Development of TaqMan Probe-Based Insulated Isothermal PCR (iiPCR) for Sensitive and Specific On-Site Pathogen Detection

Insulated isothermal PCR (iiPCR), established on the basis of Ralyeigh-Bénard convection, is a rapid and low-cost platform for nucleic acid amplification. However, the method used for signal detection, namely gel electrophoresis, has limited the application of iiPCR. In this study, TaqMan probe-based iiPCR system was developed to obviate the need of post-amplification processing. This system includes an optical detection module, which was designed and integrated into the iiPCR device to detect fluorescent signals generated by the probe. TaqMan probe-iiPCR assays targeting white spot syndrome virus (WSSV) and infectious myonecrosis virus were developed for preliminary evaluation of this system. Significant elevation of fluorescent signals was detected consistently among positive iiPCR reactions in both assays, correlating with amplicon detection by gel electrophoresis analysis. After condition optimization, a threshold value of S/N (fluorescent intensity_after/fluorescent intensity_before) for positive reactions was defined for WSSV TaqMan probe-iiPCR on the basis of 20 blank reactions. WSSV TaqMan probe-iiPCR generated positive S/Ns from as low as 10¹ copies of standard DNA and lightly infected Litopenaeus vannamei. Compared with an OIE-certified nested PCR, WSSV TaqMan probe-iiPCR showed a sensitivity of 100% and a specificity of 96.67% in 120 WSSV-free or lightly infected shrimp samples. Generating positive signals specifically and sensitively, TaqMan probe-iiPCR system has a potential as a low-cost and rapid on-site diagnostics method.     

On-site rapid detection of toxic <Emphasis Type="Italic">Alexandrium tamiyavanichii</Emphasis>: integrating the species-specific hydrolysis probe in insulated isothermal polymerase chain reaction (iiPCR)

On-site investigation of phytoplankton samples is important for rapid detection of harmful algal species and for early warning of harmful algal bloom. Molecular detection method by DNA amplification in a portable insulated isothermal PCR (iiPCR) device provides a simple and rapid detection based on fluorescent probe within an hour of reaction time. The assay was developed for a paralytic shellfish toxin-producing dinoflagellate Alexandrium tamiyavanichii. The assay presents the data as positive or negative on the presence or absence of A. tamiyavanichii cells, with a limit of detection (LOD) at five target cells per reaction. While the assay is incapable to accurately quantify cell density, it exhibits high detection accuracy and strongly correlated with quantitative PCR (qPCR) data. The user repeatability of iiPCR assay was evaluated; the results showed that no significant differences in the assay run by different operators. Field applicability of the assay was further validated by environmental samples. Despite the shortcoming of the assay, the overall performance of the assay to detect cells, its low-cost effectiveness, and portability for on-site detection, iiPCR has proven its potential as an early screening tool for harmful algae monitoring.     

Construction and verification of an infectious cDNA clone of coxsackievirus B5

Highlights:
· An infectious cDNA clone of CV-B5 was constructed.
· The rescued and parental virus possessed similar biological characteristics.
· The virulence of the rescued virus was similiar to that of the parental virus.
· Viral distribution and tissue tropism of those two viruses were in agreement.     

Identification of two novel B-cell epitopes on the nucleocapsid protein of porcine deltacoronavirus

Highlights
1. Two monoclonal antibodies against newly emerged porcine deltacoronavirus nucleocapsid protein were prepared.
2. The epitopes that these two monoclonal antibodies recognized on nucleocapsid protein were identified.
3. The monoclonal antibody 6B7 recognized a linear epitope of N protein, while the 7F8 recognized a conformational epitope.
4. Conservation of the identified epitopes between different coronaviruses was analyzed.     

Development of a biosensor assessing SARS-CoV-2 main protease proteolytic activity in living cells for antiviral drugs screening

Highlights:
The biosensor reported in our study can monitor SARS-CoV-2 M^pro activity in living cells instead of in vitro solutions.
The biosensor reported in our study is sensitive and easy to operate.
It is suitable for high-throughput screening.
It has the potential to be used in small animal models.     

Structures of SARS-CoV-2 spike protein alert noteworthy sites for the potential approaching variants

Highlights
1 Deletion of residues 156–157 warps the neighboring beta-sheet and leads NTD and RBD to shift.
2 T859N stabilizes the packing of the 630 loop motif to make RBD standing transition more difficult.
3 The overall structures of the closed state S complex from different variants resemble each other.
4 Mutations in FPPR may affect the overall structure of the trimeric spike protein.     

Saliva-based point-of-care testing techniques for COVID-19 detection

Highlights
1. The advantages of COVID-19 detection in saliva were systematically introduced.
2. Saliva-based POCT technologies for the detection of COVID-19 were reviewed.
3. A positive correlation between COVID-19 antibodies in saliva and serum was demonstrated.     

Infection and pathogenesis of the Delta variant of SARS-CoV-2 in Rhesus macaque

Highlights
1. Delta variant of SARS-CoV-2 can effectively infect the Rhesus macaque.
2. The Delta variant grows faster than the early strain isolated from Wuhan in late 2019.
3. The shedding pattern, viral load and disease severity of Delta variant are similar with the early strain isolated from Wuhan in late 2019.
4. This study supports the attributed rapid disease spread of the Delta variant.     

A single dose of recombinant VSV-RABVG vaccine provides full protection against RABV challenge

Highlights:
1. A replication-competent recombinant VSV with RABV-G protein replacement was generated.
2. Single dose of VSV-RABVG immunization induce potent antigen-specific humoral immune response, especially the virus neutralizing antibodies.
3. Mice intranasally immunized with single dose of VSV-RABVG were 100% protected upon RABV challenge.     

Differential miRNA expression profiling of highly pathogenic avian influenza virus H5N1 infected chicken lungs reveals critical microRNAs,biological pathways and genes involved in the molecular pathogenesis

Highlights
· Highthrouput sequencing of small RNA of H5N1 infected and mock infected chicken lungs.
· 297 miRNAs identified in mock-infected and 201 miRNAs identified in AIV infected chicken lungs.
· 36 miRNAs were upregulated and 90 were downregulated during H5N1 infection.
· Functional analysis and gene ontology of predicted target genes of expressed miRNAs.
· MAPK pathway, NF-κB, IGF and gga-let-7b might play important role during H5N1 pathogenesis.     

SARS-CoV-2 infection induces testicular injury in Rhesus macaque

Highlights
1 The infection of SARS-CoV-2 lead to varying degrees of testicular pathological damage.
2 The NP antigen of SARS-CoV-2 was not found in male reproductive system of rhesus macaque.
3 Infection-associated inflammatory insult and sex hormone fluctuations may account for the testicular pathophysiology.     

Enterovirus 71 3C proteolytically processes the histone H3 N-terminal tail during infection

Highlights
1. The N-terminal tail of histone H3 is specifically cleaved during EV71 infection.
2. Viral protease 3C is identified as a protease responsible for proteolytically processing the N-terminal H3 tail.
3. Our finding reveals a new epigenetic regulatory mechanism for Enterovirus 71 in virus-host interactions.     

Isolation and characterization of a novel linear-plasmid phage from the sediment of the Mariana Trench

Highlights
1. HMP1 is the first bacteriophage that was isolated from hadal sediment, the water depth at which HMP1 was isolated is the highest on record up to now.
2. The isolation of HMP1 extends the habitat of linear plasmid phages from the surface to the deep ocean.
3. The genomic and morphological features of HMP1 provide hints with regard to the vertical exchange of viral communities in the ocean.
4. HMP1 and Halomonas sp. MT08-1 contribute a useful phage-host system for in-depth analysis of the life strategy of viruses and their interactions with bacterial hosts in extreme hadal environments.     

A pair of SARS-CoV-2 nucleocapsid protein monoclonal antibodies shows high specificity and sensitivity for diagnosis

Highlights
1. Seven monoclonal antibodies (mAbs) against SARS-CoV-2 nucleocapsid protein are produced, which can be applied in ELISA, Western blotting, and immunofluorescence staining.
2. A pair of mAbs, 2G11/bio-1C7, can detect SARS-CoV-2 nucleocapsid protein as low as 15 pg/well in the double sandwich ELISA.
3. The mAb, 2G11, shows 97.4% sensitivity and 100% specificity for diagnosing the human blood samples.     

Recombinant human interferon-α1b inhibits SARS-CoV-2 better than interferon-α2b in vitro

Highlights
1) A comprehensive evaluation method for anti-SARS-CoV-2 drugs was established based on RT-qPCR, TCID₅₀ method, and immunofluorescence.
2) A significant antiviral effect of rHuIFN-α1b was shown with EC₅₀=0.12 IU/mL in Vero cells and EC₅₀=0.52 IU/mL in Calu-3 cells, which was better than rHuIFN-α2b (EC₅₀=0.25 IU/mL in Vero cells and EC₅₀=2.48 IU/mL in Calu-3 cells).
3) rHuIFN-α1b has a good potential in the application of anti-COVID-19 therapy.     

The role of photorespiration during drought stress: an analysis utilizing barley mutants with reduced activities of photorespiratory enzymes

C _i, intercellular CO₂ concentration
F_v/F_m, quantum efficiency of excitation capture by open photosystem II centres
FBPase, fructose-1,6-bisphosphatase
GAPDH, glyceraldehyde-3-phosphate dehydrogenase
GDC, glycine decarboxylase
GS-2, chloroplastic glutamine synthetase
HPR, hydroxypyruvate reductase
PFD, photon flux density
ΦCO₂, quantum efficiency of CO₂ assimilation
ΦPSII, quantum efficiency of photosystem II electron transport
ψ, water potential
q_N, non-photochemical chlorophyll a fluorescence quenching
q_P, photochemical chlorophyll a fluorescence quenching
RuBP, ribulose-1,5-bisphosphate
Rubisco, ribulose-1,5-bisphosphate carboxylase-oxygenase
SBPase, sedoheptulose-1,7-bisphosphatase
SGAT, serine : glyoxylate aminotransferase

The significance of photorespiration in drought-stressed plants was studied by withholding water from wild-type barley (Hordeum vulgare L.) and from heterozygous mutants with reduced activities of chloroplastic glutamine synthetase (GS-2), glycine decarboxylase (GDC) or serine : glyoxylate aminotransferase (SGAT). Well-watered plants of all four genotypes had identical rates of photosynthesis. Under moderate drought stress (leaf water potentials between –1 and –2 MPa), photosynthesis was lower in the mutants than in the wild type, indicating that photorespiration was increased under these conditions. Analysis of chlorophyll a fluorescence revealed that, in the GDC and SGAT mutants, the lower rates of photosynthesis coincided with a decreased quantum efficiency of photosystem II and increased non-photochemical dissipation of excitation energy. Correspondingly, the de-epoxidation state of xanthophyll-cycle carotenoids was increased several-fold in the drought-stressed GDC and SGAT mutants compared with the wild type. Accumulation of glycine in the GDC mutant was further evidence for increased photorespiration in drought-stressed barley. The effect of drought on the photorespiratory enzymes was determined by immunological detection of protein abundance. While the contents of GS-2 and P- and H-protein of the GDC complex remained unchanged as drought stress developed, the content of NADH-dependent hydroxypyruvate reductase increased. Enzymes of the Benson–Calvin cycle, on the other hand, were either not affected (ribulose-1,5-bisphosphate carboxylase-oxygenase and plastidic fructose-1,6-bisphosphatase) or declined (sedoheptulose- 1,7-bisphosphatase and NADP-dependent glyceraldehyde-3-phosphate dehydrogenase). These data demonstrate that photorespiration was enhanced during drought stress in barley and that the control exerted by photorespiratory enzymes on the rate of photosynthetic electron transport and CO₂ fixation was increased.     

The development of a novel diagnostic PCR for Madurella mycetomatis using a comparative genome approach

BackgroundEumycetoma is a neglected tropical disease most commonly caused by the fungus Madurella mycetomatis. Identification of eumycetoma causative agents can only be reliably performed by molecular identification, most commonly by species-specific PCR. The current M. mycetomatis specific PCR primers were recently discovered to cross-react with Madurella pseudomycetomatis. Here, we used a comparative genome approach to develop a new M. mycetomatis specific PCR for species identification.MethodologyPredicted-protein coding sequences unique to M. mycetomatis were first identified in BLASTCLUST based on E-value, size and presence of orthologues. Primers were then developed for 16 unique sequences and evaluated against 60 M. mycetomatis isolates and other eumycetoma causing agents including the Madurella sibling species. Out of the 16, only one was found to be specific to M. mycetomatis.ConclusionWe have discovered a predicted-protein coding sequence unique to M. mycetomatis and have developed a new species-specific PCR to be used as a novel diagnostic marker for M. mycetomatis.     

Structural and functional features of the leaves of Ranunculus trichophyllus Chaix., a freshwater submerged macrophophyte

AZA, 5-Acetamido-1,3,4-thiadiazole-2-sulphonamide
CA, carbonic anhydrase
DIC, dissolved inorganic carbon
Hepes, A-(2-hydroxyethyl)-1 piperazine-ethane sulfonic acid
IC, inorganic carbon
PAR, photosynthetic active radiation
PATAg, periodic acid-thiosemicarbazide-silver proteinate
Tris, tris (hydroxymethyl)-aminomethane

The structural and physiological strategies developed by the leaves of the freshwater macrophyte Ranunculus trichophyllus to adapt to submersed life were studied. Photosynthesis is carried out mainly by the epidermis cells of the numerous segments into which the leaf is finely dissected. In these cells, containing most of the chloroplasts, a peculiar organization of the wall has been identified by cytochemical tests. A thin compact outer region covers the cell surface and splits up forming large lacunae between adjacent cells. Below it, a thick and loose inner region rich in hydrophilic pectic acids occurs, which grows in along the cell sides giving rise to wide transfer areas. In this latter cell wall region, in which the cell/environment contact and exchanges are amplified, the systems for inorganic carbon supply to photosynthetic cells operate. The leaves of R. trichophyllus can rely on environmental CO₂ and HCO₃^– as sources of inorganic carbon for photosynthesis. A mechanism for bicarbonate utilization seems to involve its conversion to CO₂ by an apoplastic carbonic anhydrase, whose activity gains importance as the availability of environmental CO₂ decreases. Interestingly, it has been demonstrated that in this species CO₂ can also be obtained from HCO₃^– by a photodependent increase in plasmamembrane H⁺-ATPase activity in the transfer areas of the epidermis cells. This is the first time that such a mechanism has been noted in a nonpolar leaf of a submerged macrophyte.     

两种混合样品策略对揭示杜鹃花根部真菌多样性的影响

由于土壤微生物群落物种组成的高度空间异质性,混合样品(sample pooling)被广泛应用于微生物多样性与群落结构研究。在根部真菌的分子检测中,样品混合策略以及测序的克隆数或序列数均对揭示真菌群落结构的准确性有影响。【目的】为建立一套能快速准确地反映杜鹃花属植物根部真菌的物种组成与群落结构的分子检测技术平台,【方法】本研究采集锈红杜鹃和亮鳞杜鹃多份根系样品分别提取DNA,比较PCR扩增前和扩增后混合策略构建的克隆文库中真菌物种组成的差异。【结果】在2种宿主植物根系中,多份样品在PCR扩增后混合构建的克隆文库检测到的根部真菌物种丰富度、真菌群落的Shannon-Wiener多样性指数均高于扩增前混合的克隆文库。高频度的根部真菌在2种克隆文库中均检测到,但低频度的真菌物种组成在2种克隆文库中完全不同。更重要的是,当采用广泛应用的真菌通用引物ITS1f和ITS4扩增根部真菌ITS序列时,PCR扩增后混合的方法能有效地减轻杜鹃花属植物ITS序列被优先扩增的现象。真菌物种累积曲线显示,当测序的真菌ITS片段克隆数达到50个左右,即能较全面地反映2种杜鹃花根部真菌物种组成。【结论】独立扩增多份根系样品DNA,再将PCR产物混合构建克隆文库的方法能更全面地揭示杜鹃花属植物根部真菌物种丰富度与物种组成。