Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera

Cocos nucifera (coconut) is an economically important tropical crop, but opportunities for molecular breeding are limited by lack of DNA sequence information for this species. Previous assessments of coconut germplasm have been conducted based solely on phenotypic data for agronomic and quality traits, due to lack of available molecular markers. In this study, we developed 30 novel microsatellite markers from Illumina transcriptome sequence data, and used these markers to evaluate coconut genetic diversity in 30 individuals representing accessions from China (12 samples) and Southeast Asia (18 samples). The microsatellite markers displayed low to high genetic polymorphism across the population: observed heterozygosity varied from 0.06 to 0.79, with an average of 0.39 ± 0.15. Our results indicated that the Southeast Asian population had a significantly higher number of alleles (p = 0.02), but not significantly different (

Efficient isolation of high quality RNA from tropical palms for RNA-seq analysis

Currently, RNA-seq as a high throughput technology is being widely applied to various species to elucidate the complexity of the transcriptome and to discover large number of novel genes. However, the technology has had poor success in elucidating the transcriptome of tropical palms, as it is difficult to isolate high quality RNA from tropical palm tissues due to their high polysaccharide and polyphenol content. Here, we developed an RNA-isolation protocol for tropical palms, the MRIP method (Methods for RNA Isolation from Palms). The integrity of the RNA molecules extracted using this protocol was determined to be of high quality by means of gel electrophoresis and Agilent 2100 Bioanalyzer microfluidic electrophoresis chip examination with a RIN (RNA Integrity Number) value of more than 9, indicating that the mRNAs were of good integrity. Subsequently the isolated RNA was used for transcription analysis without further purification. With Illumina sequencing, we obtained 54.9 million short reads and then conducted de novo assembly to gain 57,304 unigenes with an average length of 752 base pairs. Moreover, the RNA isolated with this protocol was also successfully used for real-time RT-PCR. These results suggested that the RNA isolated was suitable for Illumina RNA sequencing and quantitative real-time RT-PCR. Furthermore, this method was also successful in isolating total RNA from the leaves of various Palmaceae species

Cellular Origins of EGFR-Driven Lung Cancer Cells Determine Sensitivity to Therapy

Targeting the epidermal growth factor receptor (EGFR) with tyrosine kinase inhibitors (TKIs) is one of the major precision medicine treatment options for lung adenocarcinoma. Due to common development of drug resistance to first- and second-generation TKIs, third-generation inhibitors, including osimertinib and rociletinib, have been developed. A model of EGFR-driven lung cancer and a method to develop tumors of distinct epigenetic states through 3D organotypic cultures are described here. It is discovered that activation of the EGFR T790M/L858R mutation in lung epithelial cells can drive lung cancers with alveolar or bronchiolar features, which can originate from alveolar type 2 (AT2) cells or bronchioalveolar stem cells, but not basal cells or club cells of the trachea. It is also demonstrated that these clones are able to retain their epigenetic differences through passaging orthotopically in mice and crucially that they have distinct drug vulnerabilities. This work serves as a blueprint for exploring how epigenetics can be used to stratify patients for precision medicine decisions

Multi-Agent Distributed Deep Deterministic Policy Gradient for Partially Observable Tracking

In many existing multi-agent reinforcement learning tasks, each agent observes all the other agents from its own perspective. In addition, the training process is centralized, namely the critic of each agent can access the policies of all the agents. This scheme has certain limitations since every single agent can only obtain the information of its neighbor agents due to the communication range in practical applications. Therefore, in this paper, a multi-agent distributed deep deterministic policy gradient (MAD3PG) approach is presented with decentralized actors and distributed critics to realize multi-agent distributed tracking. The distinguishing feature of the proposed framework is that we adopted the multi-agent distributed training with decentralized execution, where each critic only takes the agent’s and the neighbor agents’ policies into account. Experiments were conducted in the distributed tracking tasks based on multi-agent particle environments where N(N=3,N=5) agents track a target agent with partial observation. The results showed that the proposed method achieves a higher reward with a shorter training time compared to other methods, including MADDPG, DDPG, PPO, and DQN. The proposed novel method leads to a more efficient and effective multi-agent tracking

Genome-wide discovery and characterization of long noncoding RNAs in African oil palm (Elaeis guineensis Jacq.)

Long noncoding RNAs (lncRNAs) are an important class of genes and play important roles in a range of biological processes. However, few reports have described the identification of lncRNAs in oil palm. In this study, we applied strand specific RNA-seq with rRNA removal to identify 1,363 lncRNAs from the equally mixed tissues of oil palm spear leaf and six different developmental stages of mesocarp (8–24 weeks). Based on strand specific RNA-seq data and 18 released oil palm transcriptomes, we systematically characterized the expression patterns of lncRNA loci and their target genes. A total of 875 uniq target genes for natural antisense lncRNAs (NAT-lncRNA, 712), long intergenic noncoding RNAs (lincRNAs, 92), intronic-lncRNAs (33), and sense-lncRNAs (52) were predicted. A majority of lncRNA loci (77.8%–89.6%) had low expression in 18 transcriptomes, while only 89 lncRNA loci had medium to high expression in at least one transcriptome. Coexpression analysis between lncRNAs and their target genes indicated that 6% of lncRNAs had expression patterns positively correlated with those of target genes. Based on single nucleotide polymorphism (SNP) markers derived from our previous research, 6,882 SNPs were detected for lncRNAs and 28 SNPs belonging to 21 lncRNAs were associated with the variation of fatty acid contents. Moreover, seven lncRNAs showed expression patterns positively correlated expression pattern with those of genes in de novo fatty acid synthesis pathways. Our study identified a collection of lncRNAs for oil palm and provided clues for further research into lncRNAs that may regulate mesocarp development and lipid metabolism

Genome-wide identification and transferability of microsatellite markers between Palmae species

The Palmae family contains 202 genera and approximately 2800 species. Except for Elaeis guineensis and Phoenix dactylifera, almost no genetic and genomic information is available for Palmae species. Therefore, this is an obstacle to the conservation and genetic assessment of Palmae species, especially those that are currently endangered. The study was performed to develop a large number of microsatellite markers which can be used for genetic analysis in different Palmae species. Based on the assembled genome of Elaeis guineensis and Phoenix dactylifera, a total of 814 383 and 371 629 microsatellites were identified. Among these microsatellites identified in Elaeis guineensis, 734 509 primer pairs could be designed from the flanking sequences of these microsatellites. The majority (618 762) of these designed primer pairs had in silico products in the genome of Elaeis guineensis. These 618 762 primer pairs were subsequently used to in silico amplify the genome of Phoenix dactylifera. A total of 7 265 conserved microsatellites were identified between Elaeis guineensis and Phoenix dactylifera. One hundred and thirty-five primer pairs flanking the conserved SSRs were stochastically selected and validated to have high cross-genera transferability, varying from 16.7% to 93.3% with an average of 73.7%. These genome-wide conserved microsatellite markers will provide a useful tool for genetic assessment and conservation of different Palmae species in the future

A low-concentration sulfone electrolyte enables high-voltage chemistry of lithium-ion batteries

Commercial carbonate electrolytes with poor oxidation stability and high flammability limit the operating voltage of Li-ion batteries (LIBs) to ~4.3 V. As one of the most promising candidates for electrolyte solvents, sulfolane (SL) has received significant interest because of its wide electrochemical window, low flammability and high dielectric permittivity. Unfortunately, SL-based electrolytes with normal concentrations cannot achieve highly reversible Li+ intercalation/deintercalation in graphite anodes due to an ineffective solid electrolyte interface, thus undermining their potential application in LIBs. Here, a low-concentration SL-based electrolyte (LSLE) is developed for high-voltage graphite||LiNi0.8Co0.1Mn0.1O2 (NCM811) full cells. A highly reversible graphite anode can be achieved through the preferential decomposition of the dual-salt LiDFOB-LiBF4 in the LSLE. The addition of fluorobenzene further restrains the decomposition of SL, endowing uniform, robust and inorganic-rich interphases on the electrode surfaces. As a result, the LSLE with improved thermal stability can support the MCMB||NCM811 full cells at 4.4 V, evidenced by an excellent cycling performance with capacity retentions of 83% after 500 cycles at 25 ℃ and 82% after 400 cycles at 60 ℃. We believe that the design of this fluorobenzene-containing LSLE offers an effective routine for next-generation low-cost and safe electrolytes for high-voltage LIBs

SIZE AND SURFACE EFFECT OF GOLD NANOPARTICLES (AuNPs) IN NANOGOLD-ASSISTED PCR

Recently, gold nanoparticles (AuNPs) were reported to increase the specificity and efficiency of the polymerase chain reaction (PCR). In this paper, we tested the enhancement of AuNPs with five different sizes on the specificity of two-round PCR. The results showed that, except 5.02 nm AuNPs, the AuNPs that could achieve the similar enhancement happened to have nearly the same total surface area. The surface effect seems to be the key factor of nanogold-assisted PCR.PCR, gold nanoparticles, size effect