Genetic Variation Analysis of 3D Gene and Molecular Detection of Porcine Kobuvirus in 2013-2014

[Objective] This study aimed to investigate the prevalence and variation of porcine kobuvirus （PKV） in suckling piglets in China. [Method] In 2013-2014, 224 feces samples from suckling piglets with diarrhea in 27 pig farms of five provinces in China were collected to detect 3D genes of PKV with RT-PCR method; the sequences and genetic variation of 29 PKV 3D genes were analyzed. [Result] Total positive rate of PKV in feces samples from suckling piglets with diarrhea was 65.18% （146/224）; total positive rate of PKV in pig farms was 85,2% （23/27）; nucleotide sequences and the deduced amino acid sequences of 29 PKV 3D genes shared 87.0%-100% and 92.7%-100% homologies with six PKV-related 3D sequences, respectively. [Conclusion] PKV infection is prevalent in suckling piglets in China; PKV 3D genes exhibit high diversity.

Molecular Detection of Verticillium albo-atrum by PCR Based on Its Sequences

We developed one species-specific PCR assays for rapid and accurate detection of the pathogenic fungi Verticillium albo-atrum in diseased plant tissues and soil. Based on differences in internal transcribed spacer （ITS） sequences of Verticillium spp., a pair of species-specific primers, Vaal/Vaa2, was synthesized. After screening 17 isolates of V. alboatrum, 121 isolates from the Ascomycota, B asidiomycota, Deuteromycota, and Oomycota, the Vaal/Vaa2 primers amplified only a single PCR band of approximately 330 bp from V. albo-atrum. The detection sensitivity with primers Vaal/Vaa2 was 10 fg of genomic DNA. Using ITS1/ITS4 as the first-round primers, combined with Vaa1/Vaa2, the nested PCR procedures were developed, and the detection sensitivity increased 1 000-fold to 10 ag. The detection sensitivity for the soil pathogens was 100-conidiag^-1 soil. The PCR-based methods developed here could simplify both plant disease diagnosis and pathogen monitoring as well as guide plant disease management.

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 and Disease Resistance Identification of Transgenic Wheat with pti5-vp16 Gene

The immature embryos of wheat cultivars Liaochun10, Tiechun1 and Fengqiang3 were bombarded with gold particles coated with pti5 vp16 by gene gun and disease resistant regenerated plants were attained. In order to confirm that the plants are genuine transformed ones, a series of molecular tests were conducted as follows. Firstly, transient GUS expression test on embryos two days after bombardment was done. There were many obvious blue spots produced on the surface of bombarded embryos after GUS staining, in which the maximum reached to 85 blue spots per embryo. Secondly, PCR test was performed with DNA from the regenerated plants obtained after double selection with ppt. 6 plants were found PCR test positive. At last, further verification analysis using dot hybridization and southern blotting was carried out on those PCR positive plants and the strong hybridization signals appeared as expected. All the above tests were uniformly indicated that the disease resistant regenerated plants were true transgenic plants. When inoculated with Blumeria graminis, transgenic wheat plants of PCR positive results were mostly resistant(R) after 7 days, and resis tant, moderate resistant(MR), moderate susceptible(MS) at 14 days respectively. The disease severity of them was distinctively lighter than that of control.

Molecular Detection of Main Diseases of Introduced Sugarcane in Guangxi

According to the quarantine procedures for sugarcane introduction, thirty-three sugarcane varieties/materials from the United States, Bangladesh, Thailand and some other countries were quarantined. The result showed that main diseases and pests that are concerned in quarantine were undiscovered. In addition, molecular detection results of Fiji disease and leaf scald disease were negative ; detection results of mosaic in six varleties/materials were positive; detection results of yellow leaf syndrome in eight varieties/materials were positive.

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 Agricul- tural 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.

Characterization of Citrus tristeza virus Isolates by Indicators and Molecular Biology Methods

Citrus tristeza virus （CTV） exists in citrus as a large number of distinct strains differing in biological characters. The control strategies such as mild strains cross protection （MSCP） require a clear understanding of the characterization of CTV. For better understanding of the structure of CTV population and the relationship between molecular and biological characterization, 72 CTV samples collected from five provinces in China were studied, using biological indexing, p25/Hinf I restriction fragment length polymorphism （RFLP）, multiple molecular markers, and bidirectional RT-PCR assay. The mixture of severe stem pitting isolates was found to be dominant in the field. CTV isolates with p25/Hinf Ⅰ RFLP group 3 and p23/BD-PCR group Ⅰ, Ⅲ were the main cause of epidemics, and most CTV isolates were found to be the mixture of T30 and VT genotypes. More accurate identification of strain mixtures in the field and better understanding of the biological traits of the isolates may be achieved by applying the three molecular detection methods simultaneously.

Comparative genomics provide a rapid detection of Fusarium oxysporum f. sp. conglutinans

Fusarium oxysporum f. sp. conglutinans （Foc） is the causal agent of Fusarium wilt disease of Brassica oleracea. A rapid, accurate, and reliable method to detect and identify plant pathogens is vitally important to integrated disease management. In this study, using a comparative genome analysis among Fusarium oxysporum （Fo）, we developed a Foc-specific primer set （Focs-l/Focs-2） and established a multiplex-PCR assay. In the assay, the Focs-1/Focs-2 and universal primers for Fusarium species （W106PJF106S） could be used to detect Foc isolates in a single PCR reaction. With the optimized PCR parameters, the multiplex-PCR assay showed a high specificity for detecting Foc and was very sensitive to detect as little as 100 pg of pure Foc genomic DNAor 1 000 spores in 1 g of twice-autoclaved soil. We also demonstrated that Foc isolates were easily detected from infected plant tissues, as well as from natural field soils, using the multiplex-PCR assay. To our knowledge, this is a first report on detection Fo by comparative genomic method.

Transfer and Detection of barstar Gene to Maize Inbred Line 18-599 (White) by Particle Bombardment

In China, the purity of maize hybrid strain is discomforting to the development of seed industrialization. Finding a new method for reproduction of maize hybrid strain is necessary. In this study, using particle bombardment, barstar gene was transferred into maize inbred line 18-599 （White）, which is an antiviral and high quality maize inbred line. By molecular detection of the anther of transgenic maize, two plants transferred with barstar gene were gained in this study, which are two restorer lines. The two plants showed normal male spike, and lively microspores. But the capacity of the two restorer lines should be studied in the future. The aim of this study is to find a new method of reproduction of maize hybrid strain using engineering restorer lines and engineering sterility lines by gene engineering technology.

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.

Comparison of Genomic DNA Extraction Methods for Chenopodium quinoa Willd

To rapidly obtain high-quality genomic DNA from Chenopodium quinoa Willd, the genomic DAN in different tissues （leaves, stems and roots） of Chenopodi- um quinoa Willd was extracted by modified CTAB method, SDS method and high- salt Iow-pH method, respectively. The quality and yield of extracted DNA was deter- mined using agarose gel electrophoresis and UV spectrophotometry. At the same time, the PCR-SSR and SSCP molecular detection was also performed. The results showed that the gel test strips, without obvious decomposition, of all the extraction methods were relatively obvious; the genomic DNA yield extracted by modified CTAB method was highest, followed by that by SDS method, and the genomic DNA extracted by high-salt Iow-pH method was lowest： the genomic DNA yields extracted by different methods from Chenopodium quinoa Wiltd leaves were all high- er than those from roots and stems; the quality of Chenopodium quinoa Willd ge- nomic DNA extracted by modified CTAB method and high-salt Iow-pH method was better, and polyphenols, polysaccharides and other impurities were removed more completely. The PCR-SSR and SSCP detection results showed that the genomic DNA extracted by different methods from different tissues of Chenopodium quinoa Willd all could be better amplified, and high-quality strips could be obtained. So the Chenopodium quinoa Willd genomic DNA extracted by the three methods all can be used for subsequent molecular biology research.

Research on the Agronomic,Quality Traits and the Corresponding Background Genes Distribution of Wheat Germplasm Ningchun 4 and Its Parents

[Objective] The aim of this study was to observe the agronomic,yield and quality traits of Ningchun 4 and its parents under the same environmental conditions,as well as to carry out molecular detection on the background genes distribution of the corresponding traits.[Method]Ningchun 4 and its parents Sonora 64,Hongtu,Abbondanza,Quality were used as materials to detect the agronomic and quality traits,as well as to analyze the genetic variation laws by molecular determination method.[Result]Ningchun 4 had inherited the advantages of bigger spike,red and hard grain from Sonora 64 and higher 1 000-grain weight from Hongtu.However,it had also inherited the disadvantages of late-maturing from Sonora 64 and lower tillering ability from Hongtu;the grain quality of Ningchun 4 was slightly lower than the Sonora 64;Ningchun 4 had high quality subunit of 5＋10,which had good dough rheological properties.[Conclusion]Ningchun 4 had inherited the long photoperiod characteristics and no-resistant to slow-leaf rusting and stripe rust characteristics from Hongtu and low PPO activity,high yellow pigments content from parents.

Molecular Identification of Echinococcus spp. and Other Taeniid Tapeworms Using Next-Generation Sequence Analysis of PCR Amplified 18s rRNA Gene

Cystic echinococcosis (CE) is a prevalent zoonotic disease caused by Echinococcus granulosus, with a cosmopolitan distribution. The parasite is transmitted cyclically between canines and numerous intermediate herbivorous livestock animals. Also, other Taeniid tapeworms could infect domestic dogs and they pose significant veterinary and public health concerns worldwide. This study aimed to develop a sensitive molecular method for detecting Echinococcus spp. DNA in dog fecal samples using next-generation sequencing (NGS). A set of PCR primers targeting conserved regions of Taeniid tapeworms’ 18s rRNA genes was designed and tested for amplifying genomic DNA from various tapeworm species. The PCR system demonstrated high sensitivity, amplifying DNA from all tested tapeworm species, with differences observed in amplified band sizes. The primers were adapted for NGS analysis by adding forward and reverse adapters, enabling the sequencing of amplified DNA fragments. Application of the developed PCR system to dog fecal samples collected from Yatta town, Palestine, revealed the presence of E. granulosus DNA in five out of 50 samples. NGS analysis confirmed the specificity of the amplified DNA fragments, showing 98% - 99% similarity with the 18s rDNA gene of E. granulosus. This study demonstrates the utility of NGS-based molecular methods for accurate and sensitive detection of Echinococcus spp. in dog fecal samples, providing valuable insights for epidemiological surveillance and control programs of echinococcosis in endemic regions.

Prevalence of Three Shrimp Viruses in Zhejiang Province in 2008

White spot syndrome virus (WSSV),Taura syndrome virus (TSV) and Infectious hypodermal and haematopoietic necrosis virus (IHHNV) are three shrimp viruses responsible for major pandemics affecting the shrimp farming industry. Shrimps samples were collected from 12 farms in Zhejiang province,China,in 2008 and analyzed by PCR to determine the prevalence of these viruses. From the 12 sampling locations,8 farms were positive for WSSV,8 for IHHNV and 6 for both WSSV and IHHNV. An average percentage of 57.4% of shrimp individuals were infected with WSSV,while 49.2% were infected with IHHNV. A high prevalence of co-infection with WSSV and IHHNV among samples was detected from the following samples:Bingjiang (93.3%),liuao (66.7%),Jianshan (46.7%) and Xianxiang (46.7%). No samples exhibited evidence of infection with TSV in collected samples. This study provides comprehensive information of the prevalence of three shrimp viruses in Zhejiang and may be helpful for disease prevention control in this region.

Analysis of fig tree virus type and distribution in China

The common fig（Ficus carica L.）was one of the earliest horticultural crops to be domesticated.A number of different viruses can infect fig trees including Fig mosaic virus（FMV）that has been detected in several commercial fig trees in Xinjiang,China.However,the distribution of FMV and other fig-infecting viruses in China remains unknown.In the present study,a sample from an ancient fig tree growing in Xinjiang was investigated by electron microscopy（EM）followed by PCR/RT-PCR,and FMV,Fig badnavirus 1（FBV-1）and Fig leaf mottle-associated virus 1（FLMaV-1）were detected.Fig leaf samples（252）from commercial orchards across China were subjected to PCR/RT-PCR,and FMV,FBV-1 and Fig fleck-associated virus（FFka V）were relatively abundant（44.4,48.4 and 44%,respectively）,while FLMaV-1 and Fig mild mottle-associated virus（FMMa V）were much scarcer（5.6 and 0.4%,respectively）,and FLMaV-2,Fig cryptic virus（FCV）,and Fig latent virus（FLV）were not detected.The presence of disease-causing viruses in fig trees presents a significant challenge for fig producers in China.This study may help to promote actions aimed at controlling fig viruses,especially FMV.

Effects of Different Cultivation Patterns of Wheat on Population Structure of Puccinia striiformis West.f. sp. tritici

The paper was to study the effects of different cultivation patterns( mix cultivation and monocultivation) of wheat on population structure of Puccinia striiformis West. f. sp. tritici in the fields. Five race-specific-markers( CY32,CY31,CY29,CY23 and Shuiyuan pathotype) were used to survey 113 infected samples collected from two cultivation patterns. The results indicated that frequency of race-specific-markers under monocultivation was higher than that under mix cultivation; the dominant race-specific-markers were CY32 and CY29 under monocultivation,and the frequency of detection were 81. 5% and 78. 5%,respectively. The dominant race-specific-markers were CY29 and Shuiyuan pathotype under mix cultivation,and the frequency of detection are 41. 7% and 18. 8%,respectively.Several race-specific-markers were detected in single infected leaf,and 41. 7% of infected single leaf were detected with more than two race-specific-markers,58. 3% of infected single leaf were detected with one race-specific-marker under mix cultivation pattern,while there were 75. 0% infected leaves with more than two race-specific-markers and 25. 0% infected single leaf detected with one race-specific-marker under monocultivation pattern. The results indicated that mix cultivation pattern of wheat can reduce races on single leaf,affect the distribution of races in infected leaves,and suppress the occurrence frequency of dominant races of P. striiformis in the fields significantly,subsequently reduced severity and prevalence of the disease.

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.

Detection and genetic identification of Borrelia lusitaniae in questing Ixodes inopinatus tick from Tunisia

Background:Until now,there has been limited information on the prevalence and the phylogeny of Borrelia burgdorferi sensu lato in Ixodes ticks in Tunisia,particularly in Ixodes inopinatus.Methods:The present study aimed to determine the prevalence and the phylogeny of B.burgdorferi s.l.,in coexisted I.ricinus and I.inopinatus ticks collected from Northern Tunisia.One hundred questig ticks were collected during winter 2020 by tick-dragging method in Beja gouvernorate located in the north of Tunisia.Real-time PCR panel targeting B.burgdorferi s.l.23S rRNA gene were performed.Positive DNA samples were subjected to conventional PCRs targeting 457 bp fragment of the Borrelia sp.flagellin(fla)gene using primers FlaF/FlaR.The identified Borrelia sp.isolate underwent partial sequence analysis to determine genospecies and evaluate their phylogenetic position.Results:The study revealed a prevalence rate of 28%(28/100)for B.burgdorferi sensu lato in the Ixodes ticks.The prevalence rates across tick species and genders did not show significant variations(p>0.05).Interestingly,the study underlines the coexistence of I.inopinatus and I.ricinus sharing the same geographic areas in Northern Tunisia.Furthermore,DNA of B.lusitaniae was detected in I.inopinatus ticks for the first time in Tunisia.Revealed B.lusitaniae bacterium is similar to previously identified strains in Mediterranean region,but distinct from those isolated exclusively from countries of Eastern and Central Europe,such as Serbia,Romania,and Poland.This study highlights the prevalence of B.burgdorferi s.l.in I.ricinus/I.inopinatus ticks,and reveals B.lusitaniae in I.inopinatus ticks for the first time in Tunisia.Conclusion:These findings suggest the involvement of I.inopinatus as a potential vector of this pathogenic genospeciess in Tunisia.This may help understanding the ecology of Ixodes ticks,the natural infection and the transmission dynamics of Borrelia species in this country.