Rapid detection of FadA in Fusobacterium nucleatum using the quantitative LAMP colorimetric phenol red method in stool samples from colorectal cancer patients.

The study aimed to develop a quantitative colorimetric loop-mediated isothermal amplification technique using the phenol red indicator (QLAMP-PhR) for detecting Fusobacterium nucleatum (Fn) levels in colorectal cancer (CRC) patients and healthy individuals. QLAMP-PhR assays were conducted on 251 stool samples specific for the Fn FadA gene. Six primers were synthesized and utilized with master mix reagents, and a phenol red indicator was employed to enhance the QLAMP-PhR technique. A standard quantitative analysis curve was generated using a logarithmic function (absorbance vs. concentration) by serially diluting the copy number of genomic DNA templates (Fn ATCC25586). The CRC group exhibited a significantly higher abundance of Fn compared to the healthy control group (P < 0.001). These findings suggest that the QLAMP-PhR technique effectively identifies Fn specifically by its gene for the key virulence factor FadA. Additionally, ideas for developing a real-time QLAMP-PhR test were presented. Compared to the traditional polymerase chain reaction (PCR) technique, QLAMP-PhR offers several advantages including rapidity, simplicity, specificity, sensitivity, and cost-effectiveness method that can quantitatively screen for Fn presence in normal populations. The QLAMP-PhR method represents a sensitive and specific amplification assay for the rapid detection of the Fn pathogen. To the best of our knowledge, this study is the first to report the application of QLAMP-PhR for detecting FadA in Fn.

A hydrazine- and phosgene-free synthesis of tetrazinanones, precursors to 1,5-dialkyl-6-oxoverdazyl radicals.

A complementary approach to published synthetic methods for tetrazinanones, precursors to verdazyl radicals, is described herein. This approach uses carbohydrazide, a commercially available reagent, as a common starting material. Unlike previous methods described in the literature, this synthetic scheme does not rely on phosgene, phosgene substitutes, or the limited pool of commercially available monosubstituted hydrazines for its execution. A large variety of alkyl substitution patterns at the N-1 and N-5 positions of verdazyl radicals are possible, including both symmetrically and unsymmetrically substituted products. An initial condensation reaction of carbohydrazide with a specific aldehyde introduces the desired C-3 substituent in the final verdazyl radical product and protects the NH(2) groups during the subsequent N-1 and N-5 alkylation reactions. A succeeding methanolysis and concomitant ring-closing reaction gives the tetrazinanone. A number of known oxidation methods can then be employed to form the final verdazyl radical product.

Verdazyl radicals as substrates for organic synthesis: a synthesis of 3-methyl-5-aryl-1,3,4-oxadiazolones.

The synthesis of oxadiazolones under hydrolytic conditions is described for a series of 3-methyl-5-aryl-1,3,4-oxadiazolone compounds. The unique starting materials for the hydrolysis reaction are obtained from efficient 1,3-dipolar cycloaddition reactions of styrene and azomethine imine dipoles derived from verdazyl radicals via a disproportionation reaction. A proposed mechanism for the formation of these biologically relevant oxadiazolones includes an opening of the tetrazinone ring followed by a 5-exo-trig ring closure. In support of the mechanism, in one case the ring-opened intermediate was isolated and subsequently treated with acid to give the relevant oxadiazolone.

Inhibition of microbial growth by silver-starch nanocomposite thin films.

A sago starch biopolymer with embedded silver nanoparticles has been studied as a material for the prevention of microbial growth. Approximately 8 nm in size, silver nanoparticles have been synthesized by reduction of the silver salt in aqueous solution in the presence of sago starch using sodium borohydride as a reducing agent. The obtained solutions were cast on glass plates to obtain thin supported silver-starch nanocomposite films. The morphology of the nanocomposites was investigated by scanning and transmission electron microscopy. UV-Vis absorption spectroscopy showed that during the film formation a part of the silver nanoparticles has been trapped in the water present in the sample, which enabled their partial oxidation into active Ag(+) species. The oxidation of the silver nanoparticles was confirmed by X-ray photoelectron spectroscopy. The antimicrobial activity tests have shown that the nanocomposite material can be successfully employed to prevent the viability and growth of the common pathogens Staphylococcus aureus, Escherichia coli and Candida albicans.

Adsorption of sulfur onto a surface of silver nanoparticles stabilized with sago starch biopolymer.

Adsorption of sulfide ions onto a surface of starch capped silver nanoparticles upon addition of thioacetamide was investigated. UV-vis absorption spectroscopy revealed that the adsorption of the sulfide ion on the surface of the silver nanoparticles induced damping as well as blue shift of the silver surface plasmon resonance band. Further increase in thioacetamide concentration led to shift of the resonance band toward higher wavelengths indicating the formation of the continuous Ag2S layer on the silver surface. Thus fabricated nanoparticles were investigated using electron microscopy techniques (TEM, HRTEM, and HAADF-STEM) and X-ray photoelectron spectroscopy (XPS), which confirmed their core-shell structure.

Investigation of the fine structure of European populations with applications to disease association studies.

An investigation into fine-scale European population structure was carried out using high-density genetic variation on nearly 6000 individuals originating from across Europe. The individuals were collected as control samples and were genotyped with more than 300 000 SNPs in genome-wide association studies using the Illumina Infinium platform. A major East-West gradient from Russian (Moscow) samples to Spanish samples was identified as the first principal component (PC) of the genetic diversity. The second PC identified a North-South gradient from Norway and Sweden to Romania and Spain. Variation of frequencies at markers in three separate genomic regions, surrounding LCT, HLA and HERC2, were strongly associated with this gradient. The next 18 PCs also accounted for a significant proportion of genetic diversity observed in the sample. We present a method to predict the ethnic origin of samples by comparing the sample genotypes with those from a reference set of samples of known origin. These predictions can be performed using just summary information on the known samples, and individual genotype data are not required. We discuss issues raised by these data and analyses for association studies including the matching of case-only cohorts to appropriate pre-collected control samples for genome-wide association studies.