Gene expression patterns of encapsulated microbial cells

To design hybrid cellular/synthetic devices such as sensors and vaccines, understanding of how the metabolic state of living cells changes upon physical confinement within three-dimensional matrices is vital. We analyze the gene expression patterns of stationary phase Saccharomyces cerevisiae (S. cerevisiae) cells encapsulated within three distinct nanostructured silica matrices and relate those patterns to known naturally occurring metabolic states. It was found that the cells for all three-encapsulated methods enter quiescent states characteristic of response to stress, albeit to different degrees and with differences in detail. By the measure of enrichment of stress-related Gene Ontology categories, we find that the AqS+g encapsulation more amenable to the cells than CDA and SD encapsulation. We hypothesize that this differential response in the AqS+g encapsulation is related to four properties of the encapsulating gel: 1) oxygen permeability, 2) relative softness of the material, 3) development of a protective sheath around individual cells, and 4) the presence of glycerol in the gel, which has been previously noted to serve as a protectant for encapsulated cells and can serve as the sole carbon source for S. cerevisiae under aerobic conditions. This work represents a combination of experiment and analysis aimed at the design and development of 3D encapsulation procedures to induce, and perhaps control, well-defined physiological behaviors. We also report on the temporal pattern of yeast gene expression patterns during encapsulation in silica matrices via a cell-directed assembly process, and upon release. Three broad classes of patterns are seen. A major shift in expression patterns is seen upon encapsulation, relative to the beginning stationary state, similar to previously reported stress response. Significant continuing shifts are seen by sampling at different intervals during a one week encapsulation. Upon release from encapsulation and reincubation in growth medium, the cells are in a state significantly different from the state prior to encapsulation and similar to the state during encapsulation. Implications are drawn for the use of encapsulated micro-organism as sensors and effectors, and for the persister state of such organisms. Ordinarily Gene Ontology (GO) enrichment analysis is subject to an arbitrary threshold for defining significance of enriched classes. In this paper, we consider replacing an arbitrary threshold with F-measure optimization to define the p-value that divides “significant enrichment” from “non-significant”. It is found that evaluation of false negatives (essential for computing recall and thus F-measure) requires a heuristic (but reasonable) assumption. We apply F-measure optimization to two sets of genes from different organisms and use Benjamini-Hochberg and random resampling to evaluate the number of false positives. It is found that the uncorrected p- value that produces optimum F-measure varies widely from one data set to another. It is also found that all three methods of FDR calculation diverge from each other within a range of uncorrected p-values that provide F-measure optimum p-values. This study includes in Appendix II a pipeline for using resampling and F-measure optimization to create lists of enriched GO classes that provide for variable weights of precision and recall

Using Optimal F-Measure and Random Resampling in Gene Ontology Enrichment Calculations

Background: A central question in bioinformatics is how to minimize arbitrariness and bias in analysis of patterns of enrichment in data. A prime example of such a question is enrichment of gene ontology (GO) classes in lists of genes. Our paper deals with two issues within this larger question. One is how to calculate the false discovery rate (FDR) within a set of apparently enriched ontologies, and the second how to set that FDR within the context of assessing significance for addressing biological questions, to answer these questions we compare a random resampling method with a commonly used method for assessing FDR, the Benjamini-Hochberg (BH) method. We further develop a heuristic method for evaluating Type II (false negative) errors to enable utilization of F-Measure binary classification theory for distinguishing “significant” from “non-significant” degrees of enrichment.Results: The results show the preferability and feasibility of random resampling assessment of FDR over the analytical methods with which we compare it. They also show that the reasonableness of any arbitrary threshold depends strongly on the structure of the dataset being tested, suggesting that the less arbitrary method of F-measure optimization to determine significance threshold is preferable.Conclusion: Therefore, we suggest using F-measure optimization instead of placing an arbitrary threshold to evaluate the significance of Gene Ontology Enrichment results, and using resampling to replace analytical method

Course Contents of English Language Textbooks and their Relevance to Learners’ Culture in an Islamic Context

The study is an attempt at analyzing the cultural authenticity of the course contents of English as a foreign language at International Islamic University Islamabad. This study assumes that these course contents increase cultural barriers for the learners who belong to a different set of cultural values and religious and educational background. It traces the limitation of foreign textbooks writers because of their unawareness of the local culture and the social, educational and religious environment. The study on the one hand questions the suitability of such textbooks for the learners (mostly from religious institutions) and on the other hand gives proposals for the development of English textbooks based on indigenous or Islamic culture. Usually, the evaluation of course contents is descriptive in nature and is done to describe or find out a problem rather than to address it. To bring an improvement in course contents is the basic goal of course evaluation. Although, it would be irrelevant to manipulate a problem statement for this type of research yet ignoring the student factor in writing English text books and selecting these books without doing a prior research into the needs analysis of the learners can be cited as the main problem which inspired the study. This study adopts both a descriptive as well as a prescriptive approach. It analyses the contents to see what is there in the contents and what is required for the learners from a cultural perspective. On the basis of its two fold description the study has given suggestions as to what should be an ideal situation for the selection, adaptation and development of English language textbooks for the learners. The main hypothesis of the study was that there was no cultural relevance between the objectives of the learners for learning English, their social and educational background and the contents of the course book. The inappropriateness of the theories that advocate the inclusion of target language culture in language courses as an essential factor for teaching and learning English in every situation and for all learners is the secondary hypothesis of the study. The study has narrowed down its focus to the cultural relevance of the course contents being taught at the IIUI, the communication gap between the authors and the target learners, and to give suggestions regarding the possibility to include the learners’ culture in English language courses.   The study adopts a first glance evaluation in the light of guidelines provided by pedagogical theorists and deliberately avoids learners’ response method (in which learners responses are measured) because of the   researcher’s own interest in the impressionistic evaluation. The main purpose of the study was to bring the learners in the lime light of focus to make teaching of English more learners’ centered, to create awareness among the teachers, policy makers and course designers to consider learners needs in the process of textbooks selection and development. The study proves that the themes, setting, characters and worldview, presented in the contents of the book represent a foreign and unfamiliar world for the learners. The study suggests that the learners would be more motivated to learn English if language were presented in the context with which the learners could identify themselves. Keywords: language, English, Culture, Textbooks, Learner

Performance Evaluation of UK Acquiring Companies in the Pre and Post-Acquisitions Periods

This paper has two objectives: first, it examines the financial performance of twenty UK based acquiring companies over the period of five years (2009-2013) using financial ratios of Liquidity, Profitability and Solvency in order to empirically determine whether there is any significant financial performance changes in the operation of the underlying companies as a result of acquisitions. Both average ratio and paired t-test analysis have been conducted. The analysis concludes that none of the ratios proved statistical significance which shows that the underlying acquisitions did not influence changes in the financial performance of the acquiring companies. The paper also examines whether shareholders make short-term gain while opting for acquisitions by analyzing stocks return over 58 days window period i.e. 29 days prior to acquisition announcement and 29 days after acquisition announcement by applying CAPM model and AAR and CAAR analysis. The analysis concludes that none of the results show statistical significance which further asserts that UK shareholders do not make gain in the short-term as a result of the acquisition activities they have undertaken

Floristic composition, biological spectrum, and phytogeographic distribution of the Bin Dara Dir, in the western boundary of Pakistan

This study assessed the floristic composition, biological spectrum, and phytogeographical elements of the Bin Dara western boundary of Pakistan. The flora consisted of 140 plant species belonging to 47 families. The most dominant family was Poaceae (with 14 species), followed by Asteraceae (11 species). The biological spectrum showed the therophytes (71 species, 50.71%) as the dominant life form class, followed by mega -phanerophytes (27 species, 19.28%), nano-phanerophytes (15 species, 10.71%), geophytes (10 species, 7.14%), chamaephytes (9 species, 6.42%), and hemi-cryptophytes (8 species, 5.71%). Leaf size classes comprised of nanophylls (48 species, 34.28%), microphylls (32 species, 22.85%), mesophylls (22 species, 15.71%), macrophylls (17 species, 12.14%), leptophylls (12 species, 8.57), megaphylls (8 species, 5.75%), and aphyllous (1 species, 0.71%). Cosmopolitan was the most prominent form of phytogeographic elements (with 17 species, 12.14%), followed by pantropical and Euro-Siberian Mediterranean Irano-Turanian (14 species, 10%) each. The pluriregional represented (13 species, 9.28%), Holarctic and Mediterranean Irano-Turanian (10 species, 7.14%), Irano-Turanian and Western Himalayan (9 species, 6.42%) each. It is recommended that further study is needed to map the vegetation, its indicators, and rare species that face a huge threat of endangerment

PHYSIO-CHEMICAL EVALUATION AND BIOLOGICAL ACTIVITY OF AJUGA BRACTEOSA WALL. AND VIOLA ODOROTO LINN

Background: Ajuga bracteosa and Viola odorata are frequently used by the native people of Swat-Pakistan for the curing of fever, malaria, cough, urinary and stomach disorders with slightly different practice of usage like raw powdered, extracts, decoction etc. Methods and Materials: Disc Diffusion Method was used for determination of antimicrobial activities of both plants. Nutrient Agar Media was used for the culturing and growth of all microbial strains. Vitamin C and minerals contents were determined by standard method of AOAC. Na and K were analyzed by using flame photometric technique. Micro minerals i.e. “Ni, Cr, Fe, Cu, Zn, Mn, Ca, Pb, and Mg” were determined by Atomic Absorption Spectrophotometer (AAS). Total Soluble Solid (TSS) was determined by using abbe refractometer and pH was determined by using pH meter. Results: The present study demonstrates that both plants exhibited antibacterial activities against P. aeruginos, E. coli, S. typhi, B. subtilis and S. aureus. The examined plants showed zone of inhibition for aqueous fraction (50.90, 45.90 %) against P. aeruginosa; for EtOAc fraction (41.37, 57.62%) against C. Albicans and for hexane fraction (25.86, 40.57%) against K. pneumoniae, respectively. Total of 14 different minerals (Na, K, P, Ca, Mg, Fe, Zn, Mn, Co, Cr, Ni, Cu, Pb, Cd) were determined and it was also observed that both the examined plants contained significant level of these analyzed minerals. The subject plants contained highest level of magnesium (295.75, 145.85 mg 100-1g) and calcium (212.49, 44.00 mg 100-1g) and potassium (152.6, 437.45 mg 100-1g) while moderate level P, Zn, Na and lower amount of Cd, Ni, Mn and Cu using Atomic Absorption, Flame Photometry and spectrophotometric techniques. V. odorata was found to contain a higher amount of vitamin C (64.05±12.37mg 100-1g) as compared to A. bracteosa (45.45 ± 7.29 mg 100-1 g). Conclusion: Findings of this study can persuade researchers for future comprehensive phytochemical study of these plants using state of art techniques and instruments, which include not only isolation of secondary metabolites from these plants but biological evaluation of isolated compounds both in vivo and in vitr

Hypermethylation and global remodelling of DNA methylation is associated with acquired cisplatin resistance in testicular germ cell tumours

Testicular germ cell tumours (TGCTs) respond well to cisplatin-based therapy. However, cisplatin resistance and poor outcomes do occur. It has been suggested that a shift towards DNA hypermethylation mediates cisplatin resistance in TGCT cells, although there is little direct evidence to support this claim. Here we utilized a series of isogenic cisplatin-resistant cell models and observed a strong association between cisplatin resistance in TGCT cells and a net increase in global CpG and non-CpG DNA methylation spanning regulatory, intergenic, genic and repeat elements. Hypermethylated loci were significantly enriched for repressive DNA segments, CTCF and RAD21 sites and lamina associated domains, suggesting that global nuclear reorganization of chromatin structure occurred in resistant cells. Hypomethylated CpG loci were significantly enriched for EZH2 and SUZ12 binding and H3K27me3 sites. Integrative transcriptome and methylome analyses showed a strong negative correlation between gene promoter and CpG island methylation and gene expression in resistant cells and a weaker positive correlation between gene body methylation and gene expression. A bidirectional shift between gene promoter and gene body DNA methylation occurred within multiple genes that was associated with upregulation of polycomb targets and downregulation of tumour suppressor genes. These data support the hypothesis that global remodelling of DNA methylation is a key factor in mediating cisplatin hypersensitivity and chemoresistance of TGCTs and furthers the rationale for hypomethylation therapy for refractory TGCT patients

Effects of a high-dose 24-h infusion of tranexamic acid on death and thromboembolic events in patients with acute gastrointestinal bleeding (HALT-IT): an international randomised, double-blind, placebo-controlled trial

Background: Tranexamic acid reduces surgical bleeding and reduces death due to bleeding in patients with trauma. Meta-analyses of small trials show that tranexamic acid might decrease deaths from gastrointestinal bleeding. We aimed to assess the effects of tranexamic acid in patients with gastrointestinal bleeding. Methods: We did an international, multicentre, randomised, placebo-controlled trial in 164 hospitals in 15 countries. Patients were enrolled if the responsible clinician was uncertain whether to use tranexamic acid, were aged above the minimum age considered an adult in their country (either aged 16 years and older or aged 18 years and older), and had significant (defined as at risk of bleeding to death) upper or lower gastrointestinal bleeding. Patients were randomly assigned by selection of a numbered treatment pack from a box containing eight packs that were identical apart from the pack number. Patients received either a loading dose of 1 g tranexamic acid, which was added to 100 mL infusion bag of 0·9% sodium chloride and infused by slow intravenous injection over 10 min, followed by a maintenance dose of 3 g tranexamic acid added to 1 L of any isotonic intravenous solution and infused at 125 mg/h for 24 h, or placebo (sodium chloride 0·9%). Patients, caregivers, and those assessing outcomes were masked to allocation. The primary outcome was death due to bleeding within 5 days of randomisation; analysis excluded patients who received neither dose of the allocated treatment and those for whom outcome data on death were unavailable. This trial was registered with Current Controlled Trials, ISRCTN11225767, and ClinicalTrials.gov, NCT01658124. Findings: Between July 4, 2013, and June 21, 2019, we randomly allocated 12 009 patients to receive tranexamic acid (5994, 49·9%) or matching placebo (6015, 50·1%), of whom 11 952 (99·5%) received the first dose of the allocated treatment. Death due to bleeding within 5 days of randomisation occurred in 222 (4%) of 5956 patients in the tranexamic acid group and in 226 (4%) of 5981 patients in the placebo group (risk ratio [RR] 0·99, 95% CI 0·82–1·18). Arterial thromboembolic events (myocardial infarction or stroke) were similar in the tranexamic acid group and placebo group (42 [0·7%] of 5952 vs 46 [0·8%] of 5977; 0·92; 0·60 to 1·39). Venous thromboembolic events (deep vein thrombosis or pulmonary embolism) were higher in tranexamic acid group than in the placebo group (48 [0·8%] of 5952 vs 26 [0·4%] of 5977; RR 1·85; 95% CI 1·15 to 2·98). Interpretation: We found that tranexamic acid did not reduce death from gastrointestinal bleeding. On the basis of our results, tranexamic acid should not be used for the treatment of gastrointestinal bleeding outside the context of a randomised trial