Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

Background: The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the presence of glucose, but also by glycerol. This unusual regulatory behavior prompted us to study the regulation of carbon substrate utilization in different bioprocess conditions on a genome wide scale. Results: We performed microarray analysis on the total mRNA population as well as mRNA that had been fractionated according to ribosome occupancy. Translationally quiescent mRNAs were defined as being associated with single ribosomes (monosomes) and highly-translated mRNAs with multiple ribosomes (polysomes). We found that despite their lower growth rates, global translation was most active in methanol-grown P. pastoris cells, followed by excess glycerol- or glucose-grown cells. Transcript-specific translational responses were found to be minimal, while extensive transcriptional regulation was observed for cells grown on different carbon sources. Due to their respiratory metabolism, cells grown in excess glucose or glycerol had very similar expression profiles. Genes subject to glucose repression were mainly involved in the metabolism of alternative carbon sources including the control of glycerol uptake and metabolism. Peroxisomal and methanol utilization genes were confirmed to be subject to carbon substrate repression in excess glucose or glycerol, but were found to be strongly de-repressed in limiting glucose-conditions (as are often applied in fed batch cultivations) in addition to induction by methanol. Conclusions: P. pastoris cells grown in excess glycerol or glucose have similar transcript profiles in contrast to S. cerevisiae cells, in which the transcriptional response to these carbon sources is very different. The main response to different growth conditions in P. pastoris is transcriptional; translational regulation was not transcript-specific. The high proportion of mRNAs associated with polysomes in methanol-grown cells is a major finding of this study; it reveals that high productivity during methanol induction is directly linked to the growth condition and not only to promoter strength.

Computer Processing of Medieval Slavic Sources in the Institute of Literature at BAS Repertorium Project (1994–2004)

Mixed-content miscellanies (very frequent in the Byzantine and mediaeval Slavic written heritage) are usually defined as collections of works with non-occupational, non-liturgical application, and texts in them are selected and arranged according to no identifiable principle. It is a “readable” type of miscellanies which were compiled mainly on the basis of the cognitive interests of compilers and readers. Just like the occupational ones, they also appeared to satisfy public needs but were intended for individual usage. My textological comparison had shown that mixed- content miscellanies often showed evidence of a stable content – some of them include the same constituent works in the same order, regardless that the manuscripts had no obvious genetic relationship. These correspondences were sufficiently numerous and distinctive that they could not be merely fortuitous, and the only sensible interpretation was that even when the operative organizational principle was not based on independently identifiable criteria, such as the church calendar, liturgical function, or thematic considerations, mixed-content miscellanies (or, at least, portions of their contents) nonetheless fell into types. In this respect, the apparent free selection and arrangement of texts in mixed-content miscellanies turns out to be illusory. The problem was – as the corpus of manuscripts that I and my colleagues needed to examine grew – our ability to keep track of the structure of each one, and to identify structural correspondences among manuscripts within the corpus, diminished. So, at the end of 1993 I addressed a letter to Prof. David Birnbaum (University of Pittsburgh, PA) with a request to help me to solve the problem. He and my colleague Andrey Boyadzhiev (Sofia University) pointed out to me that computers are well suited to recording, processing, and analyzing large amounts of data, and to identifying patterns within the data, and their proposal was that we try to develop a computer system for description of manuscripts, for their analysis and of course, for searching the data. Our collaboration in this project is now ten years old, and our talk today presents an overview of that collaboration.

Self-monitoring of blood glucose in Black Caribbean and South Asian Canadians with non-insulin treated Type 2 diabetes mellitus:a qualitative study of patients' perspectives

Background: To examine the views and current practice of SMBG among Black Caribbean and South Asian individuals with non-insulin treated Type 2 diabetes mellitus. Methods: Twelve participants completed semi-structured interviews that were guided by the Health Belief Model and analyzed using thematic network analysis. Results: The frequency of monitoring among participants varied from several times a day to once per week. Most participants expressed similar experiences regarding their views and practices of SMBG. Minor differences across gender and culture were observed. All participants understood the benefits, but not all viewed SMBG as beneficial to their personal diabetes management. SMBG can facilitate a better understanding and maintenance of self-care behaviours. However, it can trigger both positive and negative emotional responses, such as a sense of disappointment when high readings are not anticipated, resulting in emotional distress. Health care professionals play a key role in the way SMBG is perceived and used by patients. Conclusion: While the majority of participants value SMBG as a self-management tool, barriers exist that impede its practice, particularly its cost. How individuals cope with these barriers is integral to understanding why some patients adopt SMBG more than others. © 2013 Gucciardi et al.; licensee BioMed Central Ltd.

An exploration of pharmacy-specific reasons for non-adherence to prescribed medicines in a socioeconomically deprived, ethnically diverse UK cohort

Methods - Ethical approval for the study was granted by both the local National Health Service (NHS) Research Ethics Committee (REC) and Aston University’s REC. Seven focus groups were conducted between October and December 2011 in medical or community settings within inner-city Birmingham (UK). Discussions were guided by a theme plan which was developed from key themes identified by a literature review and piloted via a Patient Consultation Group. Each focus group had between 3 and 7 participants. The groups were digitally recorded and subsequently transcribed verbatim. The transcriptions were then subjected to thematic analysis via constant comparison in order to identify emerging themes. Results - Participants recognised the pharmacist as an expert source of advice about prescribed medicines, a source they frequently felt a need to consult as a result of the inadequate supply of medicines information from the prescriber. However, an emerging theme was a perception that pharmacists had an oblique profit motive relating to the supply of generic medicines with frequent changes to the ‘brand’ of generic supplied being attributed to profit-seeking by pharmacists. Such changes had a negative impact on the patient’s perceived efficacy of the therapy which may make non-adherence more likely. Conclusions - Whilst pharmacists were recognised as medicines experts, trust in the pharmacist was undermined by frequent changes to generic medicines. Such changes have the potential to adversely impact adherence levels. Further, quantitative research is recommended to examine if such views are generalisable to the wider population of Birmingham and to establish if such views impact on adherence levels.

Target/error overlap in jargonaphasia:the case for a one-source model, lexical and non-lexical summation, and the special status of correct responses

We present three jargonaphasic patients who made phonological errors in naming, repetition and reading. We analyse target/response overlap using statistical models to answer three questions: 1) Is there a single phonological source for errors or two sources, one for target-related errors and a separate source for abstruse errors? 2) Can correct responses be predicted by the same distribution used to predict errors or do they show a completion boost (CB)? 3) Is non-lexical and lexical information summed during reading and repetition? The answers were clear. 1) Abstruse errors did not require a separate distribution created by failure to access word forms. Abstruse and target-related errors were the endpoints of a single overlap distribution. 2) Correct responses required a special factor, e.g., a CB or lexical/phonological feedback, to preserve their integrity. 3) Reading and repetition required separate lexical and non-lexical contributions that were combined at output.

Learner support and discovery in a virtual non-judgmental environment

This thesis is a qualitative case study that draws upon a grounded genre analysis approach situated within the social constructivist paradigm. The study describes the various obligatory, desired, and optional moves used by post-graduate students as they interacted within an online, non-judgmental environment in order to seek solutions to issues they were experiencing with their research projects or teaching. The postgraduate students or case participants met individually online with me at pre-arranged times to take part in Instant Messenger Cooperative Development (IMCD) (Boon, 2005) 30-minute to one hour sessions via the text-chat function of Skype. Participants took on the role of ‘Explorer’ in order to articulate their thoughts and ideas about their research. I took on the role of ‘Understander’ to provide support to each Explorer by reflecting my understanding of the ongoing articulations as the Explorers investigated their specific issues, determined possible ways to overcome them, made new discoveries, and formulated plans of action regarding the best way for them to move forward. The description of generic moves covers 32 IMCD sessions collected over a threeyear period (2009-2012) from 10 different participants (A-J). Data collected is drawn from live IMCD sessions, field notes, and post-session email feedback from participants. In particular, the thesis focuses on describing the specific generic moves of Explorers within IMCD sessions as they seek satisfactory resolutions to particular research or pedagogic puzzles. It also provides a detailed description of a longitudinal case (Participant A – four sessions), a one-session case (Participant B – one session), and an outlier case in which the Explorer underwent a negative IMCD experience. The thesis concludes by arguing that IMCD is a highly effective tool that helps facilitate the research process for both distance-learning and on-campus students and has the potential to be utilized across all disciplines at the tertiary level.

Is pregnancy a teachable moment for diet and physical activity behaviour change? An interpretative phenomenological analysis of the experiences of women during their first pregnancy

OBJECTIVES: Pregnancy may provide a 'teachable moment' for positive health behaviour change, as a time when women are both motivated towards health and in regular contact with health care professionals. This study aimed to investigate whether women's experiences of pregnancy indicate that they would be receptive to behaviour change during this period. DESIGN: Qualitative interview study. METHODS: Using interpretative phenomenological analysis, this study details how seven women made decisions about their physical activity and dietary behaviour during their first pregnancy. RESULTS: Two women had required fertility treatment to conceive. Their behaviour was driven by anxiety and a drive to minimize potential risks to the pregnancy. This included detailed information seeking and strict adherence to diet and physical activity recommendations. However, the majority of women described behaviour change as 'automatic', adopting a new lifestyle immediately upon discovering their pregnancy. Diet and physical activity were influenced by what these women perceived to be normal or acceptable during pregnancy (largely based on observations of others) and internal drivers, including bodily signals and a desire to retain some of their pre-pregnancy self-identity. More reasoned assessments regarding benefits for them and their baby were less prevalent and influential. CONCLUSIONS: Findings suggest that for women who conceived relatively easily, diet and physical activity behaviour during pregnancy is primarily based upon a combination of automatic judgements, physical sensations, and perceptions of what pregnant women are supposed to do. Health professionals and other credible sources appear to exert less influence. As such, pregnancy alone may not create a 'teachable moment'. Statement of contribution What is already known on this subject? Significant life events can be cues to action with relation to health behaviour change. However, much of the empirical research in this area has focused on negative health experiences such as receiving a false-positive screening result and hospitalization, and in relation to unequivocally negative behaviours such as smoking. It is often suggested that pregnancy, as a major life event, is a 'teachable moment' (TM) for lifestyle behaviour change due to an increase in motivation towards health and regular contact with health professionals. However, there is limited evidence for the utility of the TM model in predicting or promoting behaviour change. What does this study add? Two groups of women emerged from our study: the women who had experienced difficulties in conceiving and had received fertility treatment, and those who had conceived without intervention. The former group's experience of pregnancy was characterized by a sense of vulnerability and anxiety over sustaining the pregnancy which influenced every choice they made about their diet and physical activity. For the latter group, decisions about diet and physical activity were made immediately upon discovering their pregnancy, based upon a combination of automatic judgements, physical sensations, and perceptions of what is normal or 'good' for pregnancy. Among women with relatively trouble-free conception and pregnancy experiences, the necessary conditions may not be present to create a 'teachable moment'. This is due to a combination of a reliance on non-reflective decision-making, perception of low risk, and little change in affective response or self-concept.

Rib-cage-movement measurements as a potential new trigger signal in non-invasive mechanical ventilation

Non-invasive ventilation performed through an oronasal mask is a standard in clinical and homecare mechanical ventilation. Besides all its advantages, inevitable leaks through the mask cause errors in the feedback information provided by the airflow sensor and, hence, patient-ventilator asynchrony with multiple negative consequences. Here we investigate a new way to provide a trigger to the ventilator. The method is based on the measurement of rib cage movement at the onset of inspiration and during breathing by fibre-optic sensors. In a series of simultaneous measurements by a long-period fibre grating sensor and pneumotachograph we provide the statistical evidence of the 200 ms lag of the pneumo with respect the fibre-optic signal. The lag is registered consistently across three independent delay metrics. Further, we discuss exceptions from this trend and identify the needed improvements to the proposed fibre-sensing scheme.

Comparative analysis of a moderating and mediating model of stress, appraisal, and coping in Hispanic and non-Hispanic Alzheimer's disease caregivers

This dissertation utilizes a cross-sectional study to examine the phenomenon of caregiving within a theoretically grounded stress, appraisal, and coping model. Hispanic and non-Hispanic caregivers were studied to examine the factors associated with variance in caregiver appraisal, coping, and outcomes of caregiving strain (depression and somatic complaints) and caregiving gain (life satisfaction, mastery, and personal gain). A purposive sampling strategy was used to recruit 204 Alzheimer's disease caregivers in South Florida. A self-report questionnaire was used to collect demographic data, and to measure stress, appraisal, coping, and psychological well-being of caregivers. Regression equations were developed to compare moderating and mediating models of appraisal and coping. Emotion-focused coping skills were found to significantly moderate the effects of stress (F [1,195] = 4.62, p < .05), explaining approximately 21% of the variance in satisfaction was found to moderate the effects of stress (F [1,195] = 7.09; p < .05), explaining approximately 27% of the variance in personal gain and approximately 8% of the variance in life satisfaction (F [1,195] = 4.14; p < .05). Appraisal of Burden was found to significantly mediate the effects of stress, explaining approximately 30% of the variance in somatic complaints (F [1,196] = 31.60; p < .001) and 32% of the variance in depression (F [1,196] = 38.18; p < .001). The results of the analyses indicate that appraisal and coping skills are important variables in the stress process. The results of this study underscore the importance of accounting for positive and negative outcomes in providing a fuller understanding of the stress, appraisal and coping process of Alzheimer's Disease caregivers. ^

Sources of metals and sulfur in the mineral deposits of central Idaho, USA

A variety of mineral deposits occur in the Paleozoic sedimentary rocks and Late Cretaceous granitic rocks of central Idaho. The main objective of this project is to identify the sources of metals and sulfur in central Idaho ores. Lead isotope compositions of various crustal rocks were determined and compared with the ore lead composition in order to trace sources of lead, and by inference other metals. Sulfur isotope compositions of various sulfide minerals were also determined to trace the sources of sulfur and to explore the coupling or decoupling of metal and sulfur sources. ^ On the basis of lead and sulfur isotope compositions, two groups of ores are recognized: a sedimentary group and an igneous group. The sedimentary group ores are characterized by radiogenic lead and heavy sulfur typical of upper crustal rocks. The sedimentary group ores were formed by meteoric water-dominated hydrothermal systems that leached metals and sulfur from host Paleozoic sedimentary rocks and the underlying Precambrian crystalline basement rocks. The igneous group ores can be divided into two types, the Carrietown-type, and the non Carrietown-type. The Carrietown-type ores are isotopically different from their host granites and are characterized by low uranogenic lead isotope ratios (206Pb/204Pb and 207Pb/ 204Pb) and variable thorogenic lead isotope ratios (208Pb/ 204Pb) typical of lower crustal rocks. The non Carrietown-type ores are similar to host granites and are more radiogenic in their uranogenic lead isotope ratios when compared to the Carrietown-type ores. The differences in the lead isotope compositions of the igneous group ores are attributed to two different phases of magmatic activity. The magmatic phase exposed on the surface involved melting of shallow crustal Precambrian crystalline rocks as well as mid/lower crustal rocks while the underlying phase was derived by melting of mid/lower crustal rocks only. Igneous group ores have both light and heavy sulfur associated with them and it is a function of interaction of hydrothermal fluids with Paleozoic sedimentary rocks. ^ Paleozoic sedimentary rocks and Precambrian basement rocks are the sources of radiogenic lead, and the granites are the sources of light sulfur. Heavy sulfur comes almost entirely from Paleozoic sedimentary rocks. ^

Assessing the sources, quantities, and trends on human waste contamination along protected south Florida ecosystem: A chemical tracer based study

The common occurrence of human derived contaminants like pharmaceuticals, steroids and hormones in surface waters has raised the awareness of the role played by the release of treated or untreated sewage in the water quality along sensitive coastal ecosystems. South Florida is home to many important protected environments ranging from wetlands to coral reefs which are in close proximity to large metropolitan cities. Since large portions of South Florida and most of the Florida Keys population are not served by modern sewage treatment plants and rely heavily on the use of inefficient septic systems; a comprehensive survey of selected human waste contamination markers is needed in these areas to assess water quality with respect to non-traditional micro-constituents. ^ This study reports the development and application of new sensitive and selective analytical methods for the fast screening of multiple wastewater tracers, classified as Emergent Pollutants of Concern (EPOC). Novel methods for the trace analysis of non-traditional markers of human-specific contamination such as aminopropanone were developed and used to assess the potential of non-traditional markers as wastewater tracers. ^ During our investigation, surface water samples collected from near shore environments along the South Florida were analyzed for fifteen hormones and steroids, and five commonly detected pharmaceuticals. The compounds most frequently detected were: coprostanol, cholesterol, estrone, β-estradiol, caffeine, triclosan and DEET. Concentrations of caffeine, bisphenol A and DEET were usually higher and more prevalent than the hormonal steroids. In general, it was found that common pharmaceuticals and steroids are widely present in major coastal environments in South Florida. It is also evident that aquatic bodies in heavily urbanized sectors such as the Miami River and Key Largo Harbor contain higher concentrations of several compounds while relatively open bay waters and agricultural areas show reduced chemical signatures. Concentrations of hormones in the Little Venice area of Marathon Key were above the Lowest Observable Effect Levels (LOELs) for several species, indicating that biological resources in this area are at risk. Water quality issues in some of these coastal water environments go beyond eutrophication, thus EPOC should be the target goal for future mitigation projects. ^

Turkey and neo-Ottomanism: Domestic sources, dynamics and foreign policy

This study examined the relationship between the Turkish Islamic movements and the present government of the Justice and Development Party ( Adalet ve Kalkinma Partisi, AK Party). Since the AK Party came to power in 2002 it implemented unparalleled political reforms and pursued to improve Turkey’s relations with the EU. Opponents argued that because of the dominance of the secular military in Turkish politics, the AK Party is forced to secretly advance its Islamic agenda using the language and symbolism of democracy and human rights. This study argued that the ideas of the AK Party show similarities with the “Ottomanist” thought of the late Ottoman era. With special reference to the preservation of the Ottoman State, Ottomanism in an eclectic way was able to incorporate Islamic principles like freedom, justice and consultation into the political arena which was increasingly dominated by the secular European concepts. Literature on Islam and politics in Turkey, however, disregards the Ottoman roots of freedom and pluralism and tends to reduce the relationship between religion and state into exclusively confrontational struggles. This conceptualization of the political process relies on particular non-Turkish Muslim experiences which do not necessarily represent Islam’s venture in Turkey. Contrary to the prevailing scholarship, Islamic movements in Turkey, namely, Naqshbandi, National View and Nur, which are discussed in detail in this study, are not monolithic. They all uphold the same creedal tenets of Islam but they have sharp differences in terms of how they conceptualize the role of religious agency in politics. I argue that this diversity is a result of three distinct methodologies of Islamic religious life which are the Tariqah (Tarikat ), Shariah (Şeriat), and Haqiqah ( Hakikat). The differences between these three approaches represent a typological hierarchy in the formation of the Muslim/believer as an agent of Islamic identity. Through these different if not conflicting modes, the AK Party reconnected itself with Turkey’s Ottoman heritage in a post-Ottoman, secular setting and was able to develop an eclectic political identity of Neo-Ottomanism that is evident in the flexibility if not inconsistency of its domestic and foreign policy preferences.

Tropical seagrass-associated macroalgae distributions and trends relative to water quality

Tropical coastal marine ecosystems including mangroves, seagrass beds and coral reef communities are undergoing intense degradation in response to natural and human disturbances, therefore, understanding the causes and mechanisms present challenges for scientist and managers. In order to protect our marine resources, determining the effects of nutrient loads on these coastal systems has become a key management goal. Data from monitoring programs were used to detect trends of macroalgae abundances and develop correlations with nutrient availability, as well as forecast potential responses of the communities monitored. Using eight years of data (1996–2003) from complementary but independent monitoring programs in seagrass beds and water quality of the Florida Keys National Marine Sanctuary (FKNMS), we: (1) described the distribution and abundance of macroalgae groups; (2) analyzed the status and spatiotemporal trends of macroalgae groups; and (3) explored the connection between water quality and the macroalgae distribution in the FKNMS. In the seagrass beds of the FKNMS calcareous green algae were the dominant macroalgae group followed by the red group; brown and calcareous red algae were present but in lower abundance. Spatiotemporal patterns of the macroalgae groups were analyzed with a non-linear regression model of the abundance data. For the period of record, all macroalgae groups increased in abundance (Abi) at most sites, with calcareous green algae increasing the most. Calcareous green algae and red algae exhibited seasonal pattern with peak abundances (Φi) mainly in summer for calcareous green and mainly in winter for red. Macroalgae Abi and long-term trend (mi) were correlated in a distinctive way with water quality parameters. Both the Abi and mi of calcareous green algae had positive correlations with NO3−, NO2−, total nitrogen (TN) and total organic carbon (TOC). Red algae Abi had a positive correlation with NO2−, TN, total phosphorus and TOC, and the mi in red algae was positively correlated with N:P. In contrast brown and calcareous red algae Abi had negative correlations with N:P. These results suggest that calcareous green algae and red algae are responding mainly to increases in N availability, a process that is happening in inshore sites. A combination of spatially variable factors such as local current patterns, nutrient sources, and habitat characteristics result in a complex array of the macroalgae community in the seagrass beds of the FKNMS.

Multiple predator effects and native prey responses to two non-native Everglades cichlids

Non-native predators may have negative impacts on native communities, and these effects may be dependent on interactions among multiple non-native predators. Sequential invasions by predators can enhance risk for native prey. Prey have a limited ability to respond to multiple threats since appropriate responses may conflict, and interactions with recent invaders may be novel. We examined predator–prey interactions among two non-native predators, a recent invader, the African jewelfish, and the longer-established Mayan cichlid, and a native Florida Everglades prey assemblage. Using field enclosures and laboratory aquaria, we compared predatory effects and antipredator responses across five prey taxa. Total predation rates were higher for Mayan cichlids, which also targeted more prey types. The cichlid invaders had similar microhabitat use, but varied in foraging styles, with African jewelfish being more active. The three prey species that experienced predation were those that overlapped in habitat use with predators. Flagfish were consumed by both predators, while riverine grass shrimp and bluefin killifish were eaten only by Mayan cichlids. In mixed predator treatments, we saw no evidence of emergent effects, since interactions between the two cichlid predators were low. Prey responded to predator threats by altering activity but not vertical distribution. Results suggest that prey vulnerability is affected by activity and habitat domain overlap with predators and may be lower to newly invading predators, perhaps due to novelty in the interaction.

Determination of signature volatile odor chemicals emanating from novel biological specimens by non-invasive analytical techniques for the potential use in forensic identifications

Human scent, or the volatile organic compounds (VOCs) produced by an individual, has been recognized as a biometric measurement because of the distinct variations in both the presence and abundance of these VOCs between individuals. In forensic science, human scent has been used as a form of associative evidence by linking a suspect to a scene/object through the use of human scent discriminating canines. The scent most often collected and used with these specially trained canines is from the hands because a majority of the evidence collected is likely to have been handled by the suspect. However, the scents from other biological specimens, especially those that are likely to be present at scenes of violent crimes, have yet to be explored. Hair, fingernails and saliva are examples of these types of specimens. ^ In this work, a headspace solid phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) technique was used for the identification of VOCs from hand odor, hair, fingernails and saliva. Sixty individuals were sampled and the profiles of the extracted VOCs were evaluated to assess whether they could be used for distinguishing individuals. Preliminary analysis of the biological specimens collected from an individual (intra-subject) showed that, though these materials have some VOCs in common, their overall chemical profile is different for each specimen type. Pair-wise comparisons, using Spearman Rank correlations, were made between the chemical profiles obtained from each subject, per a specimen type. Greater than 98.8% of the collected samples were distinguished from the subjects for all of the specimen types, demonstrating that these specimens can be used for distinguishing individuals. ^ Additionally, field trials were performed to determine the utility of these specimens as scent sources for human scent discriminating canines. Three trials were conducted to evaluate hair, fingernails and saliva in comparison to hand odor, which was considered the standard source of human odor. It was revealed that canines perform similarly to these alternative human scent sources as they do to hand odor implying that, though there are differences in the chemical profiles released by these specimens, they can still be used for the discrimination of individuals by trained canines.^