DNA supercoiling with a twist

The level of torsion in double-stranded DNA regulates base-pair stability and DNA conformation. It is important in initiation and regulation of specific DNA metabolic processes as well as chromatin assembly. High mobility group proteins (HMGB) are architectural proteins whose HMG DNA binding domains confer significant preference for distorted DNA, such as supercoiled DNA and 4-way junctions. HMGB proteins play a role in transiently regulating or conserving DNA torsion. Topoisomerases regulate DNA supercoiling, which has been argued to provide a coherent explanation for the main modes of transcriptional control - stringent control, growth-rate control and growth-phase control during the normal cell growth. In this study, we have shown that HMO1, a Saccharomyces cerevisiae HMGB protein which is required for normal growth, plasmid maintenance and for regulating the susceptibility of yeast chromatin to nuclease binds linear duplex DNA but has little preference for DNA with altered conformations. Divergent box A binds DNA and contributes structure-specific binding. Unlike most HMGB proteins, HMO1 does not supercoil relaxed DNA in the presence of topoisomerase. Casein Kinase II phosphorylates HMO1, altering its DNA binding properties. We have also shown that deletion of the highly basic C-terminal tail of HMO1 localizes this otherwise both nuclear and cytoplasmic protein only to the cytoplasm. As the C-terminally truncated HMO1 has been reported to rescue the hmo1 knockout phenotype, we conclude that the main function of HMO1 lies in the cytoplasm, and not in the nucleus. Vaccinia topoisomerase I relaxes supercoiled DNA. We have shown that it interacts with enrofloxacin, a fluoroquinolone antibiotic which otherwise targets DNA gyrase and topoisomerase IV. Enrofloxacin inhibits DNA relaxation by Vaccinia topoisomerase I. When presented with relaxed DNA, the enzyme executes the reverse reaction, supercoiling the DNA. Enrofloxacin does not interfere with the catalytic cleavage site of Vaccinia topoisomerase I or its ability to bind DNA. The mechanistic implication of these observations is that protein-DNA contacts downstream of the cleavage site must contribute to DNA supercoiling, contrary to the free rotation mechanism proposed for DNA relaxation

Dynamic wave field synthesis: enabling the generation of field distributions with a large space-bandwidth product

The generation and manipulation of electromagnetic field distributions plays an essential role in physics in general, and particularly in the vast field of physical optics. In the current state of the art, one of the most convenient methods of performing this task is provided by either static or dynamic diffractive as well as holographic optical elements. Currently available dynamic optical elements, such as spatial light modulators, do offer on the one hand high temporal flexibility. They however have a limited space-bandwidth product (SBWP), and thus limited degrees of freedom. This arises primarily from a limitation in the number of controllable elements, their inherent two dimensional nature and limited lateral extent. Conventional static optical elements, such as planar or volume holographic elements, have on the other hand high degrees of freedom but low flexibility in terms of temporal applications. An optical system that facilitates dynamic synthesis of field distributions with high SBWP is thus highly desirable. This thesis presents a novel approach that facilitates the generation of a set of arbitrary orthogonal elementary waves, which can in turn be coherently superposed in order to generate optical fields with a high SBWP. To achieve this goal a hybrid system that consists of an angular multiplexed computer generated volume hologram (CGVH) as a static element and a spatial light modulator as a dynamic element is investigated, developed and characterized. CGVHs are volumetric holographic optical elements whose complex transmission function can be modeled mathematically in terms of the scattering potential of a given dielectric medium. This work presents an approach that employs perturbation theory in deriving a more elaborate mathematical model that is based on a series approximation of the complex wave field scattered from a volume hologram. The mathematical model behind this approach essentially incorporates various physical constraints that account for the discretized numerical design and a laser lithography based fabrication of the holograms in a non-linear optical material. Initial simulations and experimental work done to characterize this system show that the proposed approach facilitates a dynamic decoupling of single or a linear combination of far field projections without any detectable cross-talk between them. This work furthermore demonstrates that Bragg selectivity on the order of (change in angle = 1.1 x 10^10, i.e. approximately 4 orders of magnitude higher than the current state of the art, which is based on cascaded computer generated holograms

The Saccharomyces cerevisiae high mobility group box protein HMO1 contains two functional DNA binding domains

High mobility group box (HMGB) proteins are architectural proteins whose HMG DNA binding domains confer significant preference for distorted DNA, such as 4-way junctions. HMO1 is one of 10 Saccharomyces cerevisiae HMGB proteins, and it is required for normal growth and plasmid maintenance and for regulating the susceptibility of yeast chromatin to nuclease. Using electrophoretic mobility shift assays, we have shown here that HMO1 binds 26-bp duplex DNA with K d = 39.6 ± 5.0 nM and that its divergent box A domain participates in DNA interactions, albeit with low affinity. HMO1 has only modest preference for DNA with altered conformations, including DNA with nicks, gaps, overhangs, or loops, as well as for 4-way junction structures and supercoiled DNA. HMO1 binds 4-way junctions with half-maximal saturation of 19.6 ± 2.2 nM, with only a modest increase in affinity in the absence of magnesium ions (half-maximal saturation 6.1 ± 1.1 nM). Whereas the box A domain contributes modest structure-specific binding, the box B domain is required for high affinity binding. HMO1 bends DNA, as measured by DNA cyclization assays, facilitating cyclization of 136-, 105-, and 87-bp DNA, but not 75-bp DNA, and it has a significantly longer residence time on DNA minicircles compared with linear duplex DNA. The unique DNA binding properties of HMO1 are consistent with global roles in the maintenance of chromatin structure

Interactions between N- and C-terminal domains of the Saccharomyces cerevisiae high-mobility group protein HMO1 are required for DNA bending

The Saccharomyces cerevisiae high-mobility group protein HMO1 is composed of two DNA-binding domains termed box A and box B, of which only box B is predicted to adopt a HMG fold, and a lysine-rich C-terminal extension. To assess the interaction between individual domains and their contribution to DNA binding, several HMO1 variants were analyzed. Using circular dichroism spectroscopy, thermal stability was measured. While the melting temperatures of HMO1-boxA and HMO1-boxB are 57.2 and 47.2 °C, respectively, HMO1-boxBC, containing box B and the entire C-terminal tail, melts at 46.1 °C, suggesting little interaction between box B and the tail. In contrast, full-length HMO1 exhibits a single melting transition at 47.9 °C, indicating that interaction between box A and either box B or the tail destabilizes this domain. As HMO1-boxAB, lacking only the lysine-rich C-terminal segment, exhibits two melting transitions at 46.0 and 63.3 °C, we conclude that the destabilization of the box A domain seen in full-length HMO1 is due primarily to its interaction with the lysine-rich tail. Determination of DNA substrate specificity using electrophoretic mobility shift assays shows unexpectedly that the lysine-rich tail does not increase DNA binding affinity but instead is required for DNA bending by full-length HMO1; HMO1-boxBC, lacking the box A domain, also fails to bend DNA. In contrast, both HMO1 and HMO1-boxAB, but not the individual HMG domains, exhibit preferred binding to constrained DNA minicircles. Taken together, our data suggest that interactions between box A and the C-terminal tail induce a conformation that is required for DNA bending. © 2006 American Chemical Society

Sample-ready multiplex qPCR assay for detection of malaria

BACKGROUND: Microscopy and antigen detecting rapid diagnostic tests are the diagnostic tests of choice in management of clinical malaria. However, due to their limitations, the need to utilize more sensitive methods such as real-time PCR (qPCR) is evident as more studies are now utilizing molecular methods in detection of malaria. Some of the challenges that continue to limit the widespread utilization of qPCR include lack of assay standardization, assay variability, risk of contamination, and the need for cold-chain. Lyophilization of molecular assays can overcome some of these limitations and potentially enable widespread qPCR utilization. METHODS: A recently published multiplex malaria qPCR assay was lyophilized by freezing drying into Sample-Ready™ format (MMSR). MMSR assay contained all the required reagents for qPCR including primers and probes, requiring only the addition of water and sample to perform qPCR. The performance of the MMSR assay was compared to the non-freeze dried, “wet” assay. Stability studies were done by maintaining the MMSR assays at four different ambient temperatures of 4°C, room temperature (RT), 37°C and 42°C over a period of 42 days, tested at seven-day intervals. Plasmodium falciparum and Plasmodium vivax DNAs were used for analysis of the MMSR assay either as single or mixed parasites, at two different concentrations. The C(T) values and the standard deviations (SD) were used in the analysis of the assay performance. RESULTS: The limit of detection for the MMSR assay was 0.244 parasites/μL for Plasmodium spp. (PLU) and P. falciparum (FAL) assay targets compared to “wet” assay which was 0.39 and 3.13 parasites/μL for PLU and FAL assay targets, respectively. The MMSR assay performed with high efficiencies similar to those of the “wet” assay and was stable at 37°C for 42 days, with estimated shelf-life of 5 months. When used to analyse field clinical samples, MMSR assay performed with 100% sensitivity and specificity compared to the “wet” assay. CONCLUSION: The MMSR assay has the same robust performance characteristics as the “wet” assay and is highly stable. Availability of MMSR assay allows flexibility and provides an option in choosing assay for malaria diagnostics depending on the application, needs and budget

TgPRELID, a Mitochondrial Protein Linked to Multidrug Resistance in the Parasite Toxoplasma gondii

New drugs to control infection with the protozoan parasite Toxoplasma gondii are needed as current treatments exert toxic side effects on patients. Approaches to develop novel compounds for drug development include screening of compound libraries and targeted inhibition of essential cellular pathways. We identified two distinct compounds that display inhibitory activity against the parasite's replicative stage: F3215-0002, which we previously identified during a compound library screen, and I-BET151, an inhibitor of bromodomains, the "reader" module of acetylated lysines. In independent studies, we sought to determine the targets of these two compounds using forward genetics, generating resistant mutants and identifying the determinants of resistance with comparative genome sequencing. Despite the dissimilarity of the two compounds, we recovered resistant mutants with nonsynonymous mutations in the same domain of the same gene, TGGT1_254250, which we found encodes a protein that localizes to the parasite mitochondrion (designated TgPRELID after the name of said domain). We found that mutants selected with one compound were cross resistant to the other compound, suggesting a common mechanism of resistance. To further support our hypothesis that TgPRELID mutations facilitate resistance to both I-BET151 and F3215-0002, CRISPR (clustered regularly interspaced short palindromic repeat)/CAS9-mediated mutation of TgPRELID directly led to increased F3215-0002 resistance. Finally, all resistance mutations clustered in the same subdomain of TgPRELID. These findings suggest that TgPRELID may encode a multidrug resistance factor or that I-BET151 and F3215-0002 have the same target(s) despite their distinct chemical structures. IMPORTANCE We report the discovery of TgPRELID, a previously uncharacterized mitochondrial protein linked to multidrug resistance in the parasite Toxoplasma gondii. Drug resistance remains a major problem in the battle against parasitic infection, and understanding how TgPRELID mutations augment resistance to multiple, distinct compounds will reveal needed insights into the development of new therapies for toxoplasmosis and other related parasitic diseases

Prevalence of asymptomatic malaria infections in selected military camps in Tanzania

Background: Despite a decrease in malaria burden reported between 2000 and 2015, an increasing trend of malaria transmission has been recently reported in some endemic countries including Tanzania. Periodic monitoring to identify pocket areas for asymptomatic Plasmodium falciparum infection   is vital for malaria elimination efforts. The objective of this study was to determine prevalence of asymptomatic malaria infections among military recruits in selected camps in Tanzania. Methods: A cross-sectional study was conducted in 2015 at four military camps (Bulombora, Mgambo, Ruvu, and Rwamkoma) of National Service located in regions with varying malaria endemicity in Tanzania.  Finger prick blood samples collected from asymptomatic military recruits who had been at the camps for over two months were simultaneously tested using microscopy and malaria rapid diagnostic tests (mRDTs) to detect malaria parasite infections. Results: Malaria parasite prevalence among asymptomatic recruits was 20.3% and 19.4% by microscopy and mRDT respectively. There was moderate agreement (Kappa=0.724) between microscopy and mRDT test results. A significant difference (p<0.001) of malaria parasite prevalence among the four study camps was observed; ranging from 1.9% in Bulombora to 39.4% in Rwamkoma. The geometric mean parasite density was 11,053 asexual parasites/µl and most recruits (56.8%) had 200 to 1999 asexual parasites/µl. P. falciparum was the predominant (99.2%) malaria parasite species. Conclusion: Our study found high prevalence of asymptomatic malaria infections among military recruits in the selected camps, and this varied from one camp to another. The study has highlighted that public residence institutions such as military camps can be potential hotspots for malaria infection and therefore should not be skipped in routine national malaria surveillance system for monitoring trends of infection

falciparum dihydrofolate reductase and

Trends in drug resistance codons in Plasmodiu