Cloning and characterization of a FLORICAULA/LEAFY ortholog, PFL, in polygamous papaya

The homologous genes FLORICAULA (FLO) in Antirrhinum and LEAFY (LFY) in Arabidopsis are known to regu- late the initiation of flowering in these two distantly related plant species. These genes are necessary also for the expression of downstream genes that control floral organ identity. We used Arabidopsis LFY cDNA as a probe to clone and sequence a papaya ortholog of LFY, PFL. It encodes a protein that shares 61% identity with the Arabidopsis LFY gene and 71% identity with the LFY homologs of the two woody tree species: California sycamore (Platanus racemosa) and black cottonwood (Populus trichocarpa). Despite the high sequence similarity within two conserved regions, the N-terminal proline-rich motif in papaya PFL differs from other members in the family. This difference may not affect the gene function of papaya PFL, since an equally divergent but a functional LFY ortholog NEEDLY of Pinus radiata has been reported. Genomic and BAC Southern analyses indicated that there is only one copy of PFL in the papaya genome. In situ hybridization experiments demonstrated that PFL is expressed at a relatively low level in leaf primordia, but it is expressed at a high level in the floral meristem. Quantitative PCR analyses revealed that PFL was expressed in flower buds of all three sex types - male, female, and hermaphrodite with marginal difference between hermaphrodite and unisexual flowers. These data suggest that PFL may play a similar role as LFY in flower development and has limited effect on sex differentiation in papaya.

Adjusting Temperature and Salinity Effects on Single Capacitance Sensors

Several newly developed capacitance sensors have simplified real-time determination of soil water content.Previous work has shown that salinity and temperature can affect these sensors,but relatively little has been done to correct these effects.The objectives of this study were to evaluate the effect of media temperature and salinity on the apparent water content measured with a single capacitance sensor(SCS),and to mitigate this effect using a temperature dependent scaled voltage technique under laboratory conditions.A column study was conducted containing two media:pure deionized water and quartz sand under varying water contents(0.05 to 0.30 cm3 cm-3) and salinity(0 to 80 mmol L-1).Media temperature was varied between 5 and 45℃ using an incubator.The SCS probes and thermocouples were placed in the middle of the columns and were logged at an interval of 1 minute.There was strong negative correlation between sensor reading and temperature of deionized water with a rate of-0.779 mV ℃-1.Rates of SCS apparent output were 0.454 and 0.535 mV ℃-1 for air in heating and cooling cycles,respectively.A similar positive correlation with temperature was observed in sand at different water contents.The SCS probe was less sensitive to temperature as salinity and water content increased.Using a temperature-corrected voltage calibration model,the effect of temperature was reduced by 98%.An analytical model for salinity correction was able to minimize the error as low as ± 2% over the salinity level tested.

Green Plant Protection Innovation: Challenges and Perspectives

This issue of Engineering was compiled from papers presented at the First International Conference on Green Plant Protection Innovation(1st ICGPPI),held in Haikou in May 2018,and the Second International Conference on Green Plant Protection Innovation(2nd ICGPPI),held in Guiyang in October 2019.The conferences were sponsored by the Chinese Academy of Engineering,and the Academic Committee of the Forum of the ICGPPI,chaired by Professor Baoan Song,organized the conference.The 1st ICGPPI was attended by more than 800 people from seven countries,while the 2nd ICGPPI had more than 200 attendees from nine countries.The wide range of topics related to more environmentally sound crop protection was of great interest to all,and the meetings provided provided an opportunity for scientists from many disciplines of crop protection to exchange and share ideas and advances.

Putative Mode of Action of the Monoterpenoids Linalool, Methyl Eugenol, Estragole, and Citronellal on Ligand-Gated Ion Channels

Essential oil has been used as sedatives,anticonvulsants,and local anesthetics in traditional medical remedies;as preservatives for food,fruit,vegetable,and grain storage;and as bio-pesticides for food production.Linalool(LL),along with a few other major components such as methyl eugenol(ME),estragole(EG),and citronellal,are the active chemicals in many essential oils such as basil oil.Basil oil and the aforementioned monoterpenoids are potent against insect pests.However,the molecular mechanism of action of these chemical constituents is not well understood.It is well-known that the c-aminobutyric acid type A receptors(GABAARs)and nicotinic acetylcholine receptor(nAChR)are primary molecular targets of the synthetic insecticides used in the market today.Furthermore,the GABAAR-targeted therapeutics have been used in clinics for many decades,including barbiturates and benzodiazepines,to name just a few.In this research,we studied the electrophysiological effects of LL,ME,EG,and citronellal on GABAAR and nAChR to further understand their versatility as therapeutic agents in traditional remedies and as insecticides.Our results revealed that LL inhibits both GABAAR and nAChR,which may explain its insecticidal activity.LL is a concentration-dependent,noncompetitive inhibitor on GABAAR,as the half-maximal effective concentration(EC50)values of c-aminobutyric acid(GABA)for the rat a1b3c2L GABAAR were not affected by LL:(36.2±7.9)lmol-1 and(36.1±23.8)μmol·L-1 in the absence and presence of 5 mmol·L-1 LL,respectively.The half-maximal inhibitory concentration(IC50)of LL on GABAAR was approximately 3.2 mmol·L-1.Considering that multiple monoterpenoids are found within the same essential oil,it is likely that LL has a synergistic effect with ME,which has been previously characterized as both a GABAAR agonist and a positive allosteric modulator,and with other monoterpenoids,which offers a possible explanation for the sedative and anticonvulsant effects and the insecticidal activities of LL.

Current status and trends in forest genomics

Forests are not only the most predominant of the Earth's terrestrial ecosystems,but are also the core supply for essential products for human use.However,global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation.Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate.In the last two decades,the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies,single cell RNA-seq,clustered regularly interspaced short palindromic repeats(CRISPR)-mediated genome editing,and spatial transcriptomes,as well as bioinformatics analysis technologies,which have led to the generation of multidimensional,multilayered,and spatiotemporal gene expression data.These technologies,together with basic technologies routinely used in plant biotechnology,enable us to tackle many important or unique issues in forest biology,and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations.In this review,we recapitulated the advancement and current status of 12 research branches of forest genomics,and then provided future research directions and focuses for each area.Evidently,a shift from simple biotechnology-based research to advanced and integrative genomics research,and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.

Synthesis, Characterization, and Antifungal Evaluation of Thiolactomycin Derivatives

5-Substituted benzylidene 3-acylthiotetronic acids are antifungal.A series of 3-acylthiotetronic acid derivatives with varying substitutions at the 5-position were designed,synthesized,and characterized,based on the binding pose of 3-acyl thiolactone with the protein C171Q KasA.Fungicidal activities of these compounds were screened against Valsa Mali,Curvularia lunata,Fusarium graminearum,and Fusarium oxysporum f.sp.lycopersici.Most target compounds exhibited excellent fungicidal activities against target fungi at the concentration of 50μg·mL-1.Compounds 11c and 11i displayed the highest activity with a broad spectrum.The median effective concentration(EC50)values of 11c and 11i were 1.9–10.7 and 3.1–7.8μg·mL-1,respectively,against the tested fungi,while the EC50 values of the fungicides azoxystrobin,carbendazim,and fluopyram were respectively 0.30,4.22,and>50μg·mL-1 against V.Mali;6.7,41.7,and 0.18μg·mL-1 against C.lunata;22.4,0.42,and 0.43μg·mL-1 against F.graminearum;and 4.3,0.12,and>50μg·mL-1 against F.oxysporum f.sp.lycopersici.The structures and activities of the target compounds against C.lunata were analyzed to obtain a statistically significant comparative molecular field analysis(CoMFA)model with high prediction abilities(q2=0.9816,r2=0.8060),and its reliability was verified.The different substituents on the benzylidene at the 5-position had significant effects on the activity,while the introduction of a halogen atom at the benzene ring of benzylidene was able to improve the activity against the tested fungi.

Two aquaporins,PIP1;1 and PIP2;1,mediate the uptake of neonicotinoid pesticides in plants

Neonicotinoids(NEOs),a large class of organic compounds,are a type of commonly used pesticide for crop protection.Their uptake and accumulation in plants are prerequisites for their intra-and intercellular move-ments,transformation,and function.Understanding the molecular mechanisms that underpin NEO uptake by plants is crucial for effective application,which remains elusive.Here,we demonstrate that NEOs enter plant cells primarily through the transmembrane symplastic pathway and accumulate mainly in the cytosol.Two plasma membrane intrinsic proteins discovered in Brassica rapa,BraPIP1;1 and BraPIP2;1,were found to encode aquaporins(AQPs)that are highly permeable to NEOs in different plant species and facilitate NEO subcellular diffusion and accumulation.Their conserved transport function was further demonstrated in Xenopus laevis oocyte and yeast assays.BraPIP1;1 and BraPIP2;1 gene knockouts and interaction as-says suggested that their proteins can form functional heterotetramers.Assessment of the potential of mean force indicated a negative correlation between NEO uptake and the energy barrier of BraPIP1;1 chan-nels.This study shows that AQPs transport organic compounds with greater osmolarity than previously thought,providing new insight into the molecular mechanisms of organic compound uptake and facilitating innovations in systemic pesticides.

利用棋盘格实验直接筛选酶免疫测定的最佳包被抗原和抗体浓度

以两个单克隆抗体及其相应的包被抗原为例,研究了棋盘格实验中包被抗原与抗体浓度组合对免疫检测中0孔吸光度值A0、IC50值和标准曲线斜率的影响。结果发现,A0和IC50值随包被抗原与抗体稀释倍数的增加而降低;斜率随抗体稀释倍数增加而降低,而随包被抗原的稀释倍数增加表现出先增加后降低的趋势。在同一抗体浓度和不同包被抗原浓度的组合中,斜率最大值出现在使板吸附达到饱和的最大稀释倍数的包被抗原浓度附近。综合实验结果确认从棋盘格实验中直接筛选最佳包被抗原、抗体浓度组合的标准是:选择使板吸附达到饱和的最大包被抗原稀释倍数为最佳包被抗原浓度,在不同抗体浓度与已选择的最佳包被抗原浓度组合中使0孔吸光度值达1.0左右的抗体稀释倍数为最佳抗体浓度。

发展中国家的可再生能源:沼气的机遇和挑战

能源对于现代社会至关重要,是社会经济发展最重要的指标之一。尽管科技不断发展,但仍然有约30亿人(主要集中在发展中国家的农村地区),继续通过在传统的炉灶中燃烧生物质资源(如柴薪、秸秆、动物粪便)的方式来满足烹饪的能源需求。这种方式对环境、社会、经济、公众健康都带来极大负面影响。这些地区要实现可持续性发展,开发干净清洁、价格低廉的可再生能源就势在必行。把现有的生物质资源(动物粪便、秸秆、餐厨垃圾、绿色废弃物)提炼成更加清洁高效的能源载体(例如厌氧发酵产生的沼气),不仅具有提供清洁、可靠能源的独特潜力,同时又能保护当地和全球的环境。尽管沼气对发展中国家来说意义重大,但其面临着成本高、设备安装和维护专业知识缺乏等问题,因而在地理位置分散的社区难以广泛推广应用。因此,政府和非政府层面的通力协作就显得至关重要,从而促进沼气技术的更新改造和传播,开发尚未被开发的潜力。文章旨在通过分析沼气技术的现状、挑战和潜力,明确它在发展中国家未来的研究方向和发展传播路径。

Efficient ozonation of reverse osmosis concentrates from petroleum refinery wastewater using composite metal oxideloaded alumina

Novel Mn–Fe–Mg-and Mn–Fe–Ce-loaded alumina（Mn–Fe–Mg/Al2O3 and Mn–Fe–Ce/Al2O3） were developed to catalytically ozonate reverse osmosis concentrates generated from petroleum refinery wastewaters（PRW-ROC）. Highly dispersed 100–300-nm deposits of composite multivalent metal oxides of Mn（Mn^2＋）, Mn^3＋,and Mn^4＋, Fe（Fe^2＋）and Fe^3＋ and Mg（Mg^2＋）, or Ce（Ce^4＋） were achieved on Al2O3 supports. The developed Mn–Fe–Mg/Al2O3 and Mn–Fe–Ce/Al2O3 exhibited higher catalytic activity during the ozonation of PRW-ROC than Mn–Fe/Al2O3, Mn/Al2O-3, Fe/Al2O3, and Al2O3. Chemical oxygen demand removal by Mn–Fe–Mg/Al2O3-or Mn–Fe–Ce/Al2O3-catalyzed ozonation increased by 23.9% and23.2%, respectively, in comparison with single ozonation.Mn–Fe–Mg/Al2O3 and Mn–Fe–Ce/Al2O3 notably promoted áOH generation and áOH-mediated oxidation. This study demonstrated the potential use of composite metal oxide-loaded Al2O3 in advanced treatment of bio-recalcitrant wastewaters.

Rhamnolipids Induced by Glycerol Enhance Dibenzothiophene Biodegradation in Burkholderia sp. C3

In highly urbanized areas,pollution from anthropogenic activities has compromised the integrity of the land,decreasing soil availability for agricultural practices.Dibenzothiophene(DBT)is a heterocyclic aromatic hydrocarbon frequently found in urbanized areas,and is often used as a model chemical to study the microbial transformation of pollutants.The potential for human exposure and its health risk makes DBT a chemical of concern;thus,it needs to be environmentally managed.We utilized glycerol to stimulate Burkholderia sp.C3 in order to degrade DBT in respect to①DBT biodegradation kinetics,②bacterial growth,③rhamnolipid(RL)biosynthesis,and④RL secretion.Under an optimum glycerol-to-DBT molar ratio,the DBT biodegradation rate constants increased up to 18-fold and enhanced DBT biodegradation by 25%–30%at day 1 relative to cultivation with DBT alone.This enhancement was correlated with an increase in bacterial growth and RL biosynthesis.Proteomics studies revealed the enzymes involved in the upper and main steps of RL biosynthesis.The RL congeners Rha-C10-C10,Rha-Rha-C10-C10,Rha-Rha-C10-C12,and Rha-Rha-C12-C12 were identified in the medium supplemented with glycerol and DBT,whereas only Rha-C12-C12 was identified in cultures without glycerol or with RL inhibitors.The studies indicated that glycerol enhances DBT biodegradation via increased RL synthesis and bacterial growth.The results warrant further studies of environmental biostimulation with glycerol to advance bioremediation technologies and increase soil availability for agricultural purposes.

Heterogeneous Oxidation of Methylene Blue with Surface-Modified Iron-Amended Activated Carbon

The present study aims to develop effective adsorption and oxidation of synthetic dye in wastewater by using the newly synthesized iron-amended activated carbon. Recently synthetic dye-containing wastewater has gained more attention due to its mass discharge, high toxicity and low biodegradation. For enhancing adsorption of dye and oxidative regeneration of dye-exhausted activated carbon, the novel amendment of iron-deposited granular activated carbon (GAC) was developed. It was to amend ferrous ion onto the acid-pretreated GAC when pH of iron solution was higher than the pH at point of zero charge (pH, pzc) of the GAC. Methylene blue (MB) in water was adsorbed onto the acid-treated iron- amended GAC (Fe-GAC) followed by single or multiple applications of H2O2. Batch experiments were carried out to study the adsorption isotherm and kinetics indicating adsorption of MB onto the Fe-GAC followed Langmuir isotherm and the pseudo-second order kinetics. The Fe-GACshowed the maximum adsorption capacity (qm) of 238.1 ± 0.78 mg/g which was higher than the virgin GAC with qm of 175.4 ± 13.6 mg/g at 20?C, pH 6 and the initial concentration of 20 - 200 mg/L. The heterogeneous Fenton oxidation of MB in the Fe-GAC revealedthat increasing the H2O2 loading from 7 to 140 mmol H2O2/mmol MB led to enhancing the oxidation efficiency of MB in the GAC from 62.6% to 100% due to the increased generation of hydroxyl radicals. Further enhancement of oxidation of MB in the Fe-GAC was made by the multiple application of H2O2 while minimizing OH radical scavenging often occurring at high concentration of H2O2. Therefore, the acid-treated iron-amended GAC would provide excellent adsorption capacity for MB and high oxidation efficiency of MB in the GAC with multiple applications of H2O2 and optimum iron loading.

Laboratory studies of rice bran as a carbon source to stimulate indigenous microorganisms in oil reservoirs

There is a great interest in developing cost-efficient nutrients to stimulate microorganisms in indigenous microbial enhanced oil recovery（IMEOR） processes.In the present study,the potential of rice bran as a carbon source for promoting IMEOR was investigated on a laboratory scale.The co-applications of rice bran,K2HPO4 and urea under optimized bio-stimulation conditions significantly increased the production of gases,acids and emulsifiers.The structure and diversity of microbial community greatly changed during the IMEOR process,in which Clostridium sp.,Acidobacteria sp.,Bacillus sp.,and Pseudomonas sp.were dominant.Pressurization,acidification and emulsification due to microbial activities and interactions markedly improved the IMEOR processes.This study indicated that rice bran is a potential carbon source for IMEOR.

Molecular diagnostics in a teacup:Non-Instrumented Nucleic Acid Amplification(NINA) for rapid,low cost detection of Salmonella enterica

We report on the use of a novel non-instrumented platform to enable a Loop Mediated isothermal Amplification(LAMP) based assay for Salmonella enterica.Heat energy is provided by addition of a small amount(<150 g) of boiling water,and the reaction temperature is regulated by storing latent energy at the melting temperature of a lipid-based engineered phase change material.Endpoint classification of the reaction is achieved without opening the reaction tube by observing the fluorescence of sequence-specific FRET-based assimilating probes with a simple handheld fluorometer.At or above 22℃ ambient temperature the non-instrumented devices could maintain reactions above a threshold temperature of 61℃ for over 90 min-significantly longer than the 60 min reaction time.Using the simple format,detection limits were less than 20 genome copies for reactions run at ambient temperatures ranging from 8 to 36℃.When used with a pre-enrichment step and non-instrumented DNA extraction device,trace contaminations of Salmonella in milk close to 1 CFU/mL could be reliably detected.These findings illustrate that the non-instrumented amplification approach is a simple,viable,low-cost alternative for field-based food and agricultural diagnostics or clinical applications in developing countries.

Localization of Banana bunchy top virus and cellular compartments in gut and salivary gland tissues of the aphid vector Pentalonia nigronervosa

Banana bunchy top virus （BBTV） （Nanoviridae： Babuvirus） is transmitted by aphids of the genus Pentalonia in a circulative manner. The cellular mechanisms by which BBTV translocates from the anterior midgut to the salivary gland epithelial tissues are not understood. Here, we used multiple fluorescent markers to study the distribution and the cellular localization of early and late endosomes, macropinosomes, lysosomes, microtubules, actin filaments, and lipid raft subdomains in the gut and principal salivary glands ofPentalonia nigronervosa. We applied colabeling assays, to colocalize BBTV viral particles with these cellular compartments and structures. Our results suggest that multiple potential cellular processes, including clathrin- and caveolae-mediated endocytosis and lipid rafts, may not be involved in BBTV internalization.

GranatumX:A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data analysis.GranatumX is inspired by the interactive webtool Granatum.GranatumX enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical environment.It also offers software developers the opportunity to rapidly promote their own tools with others in customizable pipelines.The architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various platforms.GranatumX can be run on the cloud or private servers and generate reproducible results.It is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench scientists.GranatumX is freely accessible at http://garmiregroup.org/granatumx/app.

Development of a tRNA-derived small RNA diagnostic and prognostic signature in liver cancer

Liver cancer presents divergent clinical behaviors.There remain opportunities for molecular markers to improve liver cancer diagnosis and prognosis,especially since tRNA-derived small RNAs(tsRNA)have rarely been studied.In this study,a random forests(RF)diagnostic model was built based upon tsRNA profiling of paired tumor and adjacent normal samples and validated by independent validation(IV).A LASSO model was used to developed a seven-tsRNA-based risk score signature for liver cancer prognosis.Model performance was evaluated by a receiver operating characteristic curve(ROC curve)and Precision-Recall curve(PR curve).The five-tsRNA-based RF diagnosis model had area under the receiver operating characteristic curve(AUROC)88%and area under the precision–recall curve(AUPR)87%in the discovery cohort and 87%and 86%in IV-AUROC and IV-AUPR,respectively.The seven-tsRNA-based prognostic model predicts the overall survival of liver cancer patients(Hazard Ratio 2.02,95%CI 1.36–3.00,P<0.001),independent of standard clinicopathological prognostic factors.Moreover,the model successfully categorizes patients into high-low risk groups.Diagnostic and prognostic modeling can be reliably utilized in the diagnosis of liver cancer and high-low risk classification of patients based upon tsRNA characterization.

Design and Synthesis of Photoaffinity Probe Candidates for the GABA-gated Chloride Channel

In order to characterize binding sites of insecticidal compounds on GABA gated chloride channel, new photoaffinity probe candidates based on 5e-t-butyl-2e-[4-（substituted-propynyl）phenyl]-1,3-dithiane for the noncompetitive blocker （NCB） site of the γ-aminobutyric acid （GABA）-gated chloride channel were designed and synthesized, and their potency as an inhibitor on NCB was measured by 4＇-ethynyl-4-n-[2,3-^3H2]-propylbicycloorthobenzoate （^3H EBOB） assay. The synthesized compounds showed high inhibition activities with half maximum inhibition concentrations （IC50） of lower than 35 nmol/L and were very stable in binding conditions as well photoreacted quickly at 300 nm light. These new compounds are expected to be good photoaffinity labeling probes if radioisotope iodine is incorporated.

Probiotic Lactobacillus brevis CLB3 prevents azoxymethane/dextran sulfate sodium-induced colon carcinogenesis in mice by reducing amino acid transport and IL-17A levels and repressing the IL-6/AKT/p-STAT3 signaling pathway

Amino acid intake plays a crucial role in the Warburg effect of cancer.Gut microbes can regulate intestinal amino acid metabolism.However,it is still unknown whether probiotic therapy can protect the host from intestinal tumor invasion by reducing amino acid intake.With in vitro methods,three acid-tolerant strains from fermented pickles were screened out.Using azoxymethane/dextran sulfate sodium-induced colon cancer models,we evaluated the therapeutic effects of Lactobacillus brevis CLB3,Lactobacillus plantarum XLP,and Lactobacillus johnsonii CM on model mice.Their functional mechanisms were further explained through anatomy section,quantitative reverse transcription polymerase chain reaction(qRT-PCR),Western blot,and immunohistochemical staining analyses as well as database mining and gut culturomics.The Lactobacillus brevis(L.brevis)CLB3 treatment significantly improved the clinical signs and symptoms of colon cancer,alleviated colon damage,and inhibited colon carcinogenesis in mice.In addition,this treatment significantly increased gut cultivable Lactobacillus abundance,inhibited the expression and translation levels of the tumor metabolism-related solute carrier(SLC)amino acid transporter including SLC7A5 and SLC7A11,lowered circulating interleukin-6(IL-6)and interleukin-17A(IL-17A)levels,and improved the accumulation of tumor-infiltrating lymphocytes and cancer proliferation factors.These findings suggest that L.brevis CLB3 can reduce amino acid transport,inhibit mammalian target of rapamycin(mTOR)signaling and enhance intestinal anti-tumor immune responses,which provides a potential targeting amino acid transporter strategy for preventing colorectal cancer.