Single-cell omics analyses with single molecular detection:challenges and perspectives

The ultimate goal of single-cell analyses is to obtain the biomolecular content for each cell in unicellular and multicellular organisms at different points of their life cycle under variable environmental conditions.These require an assessment of:a)the total number of cells,b)the total number of cell types,and c)the complete and quantitative single molecular detection and identification for all classes of biopolymers,and organic and inorganic compounds,in each individual cell.For proteins,glycans,lipids,and metabolites,whose sequences cannot be amplified by copying as in the case of nucleic acids,the detection limit by mass spectrometry is about 105 molecules.Therefore,proteomic,glycomic,lipidomic,and metabolomic analyses do not yet permit the assembly of the complete single-cell omes.The construction of novel nanoelectrophoretic arrays and nano in microarrays on a single 1-cm-diameter chip has shown proof of concept for a high throughput platform for parallel processing of thousands of individual cells.Combined with dynamic secondary ion mass spectrometry,with 3D scanning capability and lateral resolution of 50 nm,the sensitivity of single molecular quantification and identification for all classes of biomolecules could be reached.Further development and routine application of such technological and instrumentation solution would allow assembly of complete omes with a quantitative assessment of structural and functional cellular diversity at the molecular level.

Molecular Detection of Phytophthora colocasiae of Taro Leaf Blight Based on PCR

The present PCR assay was conducted to develop rapid and sensitive detection of Phytophthora colocasiae,in order to provide a robust and reliable tool for healthy seedling production of taro and limiting the transmission and spread of the causal organism of taro leaf blight in taro planting regions.The samples were used to extract total DNA and to be detected by PCR with P.colocasiae specific primer pairs PCSP-RL F/PCSP-RL R and PCSP-T F/PCSP-T R,respectively.Distinct fragments of about 200 bp and 240 bp were amplified by PCR using primers PCSP-RL F/PCSP-RL R and PCSP-T F/PCSP-T R,respectively.The analysis of the nucleotide sequence of the PCR products were found to be 99% identical to sequence of RAS-related protein (Ypt1) and phospho-ribosylanthranilate isomerase (TRP1) in P.colocasiae,respectively.It is concluded that rapid and sensitive developed PCR assay for detection of P.colocasiae could be used in routine diagnosis and aid in management practices to mitigate taro leaf blight.

Passively and actively enhanced surface plasmon resonance sensing strategies towards single molecular detection

Surface plasmonic resonance(SPR)has been a corner stone for approaching single molecular detection due to its highsensitivity capability and simple detection mechanism,and has brought major advancements in biomedicine and life science technology.Over decades,the successful integration of SPR with versatile techniques has been demonstrated.However,several crucial limitations have hindered this technique for practical applications,such as long detection time and low overall sensitivity.This review aims to provide a comprehensive summary of existing approaches in enhancing the performance of SPR sensors based on“passive”and“active”methods.Firstly,passive enhancement is discussed from a material aspect,including signal amplification tags and modifications of conventional substrates.Then,the focus is on the most popular active enhancement methods including electrokinetic,optical,magnetic,and acoustic manipulations that are summarized with highlights on their advantageous features and ability to concentrate target molecules at the detection sites.Lastly,prospects and future development directions for developing SPR sensing towards a more practical,single molecular detection technique in the next generation are discussed.This review hopes to inspire researchers’interests in developing SPR-related technology with more innovative and influential ideas.

Molecular Techniques for Detection of Major Diseases in Sugarcane

It is necessary to rapidly diagnose diseases,identify and monitor the pathogens to achieve scientific and effective control of major diseases in sugarcane.In the present study,the molecular techniques for rapid detection of 13 pathogens that cause 10 important diseases of sugarcane including smut,rust,leaf scald,ratoon stunting,red stripe,mosaic,Fiji,yellow leaf,white leaf and bacilliform virus were established by Sugarcane Research Institute,Yunnan Academy of Agricultural Sciences after years of effort.The results will provide scientific basis for effective diagnosis and control of sugarcane diseases,detection of virus-free seedlings and quarantine management of exotic species.

Development of a loop‑mediated isothermal amplification assay for detection of Austropeplea tomentosa from environmental water samples

Lymnaeid snails are key intermediate hosts for the development and survival of Fasciola spp.,the causative agent of Fascioliasis which are economically important parasites infecting humans and livestock globally.The current control method for treating Fascioliasis is heavily reliant on anthelmintic drugs,particularly Triclabendazole(TCBZ)which has resulted in drug-resistant parasites and poses significant risk as there are no long-term efficacious alternatives available.Sustainable control measures at the farm level could include both parasite and snail control will play an important role in Fasciola spp.control and reduce the reliance on anthelmintic drugs.Implementation of such sustainable control measures requires effective identification of snails on the property however Lymnaeid snails are small and difficult to physically locate.Snail identification using an environmental DNA approach is a recent approach in which physically locating snails are not required.Austropeplea tomentosa,is the primary intermediate snail host for F.hepatica transmission in South-East Australia and we present an in-field loop-mediated isothermal amplification and water filtering method for the detection of A.tomentosa eDNA from water samples to improve current surveillance methods.This methodology is highly sensitive with a detection limit of 5×10^(−6)ng/μL,detected in<20 minutes,with cumulative sample preparation and amplification time under 1 hour.This proposed workflow could assist in monitoring areas to determine the risk of Fascioliasis infection and implement strategies to manage snail populations to ultimately reduce the risk of infection for humans and livestock.

A PCR-Based Method for Detecting Pathogen of Rice False Smut

Rice false smut is a destructive disease that affects rice grain badly.The disease seriously affects the yield and quality of rice in Heilongjiang Province.In this paper,a pair of specific primers was designed to detect the false smut pathogen rapidly and efficiently.The results showed that the pair of primers had strong specificity for false smut pathogen.In addition,the sensitivity of this primer to the genomic DNA of rice false smut pathogen in PCR reaction was 1 pg.By using these primers,the rice false smut pathogen could be detected within 48 h after inoculation,and a PCR reaction system with good specificity and high sensitivity was established.

华南三省(自治区)部分西番莲种植区花叶病病原检测及EAPV多聚蛋白基因序列分析

西番莲(Passiflora edulis Sims.)是热带亚热带地区重要经济作物,我国福建、广东、广西、海南等地广泛种植[1]。调查发现,我国南方多地西番莲花叶病为害严重,症状表现为叶片花叶、黄化、斑驳、畸形,甚至整株褪绿,严重影响西番莲的产量和品质。

A DNA origami plasmonic sensor with environment-independent read-out

DNA origami is a promising technology for its reproducibility,flexibility,scalability and biocompatibility.Among the several potential applications,DNA origami has been proposed as a tool for drug delivery and as a contrast agent,since a conformational change upon specific target interaction may be used to release a drug or produce a physical signal,respectively.However,its conformation should be robust with respect to the properties of the medium in which either the recognition or the read-out take place,such as pressure,viscosity and any other unspecific interaction other than the desired target recognition.Here we report on the read-out robustness of a tetragonal DNA-origami/gold-nanoparticle hybrid structure able to change its configuration,which is transduced in a change of its plasmonic properties,upon interaction with a specific DNA target.We investigated its response when analyzed in three different media:aqueous solution,solid support and viscous gel.We show that,once a conformational variation is produced,it remains unaffected by the subsequent physical interactions with the environment.

Analysis on virus resistance and fruit quality for T4 generation of transgenic papaya

Molecular biological characterization,fruit char-acters,and nutrients were analyzed for T4 generation of transgenic papaya.All transgenic papaya plants with the mutated replicase(RP)gene from papaya ringspot virus(PRSV)showed high resistance or immunity against PRSV in the field.The RP transgene can be steadily inherited to,and expressed at RNA level,the progenies.The growth char-acteristics of transgenic papaya were much better than non-transgenic papaya in the field.The non-transgenic papaya seedlings began to show typical symptoms caused by PRSV after being inoculated with PRSV.They died quickly and never grew to produce fruit.The adult trees developed yellow leaves and produced smaller fruits and were doomed to a slow death after some time,while most of transgenic papaya plants(about 91.8%)did not show any symptoms caused by PRSV,and produced more,bigger,and high quality fruits.Compared with non-transgenic plants,the fresh fruit length of T4 gen-eration of transgenic papaya increased 2.6%-5%,and the diameter decreased 0.6%-1.5%.The flesh thickness of fresh fruit increased 12%-15%,which made it fitter for eating.Although the fresh fruit quality changed,there was no sig-nificant difference between transgenic and non-transgenic papaya.The quality characteristics of dry fruit including the contents of water,lipid,N,protein,reduced sugar,vitamin A,vitamin C,and carotene in the T4 generation of transgenic papaya were all the same as their non-transgenic parents.This means that transgenic plants and non-transgenic plants are substantially equivalent,and the transgene has no effect on dry fruit quality.In this study,we found that vitamin A and vitamin C in red-fleshed papaya were 1.4-1.8 and 1.78-2.07 times more than the yellow-fleshed ones,respectively,while N and protein were only 84.2%-92.1%and 82.1%-98.9%of the yellow-fleshed ones.

Reproductive advance of fertility preservation in patients with early endometrial carcinoma or endometrial atypical hyperplasia

Endometrial cancer(EC)is the fourth common cancer in women worldwide with its incidence rising each year.10%–15%young patients are diagnosed of EC.For patients of childbearing age with early endometrial cancer or atypical hyperplasia,it is necessary to consider surgical removal of uterus after they have given birth.It is a big challenge for reproductive doctors and oncologists to help such patients get pregnant safely as soon as possible.In this article,we will review the latest progress in conservative treatment and candidates for fertility preservation,application of molecular detection,the fertility outcome and follow-up treatment which aims to stimulate more thinking.

Prediction of the anti-inflammatory mechanisms of curcumin by module-based protein interaction network analysis

Curcumin,the medically active component from Curcuma longa(Turmeric),is widely used to treat inflammatory diseases.Protein interaction network(PIN) analysis was used to predict its mechanisms of molecular action.Targets of curcumin were obtained based on ChE MBL and STITCH databases.Protein–protein interactions(PPIs) were extracted from the String database.The PIN of curcumin was constructed by Cytoscape and the function modules identified by gene ontology(GO) enrichment analysis based on molecular complex detection(MCODE).A PIN of curcumin with 482 nodes and 1688 interactions was constructed,which has scale-free,small world and modular properties.Based on analysis of these function modules,the mechanism of curcumin is proposed.Two modules were found to be intimately associated with inflammation.With function modules analysis,the anti-inflammatory effects of curcumin were related to SMAD,ERG and mediation by the TLR family.TLR9 may be a potential target of curcumin to treat inflammation.