Localizing introgression on the chromosome of rice by genomic in situ hybridization (GISH)

Genomic in situ hybridization was used to detect introgressed segment from Oryza australinesis onto the chromosomes of introgression line derived from the hybrid O. sativa x O. australinesis. Genomic DNA from Oryza australinesis was labeled with biotin and hybridized to the homologous sequences on the O. sativa chromosomes. The probe hybridization fluoresced green and non labeled O. sativa chromosomes appeared red or blue due to counterstaining with propidium iodide (PI) or 4,6-diamidino-2-phenylindole (DAPI). This differential painting of chromosomes unequivocally detected the introgressedsegment. Among the 200 cells analyzed, 6.5% of the cells showed  hybridization signal. Signal appeared on one chromosome in 5%, on two homologous chromosomes in 1% and on sister chromatids in 0.5%of the cells. Hybridization was seen on the short arm of the chromosome 12 of the introgression line

Application of the bacteriophage Mu-driven system for the integration/amplification of target genes in the chromosomes of engineered Gram-negative bacteria—mini review

The advantages of phage Mu transposition-based systems for the chromosomal editing of plasmid-less strains are reviewed. The cis and trans requirements for Mu phage-mediated transposition, which include the L/R ends of the Mu DNA, the transposition factors MuA and MuB, and the cis/trans functioning of the E element as an enhancer, are presented. Mini-Mu(LR)/(LER) units are Mu derivatives that lack most of the Mu genes but contain the L/R ends or a properly arranged E element in cis to the L/R ends. The dual-component system, which consists of an integrative plasmid with a mini-Mu and an easily eliminated helper plasmid encoding inducible transposition factors, is described in detail as a tool for the integration/amplification of recombinant DNAs. This chromosomal editing method is based on replicative transposition through the formation of a cointegrate that can be resolved in a recombination-dependent manner. (E-plus)- or (E-minus)-helpers that differ in the presence of the trans-acting E element are used to achieve the proper mini-Mu transposition intensity. The systems that have been developed for the construction of stably maintained mini-Mu multi-integrant strains of Escherichia coli and Methylophilus methylotrophus are described. A novel integration/amplification/fixation strategy is proposed for consecutive independent replicative transpositions of different mini-Mu(LER) units with “excisable” E elements in methylotrophic cells

AI-assisted optimization of the ECCE tracking system at the Electron Ion Collider

arXiv preprint [v2] Fri, 20 May 2022 03:23:44 UTC (2,296 KB) made available under a Creative Commons (CC BY) Attribution Licence, now in press, published by Elsevier: Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, available online 17 November 2022 at: https://doi.org/10.1016/j.nima.2022.167748The Electron-Ion Collider (EIC) is a cutting-edge accelerator facility that will study the nature of the "glue" that binds the building blocks of the visible matter in the universe. The proposed experiment will be realized at Brookhaven National Laboratory in approximately 10 years from now, with detector design and R&D currently ongoing. Notably, EIC is one of the first large-scale facilities to leverage Artificial Intelligence (AI) already starting from the design and R&D phases. The EIC Comprehensive Chromodynamics Experiment (ECCE) is a consortium that proposed a detector design based on a 1.5T solenoid. The EIC detector proposal review concluded that the ECCE design will serve as the reference design for an EIC detector. Herein we describe a comprehensive optimization of the ECCE tracker using AI. The work required a complex parametrization of the simulated detector system. Our approach dealt with an optimization problem in a multidimensional design space driven by multiple objectives that encode the detector performance, while satisfying several mechanical constraints. We describe our strategy and show results obtained for the ECCE tracking system. The AI-assisted design is agnostic to the simulation framework and can be extended to other sub-detectors or to a system of sub-detectors to further optimize the performance of the EIC detector.Office of Nuclear Physics in the Office of Science in the Department of Energy; National Science Foundation, and the Los Alamos National Laboratory Laboratory Directed Research and Development (LDRD) 20200022DR

Evaluation of appendicitis risk prediction models in adults with suspected appendicitis

Background Appendicitis is the most common general surgical emergency worldwide, but its diagnosis remains challenging. The aim of this study was to determine whether existing risk prediction models can reliably identify patients presenting to hospital in the UK with acute right iliac fossa (RIF) pain who are at low risk of appendicitis. Methods A systematic search was completed to identify all existing appendicitis risk prediction models. Models were validated using UK data from an international prospective cohort study that captured consecutive patients aged 16–45 years presenting to hospital with acute RIF in March to June 2017. The main outcome was best achievable model specificity (proportion of patients who did not have appendicitis correctly classified as low risk) whilst maintaining a failure rate below 5 per cent (proportion of patients identified as low risk who actually had appendicitis). Results Some 5345 patients across 154 UK hospitals were identified, of which two‐thirds (3613 of 5345, 67·6 per cent) were women. Women were more than twice as likely to undergo surgery with removal of a histologically normal appendix (272 of 964, 28·2 per cent) than men (120 of 993, 12·1 per cent) (relative risk 2·33, 95 per cent c.i. 1·92 to 2·84; P < 0·001). Of 15 validated risk prediction models, the Adult Appendicitis Score performed best (cut‐off score 8 or less, specificity 63·1 per cent, failure rate 3·7 per cent). The Appendicitis Inflammatory Response Score performed best for men (cut‐off score 2 or less, specificity 24·7 per cent, failure rate 2·4 per cent). Conclusion Women in the UK had a disproportionate risk of admission without surgical intervention and had high rates of normal appendicectomy. Risk prediction models to support shared decision‐making by identifying adults in the UK at low risk of appendicitis were identified

Linseed hydrogel-mediated green synthesis of silver nanoparticles for antimicrobial and wound-dressing applications

Muhammad Tahir Haseeb,1,2 Muhammad Ajaz Hussain,3 Khawar Abbas,3 Bahaa GM Youssif,4,5 Sajid Bashir,1 Soon Hong Yuk,2 Syed Nasir Abbas Bukhari5 1Faculty of Pharmacy, University of Sargodha, Sargodha, Pakistan; 2College of Pharmacy, Korea University, Sejong, Republic of Korea; 3Department of Chemistry, University of Sargodha, Sargodha, Pakistan; 4Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Assiut University, Assiut, Egypt; 5Department of Pharmaceutical Chemistry, College of Pharmacy, Aljouf University, Aljouf, Sakaka, Saudi Arabia Abstract: Polysaccharides are being extensively employed for the synthesis of silver nanoparticles (Ag NPs) having diverse morphology and applications. Herein, we present a novel and green synthesis of Ag NPs without using any physical reaction conditions. Linseed hydrogel (LSH) was used as a template to reduce Ag+ to Ag0. AgNO3 (10, 20, and 30 mmol) solutions were mixed with LSH suspension in deionized water and exposed to diffused sunlight. Reaction was monitored by noting the change in the color of reaction mixture up to 10 h. Ag NPs showed characteristic ultraviolet-visible (UV/Vis) absorptions from 410 to 437 nm in the case of sunlight and 397&ndash;410 nm in the case of temperature study. Transmission electron microscopy images revealed the formation of spherical Ag NPs in the range of 10&ndash;35 nm. Face-centered cubic array of Ag NPs was confirmed by characteristic diffraction peaks in powder X-ray diffraction spectrum. Ag NPs were stored in LSH thin films, and UV/Vis spectra recorded after 6 months indicated that Ag NPs retained their texture over the storage period. Significant antimicrobial activity was observed when microbial cultures (bacteria and fungi) were exposed to the synthesized Ag NPs. Wound-healing studies revealed that Ag NP&ndash;impregnated LSH thin films could have potential applications as an antimicrobial dressing in wound management procedures. Keywords: silver nanoparticles, green synthesis, antimicrobial studies, wound dressing, storage and stabilit