mitoSplitter: A mitochondrial variants-based method for efficient demultiplexing of pooled single-cell RNA-seq.

Single-cell RNA-seq (scRNA-seq) analysis of multiple samples separately can be costly and lead to batch effects. Exogenous barcodes or genome-wide RNA mutations can be used to demultiplex pooled scRNA-seq data, but they are experimentally or computationally challenging and limited in scope. Mitochondrial genomes are small but diverse, providing concise genotype information. We developed "mitoSplitter," an algorithm that demultiplexes samples using mitochondrial RNA (mtRNA) variants, and demonstrated that mtRNA variants can be used to demultiplex large-scale scRNA-seq data. Using affordable computational resources, mitoSplitter can accurately analyze 10 samples and 60,000 cells in 6 h. To avoid the batch effects from separated experiments, we applied mitoSplitter to analyze the responses of five non-small cell lung cancer cell lines to BET (Bromodomain and extraterminal) chemical degradation in a multiplexed fashion. We found the synthetic lethality of TOP2A inhibition and BET chemical degradation in BET inhibitor-resistant cells. The result indicates that mitoSplitter can accelerate the application of scRNA-seq assays in biomedical research.

Deconvolution algorithms for inference of the cell-type composition of the spatial transcriptome.

The spatial transcriptome has enabled researchers to resolve transcriptome expression profiles while preserving information about cell location to better understand the complex biological processes that occur in organisms. Due to technical limitations, the current high-throughput spatial transcriptome sequencing methods (known as next-generation sequencing with spatial barcoding methods or spot-based methods) cannot achieve single-cell resolution. A single measurement site, called a spot, in these technologies frequently contains multiple cells of various types. Computational tools for determining the cellular composition of a spot have emerged as a way to break through these limitations. These tools are known as deconvolution tools. Recently, a couple of deconvolution tools based on different strategies have been developed and have shown promise in different aspects. The resulting single-cell resolution expression profiles and/or single-cell composition of spots will significantly affect downstream data mining; thus, it is crucial to choose a suitable deconvolution tool. In this review, we present a list of currently available tools for spatial transcriptome deconvolution, categorize them based on the strategies they employ, and explain their advantages and limitations in detail in order to guide the selection of these tools in future studies.

The controversy about the effects of artemisinins on pancreatic α cell reprogramming and diabetes.

It has been reported that artemisinin treatment induces ß cell regeneration and alleviates hyperglycemia, although the therapeutic potential and mechanism have been questioned by various groups. We discuss the existing evidence and future plans for studies on artemisinins in the context of diabetes research.

Effects of agricultural activities on hydrochemistry in the Shiyang River Basin, China.

Agricultural water accounts for more than 80% of the available water in arid areas. Agricultural activities have a great impact on surface water and groundwater. If the impact of agricultural activities on hydrochemistry is not prevented, the risk of water quality change in arid areas may be greatly intensified. Based on the hydrochemical data of the whole Shiyang River Basin from April 2014 to October 2019, this paper analyzes the impact of agricultural activities on hydrochemistry in the basin. The results show that (i) in the middle and lower reaches of farmland with high intensity of agricultural activities, the ion concentration of groundwater in summer and autumn is significantly higher than that in winter and spring due to the influence of irrigation; (ii) the runoff ion concentration in the backflow of the river reaches recharged by irrigation water is significantly higher than that of other reaches; (iii) due to strong evaporation, different types of reservoirs will lead to an overall increase in ion concentration, which is more obvious in plain reservoirs and river tail lakes. In addition, the reservoirs have a certain removal effect on nitrates.

Population-specific, recent positive selection signatures in cultivated Cucumis sativus L. (cucumber).

Population-specific, positive selection promotes the diversity of populations and drives local adaptations in the population. However, little is known about population-specific, recent positive selection in the populations of cultivated cucumber (Cucumis sativus L.). Based on a genomic variation map of individuals worldwide, we implemented a Fisher's combination method by combining 4 haplotype-based approaches: integrated haplotype score (iHS), number of segregating sites by length (nSL), cross-population extended haplotype homozygosity (XP-EHH), and Rsb. Overall, we detected 331, 2,147, and 3,772 population-specific, recent positive selective sites in the East Asian, Eurasian, and Xishuangbanna populations, respectively. Moreover, we found that these sites were related to processes for reproduction, response to abiotic and biotic stress, and regulation of developmental processes, indicating adaptations to their microenvironments. Meanwhile, the selective genes associated with traits of fruits were also observed, such as the gene related to the shorter fruit length in the Eurasian population and the gene controlling flesh thickness in the Xishuangbanna population. In addition, we noticed that soft sweeps were common in the East Asian and Xishuangbanna populations. Genes involved in hard or soft sweeps were related to developmental regulation and abiotic and biotic stress resistance. Our study offers a comprehensive candidate dataset of population-specific, selective signatures in cultivated cucumber populations. Our methods provide guidance for the analysis of population-specific, positive selection. These findings will help explore the biological mechanisms of adaptation and domestication of cucumber.

Phosphorus-Doped Activated Coconut Shell Carbon-Anchored Highly Dispersed Pt for the Chemoselective Hydrogenation of Nitrobenzene to p-Aminophenol.

Highly dispersed Pt nanoparticles (∼2.5 nm) on phosphorus-doped activated coconut shell carbon (Pt/P-ACC) were synthesized by a two-step impregnation route. Pt/P-ACC showed a high activity, chemoselectivity, and reusability toward the hydrogenation of nitrobenzene to p-aminophenol, with hydrogen as the reducing agent in sulfuric acid. The effects of P species on the catalyst structure, surface properties, and catalytic performance were investigated. It was found that the Pt/P-ACC catalyst had an excellent catalytic activity due to its smaller Pt nanoparticles and higher content of surface-active metal compared with Pt/ACC. Besides, the experimental results and in situ infrared studies demonstrated that the interaction effect between the Pt and P species imbued the surface of Pt with an electron-rich feature, which decreased the adsorption of electron-rich substrates (that is, phenylhydroxylamine) and prevented their full hydrogenation, leading to enhanced selectivity during the hydrogenation of nitrobenzene to p-aminophenol.

Dead-End Hybridization in Walnut Trees Revealed by Large-Scale Genomic Sequence Data.

Although hybridization plays a large role in speciation, some unknown fraction of hybrid individuals never reproduces, instead remaining as genetic dead-ends. We investigated a morphologically distinct and culturally important Chinese walnut, Juglans hopeiensis, suspected to have arisen from hybridization of Persian walnut (J. regia) with Asian butternuts (J. cathayensis, J. mandshurica, and hybrids between J. cathayensis and J. mandshurica). Based on 151 whole-genome sequences of the relevant taxa, we discovered that all J. hopeiensis individuals are first-generation hybrids, with the time for the onset of gene flow estimated as 370,000 years, implying both strong postzygotic barriers and the presence of J. regia in China by that time. Six inversion regions enriched for genes associated with pollen germination and pollen tube growth may be involved in the postzygotic barriers that prevent sexual reproduction in the hybrids. Despite its long-recurrent origination and distinct traits, J. hopeiensis does not appear on the way to speciation.

Inhibition of human lung cancer cells by anti-p21Ras scFv mediated by the activatable cell-penetrating peptide.

Activatable cell-penetrating peptide (ACPP) is a tumour-targeting cell-penetrating peptide. Here, we used ACPP to carry anti-p21Ras scFv for Ras-driven cancer therapy. The ACPP-p21Ras scFv fusion protein was prepared by a prokaryotic expression system and Ni-NTA column purification. The human tumour cell lines A549, SW480, U251 and Huh7 and the normal cell line BEAS 2B were used to study the tumor-targeting and membrane-penetrating ability of ACPP-p21Ras scFv. The antitumour activity of ACPP-p21Ras scFv on A549 cells and H1299 cells in vitro was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, scratch wound healing, plate cloning and apoptosis assays. The penetration pathway of ACPP was determined by enhanced green fluorescent protein. The ACPP-p21Ras scFv fusion protein was successfully obtained at a concentration of 1.8 mg/ml. We found that ACPP-p21Ras scFv could penetrate tumour cell membranes with high expression of matrix metalloproteinase-2 (MMP-2), effectively inhibit the migration and proliferation of A549 cells and H1299 cells, and promote the apoptosis of A549 cells and H1299 cells. The membrane penetration experiment demonstrated that ACPP could enter A549 cells by direct penetration. The ability of ACPP to penetrate the membrane was affected by the addition of a membrane affinity inhibitor and a change in the potential difference across the cell membrane but not by the addition of endocytosis inhibitors and a change in temperature. The ACPP-p21Ras scFv fusion protein can penetrate tumour cells with MMP-2 expression and has antitumour activity against A549 cells and H1299 cells in vitro. This molecule is expected to become a potential antitumour drug for Ras gene-driven lung cancer.

Different rates of pollen and seed gene flow cause branch-length and geographic cytonuclear discordance within Asian butternuts.

Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance. We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance. Our findings indicate that the chloroplast genome had substantially deeper divergence (branch-length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation-by-distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome. Altogether, this study highlights a critical role of sex-biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance.

Genome sequencing and functional annotation of Bacillus sp. strain BS-Z15 isolated from cotton rhizosphere soil having antagonistic activity against Verticillium dahliae.

In the present study, antagonistic activity of bacterial strain BS-Z15, was evaluated against Verticillium dahlia. The fermented broth of BS-Z15 inhibited the growth of Verticillium dahliae. The genome of strain BS-Z15 had a total size of 4,068,702 base pairs and contained 4318 genes, of which 4196 are coding sequences and 122 are non-coding RNA. Among these genes, nine genomic islands, 86 tRNAs, 13 sRNAs, and one prophage was determined. With the help of annotation databases, most unigene functions were identified. At the same time, genomic comparison between BS-Z15 and 12 Bacillus members showed that the genes of BS-Z15 were closely related to the Bacillus group, and were conserved between the two groups, including most of the genes associated with fungal antagonism. BS-Z15 contains genes involved in a variety of antagonistic mechanisms, including genes encoding or synthesizing mycosubtilin, chitinases (but not CHIA and CHIB), glycoside hydrolases, iron nutrients, and antibiosis. However, it only contained the complete mycosubtilin- and bacilibactin-related operators in the reported main antifungal gene cluster of B. subtilis. Mycosubtilin and bacilibactin may be the main active antifungal substance. Besides, some genes could encode products related to biofilm production, which may be related to the colonization ability of the strain in plant rhizospheres. The complete genome of B. subtilis BS-Z15 provided new insights into the potential metabolites it produces related to its biocontrol activity.

CIK cell-based delivery of recombinant adenovirus KGHV500 carrying the anti-p21Ras scFv gene enhances the anti-tumor effect and safety in lung cancer.

PURPOSE: Adenovirus (Ads) is one of the most popular vectors used in gene therapy for the treatment of cancer. However, systemic therapy is limited by circulating antiviral antibodies and poor viral delivery in vivo. In this study, we used cytokine-induced killer (CIK) cells as delivery vehicles of Ads KGHV500 carrying the anti-p21Ras scFv gene to treat Ras gene-related lung cancer and investigate the anti-tumor effect in vitro and in vivo. METHODS: The human lung cancer cell line A549 was employed to investigate the anti-tumor activity of recombinant Ads KGHV500 harboring the anti-p21Ras scFv gene using MTT, wound healing, transwell invasion, and apoptosis assays in vitro. Next, CIK cells were used as delivery vehicles to deliver KGHV500 carrying the anti-p21Ras scFv gene to treat A549-transplanted tumors in nude mice, and viral replication, p21Ras scFv expression, and the therapeutic efficacy were assessed. RESULTS: In vitro studies showed that KGHV500 had potent anti-tumor activity. In addition, in vivo, this combination therapy significantly inhibited the growth of lung cancer xenografts compared with mice treated with KGHV500 alone. KGHV500 and anti-p21Ras scFv were observed in tumor tissue, but were nearly undetectable in normal tissues. CONCLUSIONS: The co-delivery of anti-p21Ras scFv by CIK cells and KGHV500 could increase the anti-tumor effect and safety, and possess considerable advantages for the treatment of Ras-related cancer.