Functional Expression of Parasite Drug Targets and Their Human Orthologs in Yeast

BACKGROUND: The exacting nutritional requirements and complicated life cycles of parasites mean that they are not always amenable to high-throughput drug screening using automated procedures. Therefore, we have engineered the yeast Saccharomyces cerevisiae to act as a surrogate for expressing anti-parasitic targets from a range of biomedically important pathogens, to facilitate the rapid identification of new therapeutic agents. METHODOLOGY/PRINCIPAL FINDINGS: Using pyrimethamine/dihydrofolate reductase (DHFR) as a model parasite drug/drug target system, we explore the potential of engineered yeast strains (expressing DHFR enzymes from Plasmodium falciparum, P. vivax, Homo sapiens, Schistosoma mansoni, Leishmania major, Trypanosoma brucei and T. cruzi) to exhibit appropriate differential sensitivity to pyrimethamine. Here, we demonstrate that yeast strains (lacking the major drug efflux pump, Pdr5p) expressing yeast ((Sc)DFR1), human ((Hs)DHFR), Schistosoma ((Sm)DHFR), and Trypanosoma ((Tb)DHFR and (Tc)DHFR) DHFRs are insensitive to pyrimethamine treatment, whereas yeast strains producing Plasmodium ((Pf)DHFR and (Pv)DHFR) DHFRs are hypersensitive. Reassuringly, yeast strains expressing field-verified, drug-resistant mutants of P. falciparum DHFR ((Pf)dhfr (51I,59R,108N)) are completely insensitive to pyrimethamine, further validating our approach to drug screening. We further show the versatility of the approach by replacing yeast essential genes with other potential drug targets, namely phosphoglycerate kinases (PGKs) and N-myristoyl transferases (NMTs). CONCLUSIONS/SIGNIFICANCE: We have generated a number of yeast strains that can be successfully harnessed for the rapid and selective identification of urgently needed anti-parasitic agents

Nutrient control of eukaryote cell growth: a systems biology study in yeast

<p>Abstract</p> <p>Background</p> <p>To elucidate the biological processes affected by changes in growth rate and nutrient availability, we have performed a comprehensive analysis of the transcriptome, proteome and metabolome responses of chemostat cultures of the yeast, <it>Saccharomyces cerevisiae</it>, growing at a range of growth rates and in four different nutrient-limiting conditions.</p> <p>Results</p> <p>We find significant changes in expression for many genes in each of the four nutrient-limited conditions tested. We also observe several processes that respond differently to changes in growth rate and are specific to each nutrient-limiting condition. These include carbohydrate storage, mitochondrial function, ribosome synthesis, and phosphate transport. Integrating transcriptome data with proteome measurements allows us to identify previously unrecognized examples of post-transcriptional regulation in response to both nutrient and growth-rate signals.</p> <p>Conclusions</p> <p>Our results emphasize the unique properties of carbon metabolism and the carbon substrate, the limitation of which induces significant changes in gene regulation at the transcriptional and post-transcriptional level, as well as altering how many genes respond to growth rate. By comparison, the responses to growth limitation by other nutrients involve a smaller set of genes that participate in specific pathways.</p> <p>See associated commentary <url>http://www.biomedcentral.com/1741-7007/8/62</url></p

The diagnostic certainty levels of junior clinicians: A retrospective cohort study

BACKGROUND: Clinical decision-making is influenced by many factors, including clinicians' perceptions of the certainty around what is the best course of action to pursue. OBJECTIVE: To characterise the documentation of working diagnoses and the associated level of real-time certainty expressed by clinicians and to gauge patient opinion about the importance of research into clinician decision certainty. METHOD: This was a single-centre retrospective cohort study of non-consultant grade clinicians and their assessments of patients admitted from the emergency department between 01 March 2019 and 31 March 2019. De-identified electronic health record proformas were extracted that included the type of diagnosis documented and the certainty adjective used. Patient opinion was canvassed from a focus group. RESULTS: During the study period, 850 clerking proformas were analysed; 420 presented a single diagnosis, while 430 presented multiple diagnoses. Of the 420 single diagnoses, 67 (16%) were documented as either a symptom or physical sign and 16 (4%) were laboratory-result-defined diagnoses. No uncertainty was expressed in 309 (74%) of the diagnoses. Of 430 multiple diagnoses, uncertainty was expressed in 346 (80%) compared to 84 (20%) in which no uncertainty was expressed. The patient focus group were unanimous in their support of this research. CONCLUSION: The documentation of working diagnoses is highly variable among non-consultant grade clinicians. In nearly three quarters of assessments with single diagnoses, no element of uncertainty was implied or quantified. More uncertainty was expressed in multiple diagnoses than single diagnoses. IMPLICATIONS: Increased standardisation of documentation will help future studies to better analyse and quantify diagnostic certainty in both single and multiple working diagnoses. This could lead to subsequent examination of their association with important process or clinical outcome measures

The diagnostic certainty levels of junior clinicians: a retrospective cohort study

Background: Clinical decision-making is influenced by many factors, including clinicians’ perceptions of the certainty around what is the best course of action to pursue. Objective: To characterise the documentation of working diagnoses and the associated level of real-time certainty expressed by clinicians and to gauge patient opinion about the importance of research into clinician decision certainty. Method: This was a single-centre retrospective cohort study of non-consultant grade clinicians and their assessments of patients admitted from the emergency department between 01 March 2019 and 31 March 2019. De-identified electronic health record proformas were extracted that included the type of diagnosis documented and the certainty adjective used. Patient opinion was canvassed from a focus group. Results: During the study period, 850 clerking proformas were analysed; 420 presented a single diagnosis, while 430 presented multiple diagnoses. Of the 420 single diagnoses, 67 (16%) were documented as either a symptom or physical sign and 16 (4%) were laboratory-result-defined diagnoses. No uncertainty was expressed in 309 (74%) of the diagnoses. Of 430 multiple diagnoses, uncertainty was expressed in 346 (80%) compared to 84 (20%) in which no uncertainty was expressed. The patient focus group were unanimous in their support of this research. Conclusion: The documentation of working diagnoses is highly variable among non-consultant grade clinicians. In nearly three quarters of assessments with single diagnoses, no element of uncertainty was implied or quantified. More uncertainty was expressed in multiple diagnoses than single diagnoses. Implications: Increased standardisation of documentation will help future studies to better analyse and quantify diagnostic certainty in both single and multiple working diagnoses. This could lead to subsequent examination of their association with important process or clinical outcome measures

H3F3A (Histone 3.3) G34W Immunohistochemistry: A Reliable Marker Defining Benign and Malignant Giant Cell Tumor of Bone

Giant cell tumor of bone (GCTB) is a locally aggressive subarticular tumor. Having recently reported that H3.3 G34W mutations are characteristic of this tumor type, we have now investigated the sensitivity and specificity of the anti-histone H3.3 G34W rabbit monoclonal antibody in a wide variety of tumors including histologic mimics of GCTB to assess its value as a diagnostic marker. We also determined the incidence of H3.3 G34 mutations in primary malignant bone tumors as assessed by genotype and H3.3 G34W immunostaining. A total of 3163 tumors were tested. Totally, 213/235 GCTB (90.6%) showed nuclear H3.3 p.G34W immunoreactivity. This was not the case for the rare variants, p.G34L, M, and V, which occurred most commonly in the small bones of the hands, patella, and the axial skeleton. If these sites were excluded from the analysis, H3.3 G34W expression was found in 97.8% of GCTB. Malignant bone tumors initially classified as osteosarcomas were the only other lesions (n=11) that showed G34W expression. Notably an additional 2 previously reported osteosarcomas with a p.G34R mutation were not immunoreactive for the antibody. A total of 11/13 of these malignant H3.3-mutant tumors exhibited an osteoclast-rich component: when imaging was available all but one presented at a subarticular site. We propose that subarticular primary malignant bone sarcoma with H3.3 mutations represent true malignant GCTB, even in the absence of a benign GCTB component

High-pitch sounds small for domestic dogs: abstract crossmodal correspondences between auditory pitch and visual size

Humans possess intuitive associations linking certain non-redundant features of stimuli - e.g. high-pitched sounds with small object size (or similarly, low-pitched sounds with large object size). This phenomenon, known as crossmodal correspondence, has been identified in humans across multiple different senses. There is some evidence that non-human animals also form crossmodal correspondences, but the known examples are mostly limited to the associations between the pitch of vocalizations and the size of callers. To investigate whether domestic dogs, like humans, show abstract pitch-size association, we first trained dogs to approach and touch an object after hearing a sound emanating from it. Subsequently, we repeated the task but presented dogs with two objects differing in size, only one of which was playing a sound. The sound was either high or low pitched, thereby creating trials that were either congruent (high pitch from small object; low pitch from large objects) or incongruent (the reverse). We found that dogs reacted faster on congruent versus incongruent trials. Moreover, their accuracy was at chance on incongruent trials, but significantly above chance for congruent trials. Our results suggest that non-human animals show abstract pitch sound correspondences, indicating these correspondences may not be uniquely human but rather a sensory processing feature shared by other species

Effects of break crops, and of wheat volunteers growing in break crops or in set-aside or conservation covers, all following crops of winter wheat, on the development of take-all (Gaeumannomyces graminis var. tritici) in succeeding crops of winter wheat

Experiments on the Rothamsted and Woburn Experimental Farms studied the effects on take-all of different break crops and of set-aside/conservation covers that interrupted sequences of winter wheat. There was no evidence for different effects on take-all of the break crops per se but the presence of volunteers, in crops of oilseed rape, increased the amounts of take-all in the following wheat. Severity of take-all was closely related to the numbers of volunteers in the preceding break crops and covers, and was affected by the date of their destruction. Early destruction of set-aside/conservation covers was usually effective in preventing damaging take-all in the following wheat except, sometimes, when populations of volunteers were very large. The experiments were not designed to test the effects of sowing dates but different amounts of take-all in the first wheats after breaks or covers apparently affected the severity of take-all in the following (second) wheats only where the latter were relatively late sown. In earlier-sown second wheats, take-all was consistently severe and unrelated to the severity of the disease in the preceding (first) wheats. Results from two very simple experiments suggested that substituting set-aside/conservation covers for winter wheat, for 1 year only, did not seriously interfere with the development of take-all disease or with the development or maintenance of take-all decline (TAD). With further research, it might be possible for growers wishing to exploit TAD to incorporate set-aside/conservation covers into their cropping strategies, and especially to avoid the worst effects of the disease on grain yield during the early stages of epidemics

Enhancing the early student experience

This paper is concerned with identifying how the early student experience can be enhanced in order to improve levels of student retention and achievement. The early student experience is the focus of this project as the literature has consistently declared the first year to be the most critical in shaping persistence decisions. Programme managers of courses with high and low retention rates have been interviewed to identify activities that appear to be associated with good retention rates. The results show that there are similarities in the way programmes with high retention are run, with these features not being prevalent on programmes with low retention. Recommendations of activities that appear likely to enhance the early student experience are provided