Com probe implemented STexS II greatly enhances specificity in SARS-CoV-2 variant detection.

The initial introduction of utilizing double helix structural oligonucleotides known as SNP typing with excellent specificity (STexS) in a standard PCR greatly improved the detection of single nucleotide polymorphisms (SNP) by enhancing amplification rates of primer-matching strands and interrupting mismatched strands by constant instability of kinetics regarding alignment attaching and detaching. The model was beneficial overall in detecting SNP variants consisting of large amounts of wildtype strands such as EGFR mutation genotyping for early detection of non-small cell lung cancer. While the STexS PCR is advantageous in detecting SNPs and biomarkers, limitations were yet observed. Despite the ability to detect variants 10 times more effective than a typical amplification-refractory mutation system PCR, it could only perform optimally in DNA concentrations around 101 ~ 105. To further enhance STexS specificity to perform detecting viral-RNA variants such as the infamous SARS-CoV-2, a novel improvement of the regular TaqMan Probe using Com-probes to inhibit high copy wild targets and amplify low copy mutant targets. By introducing the novel STexS II, omicron variants of SARS-CoV-2 were able to be successfully detected in high concentrations of normal genes.

Inclusion of double helix structural oligonucleotide (STexS) results in an enhance of SNP specificity in PCR.

Genetic mutations such as single nucleotide polymorphisms (SNP) are known as one of the most common forms which related to various genetic disorders and cancers. Among of the methods developed for efficient detection of such SNP, polymerase chain reaction (PCR) methods are widely used worldwide for its cost and viable advantages. However, the technique to discriminate small amounts of SNP mixed in abundant normal DNA is incomplete due to intrinsic technical problems of PCR such as amplification occurring even in 3'mismatched cases because of high enzyme activity of DNA polymerases. To overcome the issue, specifically designed PCR platform, STexS (SNP typing with excellent specificity) using double stranded oligonucleotides was implemented as a means to emphasize the amplification of SNP templates by decreasing unwanted amplification of 3'mismatched DNA copies. In this study, the results indicate several EGFR mutations were easily detected specifically utilizing the STexS platform. Further trials show the novel method works effectively to discriminate mutations in not only general allele specific (AS)-PCRs, but also amplification refractory mutation system (ARMS)-PCR. The STexS platform will give aid in PCRs targeting potential SNPs or genetically mutated biomarkers in human clinical samples.

Transurethral resection of fibrotic scar tissue combined with temporary urethral stent placement for patients with in anterior urethral stricture.

INTRODUCTION: Fibrotic scar formation is a main cause of recurrent urethral stricture after initial management with direct vision internal urethrotomy (DVIU). In the present study, we devised a new technique of combined the transurethral resection of fibrotic scar tissue and temporary urethral stenting, using a thermo-expandable urethral stent (Memokath(TM) 044TW) in patients with anterior urethral stricture. MATERIALS AND METHODS: As a first step, multiple incisions were made around stricture site with cold-utting knife and Collins knife electrode to release a stricture band. Fibrotic tissue was then resected with a 13Fr pediatric resectoscope before deployment of a MemokathTM 044TW stent (40 - 60mm) on a pre-mounted sheath using 0° cystoscopy. Stents were removed within12 months after initial placement. RESULTS: We performed this technique on 11 consecutive patients with initial (n = 4) and recurrent (n = 7) anterior urethral stricture (April 2009 ­ February 2013). At 18.9 months of mean follow-up (12-34 months), mean Qmax (7.8±3.9ml/sec vs 16.8 ± 4.8ml/sec, p < 0.001), IPSS (20.7 vs 12.5, p = 0.001 ), and QoL score (4.7 vs 2.2, p < 0.001) were significantly improved. There were no significant procedure-related complications except two cases of tissue ingrowth at the edge of stent, which were amenable by transurethral resection. In 7 patients, an average 1.4 times (1-5 times) of palliative urethral dilatation was carried out and no patients underwent open surgical urethroplasty during the follow-up period. CONCLUSION: Combined transurethral resection and temporary urethral stenting is a effective therapeutic option for anterior urethral stricture. Further investigations to determine the long-term effects, and safety profile of this new technique are warranted.

Transurethral resection of fibrotic scar tissue combined with temporary urethral stent placement for patients with in anterior urethral stricture

Introduction Fibrotic scar formation is a main cause of recurrent urethral stricture after initial management with direct vision internal urethrotomy (DVIU). In the present study, we devised a new technique of combined the transurethral resection of fibrotic scar tissue and temporary urethral stenting, using a thermo-expandable urethral stent (MemokathTM 044TW) in patients with anterior urethral stricture. Materials and Methods As a first step, multiple incisions were made around stricture site with cold-cutting knife and Collins knife electrode to release a stricture band. Fibrotic tissue was then resected with a 13Fr pediatric resectoscope before deployment of a MemokathTM 044TW stent (40 – 60mm) on a pre-mounted sheath using 0° cystoscopy. Stents were removed within 12 months after initial placement. Results We performed this technique on 11 consecutive patients with initial (n = 4) and recurrent (n = 7) anterior urethral stricture (April 2009 – February 2013). At 18.9 months of mean follow-up (12-34 months), mean Qmax (7.8±3.9ml/sec vs 16.8 ± 4.8ml/sec, p < 0.001), IPSS (20.7 vs 12.5, p = 0.001 ), and QoL score (4.7 vs 2.2, p < 0.001) were significantly improved. There were no significant procedure-related complications except two cases of tissue ingrowth at the edge of stent, which were amenable by transurethral resection. In 7 patients, an average 1.4 times (1-5 times) of palliative urethral dilatation was carried out and no patients underwent open surgical urethroplasty during the follow-up period. Conclusion Combined transurethral resection and temporary urethral stenting is a effective therapeutic option for anterior urethral stricture. Further investigations to determine the long-term effects, and safety profile of this new technique are warranted. .

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery.

Although the genomes of many microbial pathogens have been studied to help identify effective drug targets and novel drugs, such efforts have not yet reached full fruition. In this study, we report a systems biological approach that efficiently utilizes genomic information for drug targeting and discovery, and apply this approach to the opportunistic pathogen Vibrio vulnificus CMCP6. First, we partially re-sequenced and fully re-annotated the V. vulnificus CMCP6 genome, and accordingly reconstructed its genome-scale metabolic network, VvuMBEL943. The validated network model was employed to systematically predict drug targets using the concept of metabolite essentiality, along with additional filtering criteria. Target genes encoding enzymes that interact with the five essential metabolites finally selected were experimentally validated. These five essential metabolites are critical to the survival of the cell, and hence were used to guide the cost-effective selection of chemical analogs, which were then screened for antimicrobial activity in a whole-cell assay. This approach is expected to help fill the existing gap between genomics and drug discovery.

Draft genome sequence of Streptomyces clavuligerus NRRL 3585, a producer of diverse secondary metabolites.

Streptomyces clavuligerus is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics.

Genome sequence of the polymyxin-producing plant-probiotic rhizobacterium Paenibacillus polymyxa E681.

Paenibacillus polymyxa E681, a spore-forming, low-G+C, Gram-positive bacterium isolated from the rhizosphere of winter barley grown in South Korea, has great potential for agricultural applications due to its ability to promote plant growth and suppress plant diseases. Here we present the complete genome sequence of P. polymyxa E681. Its 5.4-Mb genome encodes functions specialized to the plant-associated lifestyle and characteristics that are beneficial to plants, such as the production of a plant growth hormone, antibiotics, and hydrolytic enzymes.

Proteome analysis of red deer antlers.

Deer antlers are the only mammalian organs capable of repeated regeneration. Although antlers are known to develop from pedicles, which arise from antlerogenic cells of cranial periosteum, their developmental process is not fully elucidated. For example, while endocrine and environmental factors influence the antler development, it is still unclear which signaling pathways are involved in the transduction of such stimuli. To study the developmental process of antlers and identify proteins functioning in their growth, we have established proteome maps of red deer (Cervus elaphus) antlers. With two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry, we analyzed more than 800 protein spots and identified approximately 130 individual proteins derived from the growing tip of antlers. The overall profile of the antler proteome was dissimilar to those of other types of tissue. Also comparison of proteomes derived from proximal bony tissue and the growing tip of antlers revealed substantial differences. Moreover several cell growth or signaling-related proteins are expressed exclusively in the growing tip, suggesting that these proteins function in the growth and differentiation of antlers. Currently, using the antler proteome maps, we are actively searching for the regulatory factor(s) that may control the antler development.

Molecular cloning and characterization of a 2-deoxystreptamine biosynthetic gene cluster in gentamicin-producing Micromonospora echinospora ATCC15835.

The organization of the 2-deoxystreptamine (DOS) biosynthetic gene cluster of Micromonospora echinospora has been determined. Sequencing of a 14.04 kb-region revealed twelve open reading frames (ORFs): four putative DOS biosynthetic genes (gtmA, B, C, and D), five amino sugars biosynthetic genes (gtmE, G, H, I, and gacB), two aminoglycoside resistance genes (gtmF and J) as well as a hypothetical ORF (gacA). One of the putative DOS biosynthetic genes, gtmA, was expressed in Escherichia coli, and the purified protein was shown to convert glucose-6-phosphate (G-6-P) to 2-deoxy-scyllo-inosose (DOI), a key step in DOS biosynthesis. In addition gtmJ was expressed in Streptomyces lividans and shown to confer gentamicin resistance. Thus gtmA and gtmJ are implicated in the biosynthesis of gentamicin and in resistance to it, respectively.

The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens.

The rumen represents the first section of a ruminant animal's stomach, where feed is collected and mixed with microorganisms for initial digestion. The major gas produced in the rumen is CO(2) (65.5 mol%), yet the metabolic characteristics of capnophilic (CO(2)-loving) microorganisms are not well understood. Here we report the 2,314,078 base pair genome sequence of Mannheimia succiniciproducens MBEL55E, a recently isolated capnophilic Gram-negative bacterium from bovine rumen, and analyze its genome contents and metabolic characteristics. The metabolism of M. succiniciproducens was found to be well adapted to the oxygen-free rumen by using fumarate as a major electron acceptor. Genome-scale metabolic flux analysis indicated that CO(2) is important for the carboxylation of phosphoenolpyruvate to oxaloacetate, which is converted to succinic acid by the reductive tricarboxylic acid cycle and menaquinone systems. This characteristic metabolism allows highly efficient production of succinic acid, an important four-carbon industrial chemical.