Research Articles (Biotechnology)

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Abolishment of morphology‑based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee
(Springer, 2023) Turner, Dann; Shkoporov, Andrey N.; van Zyl, Leonardo J.
This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratifed by vote in 2022. Signifcant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
Acyldepsipeptide analogues: A future generation antibiotics for Tuberculosis treatment
(MDPI, 2022) Cobongela, Sinazo Z. Z.; Makatini, Maya M.; Sibuyi, Nicole R. S.
Acyldepsipeptides (ADEPs) are a new class of emerging antimicrobial peptides (AMPs), which are currently explored for treatment of pathogenic infections, including tuberculosis (TB). These cyclic hydrophobic peptides have a unique bacterial target to the conventional anti-TB drugs, and present a therapeutic window to overcome Mycobacterium Tuberculosis (M. tb) drug resistance. ADEPs exerts their antibacterial activity on M. tb strains through activation of the protein homeostatic regulatory protease, the caseinolytic protease (ClpP1P2). ClpP1P2 is normally regulated and activated by the ClpP-ATPases to degrade misfolded and toxic peptides and/or short proteins. ADEPs bind and dysregulate all the homeostatic capabilities of ClpP1P2 while inducing non-selective proteolysis. The uncontrolled proteolysis leads to M. tb cell death within the host.
Adapting the yeast consolidated bioprocessing paradigm for biorefineries
(Green Wave Publishing of Canada, 2018) den Haan, Riaan
Despite decades long development, no natural or engineered organism has been isolated that can produce commodity products at the rates and yields required by industry via direct microbial conversion. However, new genomic editing tools and systems level knowledge of metabolism provides opportunities to develop yeast strains for second-generation biorefineries.
The air quality perceptions of the residents of Bayview, Mossel Bay
(NACA, 2014) Schoeman, J.P.; Schutte, D.
Background: In developing countries, it often occurs that little attention is given to air pollution emissions due to a lack of proper town planning, household combustion processes, energy production and the continuous growth in the transport sector (Norman et al., 2007:783). There is an increase in urban air pollution in most of the major cities of developing countries which is amplified by population growth and industrialization (World Resource Institute, 1998, 1999:1). Air pollution studies are not complete, and may fail if the quality of life and the perceptions of the studied community are not taken into consideration. This paper investigates the air quality perceptions of a high income residency surrounded by industrial activities and Mossel Bay was rated as to have potentially poor air quality by the South African Department of Environmental Affairs and Tourism. Methods: A cross-sectional survey was carried out in Bayview, Mossel Bay. The perceptions of the respondents were collected by a structured questionnaire. Components of perceptions that were tested included general opinion regarding air quality, visual perceptions of air quality, type of pollutants such as smoke and dust, perceptions regarding the source of air pollution, perceptions regarding the municipal health institution controlling air quality in Bayview, etc. These perceptions were investigated by age, gender, socio-economic status etc.
Alteration of Bax-to-Bcl-2 ratio modulates the anticancer activity of methanolic extract of Commelina benghalensis (Commelinaceae) in Jurkat T cells
(Academic Journals, 2008) Mbazima, Vusi G.; Mokgotho, Matlou P.; February, Faghri; Rees, Jasper G.; Mampuru, Leseilane J.
Stem extracts of Commelina benghalensis (Linn.), although not extensively documented, are frequently used in traditional medicine for the treatment of ailments such as skin malformations and outgrowths. Accordingly, the study was aimed to investigate possible molecular mechanisms that are associated with the potential anti-carcinogenic property of this agrofield weed. Jurkat T cells were exposed to different concentrations (0-600 ug/ml) of the crude methanolic extract of C. benghalensis to evaluate their growth inhibitory and apoptosis inducing effects. The extract elicited a dose- and time-dependent inhibition of cell proliferation, followed by a concomitant decrease in cell viability. The observed cytotoxicity was linked to the induction of apoptosis as determined by morphological and biochemical features known to be associated with the advent of apoptosis. Real time quantitative RT-PCR and Western blot analyses of Bax, Bcl-2 and p53 exhibited aberrant expression profiles of these genes under various treatment conditions. Taken together, the data suggest that the crude methanolic extract of C. benghalensis contains bioactive compounds that may be beneficial in the treatment of malignant growths, and that this apparent antineoplastic activity is a consequence of dysregulated expression of apoptosis-responsive genes. These observations could provide a credible scientific justification upon which the ethnopharmacological utilisation of C. benghalensis is founded.
Analysis of the differentially expressed proteins and metabolic pathways of honeybush (cyclopia subternata) in response to water deficit stress
(MDPI, 2023) Mahlare, Mary-Jane S; Husselmann, Lizex; Lewu, Muinat N
Honeybush (Cyclopia spp.) is a rich source of antioxidant properties and phenolic compounds. Water availability plays a crucial role in plant metabolic processes, and it contributes to overall quality. Thus, this study aimed to investigate changes in molecular functions, cellular components, and biological processes of Cyclopia subternata exposed to different water stress conditions, which include well-watered (as Control, T1), semi-water stressed (T2), and water-deprived (T3) potted plants. Samples were also collected from a well-watered commercial farm first cultivated in 2013 (T13) and then cultivated in 2017 (T17) and 2019 (T19). Differentially expressed proteins extracted from C. subternata leaves were identified using LC-MS/MS spectrometry. A total of 11 differentially expressed proteins (DEPs) were identified using Fisher’s exact test (p < 0.00100). Only α-glucan phosphorylase was found to be statistically common between T17 and T19 (p < 0.00100). Notably, α-glucan phosphorylase was upregulated in the older vegetation (T17) and downregulated in T19 by 1.41-fold. This result suggests that α-glucan phosphorylase was needed in T17 to support the metabolic pathway. In T19, five DEPs were upregulated, while the other six were downregulated.
Analytical studies of antimicrobial peptides as diagnostic biomarkers for the detection of bacterial and viral Pneumonia
(MDPI, 2022) Bakare, Olalekan Olanrewaju; Gokul, Arun; Keyster, Marshall
Pneumonia remains one of the leading causes of infectious mortality and significant economic losses among our growing population. The lack of specific biomarkers for correct and timely diagnosis to detect patients’ status is a bane towards initiating a proper treatment plan for the disease; thus, current biomarkers cannot distinguish between pneumonia and other associated conditions such as atherosclerotic plaques and human immunodeficiency virus (HIV). Antimicrobial peptides (AMPs) are potential candidates for detecting numerous illnesses due to their compensatory roles as theranostic molecules. This research sought to generate specific data for parental AMPs to identify viral and bacterial pneumonia pathogens using in silico technology.
Antibacterial activity of biogenic silver and gold nanoparticles synthesized from Salvia africana-lutea and Sutherlandia frutescens
(Nanotechnology, 2020) Dube, Phumuzile
Nanoparticles (NPs) synthesized using various chemical and physical methods are often cytotoxic which restricts their use in biomedical applications. In contrast, metallic biogenic NPs synthesized using biological systems such as plant extracts are said to be safer and their production more cost effective. NPs synthesized from plants with known medicinal properties can potentially have similar bioactivities as these plants. It has been shown that Salvia africana-lutea (SAL) and Sutherlandia frutescens (SF) have antibacterial activities. This study used water extracts of SAL and SF to produce biogenic silver NPs (AgNPs) and gold NPs (AuNPs). The antibacterial activity of AgNPs and AuNPs was tested against two pathogens (Staphylococcus epidermidis and P. aeruginosa). NP synthesis was optimized by varying the synthesis conditions which include synthesis time and temperature, plant extract concentration, silver nitrate (AgNO3) concentration and sodium tetrachloroaurate (III) dihydrate (NaAuCl4 · 2H2O) concentration. The NPs were characterized using Ultraviolet-visible (UV–vis) spectroscopy, dynamic light scattering, high-resolution transmission electron microscopy (HR-TEM), and Fourier transform infrared (FT-IR) spectroscopy. SAL was able to synthesize both Ag (SAL AgNP) and Au (SAL AuNP) nanoparticles, whilst SF synthesized Ag (SF AgNP) nanoparticles only. The absorbance spectra revealed the characteristic surface plasmon resonance peak between 400–500 nm and 500–600 nm for AgNP and AuNP, respectively. HR-TEM displayed the presence of spherical and polygon shaped nanoparticles with varying sizes whilst the Energy Dispersive x-ray spectra and selected area diffraction pattern confirmed the successful synthesis of the AgNPs and AuNPs by displaying the characteristic crystalline nature, optical adsorption peaks and lattice fringes. FT-IR spectroscopy was employed to identify the functional groups involved in the NP synthesis. The microtitre plate method was employed to determine the minimum inhibitory concentration (MIC) of the NPs and the extracts. The water extracts and SAL AuNP did not have significant antibacterial activity, while SAL AgNP and SF AgNP displayed high antibacterial activity. In conclusion, the data generated suggests that SAL and SF could be used for the efficient synthesis of antibacterial biogenic nanoparticles.
Antibacterial activity of rationally designed antimicrobial peptides
(Hindawi, 2020) Tincho, Marius B.; Morris, Thureyah; Meyer, Mervin
Many infectious diseases are still prevalent in the world’s populations since no effective treatments are available to eradicate them. e reasons may either be the antibiotic resistance towards the available therapeutic molecules or the slow rate of producing adequate therapeutic regimens to tackle the rapid growth of new infectious diseases, as well as the toxicity of current treatment regimens. Due to these reasons, there is a need to seek and develop novel therapeutic regimens to reduce the rapid scale of bacterial infections. Antimicrobial Peptides (AMPs) are components of the first line of defense for prokaryotes and eukaryotes and have a wide range of activities against Gram-negative and Gram-positive bacteria, fungi, cancer cells, and protozoa, as well as viruses. In this study, peptides which were initially identified for their HIV inhibitory activity were further screened for antibacterial activity through determination of their kinetics as well as their cytotoxicity. From the results obtained, the MICs of two AMPs (Molecule 3 and Molecule 7) were 12.5 μg/ml for K. pneumoniae (ATCC 700603) and 6.25 μg/ml for P. aeruginosa (ATCC 22108). e two AMPs killed these bacteria rapidly in vitro, preventing bacterial growth within few hours of treatment. Furthermore, the cytotoxic activity of these two peptides was significantly low, even at an AMP concentration of 100 μg/ml. ese results revealed that Molecule 3 and 7 have great potential as antibacterial drugs or could serve as lead compounds in the design of therapeutic regimens for the treatment of antibiotic-resistant bacteria.
Antibacterial activity of rationally designed antimicrobial peptides.
(Hindawi, 2020) Morris, Thureyah; Tincho, Marius Belmondo; Meyer, Mervin
Many infectious diseases are still prevalent in the world’s populations since no effective treatments are available to eradicate them. e reasons may either be the antibiotic resistance towards the available therapeutic molecules or the slow rate of producing adequate therapeutic regimens to tackle the rapid growth of new infectious diseases, as well as the toxicity of current treatment regimens. Due to these reasons, there is a need to seek and develop novel therapeutic regimens to reduce the rapid scale of bacterial infections. Antimicrobial Peptides (AMPs) are components of the first line of defense for prokaryotes and eukaryotes and have a wide range of activities against Gram-negative and Gram-positive bacteria, fungi, cancer cells, and protozoa, as well as viruses. In this study, peptides which were initially identified for their HIV inhibitory activity were further screened for antibacterial activity through determination of their kinetics as well as their cytotoxicity. From the results obtained, the MICs of two AMPs (Molecule 3 and Molecule 7) were 12.5 μg/ml for K. pneumoniae (ATCC 700603) and 6.25 μg/ml for P. aeruginosa (ATCC 22108). e two AMPs killed these bacteria rapidly in vitro, preventing bacterial growth within few hours of treatment. Furthermore, the cytotoxic activity of these two peptides was significantly low, even at an AMP concentration of 100 μg/ml. ese results revealed that Molecule 3 and 7 have great potential as antibacterial drugs or could serve as lead compounds in the design of therapeutic regimens for the treatment of antibiotic-resistant bacteria.
Anticancer and drug-sensitizing activities of gold nanoparticles synthesized from cyclopia genistoides (honeybush) extracts
(MDPI, 2023) Sharma, Jyoti Rajan; Sibuyi, Nicole Remaliah Samantha; Fadaka, Adewale Oluwaseun
Synthesis of gold nanoparticles (AuNPs) using phytochemicals has become tremendously prominent in biomedical applications because of its enhanced bioactivity and biocompatibility. In this study, water extracts from the leaves of Cyclopia genistoides (C. genistoides), commonly known as honeybush (HB), were used to synthesize honeybush gold nanoparticles (HB-AuNPs). The HB water extracts (HBE) served as both reducing and capping agents in the synthesis of HB-AuNPs. The HB-AuNPs were characterized by UV–Vis spectrophotometry, dynamic light scattering (DLS), and transmission electron microscopy (TEM). The cytotoxicity and apoptotic effects of the HBE and HB-AuNPs, alone and in combination with doxorubicin (Dox), were examined against various human cell lines. Spherical-shaped HB-AuNPs with a hydrodynamic diameter range of 63 to 121 nm were produced.
The antimicrobial activity of biogenic silver nanoparticles synthesized from extracts of Red and Green European pear cultivars
(Taylor & Francis, 2021-01)
Green nanotechnology stands amongst the leading giants of innovation for the twenty first century technological advances. More interesting, is the use of natural products as reducing agents. These could be recyclable materials from fruits and vegetables to produce nanoparticles (NPs) with novel properties. In the current study, silver NPs (AgNPs) were synthesized using the water extracts from the peel and flesh of two Pyrus communis L. cultivars, namely, the Forelle (Red) Pears (RPE) and Packham Triumph (Green) Pears (GPE). The AgNPs were characterized by UV-Vis spectrophotometry, Dynamic Light Scattering (DLS), High Resolution Transmission Electron Microscopy (HRTEM) and Fourier Transform Infra-Red Spectroscopy (FTIR). The antibacterial activities of the AgNPs were evaluated using agar well diffusion and microdilution assays. The cytotoxicity of the AgNPs was investigated on a rat macrophage (RAW 264.7) cells using MTT assay. Both the RPE and GPE were capable of synthesizing the AgNPs at high temperatures (70 and 100 C). The AgNPs exhibited antibacterial activity against the test strains, and also had low toxicity towards the RAW 264.7 cells. Thus, the synthesized AgNPs have a potentially viable use in bio-applications for treatment of bacterial infections.
The antimicrobial and anti-inflammatory effects of silver nanoparticles synthesised from cotyledon orbiculata aqueous extract
(MDPI, 2021) Tyavambiza, Caroline; Elbagory, Abdulrahman Mohammed; Madiehe, Abram Madimabe
Cotyledon orbiculata, commonly known as pig’s ear, is an important medicinal plant of South Africa. It is used in traditional medicine to treat many ailments, including skin eruptions, abscesses, inflammation, boils and acne. Many plants have been used to synthesize metallic nanoparticles, particularly silver nanoparticles (AgNPs). However, the synthesis of AgNPs from C. orbiculata has never been reported before. The aim of this study was to synthesize AgNPs using C. orbiculata and evaluate their antimicrobial and immunomodulatory properties. AgNPs were synthesized and characterized using Ultraviolet-Visible Spectroscopy (UV-Vis), Dynamic Light Scattering (DLS) and High-Resolution Transmission Electron Microscopy (HR-TEM).
Antimycobacterial activity and molecular docking of methanolic extracts and compounds of marine fungi from Saldanha and False Bays, South Africa
(Elsevier, 2022) Tapfuma, K; Nyambo, K; Adu-Amankwaah, F; Mavumengwana, Vuyo
The number and diversity of drugs in the tuberculosis (TB) drug development process has increased over the years, yet the attrition rate remains very high, signaling the need for continued research in drug discovery. In this study, crude secondary metabolites from marine fungi associated with ascidians collected from Saldanha and False Bays (South Africa) were investigated for antimycobacterial activity. Isolation of fungi was performed by sectioning thin inner-tissues of ascidians and spreading them over potato dextrose agar (PDA). Solid state fermentation of fungal isolates on PDA was then performed for 28 days to allow production of secondary metabolites. Afterwards, PDA cultures were dried and solid-liquid extraction using methanol was performed to extract fungal metabolites. Profiling of metabolites was performed using untargeted liquid chromatography quadrupole time-of-flight tandem mass spectrometry (LC-QTOF-MS/MS). The broth microdilution method was used to determine antimycobacterial activity against Mycobacterium smegmatis mc2155 and Mycobacterium tuberculosis H37Rv, while in silico flexible docking was performed on selected target proteins from M. tuberculosis. A total of 16 ascidians were sampled and 46 fungi were isolated. Only 32 fungal isolates were sequenced, and their sequences submitted to GenBank to obtain accession numbers. Metabolite profiling of 6 selected fungal extracts resulted in the identification of 65 metabolites. The most interesting extract was that of Clonostachys rogersoniana MGK33 which inhibited Mycobacterium smegmatis mc2155 and Mycobacterium tuberculosis H37Rv growth with minimum inhibitory concentrations (MICs) of 0.125 and 0.2 mg/mL, respectively. These results were in accordance with those from in silico molecular docking studies which showed that bionectin F produced by C. rogersoniana MGK33 is a potential inhibitor of M. tuberculosis β-ketoacyl-acyl carrier protein reductase (MabA, PDB ID = 1UZN), with the docking score observed as −11.17 kcal/mol. These findings provided evidence to conclude that metabolites from marine-derived fungi are potential sources of bioactive metabolites with antimycobacterial activity. Even though in silico studies showed that bionectin F is a potent inhibitor of an essential enzyme, MabA, the results should be validated by performing purification of bionectin F from C. rogersoniana MGK33 and in vitro assays against MabA and whole cells (M. tuberculosis).
The antioxidant and in vitro wound healing activity of cotyledon orbiculata aqueous extract and the synthesized biogenic silver nanoparticles
(MDPI, 2022) Tyavambiza, Caroline; Meyer, Mervin; Madiehe, Abram Madimabe
The synthesis of silver nanoparticles using biogenic methods, particularly plants, has led to the discovery of several effective nanoparticles. In many instances, plant-derived silver nanoparticles have been shown to have more activity than the plant extract which was used to synthesize the nanoparticles. Silver nanoparticles have been successfully synthesized using the medicinal plant, Cotyledon orbiculata. This is a shrub found in the Western Cape province of South Africa. It has a long history of use in traditional medicine in the treatment of wounds and skin infections. The C. orbiculata synthesized silver nanoparticles (Cotyledon-AgNPs) were reported to have good antimicrobial and anti-inflammatory activities; however, their wound-healing properties have not been determined. This study aimed to determine the wound healing activity of Cotyledon-AgNPs using the scratch assay. Gene expression studies were also done to determine the nanoparticles’ mechanism of action. The Cotyledon-AgNPs showed good antioxidant, growth-promoting and cell migration properties.
Antioxidant responses are associated with differences in drought tolerance between maize and sorghum
(Arid land institute, 2021) Elbasheir, Ali Ali Elnaeim; Ndiko, Ludidi
Drought is a major cause of decreased yield in crops worldwide. Sorghum (Sorghum bicolor) and maize (Zea mays) are two of the key crops in Africa serving as human food as well as livestock feed. For improved crop production, selection for drought resilient genotypes is imperative and the biological basis for drought tolerance ought to be fully understood to achieve such selection. Sorghum can tolerate drought better than maize and it is a key model for studying the physiological and biochemical mechanisms conferring drought tolerance. In this study, comparative analyses in terms of changes in growth, chlorophyll content, ROS content, lipid peroxidation level and the activity of antioxidant enzymes were investigated. Exposure to drought triggered ROS generation in both plant species. However, sorghum showed less cell damage under water deficit compared to maize. Furthermore, differences in antioxidant enzyme activity between maize and sorghum were identified. Our findings reveal differences in and association between the physiological and biochemical responses of maize and sorghum to drought, which may be relevant for breeding drought tolerant crops.
Apoptosis in cancer cells is induced by alternative splicing of hnrnpa2/b1 through splicing of bcl-x, a mechanism that can be stimulated by an extract of the South African medicinal plant, cotyledon orbiculata
(Frontiers Media S.A., 2020) Meye, Mervin; Makhafola, Tshepiso Jan; Mbele, Mzwandile
Alternative splicing is deregulated in cancer and alternatively spliced products can be linked to cancer hallmarks. Targeting alternative splicing could offer novel effective cancer treatments. We investigated the effects of the crude extract of a South African medicinal plant, Cotyledon orbiculata, on cell survival of colon (HCT116) and esophageal (OE33 and KYSE70) cancer cell lines. Using RNASeq, we discovered that the extract interfered with mRNA regulatory pathways. The extract caused hnRNPA2B1 to splice from the hnRNPB1 to the hnRNPA2 isoform, resulting in a switch in the BCL2L1 gene from Bcl-xL to Bcl-xS causing activation of caspase-3-cleavage and apoptosis. Similar splicing effects were induced by the known anti-cancer splicing modulator pladienolide B. Knockdown of hnRNPB1 using siRNA resulted in decreased cell viability and increased caspase-3-cleavage, and over-expression of hnRNPB1 prevented the effect of C.
Applications of Computational Methods in Biomedical Breast Cancer Imaging Diagnostics: A Review
(MDPI, 2020) Aruleba, Kehinde
With the exponential increase in new cases coupled with an increased mortality rate, cancer has ranked as the second most prevalent cause of death in the world. Early detection is paramount for suitable diagnosis and effective treatment of different kinds of cancers, but this is limited to the accuracy and sensitivity of available diagnostic imaging methods. Breast cancer is the most widely diagnosed cancer among women across the globe with a high percentage of total cancer deaths requiring an intensive, accurate, and sensitive imaging approach. Indeed, it is treatable when detected at an early stage. Hence, the use of state of the art computational approaches has been proposed as a potential alternative approach for the design and development of novel diagnostic imaging methods for breast cancer. Thus, this review provides a concise overview of past and present conventional diagnostics approaches in breast cancer detection. Further, we gave an account of several computational models (machine learning, deep learning, and robotics), which have been developed and can serve as alternative techniques for breast cancer diagnostics imaging. This review will be helpful to academia, medical practitioners, and others for further study in this area to improve the biomedical breast cancer imaging diagnosis.
Applications of computational methods in biomedical breast cancer imaging diagnostics: A review
(Multidisciplinary Digital Publishing Institute (MDPI), 2020) Aruleba, Kehinde; Obaido, George; Aruleba, Raphael Taiwo
With the exponential increase in new cases coupled with an increased mortality rate, cancer has ranked as the second most prevalent cause of death in the world. Early detection is paramount for suitable diagnosis and effective treatment of different kinds of cancers, but this is limited to the accuracy and sensitivity of available diagnostic imaging methods. Breast cancer is the most widely diagnosed cancer among women across the globe with a high percentage of total cancer deaths requiring an intensive, accurate, and sensitive imaging approach. Indeed, it is treatable when detected at an early stage.
Applications of computational methods in biomedical Breast cancer imaging diagnostics: A review
(MDPI, 2020) Aruleba, Kehinde; Obaido, George; Ogbuokiri, Blessing
With the exponential increase in new cases coupled with an increased mortality rate, cancer has ranked as the second most prevalent cause of death in the world. Early detection is paramount for suitable diagnosis and effective treatment of different kinds of cancers, but this is limited to the accuracy and sensitivity of available diagnostic imaging methods. Breast cancer is the most widely diagnosed cancer among women across the globe with a high percentage of total cancer deaths requiring an intensive, accurate, and sensitive imaging approach. Indeed, it is treatable when detected at an early stage. Hence, the use of state of the art computational approaches has been proposed as a potential alternative approach for the design and development of novel diagnostic imaging methods for breast cancer. Thus, this review provides a concise overview of past and present conventional diagnostics approaches in breast cancer detection. Further, we gave an account of several computational models (machine learning, deep learning, and robotics), which have been developed and can serve as alternative techniques for breast cancer diagnostics imaging. This review will be helpful to academia, medical practitioners, and others for further study in this area to improve the biomedical breast cancer imaging diagnosis.

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