Homology modeling and docking of AahII-Nanobody complexes reveal the epitope binding site on AahII scorpion toxin
- Ksouri, Ayoub, Ghedira, Kais, Abderrazek, Rahma Ben, Shankar, B A Gowri, Benkahla, Alia, Tastan Bishop, Özlem, Bouhaouala-Zahar, Balkis
- Authors: Ksouri, Ayoub , Ghedira, Kais , Abderrazek, Rahma Ben , Shankar, B A Gowri , Benkahla, Alia , Tastan Bishop, Özlem , Bouhaouala-Zahar, Balkis
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124604 , vital:35637 , https://doi.10.1016/j.bbrc.2018.01.036
- Description: Scorpion envenoming and its treatment is a public health problem in many parts of the world due to highly toxic venom polypeptides diffusing rapidly within the body of severely envenomed victims. Recently, 38 AahII-specific Nanobody sequences (Nbs) were retrieved from which the performance of NbAahII10 nanobody candidate, to neutralize the most poisonous venom compound namely AahII acting on sodium channels, was established. Herein, structural computational approach is conducted to elucidate the Nb-AahII interactions that support the biological characteristics, using Nb multiple sequence alignment (MSA) followed by modeling and molecular docking investigations (RosettaAntibody, ZDOCK software tools). Sequence and structural analysis showed two dissimilar residues of NbAahII10 CDR1 (Tyr27 and Tyr29) and an inserted polar residue Ser30 that appear to play an important role. Indeed, CDR3 region of NbAahII10 is characterized by a specific Met104 and two negatively chargedresidues Asp115 and Asp117. Complex dockings reveal that NbAahII17 and NbAahII38 share one common binding site on the surface of the AahII toxin divergent from the NbAahII10 one's. At least, a couple of NbAahII10 e AahII residue interactions (Gln38 e Asn44 and Arg62, His64, respectively) are mainly involved in the toxic AahII binding site. Altogether, this study gives valuable insights in the design and development of next generation of antivenom.
- Full Text:
- Date Issued: 2018
- Authors: Ksouri, Ayoub , Ghedira, Kais , Abderrazek, Rahma Ben , Shankar, B A Gowri , Benkahla, Alia , Tastan Bishop, Özlem , Bouhaouala-Zahar, Balkis
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124604 , vital:35637 , https://doi.10.1016/j.bbrc.2018.01.036
- Description: Scorpion envenoming and its treatment is a public health problem in many parts of the world due to highly toxic venom polypeptides diffusing rapidly within the body of severely envenomed victims. Recently, 38 AahII-specific Nanobody sequences (Nbs) were retrieved from which the performance of NbAahII10 nanobody candidate, to neutralize the most poisonous venom compound namely AahII acting on sodium channels, was established. Herein, structural computational approach is conducted to elucidate the Nb-AahII interactions that support the biological characteristics, using Nb multiple sequence alignment (MSA) followed by modeling and molecular docking investigations (RosettaAntibody, ZDOCK software tools). Sequence and structural analysis showed two dissimilar residues of NbAahII10 CDR1 (Tyr27 and Tyr29) and an inserted polar residue Ser30 that appear to play an important role. Indeed, CDR3 region of NbAahII10 is characterized by a specific Met104 and two negatively chargedresidues Asp115 and Asp117. Complex dockings reveal that NbAahII17 and NbAahII38 share one common binding site on the surface of the AahII toxin divergent from the NbAahII10 one's. At least, a couple of NbAahII10 e AahII residue interactions (Gln38 e Asn44 and Arg62, His64, respectively) are mainly involved in the toxic AahII binding site. Altogether, this study gives valuable insights in the design and development of next generation of antivenom.
- Full Text:
- Date Issued: 2018
Anti-malarial synergy of secondary metabolites from Morinda lucida Benth.
- Lakkakula, Jaya R, Matshaya, Thabo, Krause, Rui W M
- Authors: Lakkakula, Jaya R , Matshaya, Thabo , Krause, Rui W M
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125609 , vital:35800 , https://doi.org/10.1016/j.msec.2016.08.073
- Description: Ethnopharmacological relevance The roots, stem and leaves of Morinda lucida are used in some African countries as treatment against different types of fevers including yellow fever, malaria, trypanosomiasis and feverish conditions during child birth. Aim of the study To determine the in vitro cell toxicity and anti-malarial activity of the extracts of stem bark of M. lucida and to identify the secondary metabolites in the extract that may be responsible for this activity. Materials and methods The cell toxicity studies of crude extract [dichloromethane (DCM): Methanol (MeOH) in a ratio of1:1 (v/v)] as well as compounds isolated from the same extract were carried out using human cervix adenocarcinoma cells (HeLa cells); while the anti-malarial activities of the same samples were performed against Plasmodium falciparum strain 3D7 using the parasite lactate dehydrogenase (pLDH) assay. The isolation of the active compounds was carried out using chromatographic techniques (column and thin layer chromatography) where as mass spectrometry (MS), Fourier transform infrared spectroscopy (FTIR) as well as 1D- and 2D- nuclear magnetic resonance (NMR) analyses were employed in the characterisation and identification of the isolated secondary metabolites. Results The pLDH and cell toxicity assays for the crude extract and the fractions of M. lucida indicated that some fractions reduced the malaria parasite viability by approximately 50% at 100 μg/mL and they were not significantly cytotoxic. An IC50 done on the crude extract gave a value of 25 μg/mL. The % cell viability for the crude extract in cell toxicity assay remained at 100%. Seven chemical constituents i.e. asperuloside (1), asperulosidic acid (2), stigmasterol (3a), β-sitosterol (3b), cycloartenol (3c), campesterol (3d) and 5,15-O-dimethylmorindol (4) were isolated from the DCM-MeOH extract of stem bark. The isolated compounds tested were not that active by themselves individually at 20 μM but their activities were increased when the isolated compounds were combined. As seen when compounds 2, 3 and 4 (% viability: 93, 123 and 101 respectively) were combined yielding an IC50 value of 17 μM. Furthermore, this is the first report of compounds 1, 2, 3c, 3d and 4 isolated from M. lucida. Conclusion The crude extract completely suppressed the growth of P. falciparum. This indicates that the crude extract contains many compounds that might be acting in synergy. The observed activity of the crude extract and the samples containing a mixture of different compounds support the traditional use of M. lucida for the treatment of malaria.
- Full Text:
- Date Issued: 2017
- Authors: Lakkakula, Jaya R , Matshaya, Thabo , Krause, Rui W M
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125609 , vital:35800 , https://doi.org/10.1016/j.msec.2016.08.073
- Description: Ethnopharmacological relevance The roots, stem and leaves of Morinda lucida are used in some African countries as treatment against different types of fevers including yellow fever, malaria, trypanosomiasis and feverish conditions during child birth. Aim of the study To determine the in vitro cell toxicity and anti-malarial activity of the extracts of stem bark of M. lucida and to identify the secondary metabolites in the extract that may be responsible for this activity. Materials and methods The cell toxicity studies of crude extract [dichloromethane (DCM): Methanol (MeOH) in a ratio of1:1 (v/v)] as well as compounds isolated from the same extract were carried out using human cervix adenocarcinoma cells (HeLa cells); while the anti-malarial activities of the same samples were performed against Plasmodium falciparum strain 3D7 using the parasite lactate dehydrogenase (pLDH) assay. The isolation of the active compounds was carried out using chromatographic techniques (column and thin layer chromatography) where as mass spectrometry (MS), Fourier transform infrared spectroscopy (FTIR) as well as 1D- and 2D- nuclear magnetic resonance (NMR) analyses were employed in the characterisation and identification of the isolated secondary metabolites. Results The pLDH and cell toxicity assays for the crude extract and the fractions of M. lucida indicated that some fractions reduced the malaria parasite viability by approximately 50% at 100 μg/mL and they were not significantly cytotoxic. An IC50 done on the crude extract gave a value of 25 μg/mL. The % cell viability for the crude extract in cell toxicity assay remained at 100%. Seven chemical constituents i.e. asperuloside (1), asperulosidic acid (2), stigmasterol (3a), β-sitosterol (3b), cycloartenol (3c), campesterol (3d) and 5,15-O-dimethylmorindol (4) were isolated from the DCM-MeOH extract of stem bark. The isolated compounds tested were not that active by themselves individually at 20 μM but their activities were increased when the isolated compounds were combined. As seen when compounds 2, 3 and 4 (% viability: 93, 123 and 101 respectively) were combined yielding an IC50 value of 17 μM. Furthermore, this is the first report of compounds 1, 2, 3c, 3d and 4 isolated from M. lucida. Conclusion The crude extract completely suppressed the growth of P. falciparum. This indicates that the crude extract contains many compounds that might be acting in synergy. The observed activity of the crude extract and the samples containing a mixture of different compounds support the traditional use of M. lucida for the treatment of malaria.
- Full Text:
- Date Issued: 2017
Biology and rearing of Ectomyeolis ceratoniae Zeller (Lepidoptera: Pyralidae) carob moth, a pest of multiple crops in South Africa
- Thackeray, S R, Moore, Sean D, Strathie, Lorraine W, Kirkman, W, Hill, Martin P
- Authors: Thackeray, S R , Moore, Sean D , Strathie, Lorraine W , Kirkman, W , Hill, Martin P
- Date: 2017
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/59799 , vital:27652 , https://doi.org/10.4001/003.025.0474
- Description: Ectomyeolis ceratoniae Zeller (Lepidoptera: Pyralidae), carob moth, is a pest of several crops in South Africa. A laboratory culture was established from field-collected larvae infesting mummified pecan nuts. Biological parameters of larvae reared on an artificial diet were measured. The insect goes through five larval instars, and the head capsule sizes of the five instars were determined to be <0.34 mm, 0.35-0.64 mm, 0.65-0.94 mm, 0.95-1.14 mm and >0.15 mm for the five instars, respectively. The insect was reared individually and communally in glass vials, the latter to develop a mass-rearing technique. Developmental time from neonate to pupa was significantly slower when larvae were individually reared (38.18 ±1.2 days) compared to when they were communally reared (24.6 ± 0.65 days). A microsporidian infection (Nosema sp.) was recorded in the culture, causing significantly (fy6 = 14.99, P = 0.0082) higher mortality of communally reared larvae (76.25 % ± 11.87) than individually reared larvae (24.9 % ± 9.6).
- Full Text:
- Date Issued: 2017
- Authors: Thackeray, S R , Moore, Sean D , Strathie, Lorraine W , Kirkman, W , Hill, Martin P
- Date: 2017
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/59799 , vital:27652 , https://doi.org/10.4001/003.025.0474
- Description: Ectomyeolis ceratoniae Zeller (Lepidoptera: Pyralidae), carob moth, is a pest of several crops in South Africa. A laboratory culture was established from field-collected larvae infesting mummified pecan nuts. Biological parameters of larvae reared on an artificial diet were measured. The insect goes through five larval instars, and the head capsule sizes of the five instars were determined to be <0.34 mm, 0.35-0.64 mm, 0.65-0.94 mm, 0.95-1.14 mm and >0.15 mm for the five instars, respectively. The insect was reared individually and communally in glass vials, the latter to develop a mass-rearing technique. Developmental time from neonate to pupa was significantly slower when larvae were individually reared (38.18 ±1.2 days) compared to when they were communally reared (24.6 ± 0.65 days). A microsporidian infection (Nosema sp.) was recorded in the culture, causing significantly (fy6 = 14.99, P = 0.0082) higher mortality of communally reared larvae (76.25 % ± 11.87) than individually reared larvae (24.9 % ± 9.6).
- Full Text:
- Date Issued: 2017
Cationic cyclodextrin/alginate chitosan nanoflowers as 5-fluorouracil drug delivery system
- Lakkakula, Jaya R, Matshaya, Thabo, Krause, Rui W M
- Authors: Lakkakula, Jaya R , Matshaya, Thabo , Krause, Rui W M
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125587 , vital:35798 , https://doi.org/10.1016/j.msec.2016.08.073
- Description: Cyclodextrins (CDs) have widely been used as component of drug delivery systems. However unmodified cyclodextrins are associated with cytotoxicity and poor water solubility thus limiting their use in pharmaceutical industry. The cationic-β-cyclodextrin (Cat-β-CD) polymer cores were synthesized using β-CD, epichlorohydrin and choline chloride via a one-step polycondensation process. The main aim of this study was to synthesize hierarchical nanoflowers composed of cationic-β-CD as polymeric core along with alginate and chitosan “petals” (Cat-β-CD/Alg-Chi nanoflowers) as carriers for oral delivery of 5-Fluorouracil (5-FU) via an ionic-gelation technique. The drug loading capacity, particle size, zeta potential and surface morphology of the synthesized nanoflowers were determined. The prepared nanoflowers were formed with an average size of 300 nm and a zeta potential of + 9.90 mV with good encapsulation efficiency of up to 77.3%. In vitro release of 5-FU from the loaded nanoflowers showed controlled and sustained release compared to the inclusion complex alone. Cat-β-CD/Alg-Chi nanoflowers were assessed against L929 cells and found to be effectively inhibiting the growth of L929 cells in a concentration dependent manner.
- Full Text:
- Date Issued: 2017
- Authors: Lakkakula, Jaya R , Matshaya, Thabo , Krause, Rui W M
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125587 , vital:35798 , https://doi.org/10.1016/j.msec.2016.08.073
- Description: Cyclodextrins (CDs) have widely been used as component of drug delivery systems. However unmodified cyclodextrins are associated with cytotoxicity and poor water solubility thus limiting their use in pharmaceutical industry. The cationic-β-cyclodextrin (Cat-β-CD) polymer cores were synthesized using β-CD, epichlorohydrin and choline chloride via a one-step polycondensation process. The main aim of this study was to synthesize hierarchical nanoflowers composed of cationic-β-CD as polymeric core along with alginate and chitosan “petals” (Cat-β-CD/Alg-Chi nanoflowers) as carriers for oral delivery of 5-Fluorouracil (5-FU) via an ionic-gelation technique. The drug loading capacity, particle size, zeta potential and surface morphology of the synthesized nanoflowers were determined. The prepared nanoflowers were formed with an average size of 300 nm and a zeta potential of + 9.90 mV with good encapsulation efficiency of up to 77.3%. In vitro release of 5-FU from the loaded nanoflowers showed controlled and sustained release compared to the inclusion complex alone. Cat-β-CD/Alg-Chi nanoflowers were assessed against L929 cells and found to be effectively inhibiting the growth of L929 cells in a concentration dependent manner.
- Full Text:
- Date Issued: 2017
Development of Bioinformatics Infrastructure for Genomics Research:
- Mulder, Nicola J, Adebiyi, Ezekiel, Adebiyi, Marion, Adeyemi, Seun, Ahmed, Azza, Ahmed, Rehab, Akanle, Bola, Alibi, Mohamed, Armstrong, Don L, Aron, Shaun, Ashano, Efejiro, Baichoo, Shakuntala, Benkahla, Alia, Brown, David K, Chimusa, Emile Rugamika, Fadlelmola, Faisal M, Falola, Dare, Fatumo, Segun, Ghedira, Kais, Ghouila, Amel, Hazelhurst, Scott, Itunuoluwa Isewon, Segun Jung, Kassim, Samar Kamal, Kayondo, Jonathan K, Mbiyavanga, Mamana, Meintjes, Ayton, Mohammed, Somia, Mosaku, Abayomi, Moussa, Ahmed, Muhammd, Mustafa, Mungloo-Dilmohamud, Zahra, Nashiru, Oyekanmi, Odia, Trust, Okafor, Adaobi, Oladipo, Olaleye, Osamor, Victor, Oyelade, Jellili, Sadki, Khalid, Salifu, Samson Pandam, Soyemi, Jumoke, Panji, Sumir, Radouani, Fouzia, Souiai, Oussama, Tastan Bishop, Özlem
- Authors: Mulder, Nicola J , Adebiyi, Ezekiel , Adebiyi, Marion , Adeyemi, Seun , Ahmed, Azza , Ahmed, Rehab , Akanle, Bola , Alibi, Mohamed , Armstrong, Don L , Aron, Shaun , Ashano, Efejiro , Baichoo, Shakuntala , Benkahla, Alia , Brown, David K , Chimusa, Emile Rugamika , Fadlelmola, Faisal M , Falola, Dare , Fatumo, Segun , Ghedira, Kais , Ghouila, Amel , Hazelhurst, Scott , Itunuoluwa Isewon , Segun Jung , Kassim, Samar Kamal , Kayondo, Jonathan K , Mbiyavanga, Mamana , Meintjes, Ayton , Mohammed, Somia , Mosaku, Abayomi , Moussa, Ahmed , Muhammd, Mustafa , Mungloo-Dilmohamud, Zahra , Nashiru, Oyekanmi , Odia, Trust , Okafor, Adaobi , Oladipo, Olaleye , Osamor, Victor , Oyelade, Jellili , Sadki, Khalid , Salifu, Samson Pandam , Soyemi, Jumoke , Panji, Sumir , Radouani, Fouzia , Souiai, Oussama , Tastan Bishop, Özlem
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148239 , vital:38722 , DOI: 10.1016/j.gheart.2017.01.005
- Description: Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community.
- Full Text:
- Date Issued: 2017
- Authors: Mulder, Nicola J , Adebiyi, Ezekiel , Adebiyi, Marion , Adeyemi, Seun , Ahmed, Azza , Ahmed, Rehab , Akanle, Bola , Alibi, Mohamed , Armstrong, Don L , Aron, Shaun , Ashano, Efejiro , Baichoo, Shakuntala , Benkahla, Alia , Brown, David K , Chimusa, Emile Rugamika , Fadlelmola, Faisal M , Falola, Dare , Fatumo, Segun , Ghedira, Kais , Ghouila, Amel , Hazelhurst, Scott , Itunuoluwa Isewon , Segun Jung , Kassim, Samar Kamal , Kayondo, Jonathan K , Mbiyavanga, Mamana , Meintjes, Ayton , Mohammed, Somia , Mosaku, Abayomi , Moussa, Ahmed , Muhammd, Mustafa , Mungloo-Dilmohamud, Zahra , Nashiru, Oyekanmi , Odia, Trust , Okafor, Adaobi , Oladipo, Olaleye , Osamor, Victor , Oyelade, Jellili , Sadki, Khalid , Salifu, Samson Pandam , Soyemi, Jumoke , Panji, Sumir , Radouani, Fouzia , Souiai, Oussama , Tastan Bishop, Özlem
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148239 , vital:38722 , DOI: 10.1016/j.gheart.2017.01.005
- Description: Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community.
- Full Text:
- Date Issued: 2017
From Baudelaire to Beardsley: some thoughts on Poe's beast as an indicator of the tastes and fears of nineteenth-century Europe
- Authors: Beard, Margot
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/147781 , vital:38672 , https://doi.org/10.1080/00043389.2001.11876980
- Description: Charles Baudelaire (1821 1867) was one of the major influences on the French Decadent poets of the late nineteenth century whose aesthetic principles were shared, to a large extent, by a group of English poets and artists, among whom was Aubrey Beardsley (1872 1898). One of the major influences on Baude laire had been the American, Edgar Allan Poe (1809 1849), in whose short stories and poems Baudelaire had recognised a kindred spirit. Some intriguing aspects of changing nine teenth century attitudes emerge from a study of Baudelaire's 1856 translation of Poe's `The Murders in the Rue Morgue' and Beardsley's 1893 illustration to this story.
- Full Text:
- Date Issued: 2017
- Authors: Beard, Margot
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/147781 , vital:38672 , https://doi.org/10.1080/00043389.2001.11876980
- Description: Charles Baudelaire (1821 1867) was one of the major influences on the French Decadent poets of the late nineteenth century whose aesthetic principles were shared, to a large extent, by a group of English poets and artists, among whom was Aubrey Beardsley (1872 1898). One of the major influences on Baude laire had been the American, Edgar Allan Poe (1809 1849), in whose short stories and poems Baudelaire had recognised a kindred spirit. Some intriguing aspects of changing nine teenth century attitudes emerge from a study of Baudelaire's 1856 translation of Poe's `The Murders in the Rue Morgue' and Beardsley's 1893 illustration to this story.
- Full Text:
- Date Issued: 2017
Heat shock proteins as modulators and therapeutic targets of chronic disease: an integrated perspective
- Edkins, Adrienne L, Price, John T, Pockley, A Graham, Blatch, Gregory L
- Authors: Edkins, Adrienne L , Price, John T , Pockley, A Graham , Blatch, Gregory L
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/164332 , vital:41109 , DOI: 10.1098/rstb.2016.0521
- Description: Many heat shock proteins (HSPs) are essential to survival as a consequence of their role as molecular chaperones, and play a critical role in maintaining cellular proteostasis by integrating the fundamental processes of protein folding and degradation. HSPs are arguably among the most prominent classes of proteins that have been broadly linked to many human disorders, with changes in their expression profile and/or intracellular/extracellular location now being described as contributing to the pathogenesis of a number of different diseases. Although the concept was initially controversial, it is now widely accepted that HSPs have additional biological functions over and above their role in proteostasis (so-called ‘protein moonlighting’).
- Full Text:
- Date Issued: 2017
- Authors: Edkins, Adrienne L , Price, John T , Pockley, A Graham , Blatch, Gregory L
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/164332 , vital:41109 , DOI: 10.1098/rstb.2016.0521
- Description: Many heat shock proteins (HSPs) are essential to survival as a consequence of their role as molecular chaperones, and play a critical role in maintaining cellular proteostasis by integrating the fundamental processes of protein folding and degradation. HSPs are arguably among the most prominent classes of proteins that have been broadly linked to many human disorders, with changes in their expression profile and/or intracellular/extracellular location now being described as contributing to the pathogenesis of a number of different diseases. Although the concept was initially controversial, it is now widely accepted that HSPs have additional biological functions over and above their role in proteostasis (so-called ‘protein moonlighting’).
- Full Text:
- Date Issued: 2017
Improved endoglucanase production and mycelial biomass of some ericoid fungi
- Adeoyo, Olusegun R, Pletschke, Brett I, Dames, Joanna F
- Authors: Adeoyo, Olusegun R , Pletschke, Brett I , Dames, Joanna F
- Date: 2017
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61435 , vital:28026 , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209310/
- Description: Fungal species associated with ericaceous plant roots produce a number of enzymes and other bio-active metabolites in order to enhance survival of their host plants in natural environments. This study focussed on endoglucanase production from root associated ericoid mycorrhizal and dark septate endophytic fungal isolates. Out of the five fungal isolates screened, Leohumicola sp. (ChemRU330/PPRI 13195) had the highest relative enzyme activity and was tested along with isolates belonging to Hyloscyphaceae (EdRU083/PPRI 17284) and Leotiomycetes (EdRU002/PPRI 17261) for endoglucanase production under different pH and nutritional conditions that included: carbon sources, nitrogen sources and metal ions, at an optimum temperature of 28 °C. An optimal of pH 5.0 produced enzyme activity of 3.99, 2.18 and 4.31 (U/mg protein) for isolates EdRU083, EdRU002 and Leohumicola sp. respectively. Increased enzyme activities and improved mycelial biomass production were obtained in the presence of supplements such as potassium, sodium, glucose, maltose, cellobiose, tryptone and peptone. While NaFe-EDTA and Co2+ inhibited enzyme activity. The potential role of these fungi as a source of novel enzymes is an ongoing objective of this study.
- Full Text:
- Date Issued: 2017
- Authors: Adeoyo, Olusegun R , Pletschke, Brett I , Dames, Joanna F
- Date: 2017
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61435 , vital:28026 , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209310/
- Description: Fungal species associated with ericaceous plant roots produce a number of enzymes and other bio-active metabolites in order to enhance survival of their host plants in natural environments. This study focussed on endoglucanase production from root associated ericoid mycorrhizal and dark septate endophytic fungal isolates. Out of the five fungal isolates screened, Leohumicola sp. (ChemRU330/PPRI 13195) had the highest relative enzyme activity and was tested along with isolates belonging to Hyloscyphaceae (EdRU083/PPRI 17284) and Leotiomycetes (EdRU002/PPRI 17261) for endoglucanase production under different pH and nutritional conditions that included: carbon sources, nitrogen sources and metal ions, at an optimum temperature of 28 °C. An optimal of pH 5.0 produced enzyme activity of 3.99, 2.18 and 4.31 (U/mg protein) for isolates EdRU083, EdRU002 and Leohumicola sp. respectively. Increased enzyme activities and improved mycelial biomass production were obtained in the presence of supplements such as potassium, sodium, glucose, maltose, cellobiose, tryptone and peptone. While NaFe-EDTA and Co2+ inhibited enzyme activity. The potential role of these fungi as a source of novel enzymes is an ongoing objective of this study.
- Full Text:
- Date Issued: 2017
Improvement of the pharmacological activity of menthol via enzymatic β-anomer-selective glycosylation
- Choi, Ha-Young, Kim, Bo-Min, Morgan, Abubaker M A, Kim, Joong Su, Kim, Won-Gon
- Authors: Choi, Ha-Young , Kim, Bo-Min , Morgan, Abubaker M A , Kim, Joong Su , Kim, Won-Gon
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/67515 , vital:29106 , http://dx.doi.org/10.1186/s13568-017-0468-0
- Description: Publisher version , Menthol has a considerable cooling effect, but the use range of menthol is limited because of its extremely low solubility in water and inherent flavor. (−)-Menthol β-glucoside was determined to be more soluble in water (>27 times) than (−)-menthol α-glucoside; hence, β-anomer-selective glucosylation of menthol is necessary. The in vitro glycosylation of (−)-menthol by uridine diphosphate glycosyltransferase (BLC) from Bacillus licheniformis generated (−)-menthol β-glucoside and new (−)-menthol β-galactoside and (−)-menthol N-acetylglucosamine. The maximum conversion rate of menthol to (−)-menthol β-D-glucoside by BLC was found to be 58.9%. Importantly, (−)-menthol β-D-glucoside had a higher cooling effect and no flavor compared with menthol. In addition, (−)-menthol β-D-glucoside was determined to be a non-sensitizer in a skin allergy test in the human cell line activation test, whereas menthol was a sensitizer.
- Full Text:
- Date Issued: 2017
- Authors: Choi, Ha-Young , Kim, Bo-Min , Morgan, Abubaker M A , Kim, Joong Su , Kim, Won-Gon
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/67515 , vital:29106 , http://dx.doi.org/10.1186/s13568-017-0468-0
- Description: Publisher version , Menthol has a considerable cooling effect, but the use range of menthol is limited because of its extremely low solubility in water and inherent flavor. (−)-Menthol β-glucoside was determined to be more soluble in water (>27 times) than (−)-menthol α-glucoside; hence, β-anomer-selective glucosylation of menthol is necessary. The in vitro glycosylation of (−)-menthol by uridine diphosphate glycosyltransferase (BLC) from Bacillus licheniformis generated (−)-menthol β-glucoside and new (−)-menthol β-galactoside and (−)-menthol N-acetylglucosamine. The maximum conversion rate of menthol to (−)-menthol β-D-glucoside by BLC was found to be 58.9%. Importantly, (−)-menthol β-D-glucoside had a higher cooling effect and no flavor compared with menthol. In addition, (−)-menthol β-D-glucoside was determined to be a non-sensitizer in a skin allergy test in the human cell line activation test, whereas menthol was a sensitizer.
- Full Text:
- Date Issued: 2017
Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks:
- Amamuddy, Olivier S, Bishop, Nigel T, Tastan Bishop, Özlem
- Authors: Amamuddy, Olivier S , Bishop, Nigel T , Tastan Bishop, Özlem
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148261 , vital:38724 , https://0-doi.org.wam.seals.ac.za/10.1186/s12859-017-1782-x
- Description: Drug resistance in HIV treatment is still a worldwide problem. Predicting resistance to antiretrovirals (ARVs) before starting any treatment is important. Prediction accuracy is essential, as low-accuracy predictions increase the risk of prescribing sub-optimal drug regimens leading to patients developing resistance sooner. Artificial Neural Networks (ANNs) are a powerful tool that would be able to assist in drug resistance prediction. In this study, we constrained the dataset to subtype B, sacrificing generalizability for a higher predictive performance, and demonstrated that the predictive quality of the ANN regression models have definite improvement for most ARVs.
- Full Text:
- Date Issued: 2017
- Authors: Amamuddy, Olivier S , Bishop, Nigel T , Tastan Bishop, Özlem
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148261 , vital:38724 , https://0-doi.org.wam.seals.ac.za/10.1186/s12859-017-1782-x
- Description: Drug resistance in HIV treatment is still a worldwide problem. Predicting resistance to antiretrovirals (ARVs) before starting any treatment is important. Prediction accuracy is essential, as low-accuracy predictions increase the risk of prescribing sub-optimal drug regimens leading to patients developing resistance sooner. Artificial Neural Networks (ANNs) are a powerful tool that would be able to assist in drug resistance prediction. In this study, we constrained the dataset to subtype B, sacrificing generalizability for a higher predictive performance, and demonstrated that the predictive quality of the ANN regression models have definite improvement for most ARVs.
- Full Text:
- Date Issued: 2017
Oldest known naiaditid bivalve from the high-latitude Late Devonian (Famennian) of South Africa offers clues to survival strategies following the Hangenberg mass extinction
- Scholze, Frank, Gess, Robert W
- Authors: Scholze, Frank , Gess, Robert W
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/73921 , vital:30241 , https://doi.org/10.1016/j.palaeo.2017.01.018
- Description: A phased mass extinction event (which culminated in the Hangenberg event) marked the end of the Devonian period and had a significant impact on the palaeoecology and faunal diversity of vertebrate and invertebrate communities. In the present study the taxonomy of bivalves from the Waterloo Farm lagerstätte of the Upper Devonian, Famennian, Witpoort Formation (Witteberg Group, Cape Supergroup) was studied and compared with known Carboniferous examples. For the first time, Devonian bivalves of the Naiaditidae are described from a high-latitude palaeogeographic setting of Gondwana. The presented data suggests a high-latitude origin for post-Hangenberg event Naiaditidae, found at lower latitudes during the Early Carboniferous. This may have resulted from migration to lower latitudes in response to reduced global temperatures, which were associated with climatic perturbation at the time of the Hangenberg event, and which persisted into the Early Carboniferous. Taxa that were adapted to temperature ranges existing at high latitudes during the Late Devonian are likely to have followed these temperature ranges towards lower latitudes with decreasing global temperatures. Here they may have occupied free ecospace available in the aftermath of the Late Devonian extinction event.
- Full Text:
- Date Issued: 2017
- Authors: Scholze, Frank , Gess, Robert W
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/73921 , vital:30241 , https://doi.org/10.1016/j.palaeo.2017.01.018
- Description: A phased mass extinction event (which culminated in the Hangenberg event) marked the end of the Devonian period and had a significant impact on the palaeoecology and faunal diversity of vertebrate and invertebrate communities. In the present study the taxonomy of bivalves from the Waterloo Farm lagerstätte of the Upper Devonian, Famennian, Witpoort Formation (Witteberg Group, Cape Supergroup) was studied and compared with known Carboniferous examples. For the first time, Devonian bivalves of the Naiaditidae are described from a high-latitude palaeogeographic setting of Gondwana. The presented data suggests a high-latitude origin for post-Hangenberg event Naiaditidae, found at lower latitudes during the Early Carboniferous. This may have resulted from migration to lower latitudes in response to reduced global temperatures, which were associated with climatic perturbation at the time of the Hangenberg event, and which persisted into the Early Carboniferous. Taxa that were adapted to temperature ranges existing at high latitudes during the Late Devonian are likely to have followed these temperature ranges towards lower latitudes with decreasing global temperatures. Here they may have occupied free ecospace available in the aftermath of the Late Devonian extinction event.
- Full Text:
- Date Issued: 2017
Phylogeny of the Sepia officinalis species complex in the eastern Atlantic extends the known distribution of Sepia vermiculata across the Benguela upwelling region
- Healey, Amy J E, McKeown, Niall J, Potts, Warren M, de Beer, Chénelle L, Sauer, Warwick H H, Shaw, Paul W
- Authors: Healey, Amy J E , McKeown, Niall J , Potts, Warren M , de Beer, Chénelle L , Sauer, Warwick H H , Shaw, Paul W
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125631 , vital:35802 , https://doi.10.2989/1814232X.2017.1371076
- Description: Accurate species identification and biogeographic characterisation are fundamental for appropriate management of expanding cephalopod fisheries. This study addresses this topic within the common cuttlefish Sepia officinalis species complex (S. officinalis, S. hierredda and S. vermiculata), with an emphasis on occurrence in African waters. Tissue samples from the currently presumed distributions of S. vermiculata and S. hierredda (from South Africa and Ghana/Angola, respectively) were sequenced for the cytochrome c oxidase subunit I (COI) and the cytochrome b (cytb) genes of the mitochondrial genome and then compared to existing S. officinalis sequences. Three highly divergent and reciprocally monophyletic clades, corresponding to S. officinalis, S. hierredda and S. vermiculata, were resolved, representing the first molecular confirmation of the distinct species status of S. hierredda and S. vermiculata. The sequences also revealed that, contrary to expectations based on presently published information, all samples from southern Angola were S. vermiculata. These results indicate that the range of S. vermiculata extends beyond the currently described northern limit and that S. hierredda and S. vermiculata may be indiscriminately harvested in Angolan waters. Finer-scale patterns within S. vermiculata phylogeography also indicate that the Benguela Current System and/or other environmental factors serve to isolate northern and southern stocks.
- Full Text:
- Date Issued: 2017
- Authors: Healey, Amy J E , McKeown, Niall J , Potts, Warren M , de Beer, Chénelle L , Sauer, Warwick H H , Shaw, Paul W
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125631 , vital:35802 , https://doi.10.2989/1814232X.2017.1371076
- Description: Accurate species identification and biogeographic characterisation are fundamental for appropriate management of expanding cephalopod fisheries. This study addresses this topic within the common cuttlefish Sepia officinalis species complex (S. officinalis, S. hierredda and S. vermiculata), with an emphasis on occurrence in African waters. Tissue samples from the currently presumed distributions of S. vermiculata and S. hierredda (from South Africa and Ghana/Angola, respectively) were sequenced for the cytochrome c oxidase subunit I (COI) and the cytochrome b (cytb) genes of the mitochondrial genome and then compared to existing S. officinalis sequences. Three highly divergent and reciprocally monophyletic clades, corresponding to S. officinalis, S. hierredda and S. vermiculata, were resolved, representing the first molecular confirmation of the distinct species status of S. hierredda and S. vermiculata. The sequences also revealed that, contrary to expectations based on presently published information, all samples from southern Angola were S. vermiculata. These results indicate that the range of S. vermiculata extends beyond the currently described northern limit and that S. hierredda and S. vermiculata may be indiscriminately harvested in Angolan waters. Finer-scale patterns within S. vermiculata phylogeography also indicate that the Benguela Current System and/or other environmental factors serve to isolate northern and southern stocks.
- Full Text:
- Date Issued: 2017
Secondary metabolites from Tetracera potatoria stem bark with anti-mycobacterial activity.
- Fomogne-Fodjo, M C Y, Ndinteh, Derek T, Olivier, D K, Krause, Rui W M, Kempgens, Pierre, Van Vuuren, S
- Authors: Fomogne-Fodjo, M C Y , Ndinteh, Derek T , Olivier, D K , Krause, Rui W M , Kempgens, Pierre , Van Vuuren, S
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125556 , vital:35795 , https://doi.org/10.1016/j.jep.2016.11.027
- Description: Ethnopharmacological relevance Tetracera potatoria Afzel. Exg. Don (Dilleniaceae) is a medicinal plant used traditionally in Africa for the treatment of tuberculosis related ailments and respiratory infections. The antibacterial activity of the medium polar extracts of T. potatoria leaves and stem bark was recently reported against Mycobacterium smegmatis (MIC 25 µg/mL) and M. aurum (65 µg/mL), two fast-growing Mycobacterium strains used as model micro-organisms for the more pathogenic strain Mycobacterium tuberculosis (Fomogne-Fodjo et al., 2014). The aim of this study was consequently to isolate the compounds possibly contributing to this activity, and which may therefore be promising precursors to be used for the development of novel anti-TB drugs.
- Full Text:
- Date Issued: 2017
- Authors: Fomogne-Fodjo, M C Y , Ndinteh, Derek T , Olivier, D K , Krause, Rui W M , Kempgens, Pierre , Van Vuuren, S
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125556 , vital:35795 , https://doi.org/10.1016/j.jep.2016.11.027
- Description: Ethnopharmacological relevance Tetracera potatoria Afzel. Exg. Don (Dilleniaceae) is a medicinal plant used traditionally in Africa for the treatment of tuberculosis related ailments and respiratory infections. The antibacterial activity of the medium polar extracts of T. potatoria leaves and stem bark was recently reported against Mycobacterium smegmatis (MIC 25 µg/mL) and M. aurum (65 µg/mL), two fast-growing Mycobacterium strains used as model micro-organisms for the more pathogenic strain Mycobacterium tuberculosis (Fomogne-Fodjo et al., 2014). The aim of this study was consequently to isolate the compounds possibly contributing to this activity, and which may therefore be promising precursors to be used for the development of novel anti-TB drugs.
- Full Text:
- Date Issued: 2017
The temporal occurrence of flesh flies (Diptera, Sarcophagidae) at carrion-baited traps in Grahamstown, South Africa
- Villet, Martin H, Clitheroe, Crystal-Leigh, Williams, Kirstin A
- Authors: Villet, Martin H , Clitheroe, Crystal-Leigh , Williams, Kirstin A
- Date: 2017
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/59692 , vital:27639 , https://doi.org/10.3897/AfrInvertebr.58.9537
- Description: Eleven species of flesh fly were identified in a sample of 737 specimens captured during fortnightly trapping at three sites in Grahamstown, South Africa, over a year. Sarcophaga africa Wiedemann, 1824, S. inaequalis Austen, 1909, S. exuberans Pandelle, 1896 and S. tibialis Macquart, 1851 showed well-defined peaks between early October 2001 and late April 2002, and only S. africa was trapped at other times of year. These peaks occurred when average minimum and maximum ambient air temperatures were above 12°C and 22°C, respectively, and showed no obvious relationship to rainfall. There were indications of population cycles in all of these species. Sarcophaga hera Zumpt, 1972, S. arno Curran, 1934, S. inzi Curran, 1934, S. langi Curran, 1934, S. freyi Zumpt, 1953, S. nodosa Engel, 1925 and S. samia Curran, 1934 were too scarce to assess their patterns of occurrence rigorously. Insects attending a corpse are reputed to assist forensic entomologists in estimating the time of year when the body died. Some flesh flies provide more precise estimates than others, so several species should be used for cross-validation. Insect activity at a corpse depends on the weather, so that presence of a species indicates particular environmental conditions and not simply calendar dates (particularly if climate changes). Absence of a species is not necessarily evidence of specific conditions because species may not be present at all sites simultaneously, populations cycle even when their members are active, and low population densities may hamper detection of a species.
- Full Text:
- Date Issued: 2017
- Authors: Villet, Martin H , Clitheroe, Crystal-Leigh , Williams, Kirstin A
- Date: 2017
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/59692 , vital:27639 , https://doi.org/10.3897/AfrInvertebr.58.9537
- Description: Eleven species of flesh fly were identified in a sample of 737 specimens captured during fortnightly trapping at three sites in Grahamstown, South Africa, over a year. Sarcophaga africa Wiedemann, 1824, S. inaequalis Austen, 1909, S. exuberans Pandelle, 1896 and S. tibialis Macquart, 1851 showed well-defined peaks between early October 2001 and late April 2002, and only S. africa was trapped at other times of year. These peaks occurred when average minimum and maximum ambient air temperatures were above 12°C and 22°C, respectively, and showed no obvious relationship to rainfall. There were indications of population cycles in all of these species. Sarcophaga hera Zumpt, 1972, S. arno Curran, 1934, S. inzi Curran, 1934, S. langi Curran, 1934, S. freyi Zumpt, 1953, S. nodosa Engel, 1925 and S. samia Curran, 1934 were too scarce to assess their patterns of occurrence rigorously. Insects attending a corpse are reputed to assist forensic entomologists in estimating the time of year when the body died. Some flesh flies provide more precise estimates than others, so several species should be used for cross-validation. Insect activity at a corpse depends on the weather, so that presence of a species indicates particular environmental conditions and not simply calendar dates (particularly if climate changes). Absence of a species is not necessarily evidence of specific conditions because species may not be present at all sites simultaneously, populations cycle even when their members are active, and low population densities may hamper detection of a species.
- Full Text:
- Date Issued: 2017
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