Development of Sequence-Tagged Site Marker Set for Identification of J, JS, and St Sub-genomes of Thinopyrum intermedium in Wheat Background

Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) is one of the important resources for the wheat improvement. So far, a few Th. intermedium (Thi)-specific molecular markers have been reported, but the number is far from enough to meet the need of identifying alien fragments in wheat-Th. intermedium hybrids. In this study, 5,877,409 contigs were assembled using the Th. intermedium genotyping-by-sequencing (GBS) data. We obtained 5,452 non-redundant contigs containing mapped Thi-GBS markers with less than 20% similarity to the wheat genome and developed 2,019 sequence-tagged site (STS) molecular markers. Among the markers designed, 745 Thi-specific markers with amplification products in Th. intermedium but not in eight wheat landraces were further selected. The distribution of these markers in different homologous groups of Th. intermedium varied from 47 (7/12/28 on 6J/6St/6JS) to 183 (54/62/67 on 7J/7St/7JS). Furthermore, the effectiveness of these Thi-specific markers was verified using wheat-Th. intermedium partial amphidiploids, addition lines, substitution lines, and translocation lines. Markers developed in this study provide a convenient, rapid, reliable, and economical method for identifying Th. intermedium chromosomes in wheat. In addition, this set of Thi-specific markers can also be used to estimate genetic and physical locations of Th. intermedium chromatin in the introgression lines, thus providing valuable information for follow-up studies such as alien gene mining.

MRI-guided breast biopsy based on diffusion-weighted imaging: a feasibility study

Objectives This study evaluated the feasibility of DWI for lesion targeting in MRI-guided breast biopsies. Furthermore, it assessed device positioning on DWI during biopsy procedures. Methods A total of 87 biopsy procedures (5/87 bilateral) consecutively performed between March 2019 and June 2020 were retrospectively reviewed: in these procedures, a preliminary DWI sequence (b = 1300 s/mm2) was acquired to assess lesion detectability. We included 64/87 procedures on lesions detectable at DWI; DWI sequences were added to the standard protocol to localize lesion and biopsy device and to assess the site marker correct positioning. Results Mass lesions ranged from 5 to 48 mm, with a mean size of 10.7 mm and a median size of 8 mm. Non-mass lesions ranged from 7 to 90 mm, with a mean size of 33.9 mm and a median size of 31 mm. Positioning of the coaxial system was confirmed on both T1-weighted and DWI sequences. At DWI, the biopsy needle was detectable in 62/64 (96.9%) cases; it was not visible in 2/64 (3.1%) cases. The site marker was always identified using T1-weighted imaging; a final DWI sequence was acquired in 44/64 cases (68.8%). In 42/44 cases (95.5%), the marker was recognizable at DWI. Conclusions DWI can be used as a cost-effective, highly reliable technique for targeting both mass and non-mass lesions, with a minimum size of 5 mm, detectable at pre-procedural DWI. DWI is also a feasible technique to localize the biopsy device and to confirm the deployment of the site marker. Key Points • MRI-guided breast biopsy is performed in referral centers by an expert dedicated staff, based on prior MR imaging; contrast agent administration is usually needed for lesion targeting. • DWI represents a feasible, highly reliable technique for lesion targeting, avoiding contrast agent administration. • DWI allows a precise localization of both biopsy needle device and site marker.

Comparison of pendimethalin binding properties of serum albumins from various mammalian species

Background To investigate the interaction of pendimethalin (PM), a commonly used herbicide, with various mammalian serum albumins. Methods The interactions of PM with serum albumins of bovine (BSA), sheep (SSA), porcine (PSA) and rabbit (RbSA) were studied using fluorescence quenching titration and site marker displacement experiments. Results A comparison of the PM-induced quenching of the fluorescence of these albumins with that published for human serum albumin (HSA) showed similarity between BSA and HSA. The PM binding affinity of these albumins was found to follow the order: SSA>BSA>RbSA>PSA. Warfarin (WFN) displacement results also suggested similar displacing action of PM on WFN-BSA complex, when compared to the published results on WFN-HSA complex. Conclusion The results suggested close similarity between BSA and HSA in terms of PM binding characteristics and hence bovine can be selected as a suitable animal model for further toxicological studies of PM.

Conversion of a diversity arrays technology marker differentiating wild and cultivated carrots to a co-dominant cleaved amplified polymorphic site marker.

Cultivated carrot and its wild ancestor co-occur in most temperate regions of the world and can easily hybridize. The genetic basis of the process of domestication in carrot is not well understood. Recent results of an investigation on genetic diversity structure of cultivated and wild carrot and signatures for domestication using Diversity Arrays Technology (DArT) allowed identification of polymorphisms differentiating wild and cultivated accessions. We selected one of these polymorphisms, showing the strongest evidence for directional selection in the course of domestication, and converted it into a co-dominant cleaved amplified polymorphic site (CAPS) marker named cult. To achieve that, we designed site-specific primers anchored in sequences flanking the original DArT clone, amplified and sequenced the PCR products derived from cultivated and wild carrot. A PstI restriction site present in the 'cultivated' variant and absent in the 'wild' was subsequently used for routine differentiation the two variants. We validated the cult marker on 88 accessions of cultivated and wild carrot, each represented by five individuals. The allelic variant associated with the wild phenotype was only rarely observed in cultivated carrot, mostly in purple-rooted accessions originating Turkey and Iran, possibly indicating that the physical association between the diagnostic polymorphism and the putative 'domestication gene' has been broken in a group of Eastern carrots.

Spectroscopic and Molecular Modeling Studies on Binding of Sparfloxacin to Humain Serum Albumin

The interaction between sparfloxacin (SPFX) and human serum albumin (HSA) had been studied by spectroscopic and molecular modeling methods. The inner filter effect was eliminated to get accurate binding parameters. The site marker competition experiments revealed that SPFX binds to site I (subdomain IIA) of HSA and molecular docking was employed to further define the specific binding sites.