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Devil's claw is a popular natural anti-inflammatory phytomedicine. The preparation of Devil's claw products is complicated by the similarity between the morphotypes of Harpagophytum procumbens and H. zeyheri. This study investigated the potential of a validated ultra-high performance liquid chromatography coupled to mass spectrometry (UHPLC-MS) method to investigate the harpagoside content of methanol extracts of the secondary tubers of both species. In addition, DNA barcoding was used to determine the identity of the Harpagophytum species included in commercial Devil's claw products. Herbal reference material of H. procumbens and H. zeyheri, originally harvested in southern Africa, was morphologically authenticated and commercial products containing Harpagophytum were purchased on the internet using the search terms “Harpagophytum” or “Devil's claw.” High-performance thin-layer chromatography (HPTLC) and UHPLC-MS was used for the qualitative and quantitative determination of harpagoside content in commercial products. The UHPLC-MS method developed had a limit of detection (LOD) of 0.165 µg/mL and a limit of quantification (LOQ) of 0.499 µg/mL. Quantitative UHPLC-MS analysis revealed high variability in the harpagoside content for both species; H. procumbens (0.17-4.37%) and H. zeyheri (0.00-3.07%). Only 41% of H. procumbens and 17% of H. zeyheri raw materials contained harpagoside. Using HPTLC, 90% of the commercial products tested were determined to contain harpagoside. The results were congruent with the UHPLC-MS analysis where the harpagoside content was out of specification for 10% of analyzed commercial products. The harpagoside content in commercial products varied from not detected to 3.50%. PCR amplification followed by comparative sequencing analysis of trnL-F, and ycf1 plastid gene amplicons indicated specific sites in trnL-F at positions 118 and 146 and at position 538 in ycf1 amplicons suitable to distinguish the two Harpagophytum species. These sites were used to barcode the herbal products and Character-based Barcode Recognition Obtained with Nucleotide eXposes (BRONX) analyses verified the taxonomic identity of the Harpagophytum in the samples. The results revealed that 76% (16/21) of the commercial products tested were incorrectly labelled as H. procumbens and, instead, contained H. zeyheri. Our study suggests that DNA barcoding in combination with the UHPLC-MS and HPTLC could significantly support herbal product authentication. This study contributed knowledge and methods that can be implemented to enhance the quality of commercial Devil's claw products.

It has been nearly 100 years since citrus growers in two distinct regions in the northern provinces of South Africa noticed unusual symptoms in their citrus trees, causing significant crop losses. They had no idea that these symptoms would later become part of an almost global pandemic of a disease called greening or huanglongbing (HLB). The rapid spread of the disease indicated that it might be caused by a transmissible pathogen, but it took >50 years to identify the causative agent as ‘Candidatus Liberibacter africanus’. Recently, the disease appeared in more African countries, spreading by both infected planting material and Trioza erytreae. To date, five ‘Ca. L. africanus’ subspecies have been identified in various rutaceous species, with ‘Ca. L. africanus subsp. clausenae’ the only subspecies for which a biovar was detected in citrus. Efforts to detect and differentiate HLB-causing Liberibacter species are ongoing, and recent developments are discussed here. This review focuses on aspects of the African form of HLB, including its specific bacterial species and subspecies, its main insect vector, its geographic distribution, and current management strategies.

There is a causal relationship between cancer (including colorectal cancer), chronic systemic inflammation and persistent infections, and the presence of dysregulated circulating inflammatory markers. It is known that aberrant clot formation and coagulopathies occur in systemic inflammation. In colorectal cancer, there is close link between gut dysbiosis and an inflammatory profile. In this review we present evidence of the connection between gut dysbiosis, the entry of bacteria into the internal environment and the presence of their highly potent inflammagenic molecules, such as lipopolysaccharide and lipoteichoic acid, in circulation. These bacterial components may act as one of the main drivers of the inflammatory process (including hypercoagulation) in colorectal cancer. We review literature that points to the role of these bacterial inflammagens and how they contribute to colorectal carcinogenesis. Insight into the factors that promote carcinogenesis is crucial to effectively prevent and screen for colorectal cancer. Early diagnosis of an activated coagulation system and the detection of bacterial components in circulation and also in the tumour microenvironment, could therefore be important, and may also, together with modulation of the gut microbiota, serve as potential therapeutic targets.

Pneumonia is the main reason for mortality among children under five years, causing 1.6 million deaths every year; late research has exhibited that mortality is increasing in the elderly. A few biomarkers used for its diagnosis need specificity and precision, as they are related to different infections, for example, pulmonary tuberculosis and Human Immunodeficiency Virus. There is a quest for new biomarkers worldwide to diagnose the disease to defeat these previously mentioned constraints. Antimicrobial peptides (AMPs) are promising indicative specialists against infection. This research work used AMPs as biomarkers to detect viral pneumonia pathogens, for example, Respiratory syncytial virus, Influenza A and B viruses utilizing in silico technologies, such as Hidden Markov Model (HMMER). HMMER was used to distinguish putative anti-viral pneumonia AMPs against the recognized receptor proteins of Respiratory syncytial virus, Influenza A, and B viruses. The physicochemical parameters of these putative AMPs were analyzed, and their 3-D structures were determined utilizing I-TASSER. Molecular docking interaction of these AMPs against the recognized viral pneumonia proteins was carried out using the PATCHDOCK and HDock servers. The results demonstrated 27 anti-viral AMPs ranked based on their E values with significant physicochemical parameters in similarity with known experimentally approved AMPs. The AMPs additionally had a high anticipated binding potential to the pneumonia receptors of these microorganisms sensitively. The tendency of the putative anti-viral AMPs to bind pneumonia proteins showed that they would be promising applicant biomarkers to identify these viral microorganisms in the point-of-care (POC) pneumonia diagnostics. The high precision observed for the AMPs legitimizes HMM’s utilization in the disease diagnostics’ discovery process.

Histological investigations elucidate infection structure development and the subsequent colonization process of rust pathogens in their cereal hosts. No comprehensive information exists for the in...

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major disease of wheat. In Kenya, Pgt has caused sporadic but serious losses to farmers since large-scale wheat production began in...

In contrast to many other countries, the virulence and genetic diversity of the South African Puccinia triticina population before 1980 is unknown, because of the absence of regular and systematic race analysis data and viable rust cultures. Herbarium specimens housed at the National Collection of Fungi, Biosystematics Unit, Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa (SA), provided the opportunity to investigate the genetic development of the population using isolates collected between 1906 and 2010. Five subpopulations that survived between 21 and 82 years in the field were found. While three of these could represent the original races that entered SA during European settlement, two appear to be recent exotic introductions into SA, most probably from other African countries. The demise of the three oldest subpopulations might be from the release of resistant wheat cultivars. The population is clonal, where new virulence develops through single step mutations and selection for virulence. Although a possible case of somatic hybridization was found, sexual reproduction appears to be absent in SA. This study confirmed the importance of annual surveys in SA and its neighboring countries for the timely detection of new virulent races that could threaten wheat production in SA.

The density and morphology of glandular trichomes in rose geranium (Pelargonium graveolens L’Her.) are often correlated to the essential oil biosynthesis. However, whether the different organs in the same rose geranium plant are affected by hail damage, or if they recover similarly following hail damage is still unknown concerning the essential oil biosynthesis. The objective of this study was to evaluate the effects of split-applying cytokinin (CK), gibberellic acid (GA) and defoliation on rose geranium trichome morphology and density, and essential oil biosynthesis. The experiment was carried out in a hail-net covered tunnel structure during 2017-2018 growing season. The experimental design was a complete randomized blocks with a 3x3 factorial arrangement of treatments: three defoliation levels (0, 50, and 100%), two levels of split-application of CK and GA (0.32 mg L-1 CK + 150 mg L-1 GA; and 0.64 mg L-1 CK + 300 mg L-1 GA), and a control. The attenuate, peltate, and capitate trichome groups were identified in the leaf. Morphologically, the attenuate trichome group was less dense on both recovered and new plant leaves, despite split-applied CK and GA treatment. With the peltate group, brevicollate trichome density declined in all plant leaves treated with 0.64 mg L-1 CK + 300 mg L-1 GA on both leaf surfaces. Application of 0.64 mg L-1 CK + 300 mg L-1 GA led to high density of the elongated-capitate type on leaves recovered from 50 and 100% defoliation. The essential oil yield was not affected by density and morphological changes of the trichomes. However, the application of 0.32 mg L-1 CK + 150 mg L-1 GA increased the citronellol content where plants endured 100% defoliation. Results demonstrated that the effects of hail damage stress and subsequent split-applied CK and GA could transform the morphology of trichomes, subsequently increasing the density.

The unfolded protein response (UPR) is a highly conserved cellular response in eukaryotic cells to counteract endoplasmic reticulum (ER) stress, typically triggered by unfolded protein accumulation. In addition to its relevance to human diseases like cancer cell development, the induction of the UPR has a significant impact on recombinant protein production yields in microbial cell factories, including the industrial workhorse Saccharomyces cerevisiae. Being able to accurately detect and measure this ER stress response in single cells, enables the rapid optimisation of protein production conditions and high-throughput strain selection strategies. Current methodologies to monitor the UPR in S. cerevisiae are often temporally and spatially removed from the cultivation stage, or lack updated systematic evaluation. To this end we constructed and systematically evaluated a series of high-throughput UPR sensors by different designs, incorporating either yeast native UPR promoters or novel synthetic minimal UPR promoters. The native promoters of DER1 and ERO1 were identified to have suitable UPR biosensor properties and served as an expression level guide for orthogonal sensor benchmarking. Our best synthetic minimal sensor, SM1, was only 98 bp in length, had minimal homology to other native yeast sequences and displayed superior sensor characteristics. Using this synthetic minimal UPR sensor, we demonstrate its ability to accurately discriminate between cells expressing different heterologous proteins and at varying production levels. Our sensor is thus a novel high-throughput tool for determining expression/engineering strategies for optimal heterologous protein production.

Sunflower (Helianthus annuus L.) is the third largest grain crop by area planted in South Africa (SA). The annual yield is negatively affected by sunflower rust caused by Puccinia helianthi Schw. (Phe). Four Phe races were described in SA in the middle 1990s, but since then, no new race descriptions have been conducted. This has resulted in an information gap on the current Phe population, making it difficult to explain increased disease incidence and loss of resistance in previously resistant hybrids. To address this, 114 Phe field isolates along with 23 historic isolates were phenotyped using the international set of 11 sunflower differentials containing the R1, R2/R10, R3, R4a, R4b, R4c, R4d, R5, Pu6, and Radv resistance genes. Three new Phe races were identified, bringing the total number of South African races recorded to seven. No avirulence was detected attributable to the R1 gene, with the R4d and Radv genes remaining effective. Four main genetic lineages were detected with no obvious correlation between phenotype and genotype. The detection of three genetic lineages consisting exclusively of field isolates collected post-2006 suggested the possible recent entry of exotic introductions into SA. This, combined with the fact that one lineage consisted exclusively of the most virulent race Phe7721, confirmed a clear shift in the Phe population that could explain the increased virulence and occurrence of the disease in SA.

A novel Ug99-resistant wheat–Thinopyrum ponticum translocation line was produced, its chromosomal composition was analyzed and specific markers were developed. Stem rust caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn (Pgt) has seriously threatened global wheat production since Ug99 race TTKSK was first detected in Uganda in 1998. Thinopyrum ponticum is near immune to Ug99 races and may be useful for enhancing wheat disease resistance. Therefore, developing new wheat–Th. ponticum translocation lines that are resistant to Ug99 is crucial. In this study, a novel wheat–Th. ponticum translocation line, WTT34, was produced. Seedling and field evaluation revealed that WTT34 is resistant to Ug99 race PTKST. The resistance was derived from the alien parent Th. ponticum. Screening WTT34 with markers linked to Sr24, Sr25, Sr26, Sr43, and SrB resulted in the amplification of different DNA fragments from Th. ponticum, implying WTT34 carries at least one novel stem rust resistance gene. Genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), and multi-color GISH (mc-GISH) analyses indicated that WTT34 carries a T5DS·5DL-Th translocation, which was consistent with wheat660K single-nucleotide polymorphism (SNP) array results. The SNP array also uncovered a deletion event in the terminal region of chromosome 1D. Additionally, the homeology between alien segments and the wheat chromosomes 2A and 5D was confirmed. Furthermore, 51 PCR-based markers derived from the alien segments of WTT34 were developed based on specific-locus amplified fragment sequencing (SLAF-seq). These markers may enable wheat breeders to rapidly trace Th. ponticum chromosomal segments carrying Ug99 resistance gene(s).

Sickle cell disease (SCD) is caused by a point mutation in the beta-globin gene. SCD is characterized by chronic hemolytic anemia, vaso-occlusive events leading to tissue ischemia, and progressive organ failure. Chronic inflammatory state is part of the pathophysiology of SCD. Patients with SCD have extremely variable phenotypes, from mild disease to severe complications including early age death. The spleen is commonly injured in SCD. Early splenic dysfunction and progressive spleen atrophy are common. Splenomegaly and hypersplenism can also occur with the loss of the crucial splenic function. Acute, life-threatening spleen-related complications in SCD are well studied. The association of laboratory parameters with the spleen status including hyposplenism, asplenia, and splenomegaly/hypersplenism, and their implication in vaso-occlusive crisis and long-term complications in SCD remain to be determined. We evaluated the association between the spleen status with clinical and laboratory parameters in 31 SCD patients: Group a) Patients with asplenia/hyposplenism (N = 22) (including auto-splenectomy and splenectomized patients) vs. Group b) patients with splenomegaly and or hypersplenism (N = 9). Laboratory studies included: Complete Blood Count, reticulocyte count, iron metabolism parameters, C Reactive Protein (CRP), Hb variant distribution, and D-dimer. Metabolic and morphological red blood cell (RBC) studies included: density gradient (by Percoll), glucose consumption, lactate release, and K+ leakage, fetal RBC (F-Cells) and F-Reticulocytes, annexinV+, CD71+, oxidative stress measured by GSH presence in RBC and finally Howell Jolly Bodies count were all analyzed by Flow Cytometry. Scanning electron microscopy analysis of RBC was also performed. Patients with asplenia/hyposplenism showed significantly higher WBC, platelet, Hematocrit, hemoglobin S, CRP, D-dimer, Gamma Glutamyl Transferase (GGT), cholesterol, transferrin, annexin V+ RBCs, CD71+ RBCs, together with a markedly lower F Reticulocyte levels in comparison with splenomegaly/hypersplenism patients. In summary, important differences were also found between the groups in the studied RBCs parameters. Further studies are required to elucidate the effect of the spleen including hyper and hypo-splenia on laboratory parameters and in clinical manifestations, vascular pathology, and long-term complications of SCD. The benefits and risks of splenectomy compared to chronic transfusion need to be evaluated in clinical trials and the standard approach managing hypersplenism in SCD patients should be re-evaluated.

Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis) infection, is a multi-host disease which negatively affects the wildlife industry, with adverse consequences for conservation, ecotourism, and game/wildlife sales. Although interspecies transmission has been reported between some wildlife hosts, the risk of spread in complex ecosystems is largely unknown. As a controlled disease, tools for accurate detection of M. bovis infection are crucial for effective surveillance and management, especially in wildlife populations. There are, however, limited species-specific diagnostic tests available for wildlife. Hippopotamuses are rarely tested for M. bovis infection, and infection has not previously been confirmed in these species. In this study, blood and tissue samples collected from common hippopotamus (Hippopotamus amphibius) residing in a bTB-endemic area, the Greater Kruger Protected area (GKPA), were retrospectively screened to determine whether there was evidence for interspecies transmission of M. bovis, and identify tools for M. bovis detection in this species. Using the multi-species DPP® VetTB serological assay, a bTB seroprevalence of 8% was found in hippopotamus from GKPA. In addition, the first confirmed case of M. bovis infection in a free-ranging common hippopotamus is reported, based on the isolation in mycobacterial culture, genetic speciation and detection of DNA in tissue samples. Importantly, the M. bovis spoligotype (SB0121) isolated from this common hippopotamus is shared with other M. bovis-infected hosts in GKPA, suggesting interspecies transmission. These results support the hypothesis that M. bovis infection may be under recognized in hippopotamus. Further investigation is needed to determine the risk of interspecies transmission of M. bovis to common hippopotamus in bTB-endemic ecosystems and evaluate serological and other diagnostic tools in this species.

The frequency of some major mycotoxins in marker tissues (liver and kidney) and in muscle tissue of slaughter pigs and cattle, obtained from registered abattoirs in South Africa, was studied. Samples of each three bovine carcasses were obtained from two abattoirs, and samples of three porcine carcasses were from a third abattoir. All samples originated from animals from subsistence farming. All samples were analysed for aflatoxins (AFB1, AFB2, AFG1, AFG2, deoxynivalenol (DON), ochratoxin A (OTA) and zearalenone (ZEN) using immunoaffinity chromatography extract cleanup and high-performance liquid chromatography (HPLC). At a limit of quantification (LOQ) of 1 μg/kg (individual AFs, 100 μg/kg (DON), 1 μg/kg (OTA) and 20 μg/kg (ZEN)), no mycotoxins were detected in any of the samples.

Heartwater is an economically important tick-borne disease of ruminants in Africa. The current commercial vaccine uses live Ehrlichia ruminantium from blood of infected sheep, requires antibiotic treatment during infection, needs to be administered intravenously and does not protect against all South African isolates. An attenuated tissue culture vaccine not requiring antibiotic treatment and effective against different field strains in small groups of goats and sheep was reported previously. The objective of the present study was to test safety and efficacy of this vaccine administered by intramuscular (i.m.) inoculation in larger groups of sheep, Angora goats and cattle. Animals were vaccinated via intravenous (i.v.) and i.m. routes and received E. ruminantium homologous challenge by feeding of infected ticks or by i.v. inoculation of infected blood. For vaccine titration in sheep and goats, the optimum safe and efficacious dose was determined using 2 ml equivalent of 102-105 culture-derived live elementary bodies (EBs). Similarly, the vaccine was titrated in cattle using 5 ml containing 105-107 EBs. Seventy percent of i.v. vaccinated and 9.7% of i.m. vaccinated Angora goats receiving 105 EBs, developed severe reactions to vaccination and were treated. These treated animals and the remaining 90.3% of i.m.- vaccinated goats showed 100% protection against i.v. or tick challenge. Sheep and Angora goats vaccinated i.m. with 104 EBs had no vaccination reactions and were fully protected against i.v. or tick challenge. Similarly, vaccinated cattle (dose 106 EBs) did not react to vaccine inoculation and were fully protected against i.v. or tick homologous challenge. Control non-vaccinated animals reacted severely to challenge and required oxytetracycline treatment. This successfully demonstrated that Angora goats, sheep and cattle can be safely vaccinated with the attenuated E. ruminantium Welgevonden vaccine via the i.m. route, with no clinical reactions to vaccination and 100% protection against virulent i.v. and homologous tick challenge.

The production of malting barley under dryland and irrigated environments in South Africa (SA) has increased recently, making it the second most important winter crop after wheat. To assess the potential vulnerability of adapted barleys from SA to wheat stem rust (caused by Puccinia graminis f. sp. tritici, Pgt, race PTKST) and rye stem rust (Puccinia graminis f. sp. secalis, Pgs, isolate UVPgs1), 50 accessions were evaluated as seedlings and as adult plants. The same barley germplasm was tested against Pgt and Pgs cultures from the USA that have proven useful for detecting the stem rust resistance genes Rpg1 and the rpg4/Rpg5 complex. The possible presence of these resistance genes was assayed using molecular markers and sequence analysis. Barley accessions exhibited mostly resistant infection types (ITs) to the South African cultures, whilst field data revealed that several of the barley varieties displayed high severities in combination with more compatible host response types to race PTKST. The barley accessions exhibited mostly high ITs to cultures from the USA. None of the seedling IT data was sufficiently distinct to reliably postulate the presence of possible resistance genes. This result was corroborated from the molecular assays for Rpg1 and rpg4/Rpg5. Except for one line that tested heterozygous for the Rpg1 gene, none of the test entries contained this gene or a functional rpg4/Rpg5 complex due to the prevalence of mutations in the rpg4/Rpg5 + carriers. Susceptibility among barley varieties to wheat stem rust race PTKST under field conditions in the present study is of concern.

Animals partition their daily activities based on a variety of internal and external factors. For insectivorous bats, the availability of prey, weather conditions, moonlight and reproductive energy demands are proposed as the major influencers of temporal activity. This study investigated the temporal variation in activity of the subtropical cave-dwelling, migratory Natal long-fingered bat,Miniopterus natalensis, by temperature, humidity, lunar illumination and the time of moonrise per night. Using echolocation survey data collected 2014-2018 near a maternity roost in north-eastern South Africa, differences in activity between the summer maternity (1 September-28 February) and winter non-breeding (1 March-31 August) seasons were described. In the non-breeding season,M. natalensisexhibited peak activity during the early evening, with decreasing activity throughout the night. In the maternity season, a bimodal activity pattern was observed, probably related to peaks in insect activity and the energy requirements of lactating females. Predictably, temperature had the strongest positive influence on the magnitude ofM. natalensisactivity across both seasons. Humidity also positively affected activity in both seasons to a lesser extent. The time of moonrise did not affect the activity ofM. natalensisduring either of the seasons. Lunar illumination did not affect activity during the maternity season, but activity was diminished on nights with bright moonlight in the non-breeding season. Emergence and return times were not affected by lunar illumination in either season. The need ofM. natalensisto maximise resource acquisition during the maternity season is likely a strong modulator in the temporal activity of this species and outweighs predation risk in high moonlight conditions. Subsequently, this species exhibits nightly activity behaviours that balance risk factors with intrinsic needs during different seasons.

Waterbirds in stochastic environments exhibit nomadism in order to cater for the unpredictable availability of water resources. Lesser flamingos Phoeniconaias minor have long been thought to be nomadic waterbirds. In southern Africa, conservation efforts for lesser flamingos are hampered by a lack of knowledge about their movement trajectories. To investigate their movement ecology in southern Africa, we fitted GPS–GSM transmitters to 12 adults and tracked their movements over four years, from March 2016 to February 2020. Net squared displacement (NSD) was used in nonlinear least squares models classifying trajectories as nomadic, migratory, mixed-migratory, home range restricted or dispersal movement types. Data from eight of the 12 birds met the criteria for the NSD analysis. Model success was good; only 8 out of 120 (6.7%) movement type models failed to reach convergence. Goodness of fit statistics from the NSD models supported migratory and mixed migratory movement types (concordance criteria coefficient (CC) = 0.78) for more than half of the annual trajectories investigated (57.2%). Dispersal, home range-restricted and nomadic movements best described 28.6, 9.5 and 4.8% of annual trajectories, respectively, but all resulted in a mean CC of < 0.4 and thus did not fit observed NSD patterns as well as the migratory movement types. We then used nonlinear mixed effects models to account for annual and individual differences in migration parameters. Variation in the timing and duration of all migrations were more important than variation in migration distance, indicating well-established summer and winter ‘ranges’ and routes between Kamfers Dam (South Africa) and Sua Pan (Botswana). We propose that lesser flamingos in central southern Africa may be partial migrants, not true nomads, as most of their movements followed a regular, repeated pattern between two primary locations.

Introduction Several studies have explored the design of antimicrobial peptides (AMPs) for the development of therapeutic and diagnostic molecules for the treatment and identification of pathogenic diseases as well as cancer. Human cadherin-1 protein has been identified to be involved in adhesion-mediated signalling pathways in normal cells and its loss through genetic and epigenetic alterations can result in an enhanced invasion and metastasis of malignancy in tumours. Therefore, the identification of cadherin during treatment of cancer can be used as prognostic biomarker to establish the responsiveness of patients to treatment regimen. Antimicrobial peptides (AMPs) offer several compensatory advantages in biomedical applications and have been used for treatment of diseases, dietary supplements and diagnosis of diseases. The aim of this research work was to use in silico approaches to analyse retrieved human cadherin-1 as prognostic targets in cancer treatments using modelled putative anticancer AMPs. Methods The structures of the putative AMPs and cadherin-1 were modelled using I-TASSER server and the protein overall quality was validated using PROCHECK. Thereafter, the protein motifs were predicted and the molecular interaction between the putative anticancer AMPs and protein was carried out using PatchDock. Results The results revealed that all the AMPs were good prognostic molecules for cancer with BOO1 having the highest binding affinity of 15,874. Conclusion This study revealed that all the generated AMPs have good prognostic value for monitoring the progress of cancer treatment using human cadherin-1 as receptor. This is the first report where AMPs were used in prognostics of cancer using human cadherin-1.

We screened nonequine animals with unexplained neurologic signs or death in South Africa during 2010-2018 for Shuni virus (SHUV). SHUV was detected in 3.3% of wildlife, 1.1% of domestic, and 2.0% of avian species. Seropositivity was also demonstrated in wildlife. These results suggest a range of possible SHUV hosts in Africa.

Highlights • A microbiological diagnosis can currently be secured for >85% of brain abscesses. • The predominant organism is Streptococcus intermedius. • Patients typically receive six weeks of intravenous ceftriaxone (± metronidazole). • Mortality of brain abscesses remains high at >20%., Summary Background Brain abscess is an uncommon condition, but carries high mortality. Current treatment guidelines are based on limited data. Surveillance of clinical, radiological and microbiology data is important to inform patient stratification, interventions, and antimicrobial stewardship. Methods We undertook a retrospective, observational study of patients with brain abscess, based on hospital coding, in a UK tertiary referral teaching hospital. We reviewed imaging data, laboratory microbiology, and antibiotic prescriptions. Results Over a 47 month period, we identified 47 adults with bacterial brain abscess (77% male, median age 47 years). Most of the abscesses were solitary frontal or parietal lesions. A microbiological diagnosis was secured in 39/47 (83%) of cases, among which the majority were of the Streptococcus milleri group (27/39; 69%), with a predominance of Streptococcus intermedius (19/27; 70%). Patients received a median of 6 weeks of intravenous antibiotics (most commonly ceftriaxone), with variable oral follow-on regimens. Ten patients (21%) died, up to 146 days after diagnosis. Mortality was significantly associated with increasing age, multiple abscesses, immunosuppression and the presence of an underlying cardiac anomaly. Conclusion Our data suggest that there has been a shift away from staphylococcal brain abscesses, towards S. intermedius as a dominant pathogen. In our setting, empiric current first line therapy with ceftriaxone remains appropriate on microbiological grounds and narrower spectrum therapy may sometimes be justified. Mortality of this condition remains high among patients with comorbidity. Prospective studies are required to inform optimum dose, route and duration of antimicrobial therapy.

Barley, host to the wheat and rye attacking forms of the stem rust pathogen, Puccinia graminis (Pg), is considered inherently more resistant to Pg than wheat. To investigate whether this enhanced basal defence is associated with early infection or colonisation processes, adult plants of selected barley and wheat entries were inoculated with Pg f. sp. tritici (Pgt) races BNGSC and PTKST, and Pg f. sp. secalis (Pgs) isolate UVPgs1. Flag leaf sheaths on the last stem internode were sampled for analysis. Using scanning electron microscopy and epidermal stripping, early Pg infection structure development was compared between barley and wheat. Sub-stomatal vesicle appearance and production of haustorial mother cells were similar at 24 and 48 h post inoculation (hpi), respectively. Significant variation occurred among host entries (P ≤ 0.01) for colony size and fungal biomass at 120 hpi. Differences between the Pgt races and the Pgs isolate as well as the host entry-Pg isolate interaction proved insignificant (P ≥ 0.05). The period between 120 and 240 hpi may hold some explanation for the perceived lower stem rust receptivity in barley, since a steep increase in accumulated fungal biomass observed in the susceptible wheat Line 37 − 07 was not seen in the susceptible barley entries at the same time interval.

Many infectious diseases are still prevalent in the world’s populations since no effective treatments are available to eradicate them. The 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 forK. pneumoniae(ATCC 700603) and 6.25 μg/ml forP.aeruginosa(ATCC 22108). The two AMPs killed these bacteria rapidlyin 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. These 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.

Influenza A viruses (IAVs) and Newcastle disease viruses (NDVs) are major human and animal health threats with geographic differences in prevalence, characteristics and host populations. Currently, there is sparse information on IAVs and NDVs in avian species in South Africa. Because raptors feed on live wild birds which are the reservoir hosts of IAVs and NDVs, we considered them a good sentinel for surveillance. Therefore, in addition to other resident birds of prey, migratory Amur falcons (Falco amurensis) were screened for IAVs and NDVs. Oropharyngeal and cloacal samples were collected from raptor species at three sampling sites in KwaZulu-Natal Province and samples were screened for IAVs and NDVs using molecular and virus isolation methods. IAV-positive samples were further screened for the presence of H5, H7 and H9 viruses. A total of 14 samples from 11 birds (45.8% of all sampled birds) were IAV positive with C-t lower than 36 in duplicate tests. Five out of 24 birds (20.8%) were positive for IAV RNA in duplicate testing, albeit at low concentrations. Among raptor samples, three out of 24 birds (12.5%) were positive for IAVs with viral RNA detected in both cloacal and oropharyngeal swabs. One IAV-positive sample was also positive for H5 subtype (4.1%); all other samples were H5, H7 and H9 negative. Besides, all samples were NDV negative. Overall, our results support the development of more intensive and expanded influenza and other emerging virus studies in raptor species.

Background A strong correlation exists between type 2 diabetes mellitus (T2DM) and cardiovascular disease (CVD), with CVD and the presence of atherosclerosis being the prevailing cause of morbidity and mortality in diabetic populations. T2DM is accompanied by various coagulopathies, including anomalous clot formation or amyloid fibrin(ogen), the presence of dysregulated inflammatory molecules. Platelets are intimately involved in thrombus formation and particularly vulnerable to inflammatory cytokines. Methods The aim of this current study was therefore to assess whole blood (hyper)coagulability, platelet ultrastructure and receptor expression, as well as the levels of IL-1β, IL-6, IL-8 and sP-selectin in healthy and diabetic individuals. Platelet morphology was assessed through scanning electron microscopy (SEM), while assessment of GPIIb/IIIa receptor expression was performed with confocal microscopy and flow cytometry with the addition of FITC-PAC-1 and CD41-PE antibodies. IL-1β, IL-6 and IL-8 and sP-selectin levels were assessed using a multiplex assay. Results In T2DM there is significant upregulation of circulating inflammatory markers, hypercoagulation and platelet activation, with increased GPIIb/IIIa receptor expression, as seen with flow cytometry and confocal microscopy. Analyses showed that these receptors were additionally shed onto microparticles, which was confirmed with SEM. Conclusions Cumulatively, this provides mechanistic evidence that pathological states of platelets together with amyloid fibrin(ogen) in T2DM, might underpin an increased risk for cardiovascular events.

Background Modification and destruction of natural habitats are bringing previously unencountered animal populations into contact with humans, with bats considered important zoonotic transmission vectors. Caves and cave-dwelling bats are under-represented in conservation plans. In South Africa, at least two cavernicolous species are of interest as potential zoonotic hosts: the Natal long-fingered bat Miniopterus natalensis and the Egyptian fruit bat Rousettus aegyptiacus. Little information is available about the anthropogenic pressures these species face around important roost sites. Both bats are numerous and widespread throughout the country; land-use changes and urban expansions are a rising concern for both conservation and increased bat-human contact. Results Our study addressed this shortfall by determining the extent of land-cover change around 47 roosts between 2014 and 2018 using existing land cover datasets. We determined the land-cover composition around important roost sites (including maternity, hibernacula and co-roosts), distances to urban settlements and assessed the current protection levels of roost localities. We detected an overall 4% decrease in natural woody vegetation (trees) within 5 km buffer zones of all roost sites, with a 10% decrease detected at co-roost sites alone. Agricultural land cover increased the most near roost sites, followed by plantations and urban land-cover. Overall, roosts were located 4.15 ± 0.91 km from urban settlements in 2018, the distances decreasing as urban areas expand. According to the South African National Biodiversity Institute Ecosystem Threat Status assessment, 72% of roosts fall outside of well-protected ecosystems. Conclusions The current lack of regulatory protection of cavernicolous bats and their roosts, increasing anthropogenic expansions and proximity to human settlements raises concerns about increased human-bat contact. Furthermore, uncontrolled roost visitation and vandalism are increasing, contributing to bat health risks and population declines, though the extent of roosts affected is yet to be quantified. In an era where pandemics are predicted to become more frequent and severe due to land-use change, our research is an urgent call for the formal protection of bat-inhabited caves to safeguard both bats and humans.

Dual vaccines (n = 6) against both lumpy skin disease (LSD) and bovine ephemeral fever (BEF) were constructed, based on the BEFV glycoprotein (G) gene, with or without the BEFV matrix (M) protein gene, inserted into one of two different LSDV backbones, nLSDV∆SOD-UCT or nLSDVSODis-UCT. The inserted gene cassettes were confirmed by PCR, and BEFV protein was shown to be expressed by immunofluorescence. The candidate dual vaccines were initially tested in a rabbit model, neutralization assays using the South African BEFV vaccine (B-Phemeral) strain showed an African consensus G protein gene (Gb) to give superior neutralization compared to the Australian (Ga) gene. The two LSDV backbones expressing both Gb and M BEFV genes were tested in cattle and shown to elicit neutralizing responses to LSDV as well as BEFV after two inoculations 4 weeks apart. The vaccines were safe in cattle and all vaccinated animals were protected against virulent LSDV challenge, unlike a group of control naïve animals, which developed clinical LSD. Both neutralizing and T cell responses to LSDV were stimulated upon challenge. After two inoculations, all vaccinated animals produced BEFV neutralizing antibodies ≥ 1/20, which is considered protective for BEF.

Polyfunctional thiols like 3-sulfanylhexan-1-ol (3SH) and its ester 3-sulfanylhexyl acetate (3SHA) are important aroma determinants in wine with exceptionally low odor thresholds. 3SH is largely found in grape must bound to glutathione and cysteine and requires enzymatic action to be perceived sensorially. The wine yeast Saccharomyces cerevisiae is ineffective in releasing volatile thiols from their precursor configuration. For this purpose, a yeast strain was constructed that expresses the carbon-sulfur lyase encoding the tnaA gene from Escherichia coli and overexpresses its native alcohol acetyltransferase encoding genes, ATF1 and ATF2. The resulting yeast strain, which co-expresses tnaA and ATF1, showed elevated 3SH-releasing capabilities and the esterification of 3SH to its acetate ester 3SHA. Levels of over 7000 ng/L of 3SHA in Sauvignon blanc wines were achieved. Enhanced release and esterification of 3SH were also shown in the fermentation of guava and passionfruit pulp and three hop varieties. This study offers prospects for the development of flavor-enhancing yeast strains with optimized thiol-releasing and esterification capabilities in a diverse set of beverage matrices.

Resilience to abiotic stress is associated with a suite of functional traits related to defense and longevity. Stress tolerant plants are generally slow growing with extended leave lifespans and reduced allocation to reproduction. Resurrection plants are ideal systems to test for trade-offs associated with stress tolerance due to their extreme resiliency. While, growth defense trade-offs are well-characterized, few studies have tested for natural variation associated with tolerating the harshest environments. Here, we surveyed a suite of functional traits related to stress tolerance, leaf economics, and reproductive allocation in natural populations of the South African resurrection plant Myrothamnus flabellifolia. We selected three distinct field sites in South Africa ranging from mesic to xeric. Despite considerable environmental variation across the study area, M. flabellifolia plants were extremely and similarly stress tolerant at all sites. However, we detected notable variation in other life history and morphological traits. Plants in more mesic sites were larger, faster growing, and had more inflorescences. In contrast, plants from the most xeric sites appeared to invest more in persistence and defense, with lower growth rates and less reproductive allocation. Together, this suggests that desiccation tolerance is a binary trait in M. flabellifolia with little natural variation, but that other phenotypes are more labile. The trait syndromes exhibited by plants at the different study sites align with general expectations about growth defense tradeoffs associated with the colonization of extreme environments. We show that plants from the least stressful sites are more reproductive and faster growing, whereas plants from the most stressful sites were slower growing and less reproductive. These findings suggest that M. flabellifolia plants are finely tuned to their environment.

Background Bubaque is the most populous island of the Bijagos archipelago, a group of malaria-endemic islands situated off the coast of Guinea-Bissau, West Africa. Malaria vector control on Bubaque relies almost exclusively on the use of long-lasting insecticidal nets (LLINs). However, there is little information on local vector bionomics and insecticide resistance. Methods A survey of mosquito species composition was performed at the onset of the wet season (June/July) and the beginning of the dry season (November/December). Sampling was performed using indoor adult light-traps and larval dipping. Anopheles mosquitoes were identified to species level and assessed for kdr allele frequency by TaqMan PCR. Females were analysed for sporozoite positivity by CSP-ELISA. Resistance to permethrin and α-cypermethrin was measured using the CDC-bottle bioassay incorporating the synergist piperonyl-butoxide. Results Several Anopheles species were found on the island, all belonging to the Anopheles gambiae sensu lato (s.l.) complex, including An. gambiae sensu stricto, Anopheles coluzzii, Anopheles melas, and An. gambiae/An. coluzzii hybrids. Endophagic Anopheles species composition and abundance showed strong seasonal variation, with a majority of An. gambiae (50% of adults collected) caught in June/July, while An. melas was dominant in November/December (83.9% of adults collected). Anopheles gambiae had the highest sporozoite rate in both seasons, with infection rates of 13.9% and 20% in June/July and November/December, respectively. Moderate frequencies of the West African kdr allele were found in An. gambiae (36%), An. coluzzii (35%), An. gambiae/An. coluzzii hybrids (42%). Bioassays suggest moderate resistance to α-cypermethrin, but full susceptibility to permethrin. Conclusions The island of Bubaque maintained an An. gambiae s.l. population in both June/July and November/December. Anopheles gambiae was the primary vector at the onset of the wet season, while An. melas is likely to be responsible for most dry season transmission. There was moderate kdr allele frequency and synergist assays suggest likely metabolic resistance, which could reduce the efficacy of LLINs. Future control of malaria on the islands should consider the seasonal shift in mosquito species, and should employ continuous monitoring for insecticide resistance.

One-carbon compounds, such as methanol, are becoming potential alternatives to sugars as feedstocks for the biological production of chemicals, fuels, foods, and pharmaceuticals. Efficient biological production often requires extensive genetic manipulation of a microbial host strain, making well-characterised and genetically-tractable model organisms like the yeast Saccharomyces cerevisiae attractive targets for the engineering of methylotrophic metabolism. S. cerevisiae strains S288C and CEN.PK are the two best-characterised and most widely used hosts for yeast synthetic biology and metabolic engineering, yet they have unpredictable metabolic phenotypes related to their many genomic differences. We therefore sought to benchmark these two strains as potential hosts for engineered methylotrophic metabolism by comparing their growth and transcriptomic responses to methanol. CEN.PK had improved growth in the presence of methanol relative to the S288C derivative BY4741. The CEN.PK transcriptome also had a specific and relevant response to methanol that was either absent or less pronounced in the BY4741 strain. This response included up-regulation of genes associated with mitochondrial and peroxisomal metabolism, alcohol and formate dehydrogenation, glutathione metabolism, and the global transcriptional regulator of metabolism MIG3. Over-expression of MIG3 enabled improved growth in the presence of methanol, suggesting that MIG3 is a mediator of the superior CEN.PK strain growth. CEN.PK was therefore identified as a superior strain for the future development of synthetic methylotrophy in S. cerevisiae. Keywords: Yeast, Methylotrophy, Synthetic biology, Metabolic engineering, MIG3, Methanol

Parasexuality contributes to diversity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct haploid nuclei). Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), such as Ug99, are a major threat to global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation and nuclear exchange between dikaryons. Fully haplotype-resolved genome assembly and DNA proximity analysis reveal that Ug99 shares one haploid nucleus genotype with a much older African lineage of Pgt, with no recombination or chromosome reassortment. These findings indicate that nuclear exchange between dikaryotes can generate genetic diversity and facilitate the emergence of new lineages in asexual fungal populations., Strain Ug99 of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici, is a major threat to global food security. Here, the authors present genomic analyses supporting that Ug99 arose as a result of non-sexual genetic exchange between dikaryotic ancestors.

Puccinia graminis f. sp. avenae (Pga) samples were collected from cultivated oat (Avena sativa L.) in trial plots and commercial fields and from wild oat (Avena spp.) during the 2016 and 2017 seasons. Field samples were purified through selection of single pustule isolates and subsequent urediniospore increases using the susceptible cultivar Swan. For race phenotyping, a set of 12 international differential lines was used that resulted in the identification of races RSJ, RJS and RJJ. Race RSJ was the most prevalent (60% of isolates) followed by races RJS (34%) and RJJ (6%). These races varied in virulence for Pg6 and Pg12, with no avirulence recorded for Pg1, 2, 4, 8, 9, 13 and Pg15 and no virulence for Pg3, 10 and Pg16. Seedling infection types of 32 oat cultivars to the three described races showed compatible phenotypes for all cultivars towards at least one of the races. Moderate levels of adult plant resistance against races RJS and RSJ were recorded for seven cultivars during field tests in 2017 and 2018. Thirteen microsatellite markers used to assess genetic variability amongst twenty four field isolates revealed three sub-populations of which only one correlated with the race phenotype. The results contributed to our understanding of the diversity of the Pga population in South Africa, including useful resistance sources and cultivar responses.

Puccinia graminis f. sp. tritici race TTKSF+ was collected from the South African wheat cultivar ‘Matlabas’ in 2010. F2 and F3 populations derived from a Matlabas × Line 37-07 cross segregated for a single resistance gene to race TTKSF that is avirulent to Matlabas. In screening genomic DNA bulks of susceptible or resistant F2 plants with simple sequence repeat (SSR) markers, three chromosome arm 2BS markers and one multilocus marker amplified alleles present only in the resistant bulks and Matlabas. Additional 2B-specific SSR markers, incorporating markers spanning regions containing Sr9h, SrWLR, Sr28, and Sr47, were screened in the parental lines and mapped in the F2 population. Linkage and QTL mapping showed that the gene is located between Xbarc160 in the centromeric region and Xgwm47 on the long arm of chromosome 2B. When 2B-specific SNP markers were mapped, the area of interest was delimited to a 15.3 cM region on chromosome arm 2BL, with XIWA543-HRM and Xgwm47 as flanking loci. Matlabas, Webster, and related Sr9h lines all produced a similar, low infection type to race TTKSF, but were susceptible to race TTKSF+. Phenotypic data and allelic studies suggested that stem rust resistance in Matlabas was derived from an Sr9h source.

Triticale is derived from a cross between wheat and rye and the leaf rust pathogen of wheat, Puccinia triticina (Pt), and that of rye, P. recondita sensu stricto (Pr), can potentially cause disease in this crop. Recent studies showed that wheat rust fungi could adapt to warmer temperatures. In this paper, we report on the comparative virulence of three Pt races and one Pr isolate (all were collected in South Africa) on triticale as well as their in vitro response to temperature. Seedling infection types (SITs) of 169 triticale entries to Pt races 3SA144 (North American code SDDN), 3SA145 (CCPS) and 3SA248 (CFPS) and Pr isolate UVPr2 revealed that 3SA144 is the most virulent with 106 triticale entries found susceptible to this race. The three Pt races were avirulent to the four rye cultivars included as controls. UVPr2 was avirulent on all the triticale entries and 49 entries were considered resistant to the Pt races tested. Freshly harvested urediniospores of the above isolates were tested at constant temperature regimes of 10 °C, 22.5 °C and 35 °C to study germination characteristics. Mean urediniospore germination percentages as determined for 3SA144 (61.3%) and UVPr2 (62.6%) were significantly lower when compared to 3SA145 (83.7%) and 3SA248 (84.9%). Race 3SA144 was most sensitive to the higher temperature regime of 35 °C (5.2% germination). Among the investigated races, 3SA144 showed significantly lower mean germ tube elongation rates at all three incubation temperatures. This is the first report of differences in temperature adaptation between Pt races from SA.

Although rollout of combined antiretroviral treatment (cART) has blunted human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS) onset, there is increased development of cardiovascular diseases (CVDs) in HIV-infected individuals. While most HIV-infected individuals on cART achieve viral suppression, this may not necessarily result in complete immunological recovery. This study therefore evaluated T-cell-mediated changes and coagulation markers in HIV-positive individuals to ascertain their potential to increase CVD risk. Eighty participants were recruited (Worcester, South Africa), and fasted blood was collected to evaluate: 1) immune activation (CD38 expression on CD4+and CD8+T cells) and thrombus formation [tissue factor (CD142)] on CD4+and CD8+T cells; 2) monocyte subpopulations (nonclassical, intermediate, and classical); and 3) classical regulatory T (Treg) cells with activation markers [glycoprotein A repetitions predominant (GARP) and special AT-rich sequence-binding protein 1 (SATB-1)]. High- and low-density lipoprotein subclasses (Lipoprint) were also determined. This study revealed four key findings for HIV-positive patients: 1) coexpression of the CD142 coagulation marker together with immune activation on both CD4+and CD8+T cells during chronic infection stages; 2) Treg cell activation and upregulated GARP and SATB-1 contributing to Treg dysfunction in chronic HIV; 3) proatherogenic monocyte subset expansion with significant correlation between T-cell activation and macrophage activation (marker: CD163); and 4) significant correlation between immune activation and lipid subclasses, revealing crucial changes that can be missed by traditional lipid marker assessments (LDL and HDL). These data also implicate lipopolysaccharide-binding protein as a crucial link between immune activation, lipid alterations, and increased CVD risk.NEW & NOTEWORTHY With combined antiretroviral treatment rollout, HIV-AIDS patients are increasingly associated with cardiovascular diseases onset. This study demonstrated the significant interplay between adaptive immune cell activation and monocyte/macrophage markers in especially HIV-positive individuals with virological failure and on second line treatment. Our data also show a unique link between immune activation and lipid subclass alterations, revealing important changes that can be missed by traditional lipid marker assessments (e.g., LDL and HDL).

Traditional race phenotyping of cereal rusts is based on the pathogenicity of field isolates on seedlings using a set of differential host lines. These lines are regularly planted in the field, often as part of trap nurseries. In trap nurseries the primary objective is to assess the occurrence of isolates with virulence or avirulence on key resistance genes. Although it is generally accepted that field nurseries cannot be used for race identification, the correlation between seedling and adult plant response of commonly used stem rust differential lines needs further clarification. To determine if any of the wheat stem rust differential lines in South Africa contains unknown genes for adult plant resistance, or are poorly expressed in the adult stage, entries were assessed over four seasons in a nursery inoculated with race PTKST of Puccinia graminis f. sp. tritici. A strong correlation between seedling infection type and field response occurred for differential lines carrying Sr5, 6, 7b, 8a, 8b, 9a, 9b, 9d, 9e (Vernstein), 10, 11, 24, 27, 31, 36, 38, 44, McN, Kw, and Satu. However, differential lines carrying Sr9e (Vernal), 9g (Acme), 30 (Festiguay), and Sr17 (Renown) failed to accurately predict virulence under epidemic conditions in the field. Importantly, higher than expected severity and response types were recorded for differential lines carrying SrTmp and Sr21, especially under prolonged epidemic conditions. It can be concluded that field ratings of the current set of South African stem rust differential lines do not accurately describe P. graminis f. sp. tritici race PTKST.

The NRF, THRIP, and RMRD-SA in collaboration with OBP and Economic Competitiveness Support Programme and the ARC-OVR, South Africa.

BackgroundTargeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients.MethodsSpontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method.ResultsStatistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as theProteobacteria, and higher relative abundance of phyla, such asFirmicuteswhen compared to the IS-Pro method.Haemophilus,PrevotellaandStreptococcuswere most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly.ConclusionsIt is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance ofProteobacteria.However, the IS-Pro kit identified most of the important lung pathogens, such asBurkholderiaandPseudomonasand may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.

Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2)-induced infection, the cause of coronavirus disease 2019 (COVID-19), is characterized by unprecedented clinical pathologies. One of the most important pathologies, is hypercoagulation and microclots in the lungs of patients. Here we study the effect of isolated SARS-CoV-2 spike protein S1 subunit as potential inflammagen sui generis. Using scanning electron and fluorescence microscopy as well as mass spectrometry, we investigate the potential of this inflammagen to interact with platelets and fibrin(ogen) directly to cause blood hypercoagulation. Using platelet-poor plasma (PPP), we show that spike protein may interfere with blood flow. Mass spectrometry also showed that when spike protein S1 is added to healthy PPP, it results in structural changes to β and γ fibrin(ogen), complement 3, and prothrombin. These proteins were substantially resistant to trypsinization, in the presence of spike protein S1. Here we suggest that, in part, the presence of spike protein in circulation may contribute to the hypercoagulation in COVID-19 positive patients and may cause substantial impairment of fibrinolysis. Such lytic impairment may result in the persistent large microclots we have noted here and previously in plasma samples of COVID-19 patients. This observation may have important clinical relevance in the treatment of hypercoagulability in COVID-19 patients.

Prostate cancer (PCa) is the second most common form of cancer in men around the world. Due to its heterogeneity, presentations range from aggressive lethal disease to indolent disease. There is a need to identify core biomarkers that are important for early detection and progression, allowing a more precise method for the treatment and management of Pca. We obtained metastatic prostate cancer associated microRNA array profiles from the GSE28029 dataset in the GEO database. MicroRNA target prediction was done using the databases, TargetScanHuman, miRDB and DIANA microT, six target genes (FOXC1, CDKN1A, BIRC2, CTNND1, ELK1 and LRP8) were found to be common among the three different databases. Differential expression of the target genes was performed via the GENT2 database in the GPL96 platform (HG-U133A). Results indicated all genes were downregulated. Gene Ontology (GO) was used to perform enrichment analysis. The GO enrichment analysis indicated that the downregulated genes were enriched in cellular response to gamma radiation, regulation of transcription and response to drugs as well as protein binding and receptor signaling protein activity. The study suggested that CDKN1A, FOXC1 and BIRC2 might be core genes for prostate cancer that play an important role in its diagnosis, development and progression.

Psoriasis is a chronic, immune-mediated inflammatory skin disease, affecting approximately 2% of the general population, which can be accompanied by psoriatic arthritis (PsA). The condition has been associated with an increased cardiovascular burden. Hypercoagulability is a potential underlying mechanism that may contribute to the increased risk of major cardiovascular events in psoriatic individuals. Whole blood samples were collected from 20 PsA patients and 20 healthy individuals. The concentrations of inflammatory molecules (C-reactive protein, serum amyloid A, soluble intercellular adhesion molecule-1, soluble vascular cell adhesion molecule-1, and soluble P-selectin) were determined by enzyme-linked immunosorbent assays. In addition, clotting efficiency was evaluated by thromboelastography. The fibrin network architecture was also assessed by scanning electron microscopy. Elevated levels of circulating inflammatory molecules were significantly associated with the presence of psoriatic disease. Furthermore, an increased tendency towards thrombus formation was significantly predictive of disease presence. Scanning electron microscopy revealed that fibrin clots were denser in psoriatic individuals, compared to healthy controls, with an increased fibrin fibre diameter associated with psoriatic disease. Our results add to the accumulating evidence of the systemic nature of psoriasis and the subsequent risk of cardiovascular comorbidities, potentially due to an acquired hypercoagulability. We suggest that haemostatic function should be monitored carefully in psoriatic patients that present with severe disease, due to the pre-eminent risk of developing thrombotic complications.

Anthropogenic activities influence the natural equilibrium of freshwater ecosystems resulting in negative ecological impacts. Differences in the infection variables of Lamproglena clariae in relation to variable water quality influenced by metal pollution were studied at six sites along the Vaal River, South Africa (March 2017 and October 2018). From each sampling site, in situ water quality parameters, water and sediment samples, and a minimum of 10 Clarias gariepinus were collected. Lamproglena clariae specimens collected from the gills of C. gariepinus were used to calculate the prevalence, mean intensity, and mean abundance of the parasite. Metal concentrations in water and sediment were analysed with inductively coupled plasma–optical emission spectrometry and inductively coupled plasma–mass spectrometry. Parasite intensity correlated negatively with some water quality parameters (conductivity, salinity, pH, total dissolved solids, and dissolved oxygen). Negative correlations were found between L. clariae (intensity and prevalence) and metal concentrations (Cu, Cr, Zn, Cd) in water. Parasite infections were influenced negatively at sites with high metal concentrations recorded in sediment and water and high levels of organic pollution. Sites that were found to be more polluted had lower mean intensity and mean abundance of L. clariae, indicating pollution affects the survival of this ectoparasite.

Dramatic population declines of African wild dogs (Lycaon pictus) led to a managed metapopulation approach for wild dog conservation in South Africa. Monitoring the survival and habitat use of packs reintroduced into protected areas (PAs) is an essential part of adaptive management and improving the health and, ultimately, the survival of the metapopulation. Our study describes the territoriality and habitat selection of a pack of wild dogs reintroduced into Manyoni Private Game Reserve (219 km2) in northern KwaZulu-Natal, South Africa. Despite being introduced into a small PA, the pack only utilized half their available space (121 km2) and avoided the central areas of the reserve. Post hoc analysis of African lion (Panthera leo) localities suggested competitive avoidance was a strong factor in shaping the habitat usage of the pack; however, further research is required. Habitat selection also varied seasonally and with denning. Ultimately, we showed that spatio-temporal analyses can help identify high-risk areas within wild dog territories, such as hotspots of activity along fencelines. These analyses can then be used to increase targeted management of these areas, such as improving the maintenance of well-used fencelines, which is an important consideration for the sustained success of the metapopulation across small PAs. Publisher PDF