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The trajectory generated by GMR-GP cannot go through the first via-point precisely. Therefore, this paper designs an optimization method of Learning from Demonstration based on incremental GMR-GP. First, an incremental GMR-GP algorithm is designed. The advantage of the incremental GMR-GP is that the starting point of the mean trajectory can gradually approach to the real observation point while maintaining the true intention of the teaching action as much as possible. Then, an incremental GMR-GP based on importance weighting is proposed, which makes an important distinction among the new trajectories generated by the incremental GMR-GP. The generated trajectory further improves the reservation of the prior trajectory on the true teaching intention, and the uncertainty is reduced. Moreover, the availability of the proposed method is validated and analyzed by performing a series of numerical simulations and Baxter robot experiments. The results indicate that the proposed method can provide reliable solutions, which can go through the first via-point more precisely while retaining the true demonstrating intent as much as possible.

Cap-dependent initiation of translation is a canonical mechanism adopted by eukaryotic cells. Internal ribosome entry site (IRES)-dependent translation is a mechanism distinct from 5′ cap-dependent translation. IRES elements are located mainly in the 5′-untranslated regions (UTRs) of viral and eukaryotic mRNAs. In addition, IRESs are found in the coding regions of some viral and eukaryotic genomes and initiate the translation of some functional truncated isoforms. Here, via IRES-initiated expression of proteins, bicistronic vectors and ribosome profiling of the human rhinovirus 16 (HRV16), we found that the coding region of the nonstructural proteins P2 and P3 contained 5 putative IRES elements. These 5 putative IRESs were located within nucleotides 4286-4585, 5002-5126, 6245-6394, 6619-6718 and 6629-6778 and initiated green fluorescent protein (GFP) expression in vitro. This alternative mechanism might be effective and economical for eliminating the time and raw material required to synthesize the full-length polyprotein.

The characteristic secondary metabolites in tea (theanine, caffeine, and catechins) are important factors contributing to unique tea flavors. However, there has been relatively little research on molecular markers related to these metabolites. Thus, we conducted a genome-wide association analysis of the levels of these tea flavor-related metabolites in three seasons. The theanine, caffeine, and catechin levels in Population 1 comprising 191 tea plant germplasms were examined, which revealed that their heritability exceeded 0.5 in the analyzed seasons, with the following rank order (highest to lowest heritabilities): (+)-catechin > (−)-gallocatechin gallate > caffeine = (−)-epicatechin > (−)-epigallocatechin-3-gallate > theanine > (−)-epigallocatechin > (−)-epicatechin-3-gallate > catechin gallate > (+)-gallocatechin. The SNPs detected by amplified-fragment SNP and methylation sequencing divided Population 1 into three groups and seven subgroups. An association analysis yielded 307 SNP markers related to theanine, caffeine, and catechins that were common to all three seasons. Some of the markers were pleiotropic. The functional annotation of 180 key genes at the SNP loci revealed that FLS, UGT, MYB, and WD40 domain-containing proteins, as well as ATP-binding cassette transporters, may be important for catechin synthesis. KEGG and GO analyses indicated that these genes are associated with metabolic pathways and secondary metabolite biosynthesis. Moreover, in Population 2 (98 tea plant germplasm resources), 30 candidate SNPs were verified, including 17 SNPs that were significantly or extremely significantly associated with specific metabolite levels. These results will provide a foundation for future research on important flavor-related metabolites and may help accelerate the breeding of new tea varieties.

The appearance of next generation sequencing technology that features short read length with high measurement throughput and low cost has revolutionized the field of life science, medicine, and even computer science. The subsequent development of the third-generation sequencing technologies represented by nanopore and zero-mode waveguide techniques offers even higher speed and long read length with promising applications in portable and rapid genomic tests in field. Especially under the current circumstances, issues such as public health emergencies and global pandemics impose soaring demand on quick identification of origins and species of analytes through DNA sequences. In addition, future development of disease diagnosis, treatment, and tracking techniques may also require frequent DNA testing. As a result, DNA sequencers with miniaturized size and highly integrated components for personal and portable use to tackle increasing needs for disease prevention, personal medicine, and biohazard protection may become future trends. Just like many other biological and medical analytical systems that were originally bulky in sizes, collaborative work from various subjects in engineering and science eventually leads to the miniaturization of these systems. DNA sequencers that involve nanoprobes, detectors, microfluidics, microelectronics, and circuits as well as complex functional materials and structures are extremely complicated but may be miniaturized with technical advancement. This paper reviews the state-of-the-art technology in developing essential components in DNA sequencers and analyzes the feasibility to achieve miniaturized DNA sequencers for personal use. Future perspectives on the opportunities and associated challenges for compact DNA sequencers are also identified.

Objectives This study aimed to assess incidence and resistance of Mycoplasma pneumoniae MP in Qingdao children, China, in 2019. Methods 78 pharyngeal swabs of pneumonia children that were collected in 2019 in Qingdao, China. The pathogenic nucleic acid were extracted from pharyngeal swabs. MP infection were identified by qPCR. RepMP4 of P1 adhesin protein gene in MP genome, domains-V of the 23S rRNA gene and the L4, L22 ribosomal protein fragments were amplified by PCR, respectively evolutionary analyses were conducted by MEGA7 based on sequence of P1 gene. Mutations of drug-resistant gene were analyzed based on sequence of domains-V of the 23S rRNA gene and the L4, L22 ribosomal protein fragments. Results 58.97% (46/78) Mycoplasma pneumoniae (MP) infection were detected for children pneumonia in Qingdao in 2019. The average course of MP infection (8.80±2.13 days) were longer that of non MP infection (8.38±2.10 days). P1 adhesin gene and domains-V of the 23S rRNA gene and the L4, L22 ribosomal protein fragments from 21 samples were used to analysis genotype and drug resistance. According to the sequence alignment of P1 adhesin gene, total of 12 (12/21, 57.14%) were classified as type 1, and the other 9 (9/21, 42.86%) samples belonged to type 2. Drug-resistant gene A2063G mutations in domain V of the 23S rRNA gene and T508C mutation (amino acid S-P) of L22 were identified from all type 1 and type 2 MP. However, both 2064 and 2617 sites mutation of drug resistance gene were not found in this study. C162A mutation appeared in the type 2 positive samples. A430G mutation appeared in the one type 1 positive and type 2 positive samples. A new T279C mutation of L22 were found in 8 type 2 samples, not in the type 1. Simultaneous mutation of C162A, A430G and T279C were only found in type 2 MP. Conclusions The incidence of MP infection were 58.97% (46/78) in children pneumonia in Qingdao in 2019. Type 1 MP infection was slightly more than type II. Macrolide-resistant A2063G mutation and T508C mutation of L22 could be detected in all type 1 and type 2 MP. Our results indicated that the genotype of MP is gradually shifting from type I to type II in Qingdao, China

Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7 Mb chromosome-scale genome assembly of passion fruit, with 98.91% (~1327.18 Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that ‘alpha-linolenic acid metabolism’, ‘metabolic pathways’, and ‘secondary metabolic pathways’ were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.

Internal ribosome entry site (IRES)-dependent translation is a mechanism distinct from 5' cap-dependent translation. IRES elements are located mainly in the 5' untranslated regions (UTRs) of viral and eukaryotic mRNAs. However, IRESs are also found in the coding regions of some viral and eukaryotic genomes to initiate the translation of some functional truncated isoforms. Here, five putative IRES elements of human rhinovirus 16 (HRV16) were identified in the coding region of the nonstructural proteins P2 and P3 through fusion with green fluorescent protein (GFP) expression vectors and bicistronic vectors with a hairpin structure. These five putative IRESs were located at nucleotide positions 4286-4585, 5002-5126, 6245-6394, 6619-6718, and 6629-6778 in the HRV16 genome. The functionality of the five IRESs was confirmed by their ability to initiate GFP expression in vitro. This suggests that an alternative mechanism might be used to increase the efficiency of replication of HRV16.

Background: Potatoes are dicotyledonous plants of the genus Solanum, family Solanaceae, and contain large amounts of starch, proteins, and trace elements required by the human. Potato late blight is the main disease hindering potato production. In this study, Phytophthora infestans were used to quantify late blight resistance in 284 germplasm resources, and resistance genes were mined through genome-wide association analysis.Results: The results showed that among the 284 potato germplasm resources, 37 showed immunity, 15 were highly resistant to late blight, 30 were moderately resistant to late blight, 107 were moderately susceptible to late blight, and 95 were highly susceptible to late blight. Through screening and filtering, 22,489 high-quality single-nucleotide polymorphisms (SNPs) and indels were obtained. Through population structure analysis and principal-component analysis, 284 germplasm resources were divided into eight subgroups, which was consistent with the results of the phylogenetic tree analysis. The genetic diversity index of the 284 potato germplasm resources was 0.2161, and the differentiation index of each subgroup was 0.0251-0.1489. A mixed linear model was built to perform an association analysis on the diameter of the lesions identified from isolated leaves of potato affected by late blight. The genes within 100 kb of both sides of the obtained significant SNP loci were searched and functionally annotated, and 18 candidate genes were obtained. Twenty-two candidate genes were obtained from the association analysis of disease resistance grade.Conclusions: 284 potato germplasm resources were used to identify for Phytophthora infestans resistance. The potato germplasm resources were divided into 8 subgroups by population structure analysis, and the main differentiation among subgroups was moderate. Candidate genes were mined by genome-wide association analysis.The results of this study provides the foundation for the genetic improvement of potato varieties resistant to late blight.

Background: Glycolytic pathway is common in all plant organs, especially in oxygen-deficient tissues. Phosphofructokinase (PFK) is a rate-limiting enzyme in the glycolytic pathway and catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate. Cassava (Manihot esculenta) root is a huge storage organ with low amount of oxygen. However, less is known about the functions of PFK from M. esculenta (MePFK). We conducted a systematic analysis of MePFK genes to explore the function of the MePFK gene family under hypoxic stress.Results: We identified 13 MePFK genes and characterised their sequence structure. The phylogenetic tree divided the 13 genes into two groups: nine were MePFKs and four were pyrophosphate-fructose-6-phosphate phosphotransferase (MePFPs). We confirmed by green fluorescent protein fusion protein expression that MePFK03 and MePFPA1 were localised in the chloroplast and cytoplasm, respectively. The expression profiles of the 13 MePFKs detected by quantitative reverse transcription polymerase chain reaction revealed that MePFK02, MePFK03, MePFPA1, MePFPB1 and MePFPA2 displayed higher expression in leaves, root and flower. The expression of MePFK03, MePFPA1 and MePFPB1 in tuber root increased gradually with plant growth. We confirmed that hypoxia occurred in the cassava root, and the concentration of oxygen was sharply decreasing from the outside to the inside root. The expression of MePFK03, MePFPA1 and MePFPB1 decreased with the decrease in the oxygen concentration in cassava root. Waterlogging stress treatment showed that the transcript level of PPi-dependent MePFP and MeSuSy were up-regulated remarkably and PPi-dependent glycolysis bypass was promoted. Conclusion: A systematic survey of phylogenetic relation, molecular characterisation, chromosomal and subcellular localisation and cis-element prediction of MePFKs were performed in cassava. The expression profiles of MePFKs in different development stages, organs and under waterlogging stress showed that MePFPA1 plays an important role during the growth and development of cassava. Combined with the transcriptional level of MeSuSy, we found that pyrophosphate (PPi)-dependent glycolysis bypass was promoted when cassava was under waterlogging stress. The results would provide insights for further studying the function of MePFKs under hypoxic stress.

Recent studies of obstacle avoidance under the Dynamic Movement Primitives (DMPs) framework are limited on the dotted obstacles. A novel obstacle avoidance algorithm based on DMPs is proposed for shaped obstacle avoidance. By combining the steering behavior method and the potential field method with the evaluation of Euclidean distance, while absorbing the switching strategy, this new algorithm performs well in mimicking the learned DMPs trajectory and handles the fluctuations occur in the initial stage of motion. The simulations of 2D DMPs trajectory learning of one-obstacle avoidance and multi-obstacle avoidance show that the algorithm is feasible with figurate obstacles, and acquires great conformability with the learned trajectory and smoothness.

Virus entry into cells is the initial stage of infection and involves multiple steps, and interfering viral entry represents potential antiviral approaches. Ion channels are pore-forming membrane proteins controlling cellular ion homeostasis and regulating many physiological processes, but their roles during viral infection have rarely been explored. Here, the functional Kv1.3 ion channel was found to be expressed in human hepatic cells and tissues. The Kv1.3 was then revealed to restrict HCV entry via inhibiting endosome acidification-mediated viral membrane fusion. The Kv1.3 was also demonstrated to inhibit DENV and ZIKV with an endosome acidification-dependent entry, but have no effect on SeV with a neutral pH penetration. A Kv1.3 antagonist PAP-1 treatment accelerated animal death in ZIKV-infected Ifnar1-/- mice. Moreover, Kv1.3-deletion was found to promote weight loss and reduce survival rate in ZIKV-infected Kv1.3-/- mice. Altogether, the Kv1.3 ion channel behaves as a host factor restricting viral entry. These findings broaden understanding about ion channel biology.

Dengue virus (DENV) and Zika virus (ZIKV) have spread throughout many countries in the developing world and infect millions of people every year, causing severe harm to human health and the economy. Unfortunately, there are few effective vaccines and therapies available against these viruses. Therefore, the discovery of new antiviral agents is critical. Herein, a scorpion venom peptide (Smp76) characterized from Scorpio maurus palmatus was successfully expressed and purified in Escherichia coli BL21(DE3). The recombinant Smp76 (rSmp76) was found to effectively inhibit DENV and ZIKV infections in a dose-dependent manner in both cultured cell lines and primary mouse macrophages. Interestingly, rSmp76 did not inactivate the viral particles directly but suppressed the established viral infection, similar to the effect of interferon (IFN)-β. Mechanistically, rSmp76 was revealed to upregulate the expression of IFN-β by activating interferon regulatory transcription factor 3 (IRF3) phosphorylation, enhancing the type-I IFN response and inhibiting viral infection. This mechanism is significantly different from traditional virucidal antimicrobial peptides (AMPs). Overall, the scorpion venom peptide Smp76 is a potential new antiviral agent with a unique mechanism involving type-I IFN responses, demonstrating that natural AMPs can enhance immunity by functioning as immunomodulators. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12250-018-0068-4) contains supplementary material, which is available to authorized users.

Detection of species in nature at very low abundance requires innovative methods. Conventional PCR (cPCR) and real‐time quantitative PCR (qPCR) are two widely used approaches employed in environmental DNA (eDNA) detection, though lack of a comprehensive comparison of them impedes method selection. Here we test detection capacity and false negative rate of both approaches using samples with different expected complexities. We compared cPCR and qPCR to detect invasive, biofouling golden mussels (Limnoperna fortunei), in samples from laboratory aquaria and irrigation channels where this mussel was known to occur in central China. Where applicable, the limit of detection (LoD), limit of quantification (LoQ), detection rate, and false negative rate of each PCR method were tested. Quantitative PCR achieved a lower LoD than cPCR (1 × 10−7 vs. 10−6 ng/μl) and had a higher detection rate for both laboratory (100% vs. 87.9%) and field (68.6% vs. 47.1%) samples. Field water samples could only be quantified at a higher concentration than laboratory aquaria and total genomic DNA, indicating inhibition with environmental samples. The false negative rate was inversely related to the number of sample replicates. Target eDNA concentration was negatively related to distance from sampling sites to the water (and animal) source. Detection capacity difference between cPCR and qPCR for genomic DNA and laboratory aquaria can be translated to field water samples, and the latter should be prioritized in rare species detection. Field environmental samples may involve more complexities—such as inhibitors—than laboratory aquaria samples, requiring more target DNA. Extensive sampling is critical in field applications using either approach to reduce false negatives.

Rubber tree (Hevea brasiliensis) is the most important commercial producer of high-quality natural rubber in the world. Here, we identified 571,267 SNPs and 134,184 indels, and constructed the first ultra-high density genetic linkage map in rubber tree population. This map consisted of 6940 markers, with average marker density and recombination rate 0.30 cM and 0.97 cM/Mb, respectively. Then the whole genome QTL scanning for dry latex yield (DLY) trait were performed and seventeen repQTLs were obtained, among which qDFY-10 and qDFY-18-4 could explain up to 38.3% and 33.3% phenotypic variability, respectively. Numerous highly-promising QTL candidate genes were identified and then verified significant associated with DLY trait, including some first found in rubber tree, such as thioredoxin h, plastin-like protein, calmodulin binding protein, cytochrome-c oxidase and methylglutaconyl-CoA hydratase. This ultra-high density linkage map supplies a base for important traits QTL mapping and will be useful in the improvement of the assembly of genome sequences in rubber tree. The verification of candidate QTL genes showed great importance for understanding the possible function of mapped QTLs and the comprehensive relations between phenotypes and genotypes. Accurate QTL mapping will be enhance genetic studies that can be applied in rubber tree breeding programs.

Anaerobic ammonium oxidization (anammox) has been widely recognized for its importance in global nitrogen cycle. While, their distributions in the Eastern Indian Ocean (EIO) still remain unknown. This study investigated the diversity and abundance of anammox bacteria from water column (0–2000 m with seven depths) down to the surface sediments in the EIO targeting 16S rRNA gene by using clone library and quantitative real-time PCR (qPCR) analysis. Results showed a wide distribution of anammox bacteria in both water column and sediments in the EIO, with the Candidatus Scalindua sp. assemblage as the predominant group among the anammox communities. The diversity of anammox bacteria was higher in water column, but abundances (based on copy numbers of 16S rRNA gene) were lower than the corresponding sediment samples. Non-metric multidimensional scaling analysis demonstrated distinct spatial patterns (both horizontal and vertical): samples from the Bay of Bengal and the Equator showed strong stratification in different layers and were distinct from other two regions. Canonical correspondence analysis indicated that dissolved oxygen, temperature, and nitrate were the major environmental factors shaping the distribution of anammox bacteria. This is the first investigation on detailed community structure and distribution of anammox bacteria in the EIO, and the results are consistent with (i) potential contribution of sedimentary anammox bacteria towards nitrogen removal, and (ii) dispersal of anammox bacteria diversity via the ocean.

The dynamic alterations of the physiological and molecular processes in reproductive stage soybean indicated the dramatic impact caused by drought. Drought is a major abiotic stress that limits soybean (Glycine max) production. Most prior studies were focused on either model species or crops that are at their vegetative stages. It is known that the reproductive stage of soybean is more susceptible to drought. Therefore, an understanding on the responsive mechanisms during this stage will not only be important for basic plant physiology, but the knowledge can also be used for crop improvement via either genetic engineering or molecular breeding. In this study, physiological measurements and RNA-Seq analysis were used to dissect the metabolic alterations and molecular responses in the leaves of soybean grown at drought condition. Photosynthesis rate, stomata conductance, transpiration, and water potential were reduced. The activities of SOD and CAT were increased, while the activity of POD stayed unchanged. A total of 2771 annotated genes with at least twofold changes were found to be differentially expressed in the drought-stressed plants in which 1798 genes were upregulated and 973 were downregulated. Via KEGG analysis, these genes were assigned to multiple molecular pathways, including ABA biogenesis, compatible compound accumulation, secondary metabolite synthesis, fatty acid desaturation, plant transcription factors, etc. The large number of differentially expressed genes and the diverse pathways indicated that soybean employs complicated mechanisms to cope with drought. Some of the identified genes and pathways can be used as targets for genetic engineering or molecular breeding to improve drought resistance in soybean.

A combination of advanced sequencing and mapping techniques is used to produce a reference genome of Aegilops tauschii, progenitor of the wheat D genome, providing a valuable resource for comparative genetic studies. Supplementary information The online version of this article (doi:10.1038/nature24486) contains supplementary material, which is available to authorized users., Genome of common wheat ancestor Sequencing the genomes of crops plants provides useful resources for crop improvement and breeding. Jan Dvořák, Katrien Devos, Steven Salzberg and colleagues report a reference genome for Aegilops tauschii, the diploid progenitor of the D genome of hexaploid wheat. They use a combination of ordered-clone genome sequencing, whole-genome shotgun sequencing and BioNano optical genome mapping to assemble this large and highly repetitive genome. This provides a useful resource for comparative genomics studies of wheat. Supplementary information The online version of this article (doi:10.1038/nature24486) contains supplementary material, which is available to authorized users., Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat1 (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat2,3,4. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence5. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution. Supplementary information The online version of this article (doi:10.1038/nature24486) contains supplementary material, which is available to authorized users.

Management of non-indigenous invasive species (NIS) is challenging owing in part to limitations of early detection and identification. The advent of environmental DNA (eDNA) techniques provides an efficient way to detect NIS when their abundance is extremely low. However, eDNA-based methods often suffer from uncertain detection sensitivity, which requires detailed testing before applying these methods in the field. Here we developed an eDNA tool for early detection of the highly invasive golden mussel, Limnoperna fortunei, based on the mitochondrial cytochrome c oxidase subunit I gene (COI). Further, we tested technical issues, including sampling strategy and detection sensitivity, based on a laboratory experiment. We then applied the method to field samples collected from water bodies in China where this mussel has or is expected to colonize. Results showed that the detection limit varied extensively among our newly developed primer pairs, ranging from 4 × 10−2 to 4 × 10−6 ng of total genomic DNA. Laboratory detection was affected by the availability of eDNA (i.e., both mussel abundance and incubation time). Detection capacity was higher in laboratory samples containing re-suspended matter from the bottom layer versus that collected from the surface. Among 25 field sites, detection was 100% at sites with high mussel abundance and as low as 40% at sites with low abundance when tested using our most sensitive primer pair. Early detection of NIS present at low abundance in nature requires not only sensitive primers, but also an optimized sampling strategy to reduce the occurrence of false negatives. Careful selection and detailed testing of primer pairs ensures effective eDNA-based species detection in surveillance and management programs.

The quagga mussel (Dreissena rostriformis bugensis) is a filter-feeding invasive species that has re-engineered many freshwater ecosystems worldwide. High clearance rates (CRs) and dense populations underpin their ecological impacts. CRs, however, are highly variable, as are environmental factors that regulate them. Despite their widespread distribution in Europe and North America, knowledge of how multiple environmental factors regulate CRs of quagga mussels remains limited. We investigated quagga mussel CRs under varying conditions including water temperature, food availability, habitat depth, flow velocity, and duration of incubation in chambers with both static and flowing water. We found that CR was positively related to water temperature and initial food concentration in static chambers. When coupled with limited food concentration, cold water (7.5 °C), due to a deep-water upwelling event, produced very low CR (~ 10× lower) compared to warmer water (12–24 °C) (0.47 vs. 3.12–5.84 L g−1 DW h−1). Mussels from deeper water (20 m) had CRs that were ~ 3.5× higher than from shallower depths (2–10 m) and CRs were inversely affected by total mussel dry weight. Flow rates from 1 to 22 cm s−1 generated a unimodal pattern of CR with an optimal flow velocity of 6–12 cm s−1 (~ 2× higher than suboptimal CRs). Enhanced flow velocity (22 cm s−1), reflective of storm conditions in shallow waters, significantly increased the closing/reopening activity of mussel valves relative to lower velocities (1–12 cm s−1). Incubation time had a strong negative effect (~ 2–4× reduction) on CRs likely reflecting refiltration in static chambers versus food saturation of mussels in flowing chambers, respectively. Our findings highlight how multiple factors can influence quagga mussel CRs by factors of 2–10. Given widespread habitat heterogeneity in large aquatic ecosystems, whole-lake estimates of mussel impacts should include multiple regulatory factors that affect mussel filtration.

Three kinds of decision models for closed-loop supply chain (CLSC) with trade-ins are developed in this paper, including the centralized collection (Model C), the retailer collection (Model R), and the manufacturer collection (Model M). By analyzing these models, we argue that there are three types of optimal collection strategies, namely, no collection, partial collection, and full collection. We provide conditions under which one of these three collection strategies is optimal for different supply chain models. By comparing the impact of trade-ins on these different supply chain models, we find that only when the direct net value of a used product derived from the trade-ins for the whole CLSC system including the consumers is high enough can trade-in strategy be adopted to stimulate consumer demand and improve the manufacturer׳s and retailer׳s profit. Based on the life-cycle assessment method, we find that when the marginal effect of the product on environment in the continue-to-use phase is more significant than in other phases, trade-ins can promote the environmental performance of the CLSC system. Further, by comparing the optimal solutions for the different models, we find that one collection model may dominate the others in terms of the economic performance of the involved parties. Specifically, Model M dominates Model R in terms of the profits of the manufacturer and the profits of the whole supply chain; Model R dominates Model M in terms of retailer׳s profit; and Model R dominates all other models in terms of environmental performance.

Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics. Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not. Here, we investigated the transcriptional differences of eight cDNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line, W14, using next generation sequencing system. A total of 41302 assembled transcripts were obtained and from these, 25961 transcripts with FPKM ≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and 3584 transcripts were found to be differentially expressed in leaf, stem and storage root (150 d after planting), respectively, between Arg7 and W14 and ascribed to 103, 93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I (PSA) and photosystem II (PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes (PFK, PGK and PK, GAPDH) coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation (INVs), amylose synthesis (GBSS) and hydrolysis (RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation (ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed the relationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.

A full-length cDNA library from leaf and root tissues of cassava (Manihot esculenta) Arg7 and one accession of its wild ancestor W14 (M. esculenta ssp. flabellifolia) has been constructed. The library is comprised of four sub-libraries, containing 32640 recombinant clones, 6028 cDNA clones from their 5′ ends, and 128 clones from the 3′ ends were sequenced. In total, 5013 high-quality expressed sequence tags (ESTs) and 1259 unigenes were obtained. Of these, 746 unigenes were identified by their sequence homologies to ESTs from model plants, and 323 unigenes were mapped onto 114 different KEGG pathways. From these, 24 differentially expressed genes involved in starch metabolism and photosynthesis were identified and five of them were selected to compare their expression level between Arg7 and W14. Notably, Arg7 has a higher net photosynthesis rate in leaves, higher ribulose-1,5-bisphosphate carboxy-lase oxygenase activities in leaves, and higher AGPase activity in roots. This resource is the first EST collection from wild cassava and should be of value for gene discovery, genome annotation and studies of Manihot evolution.

Inactivation of the p53 tumor suppressor by mutation or overexpression of negative regulators occurs frequently in cancer. As p53 plays a key role in regulating proliferation or apoptosis in response to DNA-damaging chemotherapies, strategies aimed at reactivating p53 are increasingly being sought. Strategies to reactivate wild-type p53 include the use of small molecules capable of releasing wild-type p53 from key, cellular negative regulators, such as Hdm2 and HdmX. Derivatives of the Hdm2 antagonist Nutlin-3 are in clinical trials. However, Nutlin-3 specifically disrupts Hdm2-p53, leaving tumors harboring high levels of HdmX resistant to Nutlin-3 treatment. Here, we identify CTX1, a novel small molecule that overcomes HdmX-mediated p53 repression. CTX1 binds directly to HdmX to prevent p53–HdmX complex formation, resulting in the rapid induction of p53 in a DNA damage–independent manner. Treatment of a panel of cancer cells with CTX1 induced apoptosis or suppressed proliferation and, importantly, CTX1 demonstrates promising activity as a single agent in a mouse model of circulating primary human leukemia. CTX1 is a small molecule HdmX inhibitor that demonstrates promise as a cancer therapeutic candidate. Mol Cancer Ther; 15(4); 574–82. ©2016 AACR.

Arboviruses, especially Dengue virus (DENV) and Zika virus (ZIKV), have been a severe threat to human health in the last few years due to uncontrollable transmission. There are no approved vaccines or clinical drugs available for use to prevent and treat their infections. Transient receptor potential mucolipin 2 and 3 (TRPML2 and TRPML3) were reported to modulate viral entry, but the antiviral function of these modulators was unknown. Here, we reported that ML-SA1, a TRPML agonist, inhibited DENV2 and ZIKV in vitro in a dose-dependent manner. Time-of-drug-addition experiments showed that ML-SA1 mainly restricted viral entry. Moreover, the selective TRPML3 activator SN-2 was found to share a similar antiviral effect against DENV2 and ZIKV, but the specific TRPML1 agonist MK6-83 was not effective. Although ML-SA1 was further revealed to induce autophagy, its antiviral role was independent of autophagy induction. Finally, ML-SA1 was found to inhibit DENV2 and ZIKV by promoting lysosome acidification and protease activity to cause viral degradation. Together, our study identifies two TRPML agonists, ML-SA1 and SN-2, as potent inhibitors of DENV2 and ZIKV, which may lead to the discovery of new candidates against viruses.

Understanding the physiological and molecular processes in response to heat in soybean is important to implement strategies to breed more heat tolerant soybean. In this study, physiological and RNA-Seq analysis were used to dissect the physiological alterations and molecular responses in the leaves of reproductive stage soybean grown at heat condition. Stomata conductance and transpiration rate were increased but photosynthesis and relative water content were reduced in response to heat. Among the three measured antioxidant enzymes, the activity of peroxidase was increased but no changes were detected for catalase and superoxide dismutase. A total of 633 annotated genes were found to be differentially expressed in heat stressed plants in which the expression levels of 417 genes were up-regulated and 216 were down-regulated. Most dramatic responses are related to flowering, oxidative stress, protein and mRNA folding and degradation, protective compounds synthesis, and ethylene biosynthesis and signaling. The diverse pathways identified in this study indicated that soybean employs complicated mechanisms to cope with heat. A few of the identified genes and pathways may be manipulated to improve heat resistance ability in soybean via either genetic engineering or molecular breeding method.

Viral infections still threaten human health all over the world, and many people die from viral diseases every year. However, there are no effective vaccines or drugs for preventing or managing most viral diseases. Thus, the discovery and development of broad-spectrum antiviral agents remain urgent. Here, we expressed and purified a venom peptide, Ev37, from the scorpion Euscorpiops validus in a prokaryotic system. We found that rEv37 can inhibit dengue virus type 2 (DENV-2), hepatitis C virus (HCV), Zika virus (ZIKV), and herpes simplex virus type 1 (HSV-1) infections in a dose-dependent manner at noncytotoxic concentrations, but that it has no effect on Sendai virus (SeV) and adenovirus (AdV) infections in vitro. Furthermore, rEv37 alkalized acidic organelles to prevent low pH–dependent fusion of the viral membrane–endosomal membrane, which mainly blocks the release of the viral genome from the endosome to the cytoplasm and then restricts viral late entry. Taken together, our results indicate that the scorpion venom peptide Ev37 is a broad-spectrum antiviral agent with a specific molecular mechanism against viruses undergoing low pH–dependent fusion activation during entry into host cells. We conclude that Ev37 is a potential candidate for development as an antiviral drug.

Biofouling by the invasive mussel species Limnoperna fortunei has caused severe negative consequences in various freshwater ecosystems, but there is still a lack of effective antifouling strategies for this species, particularly in drinking water treatment systems where many existing strategies cannot be used. Chemical oxidants have been proposed to potentially control fouling mussels by influencing 3,4‑dihydroxyphenylalanine oxidation involved in byssus adhesion. To test this potential control strategy, L. fortunei adults were exposed to four oxidants: sodium hypochlorite (NaClO), potassium permanganate (KMnO4), hydrogen peroxide (H2O2) and chloramine T (CAT) at concentrations of 0.5, 1.0, 3.0 and 5.0 mg L−1 for one week. The results showed that low concentrations of KMnO4 stimulated foot protein secretion, which was beneficial to byssus production (number and length). NaClO and H2O2, but not KMnO4 and CAT, significantly inhibited byssus production and reduced breaking force, causing an increased byssus shedding rate. However, only NaClO dissolved byssus and altered the failure location from the byssal thread to adhesive plaque, even when exposed at low concentrations, showing its great impacts on byssus adhesion. Further analysis of polyphenoloxidase activities and gene expression profiles of LfBP-1, LfFP-2 and LfBP-3 revealed that chemical oxidants affected byssus adhesion by altering Dopa oxidation and foot protein gene expressions. This study, therefore, suggests that a low concentration of NaClO can be used as an alternative and environmentally friendly chemical for controlling L. fortunei biofouling by weakening byssus adhesion.

The dynamic alterations of the physiological and molecular processes in reproductive stage soybean indicated the dramatic impact caused by drought. Drought is a major abiotic stress that limits soybean (Glycine max) production. Most prior studies were focused on either model species or crops that are at their vegetative stages. It is known that the reproductive stage of soybean is more susceptible to drought. Therefore, an understanding on the responsive mechanisms during this stage will not only be important for basic plant physiology, but the knowledge can also be used for crop improvement via either genetic engineering or molecular breeding. In this study, physiological measurements and RNA-Seq analysis were used to dissect the metabolic alterations and molecular responses in the leaves of soybean grown at drought condition. Photosynthesis rate, stomata conductance, transpiration, and water potential were reduced. The activities of SOD and CAT were increased, while the activity of POD stayed unchanged. A total of 2771 annotated genes with at least twofold changes were found to be differentially expressed in the drought-stressed plants in which 1798 genes were upregulated and 973 were downregulated. Via KEGG analysis, these genes were assigned to multiple molecular pathways, including ABA biogenesis, compatible compound accumulation, secondary metabolite synthesis, fatty acid desaturation, plant transcription factors, etc. The large number of differentially expressed genes and the diverse pathways indicated that soybean employs complicated mechanisms to cope with drought. Some of the identified genes and pathways can be used as targets for genetic engineering or molecular breeding to improve drought resistance in soybean.

Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10-4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10-4, 1.01 × 10-4, and 1.89 × 10-4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava.

Calcium (Ca2+) plays a crucial role in plant development and responses to environmental stimuli. Currently, calmodulins (CaMs), calmodulin-like proteins (CMLs), and calcineurin B-like proteins (CBLs), such as Ca2+ sensors, are not well understood in cassava (Manihot esculenta Crantz), an important tropical crop. In the present study, 8 CaMs, 48 CMLs, and 9 CBLs were genome-wide identified in cassava, which were divided into two, four, and four groups, respectively, based on evolutionary relationship, protein motif, and gene structure analyses. Transcriptomic analysis revealed the expression diversity of cassava CaMs-CMLs-CBLs in distinct tissues and in response to drought stress in different genotypes. Generally, cassava CaMs-CMLs-CBLs showed different expression profiles between cultivated varieties (Arg7 and SC124) and wild ancestor (W14) after drought treatment. In addition, numerous CaMs-CMLs-CBLs were significantly upregulated at 6 h, 12 h, and 48 h after harvest, suggesting their possible role during storage roots (SR) deterioration. Further interaction network and co-expression analyses suggested that a CBL-mediated interaction network was widely involved in SR deterioration. Taken together, this study provides new insights into CaMs-CMLs-CBLs-mediated drought adaption and SR deterioration at the transcription level in cassava, and identifies some candidates for the genetic improvement of cassava.

GENERAL REGULATORY FACTOR (GRF) proteins play vital roles in the regulation of plant growth, development, and response to abiotic stress. However, little information is known for this gene family in cassava (Manihot esculenta). In this study, 15 MeGRFs were identified from the cassava genome and were clustered into the ε and the non-ε groups according to phylogenetic, conserved motif, and gene structure analyses. Transcriptomic analyses showed eleven MeGRFs with constitutively high expression in stems, leaves, and storage roots of two cassava genotypes. Expression analyses revealed that the majority of GRFs showed transcriptional changes under cold, osmotic, salt, abscisic acid (ABA), and H2O2 treatments. Six MeGRFs were found to be commonly upregulated by abiotic stress, ABA, and H2O2 treatments, which may be the converging points of multiple signaling pathways. Interaction network analysis identified 18 possible interactors of MeGRFs. Taken together, this study elucidates the transcriptional control of MeGRFs in tissue development and the responses of abiotic stress and related signaling in cassava. Some constitutively expressed, tissue-specific, and abiotic stress-responsive candidate MeGRF genes were identified for the further genetic improvement of crops.

Calcium-dependent protein kinases (CPKs) play important roles in regulating plant tolerance to abiotic stress and signal transduction; however, no data are currently available regarding the CPK family in cassava. Herein, we identified 27 CPK genes from cassava based on our previous genome sequencing data. Phylogenetic analysis showed that cassava CPKs could be clustered into three groups, which was further supported by gene structure and conserved protein motif analyses. Global expression analysis suggested that MeCPK genes showed distinct expression patterns in different tissues between wild subspecies and cultivated varieties, indicating their involvement in the functional diversity of different varieties. Transcriptomics, interaction networks, and co-expression assays revealed a broad transcriptional response of cassava CPKs and CPK-mediated networks to drought stress and their differential expression profiles in different varieties, implying their contribution to drought stress tolerance in cassava. Expression analysis of eight MeCPK genes suggested a comprehensive response to osmotic stress, salt, cold, abscisic acid, and H2O2, which indicated that cassava CPKs might be convergence points for different signaling pathways. This study provides a basis for crop improvements and understanding of abiotic stress responses and signal transduction mediated by CPKs in cassava.

Starch branching enzyme (SBE) is one of the key enzymes involved in starch biosynthetic metabolism. In this study, six SBE family genes were identified from the cassava genome. Phylogenetic analysis divided the MeSBE family genes into dicot family A, B, C, and the new group. Tissue-specific analysis showed that MeSBE2.2 was strongly expressed in leaves, stems cortex, and root stele, and MeSBE3 had high expression levels in stem cortex and root stele of plants in the rapid growth stage under field condition, whereas the expression levels of MeSBE2.1, MeSBE4, and MeSBE5 were low except for in stems cortex. The transcriptional activity of MeSBE2.2 and MeSBE3 was higher compared with other members and gradually increased in the storage roots during root growth process, while the other MeSBE members normally remained low expression levels. Expression of MeSBE2.2 could be induced by salt, drought, exogenous abscisic acid, jasmonic acid, and salicylic acid signals, while MeSBE3 had positive response to drought, salt, exogenous abscisic acid, and salicylic acid in leaves but not in storage root, indicating that they might be more important in starch biosynthesis pathway under diverse environments.

Additional file 1: Figure S1. Recombination hotspots in 11 LGs. Figure S2. Distribution of r2 values between markers for Jatropha. Figure S3. Genome-wide LD decay (mean r2) estimated using 3422 markers that are mapped on 11 LGs of Jatropha ultra-high density genetic map. Table S1. Recombination hotspots in 11 LGs. Table S2. Genome-wide LD estimates among marker-pairs mapped across 11 LGs of ultra-high density genetic map for Jatropha.

Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10-4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10-4, 1.01 × 10-4, and 1.89 × 10-4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava.

Mitogen-activated protein kinase kinase kinases (MAPKKKs), an important unit of MAPK cascade, play crucial roles in plant development and response to various stresses. However, little is known concerning the MAPKKK family in the important subtropical and tropical crop cassava. In this study, 62 MAPKKK genes were identified in the cassava genome, and were classified into 3 subfamilies based on phylogenetic analysis. Most of MAPKKKs in the same subfamily shared similar gene structures and conserved motifs. The comprehensive transcriptome analysis showed that MAPKKK genes participated in tissue development and response to drought stress. Comparative expression profiles revealed that many MAPKKK genes were activated in cultivated varieties SC124 and Arg7 and the function of MeMAPKKKs in drought resistance may be different between SC124/Arg7 and W14. Expression analyses of the 7 selected MeMAPKKK genes showed that most of them were significantly upregulated by osmotic, salt and ABA treatments, whereas slightly induced by H2O2 and cold stresses. Taken together, this study identified candidate MeMAPKKK genes for genetic improvement of abiotic stress resistance and provided new insights into MAPKKK -mediated cassava resistance to drought stress.