Optimization of Plant Growth Regulators for In Vitro Mass Propagation of a Disease-Free 'Shine Muscat' Grapevine Cultivar.

This study addresses the propagation challenges faced by 'Shine Muscat', a newly introduced premium grapevine cultivar in South Korea, where multiple viral infections pose considerable economic loss. The primary objective was to establish a robust in vitro propagation method for producing disease-free grapes and to identify effective plant growth regulators to facilitate large-scale mass cultivation. After experimentation, 2.0 µM 6-benzyladenine (BA) exhibited superior shoot formation in the Murashige and Skoog medium compared with kinetin and thidiazuron. Conversely, α-naphthaleneacetic acid (NAA) hindered shoot growth and induced callus formation, while indole-3-butyric acid (IBA) and indole-3-acetic acid (IAA) demonstrated favorable root formation, with IBA showing better results overall. Furthermore, inter simple sequence repeat analysis confirmed the genetic stability of in vitro-cultivated seedlings using 2.0 µM BA and 1.0 µM IBA, validating the suitability of the developed propagation method for generating disease-free 'Shine Muscat' grapes. These findings offer promising prospects for commercial grape cultivation, ensuring a consistent supply of healthy grapes in the market.

Effect of the size of the bony access window and the collagen barrier over the window in sinus floor elevation: a preclinical investigation in a rabbit sinus model.

PURPOSE: The aim of this study was to investigate the effect of (1) the size of the bony access window and (2) collagen membrane coverage over the window in sinus floor elevation in a rabbit sinus model. METHODS: Small bony access windows (SW; ø 2.8 mm) were made in 6 rabbits and large windows (LW; ø 6 mm) in 6 other rabbits. Both sinuses in each rabbit were allocated to groups with or without coverage of a collagen membrane (CM) on the window, resulting in 4 groups: SW, LW, SW+CM, and LW+CM. After 4 weeks of healing, micro-computed tomographic, histologic, and histomorphometric analyses were performed. RESULTS: Bony healing in the window area was incomplete in all groups, but most bone graft particles were well confined in the augmented cavity. Histologically, the pattern of new bone formation was similar in all groups. Histomorphometrically, the percentage of newly formed bone was greater in the groups with CM than in the groups without CM, and in the groups with SW than in the groups with LW (12.92%±6.40% in the SW+CM group, 4.21%±7.73% in the SW group, 10.45%±4.81% in the LW+CM group, 11.77%±3.83% in the LW group). The above differences were not statistically significant (P>0.05). CONCLUSIONS: The combination of a small bony access window and the use of a collagen membrane over the window favored new bone formation compared to other groups, but this result should be further investigated due to the limitations of the present animal model.

Total integrated slidable and valveless solid phase extraction-polymerase chain reaction-capillary electrophoresis microdevice for mini Y chromosome short tandem repeat genotyping.

A fully integrated slidable and valveless microsystem, which performs solid phase DNA extraction (SPE), micro-polymerase chain reaction (µPCR) and micro-capillary electrophoresis (µCE) coupled with a portable genetic analyser, has been developed for forensic genotyping. The use of a slidable chip, in which a 1 µL-volume of the PCR chamber was patterned at the center, does not necessitate any microvalves and tubing systems for fluidic control. The functional micro-units of SPE, µPCR, and µCE were fabricated on a single glass wafer by conventional photolithography, and the integrated microdevice consists of three layers: from top to bottom, a slidable chip, a channel wafer in which a SPE chamber, a mixing microchannel, and a CE microchannel were fabricated, and a Ti/Pt resistance temperature detector (RTD) wafer. The channel glass wafer and the RTD glass wafer were thermally bonded, and the slidable chip was placed on the designated functional unit. The entire process from the DNA extraction using whole human blood sample to identification of target Y chromosomal short tandem repeat (STR) loci was serially carried out with simply sliding the slidable chamber from one to another functional unit. Monoplex and multiplex detection of amelogenin and mini Y STR loci were successfully analysed on the integrated slidable SPE-µPCR-µCE microdevice by using 1 µL whole human blood within 60 min. The proposed advanced genetic analysis microsystem is capable of point-of-care DNA testing with sample-in-answer-out capability, more importantly, without use of complicated microvalves and microtubing systems for liquid transfer.

Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup distribution in Pathans of Pakistan.

We analyzed haplotypes for 22 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and five additional STRs (DYS388, DYS446, DYS447, DYS449 and DYS464), and Y chromosomal haplogroup distribution in 270 unrelated individuals from the Pathans residing in the Federally Administered Tribal Areas and the North-West Frontier Province of Pakistan using in-house multiplex PCR systems. Each Y-STR showed diversities ranging from 0.2506 to 0.8538, and the discriminatory capacity (DC) was 73.7% with 199 observed haplotypes using 17 Yfiler loci. By the addition of 5 Y-STRs to the Yfiler system, the DC was increased to 85.2% while showing 230 observed haplotypes. Among the additional 5 Y-STRs, DYS446, DYS447 and DYS449 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Pathans of this study showed significant differences from other Pathan populations as well as neighboring population sets. In Y-SNP analysis, a total of 12 Y chromosomal haplogroups were observed and the most frequent haplogroup was R1a1a with 49.3% frequency. To obtain insights on the origin of Pathans, the network analysis was performed for the haplogroups G and Q observed from the Pathans and the Jewish population groups including Ashkenazim and Sephardim, but little support for a Jewish origin could be found. In the present study, we report Y-STR population data in Pathans of Pakistan, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity.

High-throughput STR analysis for DNA database using direct PCR.

Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner.

Collaborative genetic mapping of 12 forensic short tandem repeat (STR) loci on the human X chromosome.

A large number of short tandem repeat (STR) markers spanning the entire human X chromosome have been described and established for use in forensic genetic testing. Due to their particular mode of inheritance, X-STRs often allow easy and informative haplotyping in kinship analyses. Moreover, some X-STRs are known to be tightly linked so that, in combination, they constitute even more complex genetic markers than each STR taken individually. As a consequence, X-STRs have proven particularly powerful in solving complex cases of disputed blood relatedness. However, valid quantification of the evidence provided by X-STR genotypes in the form of likelihood ratios requires that the recombination rates between markers are exactly known. In a collaborative family study, we used X-STR genotype data from 401 two- and three-generation families to derive valid estimates of the recombination rates between 12 forensic markers widely used in forensic testing, namely DXS10148, DXS10135, DXS8378 (together constituting linkage group I), DXS7132, DXS10079, DXS10074 (linkage group II), DXS10103, HPRTB, DXS10101 (linkage group III), DXS10146, DXS10134 and DXS7423 (linkage group IV). Our study is the first to simultaneously allow for mutation and recombination in the underlying likelihood calculations, thereby obviating the bias-prone practice of excluding ambiguous transmission events from further consideration. The statistical analysis confirms that linkage groups I and II are transmitted independently from one another whereas linkage groups II, III and IV are characterised by inter-group recombination fractions that are notably smaller than 50%. Evidence was also found for recombination within all four linkage groups, with recombination fraction estimates ranging as high as 2% in the case of DXS10146 and DXS10134.

DNA typing for the identification of old skeletal remains from Korean War victims.

The identification of missing casualties of the Korean War (1950-1953) has been performed using mitochondrial DNA (mtDNA) profiles, but recent advances in DNA extraction techniques and approaches using smaller amplicons have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Therefore, 21 skeletal remains of Korean War victims and 24 samples from biological relatives of the supposed victims were selected based on circumstantial evidence and/or mtDNA-matching results and were analyzed to confirm the alleged relationship. Cumulative likelihood ratios were obtained from autosomal short tandem repeat, Y-chromosomal STR, and mtDNA-genotyping results, and mainly confirmed the alleged relationship with values over 105. The present analysis emphasizes the value of mini- and Y-STR systems as well as an efficient DNA extraction method in DNA testing for the identification of old skeletal remains.

Simple and highly effective DNA extraction methods from old skeletal remains using silica columns.

The recovery of DNA data from old skeletal remains is often difficult due to degraded and very low yield of extracted DNA and the presence of PCR inhibitors. Herein, we compared several silica-based DNA extraction methods from artificially degraded DNA, DNA with PCR inhibitors and DNA from old skeletal remains using quantitative real-time PCR. We present a modified large-scale silica-based extraction combined with complete demineralization, that enables maximum DNA recovery and efficient elimination of PCR inhibitors. This is performed with high concentration of EDTA solution for demineralization of bone powder followed by QIAamp spin columns and buffers from the QIAquick PCR purification kit. We have successfully used this modified technique to perform STR analysis for 55-year-old skeletal remains. The results of this study will contribute to solve the forensic cases dealing with skeletal remains.

Population genetic study of four closely-linked X-STR trios in Koreans.

We investigated four X chromosomal short tandem repeat (X-STR) markers (DXS10079, DXS10103, DXS10146, and DXS10148) in 450 unrelated Koreans (300 males and 150 females), and evaluated their forensic usage in relation to the four X-STR linkage groups. Forensic statistical parameters for these X-STR markers indicated that they are highly informative for forensic application in Koreans. No significant deviations from Hardy-Weinberg equilibrium were observed in any of the four X-STR markers. In addition, we present haplotypes and their frequency data for four linkage groups each comprised of three X-STRs (DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074, DXS10103-HPRTB-DXS10101, and DXS10146-DXS10134-DXS7423) in 300 males. Haplotype diversity values in the four linkage trios were all higher than 0.98, and 77.1% of all haplotypes showed a frequency less than 0.01. Therefore, the four closely-linked X-STR trios will contribute to complex kinship testing in Koreans.

Genetic polymorphism and haplotype analysis of 4 tightly linked X-STR duos in Koreans.

AIM: To investigate genetic polymorphism and haplotypes of tightly linked X-chromosomal short tandem repeat (X-STR) clusters in Koreans. METHODS: Four X-STR duos in the linkage group 1-4 (DXS10135-DXS8378, DXS7132-DXS10074, HPRTB-DXS10101, and DXS10134-DXS7423) were investigated in 450 unrelated Koreans (300 men and 150 women) using the Mentype Argus X-8 Polymerase Chain Reaction Amplification Kit. RESULTS: No significant deviation from Hardy-Weinberg equilibrium was observed in any of the 8 loci. DXS10135 was the most polymorphic X-STRs, with 25 alleles and DXS7423 was the least informative, with 5 alleles. Eleven off-ladder alleles and a triallelic pattern were observed, and these alleles were characterized by cloning and sequencing analysis. In 300 Korean men, 38 to 59 haplotypes were observed for each linkage duo with 91.6-96.6% of haplotype diversities. However, due to the low genetic diversity of DXS7423, the X-STR duo in linkage group 4 (DXS10134-DXS7423), in comparison with other linkage duos, had considerably lower haplotype diversity values (91.6%) with 3 common haplotypes (35-15, 36-15, and 37-15) observed in 44.3% of Koreans. CONCLUSION: Four X-STR duos in the linkage group 1-4 will be able to provide a powerful tool for solving complex kinship cases in Koreans. However, to increase the haplotype diversity in the linkage group 4, it will be useful to discover a new marker for Asians that can serve as an adequate substitute for DXS7423 or at least complement the existing linkage duo of DXS10134-DXS7423.