Effect of probe characteristics on the subtractive hybridization efficiency of human genomic DNA

<p>Abstract</p> <p>Background</p> <p>The detection sensitivity of low abundance pathogenic species by polymerase chain reaction (PCR) can be significantly enhanced by removing host nucleic acids. This selective removal can be performed using a magnetic bead-based solid phase with covalently immobilized capture probes. One of the requirements to attain efficient host background nucleic acids subtraction is the capture probe characteristics.</p> <p>Findings</p> <p>In this study we investigate how various capture probe characteristics influence the subtraction efficiency. While the primary focus of this report is the impact of probe length, we also studied the impact of probe conformation as well as the amount of capture probe attached to the solid phase. The probes were immobilized on magnetic microbeads functionalized with a phosphorous dendrimer. The subtraction efficiency was assessed by quantitative real time PCR using a single-step capture protocol and genomic DNA as target. Our results indicate that short probes (100 to 200 bp) exhibit the best subtraction efficiency. Additionally, higher subtraction efficiencies with these probes were obtained as the amount of probe immobilized on the solid phase decreased. Under optimal probes condition, our protocol showed a 90 - 95% subtraction efficiency of human genomic DNA.</p> <p>Conclusions</p> <p>The characteristics of the capture probe are important for the design of efficient solid phases. The length, conformation and abundance of the probes determine the capture efficiency of the solid phase.</p

Structural Requirements for Dihydrobenzoxazepinone Anthelmintics: Actions against Medically Important and Model Parasites: Trichuris muris, Brugia malayi, Heligmosomoides polygyrus, and Schistosoma mansoni.

Nine hundred million people are infected with the soil-transmitted helminths Ascaris lumbricoides (roundworm), hookworm, and Trichuris trichiura (whipworm). However, low single-dose cure rates of the benzimidazole drugs, the mainstay of preventative chemotherapy for whipworm, together with parasite drug resistance, mean that current approaches may not be able to eliminate morbidity from trichuriasis. We are seeking to develop new anthelmintic drugs specifically with activity against whipworm as a priority and previously identified a hit series of dihydrobenzoxazepinone (DHB) compounds that block motility of ex vivo Trichuris muris. Here, we report a systematic investigation of the structure-activity relationship of the anthelmintic activity of DHB compounds. We synthesized 47 analogues, which allowed us to define features of the molecules essential for anthelmintic action as well as broadening the chemotype by identification of dihydrobenzoquinolinones (DBQs) with anthelmintic activity. We investigated the activity of these compounds against other parasitic nematodes, identifying DHB compounds with activity against Brugia malayi and Heligmosomoides polygyrus. We also demonstrated activity of DHB compounds against the trematode Schistosoma mansoni, a parasite that causes schistosomiasis. These results demonstrate the potential of DHB and DBQ compounds for further development as broad-spectrum anthelmintics

Medical student and academic staff perceptions of role models: an analytical cross-sectional study

BACKGROUND: This study explored the associations between the perceptions of students and the perceptions of academic staff about the characteristics of clinical lecturers at the Department of Internal Medicine at Kerman University of Medical Sciences (KUMS). It also assessed what characteristics constitute a 'role model' from the point of view of students and staff. METHODS: Staff and students were questioned about the characteristics of their colleagues and lecturers, respectively. They were asked about 15 characteristics under four headings: personality, teaching skill, group working and overall performance as a role model. Associations between lecturers' characteristics were explored using Pearson correlation and characteristics were allocated into groups by partition cluster method. In addition, predictors of being a valuable lecturer were assessed using logistic regression analysis. RESULTS: Based on staff responses, the strongest association observed was between honesty and being respectful (r = 0.93, p < 0.0001). Based on student responses, the strongest association observed was between being professional and honesty (r = 0.98, p < 0.0001). None of the correlations between student and staff perceptions were significant for any characteristic. Two groups were recognized among the characteristics. group one contained those characteristics which were related to the lecturer's activity; while the second group contained characteristics that were related to the personality or teaching performance of the lecturer. The predictors of lecturer as 'role model' (i.e., perceptions of students) consisted mostly of characteristics from the first group, while the predictors of a 'role model' by fellow academic staff consisted of characteristics that were in both groups. CONCLUSION: These findings showed considerable differences between the perceptions of students about their lecturers when compared with perceptions of staff about their colleagues. Students were more concerned with the personality of their lecturers, while staff also considered their ideas and behaviors. This suggests that a more comprehensive assessment of a lecturer's performance could be obtained by taking into account feedback from both students and colleagues

Rise to modern levels of ocean oxygenation coincided with the Cambrian radiation of animals.

The early diversification of animals (∼630 Ma), and their development into both motile and macroscopic forms (∼575-565 Ma), has been linked to stepwise increases in the oxygenation of Earth's surface environment. However, establishing such a linkage between oxygen and evolution for the later Cambrian 'explosion' (540-520 Ma) of new, energy-sapping body plans and behaviours has proved more elusive. Here we present new molybdenum isotope data, which demonstrate that the areal extent of oxygenated bottom waters increased in step with the early Cambrian bioradiation of animals and eukaryotic phytoplankton. Modern-like oxygen levels characterized the ocean at ∼521 Ma for the first time in Earth history. This marks the first establishment of a key environmental factor in modern-like ecosystems, where animals benefit from, and also contribute to, the 'homeostasis' of marine redox conditions

Quantum Gravity in 2+1 Dimensions: The Case of a Closed Universe

In three spacetime dimensions, general relativity drastically simplifies, becoming a ``topological'' theory with no propagating local degrees of freedom. Nevertheless, many of the difficult conceptual problems of quantizing gravity are still present. In this review, I summarize the rather large body of work that has gone towards quantizing (2+1)-dimensional vacuum gravity in the setting of a spatially closed universe.Comment: 61 pages, draft of review for Living Reviews; comments, criticisms, additions, missing references welcome; v2: minor changes, added reference

Enhanced susceptibility to infections in a diabetic wound healing model

<p>Abstract</p> <p>Background</p> <p>Wound infection is a common complication in diabetic patients. The progressive spread of infections and development of drug-resistant strains underline the need for further insights into bacterial behavior in the host in order to develop new therapeutic strategies. The aim of our study was to develop a large animal model suitable for monitoring the development and effect of bacterial infections in diabetic wounds.</p> <p>Methods</p> <p>Fourteen excisional wounds were created on the dorsum of diabetic and non-diabetic Yorkshire pigs and sealed with polyurethane chambers. Wounds were either inoculated with 2 × 10⁸Colony-Forming Units (CFU) of <it>Staphylococcus aureus </it>or injected with 0.9% sterile saline. Blood glucose was monitored daily, and wound fluid was collected for bacterial quantification and measurement of glucose concentration. Tissue biopsies for microbiological and histological analysis were performed at days 4, 8, and 12. Wounds were assessed for reepithelialization and wound contraction.</p> <p>Results</p> <p>Diabetic wounds showed a sustained significant infection (>10⁵CFU/g tissue) compared to non-diabetic wounds (p < 0.05) over the whole time course of the experiment. <it>S. aureus</it>-inoculated diabetic wounds showed tissue infection with up to 8 × 10⁷CFU/g wound tissue. Non-diabetic wounds showed high bacterial counts at day 4 followed by a decrease and no apparent infection at day 12. Epidermal healing in <it>S. aureus</it>-inoculated diabetic wounds showed a significant delay compared with non-inoculated diabetic wounds (59% versus 84%; p < 0.05) and were highly significant compared with healing in non-diabetic wounds (97%; p < 0.001).</p> <p>Conclusion</p> <p>Diabetic wounds developed significantly more sustained infection than non-diabetic wounds. <it>S. aureus </it>inoculation leads to invasive infection and significant wound healing delay and promotes invasive co-infection with endogenous bacteria. This novel wound healing model provides the opportunity to closely assess infections during diabetic wound healing and to monitor the effect of therapeutical agents <it>in vivo</it>.</p

Culturally valuable minority crops provide a succession of floral resources for flower visitors in traditional orchard gardens

Agricultural intensification typically has detrimental effects on pollinator communities, but diverse cropping systems that contain sequentially-flowering crops have the potential to benefit pollinators through the provision of additional floral resources. In this study we investigate the importance of cultivated flora for flower visitors in ten agricultural gardens in South Sinai, Egypt. Insect-flower interactions in gardens and unmanaged plots were surveyed across a four-month period in two environmentally distinct years (pre-flood and post-flood). Despite containing an equal abundance and diversity of wild plants as unmanaged habitat, gardens supported a higher abundance and diversity of flower visitors due to the additional presence of cultivated flora. Visitation networks exhibited dramatic intra-annual changes in composition, with cultivated plants becoming increasingly important in later months. Trends were highly conserved across 2 years despite highly contrasting rainfall. Several key crop species were strongly involved in shaping the structure of the networks, the majority of which were herbs with strong cultural significance (fennel, rosemary, mint) and grown incidentally alongside the primary orchard crops. Minority crops are frequently overlooked in agricultural systems due to their low economic value, but we show that they can have a dramatic influence upon the structure of visitation networks, increasing both pollinator abundance and diversity, and emphasising the link between cultural practices and biodiversity conservation

ST6GAL1-mediated aberrant sialylation promotes prostate cancer progression

Aberrant glycosylation is a universal feature of cancer cells, and cancer-associated glycans have been detected in virtually every cancer type. A common change in tumour cell glycosylation is an increase in α2,6 sialylation of N-glycans, a modification driven by the sialyltransferase ST6GAL1. ST6GAL1 is overexpressed in numerous cancer types, and sialylated glycans are fundamental for tumour growth, metastasis, immune evasion, and drug resistance, but the role of ST6GAL1 in prostate cancer is poorly understood. Here, we analyse matched cancer and normal tissue samples from 200 patients and verify that ST6GAL1 is upregulated in prostate cancer tissue. Using MALDI imaging mass spectrometry (MALDI-IMS), we identify larger branched α2,6 sialylated N-glycans that show specificity to prostate tumour tissue. We also monitored ST6GAL1 in plasma samples from >400 patients and reveal ST6GAL1 levels are significantly increased in the blood of men with prostate cancer. Using both in vitro and in vivo studies, we demonstrate that ST6GAL1 promotes prostate tumour growth and invasion. Our findings show ST6GAL1 introduces α2,6 sialylated N-glycans on prostate cancer cells and raise the possibility that prostate cancer cells can secrete active ST6GAL1 enzyme capable of remodelling glycans on the surface of other cells. Furthermore, we find α2,6 sialylated N-glycans expressed by prostate cancer cells can be targeted using the sialyltransferase inhibitor P-3FAX-Neu5Ac. Our study identifies an important role for ST6GAL1 and α2,6 sialylated N-glycans in prostate cancer progression and highlights the opportunity to inhibit abnormal sialylation for the development of new prostate cancer therapeutics

Large sub-clonal variation in <i>Phytophthora infestans</i> from recent severe late blight epidemics in India

Abstract The population structure of the Phytophthora infestans populations that caused the recent 2013–14 late blight epidemic in eastern India (EI) and northeastern India (NEI) was examined. The data provide new baseline information for populations of P. infestans in India. A migrant European 13_A2 genotype was responsible for the 2013–14 epidemic, replacing the existing populations. Mutations have generated substantial sub-clonal variation with 24 multi-locus genotypes (MLGs) found, of which 19 were unique variants not yet reported elsewhere globally. Samples from West Bengal were the most diverse and grouped alongside MLGs found in Europe, the UK and from neighbouring Bangladesh but were not linked directly to most samples from south India. The pathogen population was broadly more aggressive on potato than on tomato and resistant to the fungicide metalaxyl. Pathogen population diversity was higher in regions around the international borders with Bangladesh and Nepal. Overall, the multiple shared MLGs suggested genetic contributions from UK and Europe in addition to a sub-structure based on the geographical location within India. Our data indicate the need for improved phytosanitary procedures and continuous surveillance to prevent the further introduction of aggressive lineages of P. infestans into the country