation and transdifferentiation, and we validated this prediction by showing that mechanical strain-treated mouse cumulus cells (CCs) exhibit significantly improved somatic cell nuclear transfer (SCNT) reprogramming efficiency. We found that the chromatin accessibility of CCs was globally increased by mechanical strain treatment and that this increase was partially mediated by the induction of the YAP-TEAD interaction. Moreover, using mechanical strain-treated CCs could prevent transcriptional dysregulation in SCNT embryos. Taken together, our study results demonstrated that modulating cell mechanical properties to regulate epigenetic status is a promising approach to facilitate cell fate transition.

Bacteria-mediated tumor-targeted delivery of tumstatin (54-132) significantly suppresses tumor growth in mouse model by inhibiting angiogenesis and promoting apoptosis.

Tumor growth is an angiogenesis-dependent process and accompanied by the formation of hypoxic areas. Tumstatin is a tumor-specific angiogenesis inhibitor that suppresses the proliferation and induces the apoptosis of tumorous vascular endothelial cells. VNP20009, an attenuated Salmonella typhimurium strain, preferentially accumulates in the hypoxic areas of solid tumors. In this study, a novel Salmonella-mediated targeted expression system of tumstatin (VNP-Tum5) was developed under the control of the hypoxia-induced J23100 promoter to obtain anti-tumor efficacy in mice. Treatment with VNP-Tum5 effectively suppressed tumor growth and prolonged survival in the mouse model of B16F10 melanoma. VNP-Tum5 exhibited a higher efficacy in inhibiting the proliferation and inducing the necrosis and apoptosis of B16F10 cells in vitro and in vivo compared with VNP (control). VNP-Tum5 significantly inhibited the proliferation and migration of mouse umbilical vascular endothelial cells to impede angiogenesis. VNP-Tum5 downregulated the expression of anti-vascular endothelial growth factor A, platelet endothelial cell adhesion molecule-1, phosphorylated phosphoinositide 3 kinase, and phosphorylated protein kinase B and upregulated the expression of cleaved-caspase 3 in tumor tissues. This study is the first to use tumstatin-transformed VNP20009 as a tumor-targeted system for treatment of melanoma by combining anti-tumor and anti-angiogenic effects.

Optimization of the Transformation Protocol for Increased Efficiency of Genetic Transformation in Hevea brasiliensis.

The recurring growth of bacterium in newly developed resistant cells and a minimal level of bacterial infection rate are the main limiting factors of Agrobacterium-mediated transformation experiments in Hevea brasiliensis. The current study aimed to optimize crucial factors of the transformation protocol in order to obtain an efficient transformation experimental model for Hevea using cotyledonary somatic embryos as explants. Transformation conditions such as antibiotic concentration, preculture duration, Agrobacterium concentration, sonication and cocultivation conditions were analyzed using the binary vector pCAMBIA2301. Transient transformation was confirmed by GUS histochemical staining. The best transformation efficiency was observed when the explants were not cultured on a preculture medium that contained acetosyringone at a level of 100 µM. The best results were obtained using a bacterial density of 0.45 at OD 600 nm, 50 s of sonication of explants in a bacterial liquid culture and a total incubation time of 18 min in the same bacterial suspension. Transmission electron microscopical analysis confirmed the impacts of sonication on bacterial infection efficiency. Cocultivation conditions of 22 °C and 84 h of darkness were optimal for the transfer of T-DNA. Agrobacterium was eliminated with 500 mg/L of timentin, and the selection of transformants was performed using 100 mg/L of kanamycin in the selection medium. The presence of transgene was confirmed in the resistant embryos by polymerase chain reaction (PCR). The improved method of genetic transformation established in the present study will be useful for the introduction of foreign genes of interest into the Hevea genome for the breeding of this economically important plant species in the future.

Generation of functional oligopeptides that promote osteogenesis based on unsupervised deep learning of protein IDRs.

Deep learning (DL) is currently revolutionizing peptide drug development due to both computational advances and the substantial recent expansion of digitized biological data. However, progress in oligopeptide drug development has been limited, likely due to the lack of suitable datasets and difficulty in identifying informative features to use as inputs for DL models. Here, we utilized an unsupervised deep learning model to learn a semantic pattern based on the intrinsically disordered regions of ~171 known osteogenic proteins. Subsequently, oligopeptides were generated from this semantic pattern based on Monte Carlo simulation, followed by in vivo functional characterization. A five amino acid oligopeptide (AIB5P) had strong bone-formation-promoting effects, as determined in multiple mouse models (e.g., osteoporosis, fracture, and osseointegration of implants). Mechanistically, we showed that AIB5P promotes osteogenesis by binding to the integrin α5 subunit and thereby activating FAK signaling. In summary, we successfully established an oligopeptide discovery strategy based on a DL model and demonstrated its utility from cytological screening to animal experimental verification.

Real-world outcomes of regorafenib combined with immune checkpoint inhibitors in patients with advanced or metastatic microsatellite stable colorectal cancer: A multicenter study.

BACKGROUND: Treatment strategies are limited for patients with chemotherapy refractory microsatellite stable (MSS) colorectal cancer. We aim to evaluate the efficacy and safety of immune checkpoint inhibitors (ICIs) combined with regorafenib in this population in routine clinical practice. METHODS: We retrospectively analyzed patients with advanced or metastatic colorectal cancer who received at least one dose of ICIs combined with regorafenib in 14 Chinese medical centers. The primary outcome was objective response rate (ORR). This study was registered at ClinicalTrials.gov on February 2020 (NCT04771715). RESULTS: Eighty-four patients received ICIs combined with regorafenib from January 2019 to January 2021. Most patients (91%) received two or more systemic treatment lines before the study treatment. Seventy-six patients (90%) had confirmed MSS status. At a median follow-up of 5.5 months, four patients achieved partial response (5%) and 37 patients achieved stable disease (45%) as the best response. The median progression-free survival (PFS) was 3.1 months, and the median overall survival was 17.3 months. Eleven patients (13%) remained progression-free for more than 6 months. Baseline liver metastasis (HR 1.98, 95%CI 1.07-3.69, P = 0.03) and neutrophil-lymphocyte ratio (NLR) of ≥ 1.5 (HR 2.83, 95%CI 1.00-7.98, P = 0.05) were associated with shorter PFS in multivariate analysis. Grade 3 or higher treatment-related adverse events (TRAEs) occurred in 16 patients (19%). CONCLUSION: The combination of ICIs with regorafenib can be a valuable treatment option for a proportion of patients with chemotherapy refractory MSS colorectal cancer. Patients with no liver metastasis and a low NLR at baseline may derive most benefit from this strategy.

CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data.

MOTIVATION: The increasing amount of time-series single-cell RNA sequencing (scRNA-seq) data raises the key issue of connecting cell states (i.e. cell clusters or cell types) to obtain the continuous temporal dynamics of transcription, which can highlight the unified biological mechanisms involved in cell state transitions. However, most existing trajectory methods are specifically designed for individual cells, so they can hardly meet the needs of accurately inferring the trajectory topology of the cell state, which usually contains cells assigned to different branches. RESULTS: Here, we present CStreet, a computed Cell State trajectory inference method for time-series scRNA-seq data. It uses time-series information to construct the k-nearest neighbor connections between cells within each time point and between adjacent time points. Then, CStreet estimates the connection probabilities of the cell states and visualizes the trajectory, which may include multiple starting points and paths, using a force-directed graph. By comparing the performance of CStreet with that of six commonly used cell state trajectory reconstruction methods on simulated data and real data, we demonstrate the high accuracy and high tolerance of CStreet. AVAILABILITY AND IMPLEMENTATION: CStreet is written in Python and freely available on the web at https://github.com/TongjiZhanglab/CStreet and https://doi.org/10.5281/zenodo.4483205. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization.

BACKGROUND: Germline cells are important carriers of genetic and epigenetic information transmitted across generations in mammals. During the mammalian germline cell development cycle (i.e., the germline cycle), cell potency changes cyclically, accompanied by dynamic transcriptional changes and epigenetic reprogramming. Recently, to understand these dynamic and regulatory mechanisms, multiomic analyses, including transcriptomic and epigenomic analyses of DNA methylation, chromatin accessibility and histone modifications of germline cells, have been performed for different stages in human and mouse germline cycles. However, the long time span of the germline cycle and material scarcity of germline cells have largely limited the understanding of these dynamic characteristic changes. A tool that integrates the existing multiomics data and visualizes the overall continuous dynamic trends in the germline cycle can partially overcome such limitations. RESULTS: Here, we present GLEANER, a web server for GermLine cycle Expression ANalysis and Epigenetics Roadmap visualization. GLEANER provides a comprehensive collection of the transcriptome, DNA methylome, chromatin accessibility, and H3K4me3, H3K27me3, and H3K9me3 histone modification characteristics in human and mouse germline cycles. For each input gene, GLEANER shows the integrative analysis results of its transcriptional and epigenetic features, the genes with correlated transcriptional changes, and the overall continuous dynamic trends in the germline cycle. We further used two case studies to demonstrate the detailed functionality of GLEANER and highlighted that it can provide valuable clues to the epigenetic regulation mechanisms in the genetic and epigenetic information transmitted during the germline cycle. CONCLUSIONS: To the best of our knowledge, GLEANER is the first web server dedicated to the analysis and visualization of multiomics data related to the mammalian germline cycle. GLEANER is freely available at http://compbio-zhanglab.org/GLEANER .

Comparative analysis of latex transcriptomes reveals the potential mechanisms underlying rubber molecular weight variations between the Hevea brasiliensis clones RRIM600 and Reyan7-33-97.

BACKGROUND: The processabilities and mechanical properties of natural rubber depend greatly on its molecular weight (MW) and molecular weight distribution (MWD). However, the mechanisms underlying the regulation of molecular weight during rubber biosynthesis remain unclear. RESULTS: In the present study, we determined the MW and particle size of latex from 1-year-old virgin trees and 30-year-old regularly tapped trees of the Hevea clones Reyan7-33-97 and RRIM600. The results showed that both the MW and the particle size of latex varied between these two clones and increased with tree age. Latex from RRIM600 trees had a smaller average particle size than that from Reyan7-33-97 trees of the same age. In 1-year-old trees, the Reyan7-33-97 latex displayed a slightly higher MW than that of RRIM600, whereas in 30-year-old trees, the RRIM600 latex had a significantly higher MW than the Reyan7-33-97 latex. Comparative analysis of the transcriptome profiles indicated that the average rubber particle size is negatively correlated with the expression levels of rubber particle associated proteins, and that the high-MW traits of latex are closely correlated with the enhanced expression of isopentenyl pyrophosphate (IPP) monomer-generating pathway genes and downstream allylic diphosphate (APP) initiator-consuming non-rubber pathways. By bioinformatics analysis, we further identified a group of transcription factors that potentially regulate the biosynthesis of IPP. CONCLUSIONS: Altogether, our results revealed the potential regulatory mechanisms involving gene expression variations in IPP-generating pathways and the non-rubber isoprenoid pathways, which affect the ratios and contents of IPP and APP initiators, resulting in significant rubber MW variations among same-aged trees of the Hevea clones Reyan7-33-97 and RRIM600. Our findings provide a better understanding of rubber biosynthesis and lay the foundation for genetic improvement of rubber quality in H. brasiliensis.

Cloning and functional analysis of five TERMINAL FLOWER 1/CENTRORADIALIS-like genes from Hevea brasiliensis.

Five TERMINAL FLOWER 1 (TFL1)/CENTRORADIALIS (CEN)-like genes were isolated and characterized from rubber tree (Hevea brasiliensis). All genes, except HbCEN1, were found to have conserved genomic organization, characteristic of the phosphatidyl ethanolamine-binding protein (PEBP) family. Overexpression of all of them delayed flowering and altered flower architecture compared with the wild-type (wt) counterpart. In addition, as premature-flowering of the terminal bud was successfully overcome in the tfl1-1 mutant of Arabidopsis, all these genes have a potential function similar to TFL1. Quantitative reverse transcriptase-polymerase chain reaction analysis showed higher expressions of HbCEN1 and HbCEN2 in the shoot apices and stems of both immature and mature rubber trees than in reproductive organs. HbTFL1-1 and HbTFL1-2 expression was confined to roots of 3-month-old seedlings and HbTFL1-3 was significantly higher in the shoot apices of these seedlings. These results suggested that HbCEN1 and HbCEN2 could be associated with the development of vegetative growth, whereas HbTFL1-1, HbTFL1-2 and HbTFL1-3 seem to be mainly related with maintenance of juvenility. In addition, four of the five genes displayed variable diurnal expression, HbTFL1-1 and HbTFL1-3 being mainly expressed during the night whereas HbCEN1 and HbCEN2 showed irregular diurnal rhythms.

The rubber tree genome reveals new insights into rubber production and species adaptation.

The Para rubber tree (Hevea brasiliensis) is an economically important tropical tree species that produces natural rubber, an essential industrial raw material. Here we present a high-quality genome assembly of this species (1.37 Gb, scaffold N50 = 1.28 Mb) that covers 93.8% of the genome (1.47 Gb) and harbours 43,792 predicted protein-coding genes. A striking expansion of the REF/SRPP (rubber elongation factor/small rubber particle protein) gene family and its divergence into several laticifer-specific isoforms seem crucial for rubber biosynthesis. The REF/SRPP family has isoforms with sizes similar to or larger than SRPP1 (204 amino acids) in 17 other plants examined, but no isoforms with similar sizes to REF1 (138 amino acids), the predominant molecular variant. A pivotal point in Hevea evolution was the emergence of REF1, which is located on the surface of large rubber particles that account for 93% of rubber in the latex (despite constituting only 6% of total rubber particles, large and small). The stringent control of ethylene synthesis under active ethylene signalling and response in laticifers resolves a longstanding mystery of ethylene stimulation in rubber production. Our study, which includes the re-sequencing of five other Hevea cultivars and extensive RNA-seq data, provides a valuable resource for functional genomics and tools for breeding elite Hevea cultivars.

Effects of resistant and susceptible rubber germplasms on development, reproduction and protective enzyme activities of Eotetranychus sexmaculatus (Acari: Tetranychidae).

Systematic research or technical support regarding rubber germplasm resistance against mites was not performed yet. To develop a preliminary understanding of the mite-resistance mechanisms of rubber germplasms, stably resistant rubber germplasms were obtained, the development and reproduction of Eotetranychus sexmaculatus that fed on leaves of resistant and susceptible rubber germplasms were examined in the laboratory, and the activities of protective enzymes in this mite species were also compared. The results indicated that: (1) among the 23 rubber core germplasms identified, five (IRCI12, Reyan87-6-5, IAN717, RRIM600 and RRIC52) steadily developed resistance to E. sexmaculatus; (2) E. sexmaculatus that fed on the highly resistant germplasm IRCI12 did not complete development and reproduction-the female adults laid only 4.90 eggs on average, and none of these eggs hatched; (3) the resistant germplasms extended the duration of each developmental stage, reduced the fecundity, egg hatchability, and female offspring percentage, and significantly decreased the offspring survival rate compared with the susceptible germplasms; and (4) during each developmental stage of the mites that fed on resistant rubber germplasms, decreased activities (by 0.25-fold to 0.63-fold times) of the protective enzymes peroxidase, ascorbate peroxidase, polyphenol oxidase, superoxide dismutase and catalase were observed compared with those in the mites that fed on susceptible rubber germplasms (P < 0.05). These findings may explain why E. sexmaculatus did not complete their development and reproduction on the resistant rubber germplasms. This study lays a foundation for elucidation of the mechanism of rubber resistance to mites and provides experimental material and technical support for the breeding of mite-resistant rubber plants.

Identification, Functional Study, and Promoter Analysis of HbMFT1, a Homolog of MFT from Rubber Tree (Hevea brasiliensis).

A homolog of MOTHER OF FT AND TFL1 (MFT) was isolated from Hevea brasiliensis and its biological function was investigated. Protein multiple sequence alignment and phylogenetic analysis revealed that HbMFT1 conserved critical amino acid residues to distinguish MFT, FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1)-like proteins and showed a closer genetic relationship to the MFT-like group. The accumulation of HbMFT1 was generally detected in various tissues except pericarps, with the highest expression in embryos and relatively higher expression in roots and stems of seedlings, flowering inflorescences, and male and female flowers. HbMFT1 putative promoter analysis showed that tissue-specific, environmental change responsive and hormone-signaling responsive elements were generally present. HbMFT1 was strongly induced under a short-day condition at 28 °C, with the highest expression after the onset of a day. Overexpression of HbMFT1 inhibited seed germination, seedling growth, and flowering in transgenic Arabidopsis. The qRT-PCR further confirmed that APETALA1 (AP1) and FRUITFULL (FUL) were drastically down-regulated in 35S::HbMFT1 plants. A histochemical ß-glucuronidase (GUS) assay showed that HbMFT1::GUS activity was mainly detected in stamens and mature seeds coinciding with its original expression and notably induced in rosette leaves and seedlings of transgenic Arabidopsis by exogenous abscisic acid (ABA) due to the presence of ABA cis-elements in HbMFT1 promoter. These results suggested that HbMFT1 was mainly involved in maintenance of seed maturation and stamen development, but negatively controlled germination, growth and development of seedlings and flowering. In addition, the HbMFT1 promoter can be utilized in controlling transgene expression in stamens and seeds of rubber tree or other plant species.

[Construction of a methylation filtration library in Hevea brasiliensis.].

In order to enrich gene encoding region of Hevea brasiliensis, a methylation filtration library was constructed using Escherichia coli McrBC restriction-modification system. The titers of the non-amplified library and the amplified library were 2.6×106 pfu/ml and 9.0×109, respectively. The rate of positive clones was 86.4%. The lengths of inserted DNA sequence ranged from 1 kb to 2.5 kb and the average size of inserts was 1.2 kb. One hundred clones were selected randomly for sequencing, resulting in splicing out of 81 non-redundant sequences, including 6 contigs and 75 singlets. The redundancy was 17.35%. Blast analysis showed that 39.5% of non-redundant sequences were homologous with the Nr database, 14.81% with the EST database, and 32.1% were unknown sequences. Some sequences were related genes for flowering, insect and disease resistance. Therefore, the rubber tree methylation library is helpful for discovery and cloning of functional genes.

[Genomic in situ hybridization in intergeneric hybrids between Raphanus sativus and Brassica oleracea].

Genomic in situ hybridization (GISH) was applied to study the meiosis of F1 plants from intergeneric hybrids between radish (Raphanus sativus, 2n=18, RR) and cabbage (Brassica oleracea, 2n=18, CC). The result showed that its somatic cells had the expected chromosomes, RC, 2n=18; but the pollen mother cells (PMCs) were different. There were three main kinds of PMCs. The first one was RC (2n=18), and the mean chromosome pairing pattern was 14.87I+1.20II+0.04III+0.06IV on Diakinesis. GISH indicated that most bivalents resulted from chromosome pairing between radish and cabbage, and the nine chromosomes of R-genome were separated mostly in the ratio 5/4 and 6/3 at Anaphase, so the chromosome number and components in gametes were not in equilibrium and the gametes were sterile. The second was RRCC (2n=36) with normal chromosome pairing and separation, producing unreduced gametes. And the third was nullisomic of RRCC in PMCs (2n<36) GISH showed that some radish chromosomes were lost in those PMCs, and its gametes had nine cabbage chromosomes and partial radish chromosomes. The mechanism of this chromosome reduplication was discussed in this paper.

Parental genome separation and elimination of cells and chromosomes revealed by AFLP and GISH analyses in a Brassica carinata x Orychophragmus violaceus cross.

BACKGROUND AND AIMS: The phenomenon of parental genome separation during the mitotic divisions of hybrid cells was proposed to occur under genetic control in intergeneric hybrids between cultivated Brassica species and Orychophragmus violaceus (2n = 24). To elucidate further the cytological and molecular mechanisms behind parental genome separation, Brassica carinata (2n = 34) x O. violaceus hybrids were resynthesized and their chromosome/genomic complements analysed. METHODS: F(1) hybrids of the cross were obtained following embryo rescue, and were investigated for their cytological behaviour and subjected to genomic in situ hybridization (GISH) and amplified fragment length polymorphism (AFLP) to determine the contribution of parental genomes. KEY RESULTS: All the F(1) plants with high fertility closely resembled B. carinata in morphological attributes. These were mixoploids with 2n chromosome numbers ranging from 17 to 35; however, 34, the same number as in B. carinata, was the most frequent number of chromosomes in ovary and pollen mother cells (PMCs). GISH clearly identified 16 chromosomes of B. nigra in ovary cells and PMCs with 2n = 34 and 35. However, no O. violaceus chromosome was detected, indicating the presence of the intact B. carinata genome and elimination of the entire O. violaceus genome. However, some AFLP bands specific for O. violaceus and novel for the two parents were detected in the leaves. Cells with fewer than 34 chromosomes had lost some B. oleracea chromosomes. F(2) plants were predominantly like B. carinata, but some contained O. violaceus characters. CONCLUSIONS: The cytological mechanism for the results involves complete and partial genome separation at mitosis in embryos of F(1) plants followed by chromosome doubling, elimination of cells with O. violaceus chromosomes and some introgression of O. violaceus genetic information.

[Chromosomal behaviors in plant wide hybridizations and their genetic and evolutionary implications].

The wide hybridization and polyploidization play a significant role in the evolution of higher plants. On the contrary, the artificially synthesized allopolyploids are genetically unstable and fail to be used as crops. One reason for this situation may be that the allopolyploids in nature are the products of natural selection and evolution and it is difficult for human to repeat and perform the process in short periods. Another reason is that we know little about the interaction mechanisms between the genomes of different origins. So the genetics and epigenetics after allopolyploidizations are now studied by multidisciplinary approaches. The spatial separation of parental genomes in hybrid cells have been observed in some sexual and somatic hybrids, but the biological meanings remain to clarify. The abnormal chromosome behaviors in plant wide crosses, such as pseudogamy, semigamy, chromosome elimination and the mitotic and meiotic separation of parental genomes, may indicate the incompatibility of two parental species at gametic and chromosomal levels. The systematic studies at different levels on chromosomal behavior and genetics in plant hybridizations are needed to undermine the mechanisms responsible for the formation and evolution of new species.