Streptococcal Bacteriocin-Like Inhibitory Substances: Some Personal Insights into the Bacteriocin-Like Activities Produced by Streptococci Good and Bad

The background to the discovery and commercial development of the first Streptococcus salivarius probiotic is documented. A 40-year search of the genus Streptococcus for a harmless natural antagonist of Streptococcus pyogenes had as its operational basis a simple deferred antagonism “fingerprinting” procedure, the application of which results in each tested strain being accorded an inhibitor production (P)-type and inhibitor sensitivity (S)-type profile. Systematic application of this schema has opened a “Pandora’s Box” of novel streptococcal bacteriocin-like inhibitory substances (BLIS). The numerically prominent commensal S. salivarius is proposed to have a pivotal population-modulating role within the oral microbiota of humans. The probiotic strain S. salivarius K12 produces several megaplasmid-encoded BLIS including the lantibiotics salivaricin A and salivaricin B. Strain K12 and other BLIS-producing S. salivarius are currently in use or under development for application to the control of a variety of common maladies and infections of the human oral cavity.     

Insights into the demographic history of African Pygmies from complete mitochondrial genomes

Pygmy populations are among the few hunter-gatherers currently living in sub-Saharan Africa and are mainly represented by two groups, Eastern and Western, according to their current geographical distribution. They are scattered across the Central African belt and surrounded by Bantu-speaking farmers, with whom they have complex social and economic interactions. To investigate the demographic history of Pygmy groups, a population approach was applied to the analysis of 205 complete mitochondrial DNA (mtDNA) sequences from ten central African populations. No sharing of maternal lineages was observed between the two Pygmy groups, with haplogroup L1c being characteristic of the Western group but most of Eastern Pygmy lineages falling into subclades of L0a, L2a, and L5. Demographic inferences based on Bayesian coalescent simulations point to an early split among the maternal ancestors of Pygmies and those of Bantu-speaking farmers (～ 70,000 years ago [ya]). Evidence for population growth in the ancestors of Bantu-speaking farmers has been observed, starting ～ 65,000 ya, well before the diffusion of Bantu languages. Subsequently, the effective population size of the ancestors of Pygmies remained constant over time and ～ 27,000 ya, coincident with the Last Glacial Maximum, Eastern and Western Pygmies diverged, with evidence of subsequent migration only among the Western group and the Bantu-speaking farmers. Western Pygmies show signs of a recent bottleneck 4,000-650 ya, coincident with the diffusion of Bantu languages, whereas Eastern Pygmies seem to have experienced a more ancient decrease in population size (20,000-4,000 ya). In conclusion, the results of this first attempt at analyzing complete mtDNA sequences at the population level in sub-Saharan Africa not only support previous findings but also offer new insights into the demographic history of Pygmy populations, shedding new light on the ancient peopling of the African continent.     

Microbiological Quality of Protein Feed Supplements Produced by Rendering Plants

Samples of protein feed supplements produced by rendering plants were examined for salmonellae, total aerobic bacterial counts, coliform counts, and enterococci. Isolations of salmonellae were more frequent from products with high counts; however, 6% of the samples with total counts of less than 1,000 per gram and 14% of the samples with coliform counts of less than 1 per gram contained salmonellae. Serotypes of Escherichia coli which have been associated with disease in domestic animals and poultry were also isolated from products. Although the distribution of serotypes of salmonellae isolated from environmental swabs and flies was similar to that isolated from products, the isolation of several serotypes from flies which had not been isolated in plants suggested that flies may be a potential source of contamination.     

Structural Insights into Substrate Specificity in Variants of N-Acetylneuraminic Acid Lyase Produced by Directed Evolution

The substrate specificity of Escherichia coli N-acetylneuraminic acid lyase was previously switched from the natural condensation of pyruvate with N-acetylmannosamine, yielding N-acetylneuraminic acid, to the aldol condensation generating N-alkylcarboxamide analogues of N-acetylneuraminic acid. This was achieved by a single mutation of Glu192 to Asn. In order to analyze the structural changes involved and to more fully understand the basis of this switch in specificity, we have isolated all 20 variants of the enzyme at position 192 and determined the activities with a range of substrates. We have also determined five high-resolution crystal structures: the structures of wild-type E. coli N-acetylneuraminic acid lyase in the presence and in the absence of pyruvate, the structures of the E192N variant in the presence and in the absence of pyruvate, and the structure of the E192N variant in the presence of pyruvate and a competitive inhibitor (2R,3R)-2,3,4-trihydroxy-N,N-dipropylbutanamide. All structures were solved in space group P2₁ at resolutions ranging from 1.65 Å to 2.2 Å. A comparison of these structures, in combination with the specificity profiles of the variants, reveals subtle differences that explain the details of the specificity changes. This work demonstrates the subtleties of enzyme-substrate interactions and the importance of determining the structures of enzymes produced by directed evolution, where the specificity determinants may change from one substrate to another.     

Secretarybird Sagittarius serpentarius Population Trends and Ecology: Insights from South African Citizen Science Data

Data from two long-term citizen science projects were used to examine the status and ecology of a Red List species, the Secretarybird Sagittarius serpentarius (Vulnerable), in South Africa. The first phase of the Southern African Bird Atlas Project operated from 1987 until 1992, and the second phase began in 2007. The Coordinated Avifaunal Roadcounts (CAR) project began in 1993 and by 1998 had expanded to cover much of the south-eastern half of the country. Data submitted up until April 2013 were used. A new method of comparing reporting rates between atlas projects was developed. Changing reporting rates are likely to reflect changes in abundance; in this instance the data suggest that the Secretarybird population decreased across much of South Africa between the two atlas projects, with a widespread important decrease in the Kruger National Park. Habitat data from the CAR project were analysed to gain insight into the ecology of the species. Secretarybirds tended to avoid transformed habitats across much of the area covered by the CAR project. In the winter rainfall region of the Western Cape, which is characterised by heavily transformed fynbos vegetation, at least 50% of Secretarybirds recorded were in transformed environments. This implies that in the Fynbos biome, at least, Secretarybirds have adapted to transformed environments to some degree. However, in the rest of the country it is likely that habitat loss, largely through widespread bush encroachment but also through agriculture, afforestation, and urbanisation, is a major threat to the species. The methods developed here represent a new approach to analysing data from long-term citizen science projects, which can provide important insights into a species'' conservation status and ecology.     

Insights into the Management of Large Carnivores for Profitable Wildlife-Based Land Uses in African Savannas

Large African predators, especially lions (Panthera leo) and leopards (Panthera pardus), are financially valuable for ecotourism and trophy hunting operations on land also utilized for the production of other wildlife species for the same purpose. Predation of ungulates used for trophy hunting can create conflict with landholders and trade off thus exists between the value of lions and leopards and their impact on ungulate populations. Therefore productionist and conservation trade-offs are complexly graded and difficult to resolve. We investigated this with a risk-benefit analysis on a large private wildlife production area in Zimbabwe. Our model showed that lions result in substantial financial costs through predation on wild ungulates that may not be offset by profits from hunting them, whereas the returns from trophy hunting of leopards are projected to exceed the costs due to leopard predation. In the absence of additional income derived from photo-tourism the number of lions may need to be managed to minimize their impact. Lions drive important ecological processes, but there is a need to balance ecological and financial imperatives on wildlife ranches, community wildlife lands and other categories of multiple use land used for wildlife production. This will ensure the competitiveness of wildlife based land uses relative to alternatives. Our findings may thus be limited to conservancies, community land-use areas and commercial game ranches, which are expansive in Africa, and should not necessarily applied to areas where biodiversity conservation is the primary objective, even if hunting is allowed there.     

Insights into the inhibition of xanthine oxidase by curcumin

As a natural pigment, curcumin exhibits multiple biological activities. Previous studies have investigated the inhibition of xanthine oxidase (XO) by curcumin. In the present work, based on the molecular docking simulations, it is interesting to find that parent curcumin binds weakly to XO, while its degradation products, for example, trans-6-(4′-hydroxy-3′-methoxyphenyl)-2,4-dioxo-5-hexenal, exhibit effective inhibitory activities against XO. The findings shed new light on the underlying mechanisms of curcumin in inhibiting XO and also have potential implication that both parent curcumin and its degradation products should be taken into account when exploring the mechanisms of curcumin’s biological activities.     

Insights into the Dual Activity of SIVmac239 Vif against Human and African Green Monkey APOBEC3G

Human immunodeficiency virus type 1 (HIV-1) Vif is essential for viral evasion of the host antiviral protein APOBEC3G (APO3G). The Vif protein from a distantly related African green monkey (Agm) simian immunodeficiency virus (SIVagm) is unable to suppress the antiviral activity of human APO3G but is active against Agm APO3G. SIVmac Vif on the other hand, possesses antiviral activity against both human and Agm APO3G. In this study, we were interested in mapping domains in SIVmac Vif that are responsible for its dual activity against human and Agm APO3G. We constructed a series of Vif chimeras by swapping domains in SIVmac Vif with equivalent regions from SIVagm Vif and determined their activity against human and Agm APO3G. We found that replacing any region in SIVmac Vif by corresponding fragments from SIVagm Vif only moderately reduced the activity of the chimeras against Agm APO3G but in all cases resulted in a severe loss of activity against human APO3G. These results suggest that the domains in SIVmac Vif required for targeting human and Agm APO3G are distinct and cannot be defined as linear amino acid motifs but rather appear to depend on the overall structure of full-length SIVmac Vif.     

Insights into mechanism of tumour promotion by mezerein

The objective of this study was to gather insights and compare the mode of action of the non phorbol, diterpene mezerein with the phorbol ester, phorbol-12-myristate-13 acetate, in normal and transformed cells. Both phorbol-12-myristate-13 acetate and mezerein are shown to activate the signal transduction pathways involving post translational modification of proteins by poly ADP-ribosylation and by protein kinase C, but to varying extents and showed different time kinetics and cell type differences. Multiple nuclear proteins, especially histones H3d, A24 and HI served as acceptors of poly ADP-ribose in response to PMA in both NIH 3T3 and HDCS cells whereas H1 and H2B were the major acceptors in case of mezerein treatment, similarly in both NIH 3T3 and HDCS cells. The results suggest an epigenetic mechanism (s) in tumour promotion by mezerein.     

Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes

Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1) and two novel loci (HLA-B and INS-IGF2) at genome-wide significance (4.15×10⁻⁹⁴<P<5×10⁻⁸, odds ratio (OR) = 1.09 to 1.36). Fine-mapping revealed that 88 of 158 previously identified T2D or glucose homeostasis loci demonstrated nominal to highly significant association (2.2×10⁻²³ < locus-wide P<0.05). These novel and previously identified loci yielded a sibling relative risk of 1.19, explaining 17.5% of the phenotypic variance of T2D on the liability scale in African Americans. Overall, this study identified two novel susceptibility loci for T2D in African Americans. A substantial number of previously reported loci are transferable to African Americans after accounting for linkage disequilibrium, enabling fine mapping of causal variants in trans-ethnic meta-analysis studies.     

New Insights into the Pelletization Mechanism by Extrusion/Spheronization

Pellet manufacturing by extrusion/spheronization is quite common in the pharmaceutical field because the obtained product is characterized by a high sphericity as well as a narrow particle size distribution. The established mechanisms only consider deformation of the initially fractured particles but do not account for mass transfer between the particles as a factor in achieving spherical particles. This study dealt with the visualization of mass transfer during spheronization. Therefore, two common pelletization aids, microcrystalline cellulose and kappa-carrageenan, were used alone as well as in combination with lactose as a filler. This study proves that mass transfer between particles must be considered in addition to plastic deformation in order to capture the spheronization mechanism. Moreover, it is evident that there are regional distinctions in the amount of mass transfer at the particle surface. Therefore, the commonly espoused pelletization mechanisms need to be extended to account for material transfer between pellet particles, which has not been considered before.     

Insights into the molecular mechanism of mitochondrial toxicity by AIDS drugs

Several of the nucleoside analogs used in the treatment of AIDS exhibit a delayed clinical toxicity limiting their usefulness. The toxicity of nucleoside analogs may be related to their effects on the human mitochondrial DNA polymerase (Pol gamma), the polymerase responsible for mitochondrial DNA replication. Among the AIDS drugs approved by the FDA for clinical use, two are modified cytosine analogs, Zalcitabine (2',3'-dideoxycytidine (ddC)) and Lamivudine (beta-d-(+)-2',3'-dideoxy-3'-thiacytidine ((-)3TC])). (-)3TC is the only analog containing an unnatural l(-) nucleoside configuration and is well tolerated by patients even after long term administration. In cell culture (-)3TC is less toxic than its d(+) isomer, (+)3TC, containing the natural nucleoside configuration, and both are considerably less toxic than ddC. We have investigated the mechanistic basis for the differential toxicity of these three cytosine analogs by comparing the effects of dideoxy-CTP), (+)3TC-triphosphate (TP), and (-)3TC-TP on the polymerase and exonuclease activities of recombinant human Pol gamma. This analysis reveals that Pol gamma incorporates (-)3TC-triphosphate 16-fold less efficiently than the corresponding (+)isomer and 1140-fold less efficiently than dideoxy-CTP, showing a good correlation between incorporation rate and toxicity. The rates of excision of the incorporated analogs from the chain-terminated 3'-end of the DNA primer by the 3'-5'-exonuclease activity of Pol gamma were similar (0.01 s(-)1) for both 3TC analogs. In marked contrast, the rate of exonuclease removal of a ddC chain-terminated DNA occurs at least 2 orders of magnitude slower, suggesting that the failure of the exonuclease to remove ddC may play a major role in its greater toxicity. This study demonstrates that direct analysis of the mitochondrial DNA polymerase structure/function relationships may provide valuable insights leading to the design of less toxic inhibitors.     

Insights into the mechanism of oxidative deamination catalyzed by DOPA decarboxylase

The unusual oxygen-consuming oxidative deamination reaction catalyzed by the pyridoxal 5'-phosphate (PLP) enzyme DOPA decarboxylase (DDC) was here investigated. Either wild-type or Y332F DDC variant is able to perform such oxidation toward aromatic amines or aromatic l-amino acids, respectively, without the aid of any cofactor related to oxygen chemistry. Oxidative deamination produces, in equivalent amounts, a carbonyl compound and ammonia, accompanied by dioxygen consumption in a 1:2 molar ratio with respect to the products. Kinetic studies either in the pre-steady or in the steady state, together with HPLC analyses of reaction mixtures under varying experimental conditions, revealed that a ketimine accumulates during the linear phase of product formation. This species is reactive since it is converted back to PLP when the substrate is consumed. Rapid-mixing chemical quench studies provide evidence that the ketimine is indeed an intermediate formed during the first catalytic cycle. Moreover, superoxide anion and hydrogen peroxide are both generated during the catalytic cycles. On this basis, a mechanism of oxidative deamination consistent with the present data is proposed. Furthermore, the catalytic properties of the T246A DDC mutant together with those previously obtained with H192Q mutant allow us to propose that the Thr246-His192 dyad could act as a general base in promoting the first step of the oxidative deamination of aromatic amines.