Bacteriophages of marine Roseobacter

The oceans cover ca. 70% of the Earth’s surface and due to their depth encompass around 300 times the habitable volume of the terrestrial environment. The exact proportion of life on Earth that exists in the oceans is unknown as many ocean species remain undiscovered; in particular this holds true for the viruses that infect marine bacterioplankton. It is currently thought that viruses that infect bacteria, bacteriophages or phages, can numerically exceed their hosts by a factor of ten, however, this abundant and diverse group of organisms is still poorly understood. This is especially true of phages that infect members of the Roseobacter clade. Globally, members of the Roseobacter lineage can comprise up to a quarter of the marine microbial community and often dominate the alga-associated bacterial community. In this study phages capable of infecting species of Roseobacter were isolated and characterised. Two Roseovarius-specific phages, RLP1 and RPP1, were isolated from UK coastal waters; morphological and sequence data identified them as belonging to the N4-like genus of Podoviridae. Comparative genomic analysis of both Roseovarius phages to other N4-like phages such as Escherichia coli phage N4 and Sulfitobacter sp. EE-36 phage EE36Φ1, revealed a number of conserved core genes involved in DNA metabolism, transcription control and virion structure. Comparison of N4-like Roseobacter phages (RLP1, RPP1, EE36Φ1 and Ruegeria pomeroyi DSS-3 phage DSS3Φ2) also revealed a number of peripheral genes which are likely to interact directly with host proteins/machinery specific to the Roseobacter group. Unusually, both RLP1 and RPP1 appeared to only infect host cells when in semi-solid agar matrix, but not in liquid culture. Comparison of the outer surface of agar-embedded and planktonic cells revealed different outer-membrane protein and lipopolysaccharide expression profiles. This suggests that some Roseobacter species (spp.) change components of their bacterial cell surface according to their physiological state: agar-embedded/sessile or planktonic and RLP1 and RPP1 exploit this by binding to (a) receptor(s) only expressed during sessile conditions. A number of prophage-like elements were also induced from three Roseobacter spp. by exposure of growing cultures to the DNA-damaging chemical Mitomycin C. These were identified by electron microscopy as belonging to the Siphoviridae family. The results of this project suggest that within the marine environment there remain many uncharacterised phages with peculiar biochemical properties and a wealth of genomic information

Managing Pharmacotherapy in People Living With HIV and Concomitant Malignancy.

Objective: To describe data with selected malignancies in people living with HIV (PLWH) and HIV in individuals affected by both conditions and to summarize drug-drug interactions (DDIs) with clinical recommendations for point-of-care review of combination therapies. Data Sources: Literature searches were performed (2005 to December 2018) in MEDLINE and EMBASE to identify studies of malignancies in PLWH in the modern era. Study Selection and Data Extraction: Article bibliographies and drug interaction databases were reviewed. Search terms included HIV, antiretroviral therapy, antineoplastic agents, malignancies, and drug interactions. Data Synthesis: In the pre-antiretroviral therapy (ART) era, malignancies in PLWH were AIDS-defining illnesses, and life expectancy was shorter. Nowadays, PLWH are living longer and developing malignancies, including lung, anal, and prostate cancers. Concurrently, the oncology landscape has evolved, with novel oral targeted agents and immunotherapies becoming routine elements of care. The increased need for and complexity with antineoplastics in PLWH has led to recommendations for multidisciplinary care of this unique population. Evaluation of DDIs requires review of metabolic pathways, absorption mechanisms, and various drug transporters associated with antineoplastics and ART. Relevance to Patient Care and Clinical Practice: This review summarizes available data of non-AIDS-defining malignancies, principles of HIV care in the patient with malignancy, and guidance for assessing DDIs between antineoplastics and ART. Summary DDI tables provide point-of-care recommendations. Conclusions: The availability of ART has transformed AIDS into a chronic medical condition, and PLWH are experiencing age-related malignancies. Pharmacists play an important role in the management of this patient population

Defining bacterial species in the genomic era : insights from the genus Acinetobacter

Background: Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data. Results: In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species. Conclusion: We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin’s vision of classification becoming, as far as is possible, genealogical

Reinforcement of Shear Thinning Protein Hydrogels by Responsive Block Copolymer Self-Assembly

Shear thinning hydrogels are promising materials that exhibit rapid self-healing following the cessation of shear, making them attractive for applications including injectable biomaterials. Here, self-assembly is demonstrated as a strategy to introduce a reinforcing network within shear thinning artificially engineered protein gels, enabling a responsive transition from an injectable state at low temperatures with a low yield stress to a stiffened state at physiological temperatures with resistance to shear thinning, higher toughness, and reduced erosion rates and creep compliance. Protein-polymer triblock copolymers capable of the responsive self-assembly of two orthogonal networks are synthesized. Midblock association forms a shear-thinning network, while endblock aggregation at elevated temperatures introduces a second, independent physical network into the protein hydrogel. These reversible crosslinks introduce extremely long relaxation times and lead to a five-fold increase in the elastic modulus, significantly larger than is expected from transient network theory. Thermoresponsive reinforcement reduces the high temperature creep compliance by over four orders of magnitude, decreases the erosion rate by at least a factor of five, and increases the yield stress by up to a factor of seven. Combined with the demonstrated potential of shear thinning artificial protein hydrogels for various uses, this reinforcement mechanism broadens the range of applications that can be addressed with shear-thinning physical gels

Analysing Causal Complexities in IT Business Value Research

In the study of IT business value (ITBV), the notion of complementarities has been used to explain why firms with similar level of IT investments have received varying level of returns. Complementarities suggest that greater business value can be derived when IT investment is accompanied by other complementary organizational investments. This paper introduces a novel analytical approach called fuzzy set Qualitative Comparative Analysis (fsQCA). The method is based on principles of comparison used in the field of social and political science, and can be applied to explain the complex causality of IT business value. We have found that fsQCA was able to show that organizational factors in complex configurations may play different roles as core and periphery factors in affecting organizational performance. Such organizational practices have often been overlooked in many empirical studies but can play a non-trivial role in the organizational processes

Teachers, policymakers and project learning: The questionable use of ‘hard’ and ‘soft’ policy instruments to influence the implementation of curriculum reform in Hong Kong

Following the return of Hong Kong to Chinese sovereignty in 1997, the government of the Hong Kong Special Administrative Region developed wide-ranging curriculum reforms, including project learning. A recent survey has indicated that over 80% of Hong Kong primary and secondary schools have adopted project learning as a curriculum task. Such an outcome is hard to reconcile both with the culture of Hong Kong schools and the generally bleak picture that pervades the literature on educational change. In seeking an explanation for this apparent success we focus attention on the policy instruments that were used by government agencies to facilitate the process of implementation. Our analysis revealed that teachers were caught in a pincer movement that involved voluntary activities promoting project learning and coercive measures that monitored and evaluated successful implementation. Teachers’ views of these policy instruments differed markedly from those of policymakers. This confluence of mixed approaches, while apparently successful, is also shown to be problematic. Finally, the paper is located in a theoretical framework with its origins in recent policy theory that to date has not been applied to educational contexts

Transition in Occupations of Refugees During Resettlement

Purpose: In 2016, there were 22.5 million refugees worldwide (UNHCR, 2017). California resettled just over 5,000 of those 85,000 (Igielnik & Krogstad, 2017). Limited research has been conducted in the United States (U.S.) focusing on the refugee experience; furthermore, there is a significant gap in research regarding the impact of the refugee experience on the occupations of refugees as they transition to living in the U.S. Smith (2012) explored the adaptation of cultural weaving among Karen refugees to maintain their previous occupations and the impact of daily weaving on their lives within Western culture; however, the study focused only on work occupations. This study sought to capture the experience of refugees and the impact of their transition on a broad array of occupations. Adding to occupational science literature regarding the occupational impact of the refugee experience, as well as aiding in addressing issues of occupational justice (Townsend, & Wilcock, 2004). Methods: This research was a qualitative-descriptive, phenomenological study. Data was collected through semi-structured interviews. Questions were guided by Person-Environment-Occupation model (Law, et al., 1996) and Transitions Theory (Blair, 2000), to address personal and cultural values, environments where occupations are performed, and occupational patterns to identify changes in meaningful occupations due to the refugee process. Participants have legal status as refugees, have been in the U.S. between one and five years, resettled in Northern California, are at least 18 years old and were not required to speak English. As this study aimed to capture a broad experience of transition and limit confounding factors influencing how the participant responded to changes in occupations, participants could be of any ethnicity, country of origin, or gender. Two participants were recruited through snowball sampling. Interviews were audio taped and transcribed. Interviews were coded using Thematic Analysis to generate common themes across cases (Braun & Clarke, 2006). Rigor was strengthened through member checks and peer review. Findings: Through analysis of the interviews, the researchers found five major themes: contextual barriers, internal factors, adaptation, belonging, and transition. The first four themes form a loop and influence each other both positively and negatively and, ultimately, affect engagement in occupations. Transition is the theme that envelops and influences the whole. Using these five themes, the researchers developed the Transition-related Effects on Refugee Occupations (TERO) Model. Key findings include that refugees may experience more meaning and role change/loss in their occupations, rather than adoption of new occupations. Additionally, the researchers found social network to be important for positive occupational engagement throughout country transition. Implications: As occupational therapists, the tendency towards working with refugee populations may be to focus on their transitions to new occupations. However, data from this study indicates that it may be more pertinent to address role and meaning change/loss in current occupations

Transition in Occupations of Refugees During Resettlement

Background: Human displacement is a social problem that has occupational implications. There is a significant gap in the research focusing on the refugee experience and the impact of this experience on their occupations as they transition to living in the US. This study seeks to capture the experience of refugees and the impact of this transition to the US on a broad array of occupations. Method: This research is a qualitative study. Data was collected through semi-structured interviews with two participants who have legal status as refugees living in the US. Results: Thematic analysis generated three themes: (a) contextual barriers to occupation, (b) belonging, and (c) adaptation. Refugees experienced a variety of contextual barriers, both systemic and socio-cultural, that impacted their ability to engage in meaningful occupation leading to a lack of belonging. Refugees adapted to these barriers by adapting their occupations. In addition, the researchers found social networks to be important for positive occupational engagement throughout country transition. Conclusion: This research adds to occupational science literature regarding the occupational impact of the refugee experience, as well as supporting occupational therapists to address issues of occupational deprivation with refugee populations

Transition in Occupations of Refugees During Resettlement

Purpose: In 2016, there were 22.5 million refugees worldwide (UNHCR, 2017). California resettled just over 5,000 of those 85,000 (Igielnik & Krogstad, 2017). Limited research has been conducted in the United States (U.S.) focusing on the refugee experience; furthermore, there is a significant gap in research regarding the impact of the refugee experience on the occupations of refugees as they transition to living in the U.S. Smith (2012) explored the adaptation of cultural weaving among Karen refugees to maintain their previous occupations and the impact of daily weaving on their lives within Western culture; however, the study focused only on work occupations. This study sought to capture the experience of refugees and the impact of their transition on a broad array of occupations. Adding to occupational science literature regarding the occupational impact of the refugee experience, as well as aiding in addressing issues of occupational justice (Townsend, & Wilcock, 2004). Methods: This research was a qualitative-descriptive, phenomenological study. Data was collected through semi-structured interviews. Questions were guided by Person-Environment-Occupation model (Law, et al., 1996) and Transitions Theory (Blair, 2000), to address personal and cultural values, environments where occupations are performed, and occupational patterns to identify changes in meaningful occupations due to the refugee process. Participants have legal status as refugees, have been in the U.S. between one and five years, resettled in Northern California, are at least 18 years old and were not required to speak English. As this study aimed to capture a broad experience of transition and limit confounding factors influencing how the participant responded to changes in occupations, participants could be of any ethnicity, country of origin, or gender. Two participants were recruited through snowball sampling. Interviews were audio taped and transcribed. Interviews were coded using Thematic Analysis to generate common themes across cases (Braun & Clarke, 2006). Rigor was strengthened through member checks and peer review. Findings: Through analysis of the interviews, the researchers found five major themes: contextual barriers, internal factors, adaptation, belonging, and transition. The first four themes form a loop and influence each other both positively and negatively and, ultimately, affect engagement in occupations. Transition is the theme that envelops and influences the whole. Using these five themes, the researchers developed the Transition-related Effects on Refugee Occupations (TERO) Model. Key findings include that refugees may experience more meaning and role change/loss in their occupations, rather than adoption of new occupations. Additionally, the researchers found social network to be important for positive occupational engagement throughout country transition. Implications: As occupational therapists, the tendency towards working with refugee populations may be to focus on their transitions to new occupations. However, data from this study indicates that it may be more pertinent to address role and meaning change/loss in current occupations.https://scholar.dominican.edu/ug-student-posters/1082/thumbnail.jp

Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine

Streptococcus pneumoniae causes invasive infections, primarily at the extremes of life. A seven-valent conjugate vaccine (PCV7) is used to protect against invasive pneumococcal disease in children. Within three years of PCV7 introduction, we observed a fourfold increase in serotype 6C carriage, predominantly due to a single clone. We determined the whole-genome sequences of nineteen S. pneumoniae serotype 6C isolates, from both carriage (n = 15) and disease (n = 4) states, to investigate the emergence of serotype 6C in our population, focusing on a single multi-locus sequence type (MLST) clonal complex 395 (CC395). A phylogenetic network was constructed to identify different lineages, followed by analysis of variability in gene sets and sequences. Serotype 6C isolates from this single geographical site fell into four broad phylogenetically distinct lineages. Variation was seen in the 6C capsular locus and in sequences of genes encoding surface proteins. The largest clonal complex was characterised by the presence of lantibiotic synthesis locus. In our population, the 6C capsular locus has been introduced into multiple lineages by independent capsular switching events. However, rapid clonal expansion has occurred within a single MLST clonal complex. Worryingly, plasticity exists within current and potential vaccine-associated loci, a consideration for future vaccine use, target selection and design