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Developing student heuristic characterizations to help them “Bond” with organic chemistry
(University of California Press, 2024-03) Mirkin, Philip Joshua
The volume of content and abstract nature of organic chemistry is challenging and potentially intimidating for students. I describe a strategy for facilitating student development of heuristic tools for engaging with the subject. By using experimental and researched data on carbon, oxygen, nitrogen, and hydrogen, the bulk chemical elements of organic chemistry, my students were encouraged to develop a “character reference” for each. The heuristics of characterization enabled them to relate more easily and engage more creatively with the work, including when working with complex organic molecules later on. I used this approach when teaching carbohydrates, alcohols, fats and proteins to 12- to 14-year-old students.
Executive compensation and gaps in South Africa's regulatory framework : a structured literature review and future agenda
(Allied Business Academies, 2024-02-08) Matemane, Matwale Reon; Moloi, Tankiso; Adelowotan, Michael
South Africa is a country with huge income gaps. Further, currently, there is trust deficit that is pervasive in many sectors of the economy which has been fueled by recent corporate scandals. As such, the study sought to determine whether the regulatory and disclosure framework currently in place is geared to address these challenges. A systematic literature review focusing on cross-country comparative study found several areas in which South Africa’s regulatory and disclosure requirements, particularly as it relates to the executive compensation could be enhanced. As such, the study suggests that practices deployed in countries that have faced trust deficit and are addressing these through enhanced practices could be adopted to enhance South Africa’s position. There are merits for policy makers to consider principles and practices such as mandatory pay-ratio disclosure, claw-back provision, binding shareholders’ say on pay, codetermination, inclusivity and mandating the supreme audit institution to conduct monitoring and evaluation as part of regulatory and disclosure regime. The deficiencies of the current regulatory and disclosure requirements open the system up to be exploited by greed.
Molecular characterization of hepatitis B virus in people living with HIV in rural and peri-urban communities in Botswana
(MDPI, 2024-07-14) Phinius, Bonolo B.; Choga , Wonderful T.; Anderson , Motswedi; Mokomane , Margaret; Gobe , Irene; Ratsoma, Tsholofelo; Phakedi , Basetsana; Mpebe , Gorata; Bhebhe , Lynnette; Gaolathe , Tendani; Mosepele, Mosepele; Makhema , Joseph; Shapiro , Roger; Lockman , Shahin; Musonda, Rosemary; Moyo, Sikhulile; Gaseitsiwe, Simani
BACKGROUND : Hepatitis B virus (HBV) sequencing data are important for monitoring HBV evolution. We aimed to molecularly characterize HBV sequences from participants with HBV surface antigen-positive (HBsAg+) serology and occult hepatitis B infection (OBI+).
METHODS : We utilized archived plasma samples from people living with human immunodeficiency virus (PLWH) in Botswana. HBV DNA was sequenced, genotyped and analyzed for mutations. We compared mutations from study sequences to those from previously generated HBV sequences in Botswana. The impact of OBI-associated mutations on protein function was assessed using the Protein Variation Effect Analyzer.
RESULTS : Sequencing success was higher in HBsAg+ than in OBI+ samples [86/128 (67.2%) vs. 21/71 (29.2%)]. Overall, 93.5% (100/107) of sequences were genotype A1, 2.8% (3/107) were D3 and 3.7% (4/107) were E. We identified 13 escape mutations in 18/90 (20%) sequences with HBsAg coverage, with K122R having the highest frequency. The mutational profile of current sequences differed from previous Botswana HBV sequences, suggesting possible mutational changes over time. Mutations deemed to have an impact on protein function were tpQ6H, surfaceV194A and preCW28L.
CONCLUSIONS : We characterized HBV sequences from PLWH in Botswana. Escape mutations were prevalent and were not associated with OBI. Longitudinal HBV studies are needed to investigate HBV natural evolution.
Advanced analysis of single-molecule spectroscopic data
(Cell Press, 2024-09) Botha, Joshua Leon; Van Heerden, Bertus; Kruger, T.P.J. (Tjaart); tjaart.kruger@up.ac.za
We present Full SMS, a multipurpose graphical user interface (GUI)-based software package for analyzing single-molecule spectroscopy (SMS) data. SMS typically delivers multiparameter data—such as fluorescence brightness, lifetime, and spectra—of molecular- or nanometer-scale particles such as single dye molecules, quantum dots, or fluorescently labeled biological macromolecules. Full SMS allows an unbiased statistical analysis of fluorescence brightness through level resolution and clustering, analysis of fluorescence lifetimes through decay fitting, as well as the calculation of second-order correlation functions and the display of fluorescence spectra and raster-scan images. Additional features include extensive data filtering options, a custom HDF5-based file format, and flexible data export options. The software is open source and written in Python but GUI based so it may be used without any programming knowledge. A multi-process architecture was employed for computational efficiency. The software is also designed to be easily extendable to include additional import data types and analysis capabilities.
Molecular epidemiology of carbapenemase‑producing Klebsiella pneumoniae in Gauteng South Africa
(Nature Research, 2024-11-09) Salvador-Oke, Kafilat Taiwo; Pitout, Johann D.D.; Peirano, Gisele; Strydom, Kathy‑Anne; Kingsburgh, Chanel; Ehlers, Marthie Magdaleen; Ismail, Arshad; Takawira, Faustinos T.; Kock, Marleen M.; marleen.kock@up.ac.za
Klebsiella pneumoniae multidrug-resistant (MDR) high-risk clones drive the spread of antimicrobial resistance (AMR) associated infections, resulting in limited therapeutic options. This study described the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa. Representative carbapenem-resistant [K. pneumoniae carbapenemase (KPC)-2, New-Delhi metallo-beta (β)-lactamase (NDM)-1, oxacillinase (OXA)-181, OXA-232, OXA-48, Verona integron-encoded metallo-β-lactamase (VIM)-1] K. pneumoniae isolates (n = 22) obtained from inpatient and outpatient’s urine (n = 9) and inpatients rectal carriage (n = 13) were selected for short-read whole genome sequencing. Klebsiella pneumoniae population include sequence type (ST)-307 (n = 3), ST2497 (n = 5) and ST17 (n = 4). The ST17 strains were exclusively obtained from rectal screening. Ten isolates co-harboured carbapenemase genes including β-lactamase gene encoding KPC-2 + OXA-181, NDM-1 + OXA-48 and NDM-1 + OXA-181. One ST307 isolate (UP-KT-73CKP) co-harboured three carbapenemase genes (blaNDM-1 + blaOXA-48 + blaOXA-181), while all the ST2497 strains co-harboured (blaNDM-1 + blaOXA-232). Phenotypically, hypermucoviscosity was observed in a single ST307 isolate. The ST307 isolate UP-KT-151UKP harboured colibactin genotoxins. The following mobile genetic elements were detected: plasmids [incompatibility group (Inc)-FIB(K), IncX3], and bacteriophages [e.g. Klebsi_ST16_OXA48phi5.4_NC_049450, Klebsi_3LV2017_NC_047817(36)]. The study highlights the importance of local genomic surveillance systems to characterise K. pneumoniae MDR high-risk clones. This data will aid in designing infection and prevention measures for limiting the spread of carbapenemase-producing K. pneumoniae in Gauteng, South Africa.