High-throughput screening and sensitized bacteria identify an M. tuberculosis dihydrofolate reductase inhibitor with whole cell activity

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is a bacterial pathogen that claims roughly 1.4 million lives every year. Current drug regimens are inefficient at clearing infection, requiring at least 6 months of chemotherapy, and resistance to existing agents is rising. There is an urgent need for new drugs that are more effective and faster acting. The folate pathway has been successfully targeted in other pathogens and diseases, but has not yielded a lead drug against tuberculosis. We developed a high-throughput screening assay against Mtb dihydrofolate reductase (DHFR), a critical enzyme in the folate pathway, and screened a library consisting of 32,000 synthetic and natural product-derived compounds. One potent inhibitor containing a quinazoline ring was identified. This compound was active against the wild-type laboratory strain H37Rv (MIC(99)?=?207 μM). In addition, an Mtb strain with artificially lowered DHFR levels showed increased sensitivity to this compound (MIC(99)?=?70.7 μM), supporting that the inhibition was target-specific. Our results demonstrate the potential to identify Mtb DHFR inhibitors with activity against whole cells, and indicate the power of using a recombinant strain of Mtb expressing lower levels of DHFR to facilitate the discovery of antimycobacterial agents. With these new tools, we highlight the folate pathway as a potential target for new drugs to combat the tuberculosis epidemic.     

Arsenal of elevated defense proteins fails to protect tomato against Verticillium dahliae

Although the hypersensitive reaction in foliar plant diseases has been extensively described, little is clear regarding plant defense strategies in vascular wilt diseases affecting numerous economically important crops and trees. We have examined global genetic responses to Verticillium wilt in tomato (Lycopersicon esculentum Mill.) plants differing in Ve1 resistance alleles. Unexpectedly, mRNA analyses in the susceptible plant (Ve1-) based on the microarrays revealed a very heroic but unsuccessful systemic response involving many known plant defense genes. In contrast, the response is surprisingly low in plants expressing the Ve1+ R-gene and successfully resisting the pathogen. Similarly, whole-cell protein analyses, based on 2D gel electrophoresis and mass spectrometry, demonstrate large systemic increases in a variety of known plant defense proteins in the stems of susceptible plants but only modest changes in the resistant plant. Taken together, the results indicate that the large systemic increases in plant defense proteins do not protect the susceptible plant. Indeed, since a number of the highly elevated proteins are known to participate in the plant hypersensitive response as well as natural senescence, the results suggest that some or all of the disease symptoms, including ultimate plant death, actually may be the result of this exaggerated plant response.     

Methylome analysis using MeDIP-seq with low DNA concentrations

DNA methylation is an epigenetic mark that has a crucial role in many biological processes. To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome-wide analysis should be embraced. This in turn requires a technique that balances accuracy, genome coverage, resolution and cost, yet is low in DNA input in order to minimize the drain on precious samples. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) fulfils these criteria, combining MeDIP with massively parallel DNA sequencing. Here we report an improved protocol using 100-fold less genomic DNA than that commonly used. We show comparable results for specificity (>97%) and enrichment (>100-fold) over a wide range of DNA concentrations (5,000-50 ng) and demonstrate the utility of the protocol for the generation of methylomes from rare bone marrow cells using 160-300 ng of starting DNA. The protocol described here, i.e., DNA extraction to generation of MeDIP-seq library, can be completed within 3-5 d.     

Mutational analysis of the subunit C (Vma5p) of the yeast vacuolar H+-ATPase.

Subunit C is a V(1) sector subunit found in all vacuolar H(+)-ATPases (V-ATPases) that may be part of the peripheral stalk connecting the peripheral V(1) sector with the membrane-bound V(0) sector of the enzyme (Wilkens, S., Vasilyeva, E., and Forgac, M. (1999) J. Biol. Chem. 274, 31804--31810). To elucidate subunit C function, we performed random and site-directed mutagenesis of the yeast VMA5 gene. Site-directed mutations in the most highly conserved region of Vma5p, residues 305--325, decreased catalytic activity of the V-ATPase by up to 48% without affecting assembly. A truncation mutant (K360stop) identified by random mutagenesis suggested a small region near the C terminus of the protein (amino acids 382--388) might be important for subunit stability. Site-directed mutagenesis revealed that three aromatic amino acids in this region (Tyr-382, Phe-385, and Tyr-388) in addition to four other conserved aromatic amino acids (Phe-260, Tyr-262, Phe-296, Phe-300) are essential for stable assembly of V(1) with V(0), although alanine substitutions at these positions support some activity in vivo. Surprisingly, three mutations (F260A, Y262A, and F385A) greatly decrease the stability of the V-ATPase in vitro but increase its k(cat) for ATP hydrolysis and proton transport by at least 3-fold. The peripheral stalk of V-ATPases must balance the stability essential for productive catalysis with the dynamic instability involved in regulation; these three mutations may perturb that balance.     

Selenium status of idiopathic infertile Nigerian males

Selenium concentration in the sera and seminal plasma of 60 infertile males (40 oligospermia and 20 azoospermia) and 40 males with proven evidence of fertility (normospermia; control group) were estimated using atomic absorption spectrophotometry. Results were correlated with spermatogram and hormonal levels in order to determine their relationship and significance in male infertility. The mean serum concentrations of selenium was found to be significantly increased in oligospermic compared to azoospermic subjects and controls (p<0.01), whereas the seminal plasma level was significantly higher in azoospermic compared to oligospermic subjects and controls (p<0.001). Thus, the ratio of serum selenium to seminal plasma selenium was 1∶1 in controls, 4∶1 in oligospermia, and 1∶2 in azoospermic subject. A significant inverse correlation was observed between serum selenium level and sperm count (p<0.01). Similarly, seminal plasma selenium correlated with spermatozoa motility, viability, and morphology. Serum selenium level shows positive correlation with the serum testosterone level (p<0.01). In conclusion, there appears to be a physiological balance in the distribution of selenium in serum and seminal plasma compartment of control males. A disturbance in this balance has a significant influence on spermatogenesis. Selenium appears to have a positive influence on Leydig cells, thus influencing the secretion of testosterone.     

Glucose uptake stimulatory effect of akuammicine from Picralima nitida (Apocynaceae)

A bioactivity-guided fractionation of the chloroform extract of the seeds of Picralima nitida using glucose uptake in fully differentiated 3T3-L1 adipocytes afforded six indole alkaloids (akuammicine, 10-deoxyakuammine, akuammine, akuammidine, burnamine and picraline) and a mixture of four 5-hydroxy tryptamine amides. Akuammicine accounted for the increase in glucose uptake observed in the chloroform extract.     

Mass administration of medicines in changing contexts: Acceptability,adaptability and community directed approaches in Kaduna and Ogun States,Nigeria

Nigeria has the highest burden of NTDs in sub-Saharan Africa. Commitments to reach the control and elimination of many Neglected Tropical Diseases (NTDs), particularly those amenable to preventive chemotherapy (onchocerciasis, schistosomiasis, soil transmitted helminths, lymphatic filariasis and trachoma) by 2020 are detailed in the London declaration. Strategies to reach targets build on existing approaches, one of which is the use of community directed intervention (CDI) methods to deliver the mass administration of medicines (MAM). However, treatment using this approach has been inconsistent and there are questions about the acceptability and adaptability of these interventions during periods of programmatic, social, and political change. This paper explores the current strengths and weaknesses of CDI approaches in MAM delivery. We consider the acceptability and adaptability of existing MAM approaches to ensure equity in access to essential treatments. Using qualitative methods, we explore implementer perspectives of MAM delivery. We purposively selected programme implementers to ensure good programmatic knowledge and representation from the different levels of health governance in Nigeria. Data collection took place across two States (Kaduna and Ogun). Our results indicate that CDI approaches have underpinned many historic successes in NTD programme acceptance in Nigeria, specifically in Kaduna and Ogun State. However, our results also show that in some contexts, factors that underpin the success of CDI have become disrupted presenting new challenges for programme implementers. Capturing the tacit knowledge of health implementers at varying levels of the health system, we present the current and changing context of MAM delivery in Kaduna and Ogun States and consolidate a platform of evidence to guide future programme delivery and research studies. We situate our findings within the broader NTD literature, specifically, in identifying how our findings align to existing reviews focused on factors that shape individual acceptance of MAM.     

Genetic characteristics, coreceptor usage potential and evolution of Nigerian HIV-1 subtype G and CRF02_AG isolates

HIV-1 CRF02_AG and subtype G (HIV-1G) account for most HIV infections in Nigeria, but their evolutionary trends have not been well documented. To better elucidate the dynamics of the epidemic in Nigeria we characterised the gag and env genes of North-Central Nigerian HIV-1 isolates from pregnant women. Of 28 samples sequenced in both genes, the predominant clades were CRF02_AG (39%) and HIV-1G (32%). Higher predicted proportion of CXCR4-tropic (X4) HIV-1G isolates was noted compared to CRF02_AG (p = 0.007, Fisher''s exact test). Phylogenetic and Bayesian analysis conducted on our sequences and all the dated available Nigerian sequences on the Los Alamos data base showed that CRF02_AG and HIV-1G entered into Nigeria through multiple entries, with presence of HIV-1G dating back to early 1980s. This study underlines the genetic complexity of the HIV-1 epidemic in Nigeria, possible subtype-specific differences in co-receptor usage, and the evolutionary trends of the predominant HIV-1 strains in Nigeria, which may have implications for the design of biomedical interventions and better understanding of the epidemic.     

Endophyte-induced Verticillium protection in tomato is range-restricted

Endophytes, bacterial, fungal or viral, colonize plants often without causing visible symptoms. More important, they may benefit host plants in many ways, most notably by preventing diseases caused by normally virulent pathogens. Previous studies have shown that an isolate of V. dahliae from eggplant, Dvd-E6, can colonize tomato endophytically, producing taller and more robust tomato plants while providing protection against a virulent V. dahliae, race 1 (Vd1) isolate. Expression analyses suggest this requires interplay between Dvd-E6 and the plant that involves resistance and defense genes. To examine the possibility of a broader effect, dual interactions have been further examined with a more distantly related pathogen, Verticillium albo-atrum (Vaa). The results indicate Dvd-E6 colonization selectively modifies the expression of specific tomato genes to be detrimental to Vd1 but not Vaa, providing evidence that Verticillium-induced protection is range-restricted.Key words: cross-protection, endophyte, lycopersicon, tolerance, VerticilliumAn “endophyte” commonly is defined as a “fungus or bacterium living within plants without causing visible symptoms of disease”; a “pathogen” is regarded as “a disease causing biological agent”. Historically, plant biologists have tended to consider these as two very different and distinct classes of organisms but accumulating evidence now suggests that the boundaries between mutualism and parasitism are not as defined as previously thought. Many organisms can occupy both ecological niches¹ depending on the genotype of the host, the genotype of the organism itself and interaction with the environment. Indeed, this “dual life style” may be a significant factor in the evolutionary dynamics of pathogen resistance, tolerance and susceptibility.²One of the more recent additions to the growing list of dual life style (endophyte/pathogen) fungi is Verticillium dahliae,³ a causal agent of vascular wilt disease or early dying syndrome in a broad range of the plant species.⁴ When Verticillium infects a plant three different host responses can occur: resistance, susceptibility or tolerance. The phenomenon of tolerance has been associated with Verticillium spp. for decades but research on mechanisms governing the development of the plant/Verticillium interaction has focused on the compatible and incompatible interactions and little is known about the tolerant state (reviewed in ref. ⁵). In a recent series of papers we have identified an isolate of Verticillium dahliae, known as Dvd-E6, that colonizes tomatoes, cv Craigella, resulting in a stable tolerant condition, that we have used as a model system to investigate the biological and molecular bases of plant tolerance to Verticillium spp. The Craigella/Dvd E6 interaction has a number of interesting but unanticipated properties. Host plants tend to be taller and more robust than their uninfected counterparts⁶ and colonization of Craigella by Dvd-E6 provides protection against its virulent Verticillium dahliae race 1 (Vd1) cousin, limiting both Vd1 colonization and symptom development during dual infections.⁷ Such attributes normally are associated with plant/endophyte partnerships, strongly suggesting that under some conditions, Verticillium dahliae can assume an endophytic role. Apparently interplay between Dvd-E6 and the plant establishes protection against the virulent Vd1.⁷Many endophytic infections provide protection for the host against a broad range of pathogens.¹ To test the ability of Dvd-E6 infection to protect Craigella against a more distantly related Verticillium pathogen we have now examined dual interactions with Verticillium albo-atrum (Vaa). Susceptible Craigella⁸ seedlings again were inoculated at the 4-leaf stage by dipping the roots in Vd1, Dvd-E6 or Vaa conidial suspensions (1 × 10⁷ spores/ml in 0.5% gelatin solution) to establish homogeneous interactions (reviewed in ref. ⁷). For dual interactions, seedlings were inoculated with Dvd-E6 spores at the 3-leaf stage and reinoculated at the 4-leaf stage with either Vd1 or Vaa spore suspension to establish the mixed infections. Control seedlings were root dipped in gelatin solution alone. Plants were scored for symptom expression on a 0 (no symptoms) to 5 (plant dead) scale as described by Shittu and co-workers (2009) and the top two-thirds of the stems harvested at 5 and 10 days post inoculation (d.p.i.) for extraction and fungal DNA assays.^7,9All experimental results are summarized in Figure 1. At 10 d.p.i., the disease scores for Dvd-E6-infected plants were approximately one-third that of the Vd1-or Vaa-infected plants. More interesting were the symptoms in the dual interactions, Dvd-E6/Vd1 mimicking the tolerant plants with low disease and Dvd-E6/Vaa-infected plants exhibiting the highest disease scores, similar to Vd1-or Vaa-infected plants. When the amount of fungal DNA in the stems was assessed, the total fungal biomass in both dual infections as well as the Dvd-E6 and Vd1-infected plants at 5 and 10 dpi was similar (light and dark gray bars), the amount of Vaa being somewhat lower. In the mixed infections, however, most of the DNA (>90%) was of Dvd-E6 origin (white bars). More important, the Vd1 DNA level in Dvd-E6/Vd1 plants was substantially reduced relative to plants infected with Vd1 alone while the Vaa DNA levels stayed about the same in the single and double infections. This indicates that Vd1 colonization is restricted⁷ by the presence of Dvd-E6 while Vaa is not.Open in a separate windowFigure 1Comparison of symptoms and levels of V. dahliae 1 or V. albo-atrum DNA in susceptible Craigella tomato simultaneously infected with V. dahliae Dvd-E6. Individual (E6, Vd1 and Vaa) and mixed (E6/Vd1 and E6/Vaa) infections were established as previously described.⁷ Plants were scored (upper) at 5 (light gray bars) and 10 (dark gray bars) dpi for symptoms (i.e., disease scores ± SD) or assayed⁷ for total levels of Verticillium DNA (i.e., ng/g plant tissue ± SD) in the stems (lower). In mixed infections levels for each fungus also were determined (black and white bars, respectively). Results summarize the data for 9–12 plants per time point for each interaction.These results demonstrate that Dvd-E6 infection protects Craigella tomatoes against colonization by and symptom development from Vd1 but not Vaa. Past studies often have suggested that the protective effect stems from an endophyte-induced activation of systemic acquired resistance (SAR) in the host providing protection against a broad range of pathogens.¹⁰ However, in the tolerant CS//Dvd-E6 interaction the protective effect appears to be targeted more directly, allowing Dvd-E6 to effectively restrict it''s virulent cousin, Vd1. In this context, it may be important that both of the Verticillium dahliae isolates from tomato are endemic to Ontario^7,11 and potentially in direct competition, while Verticillium albo-atrum from tomato is not. Previous molecular analyses suggested that the protective effect provided by Dvd-E6 colonization requires a genetic interplay with the host, selectively modifying the expression of specific tomato genes to be detrimental to Vd1. The experimental results presented here provide evidence that Verticillium-induced protection is restricted in range.