Computational discovery of antibiotic resistance genes and their horizontal transfer

Antibiotic resistance is increasing among clinical infections and represents one of the most serious threats to public health. Pathogens often become resistant by acquiring mobile antibiotic resistance genes (ARGs) via horizontal gene transfer (HGT). To limit the spread of new ARGs, it is important that we identify emerging threats early, and that we improve our understanding of what drives the HGT of ARGs. The three papers encompassing this thesis aim to increase our knowledge about ARGs and their mobility. In paper I, computational screening of large genomic datasets was used to identify new resistance genes for macrolide antibiotics, and to clarify their evolution. A large diversity of new erm and mph genes was identified, including six new families of mobile ARGs carried by pathogens, that showed varied phylogenetic origins. Of the tested genes, 70% induced resistance in Escherichia coli. In paper II, we identified previously undiscovered mobile genes giving resistance to aminoglycoside antibiotics in pathogens, further demonstrating how computational methods can discover potential emerging ARGs. Close to one million bacterial genomes were screened for aac and aph genes, and the mobility of each predicted gene was evaluated. A total of 50 families of new mobile ARGs were identified in pathogens. When new ARGs were tested in E. coli. 86% were functional, with 39% giving clinical resistance. In paper III, the factors influencing the HGT of ARGs were investigated. Phylogenetic analysis was used to identify HGT events from a large set of ARGs. For each event, the genetic compatibility of the involved gene(s) and genomes, as well as the co-occurrence of donor and recipient in different environments, were computed and used as input to train random forest classifiers. The resulting models suggested that the most important factor for determining if a mobile ARG successfully undergoes horizontal transfer is the genetic compatibility between the gene and the recipient genome. The findings presented in this thesis increase our knowledge about new genes giving resistance to two important classes of antibiotics. Furthermore, the results provide new insights into the horizontal transfer of resistance genes

Gulf Stream temperature, salinity and transport during the last millennium

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February, 2006Benthic and planktonic foraminiferal δ18O (δ18Oc) from a suite of well-dated, high-resolution cores spanning the depth and width of the Straits of Florida reveal significant changes in Gulf Stream cross-current density gradient during the last millennium. These data imply that Gulf Stream transport during the Little Ice Age (LIA: 1200-1850 A.D.) was 2-3 Sv lower than today. The timing of reduced flow is consistent with cold conditions in Northern Hemisphere paleoclimate archives, implicating Gulf Stream heat transport in centennial-scale climate variability of the last 1,000 years. The pattern of flow anomalies with depth suggests reduced LIA transport was due to weaker subtropical gyre wind stress curl. The oxygen isotopic composition of Florida Current surface water (δ18O w) near Dry Tortugas increased 0.4% during the course of the Little Ice Age (LIA: ~1200-1850 A.D.), equivalent to a salinity increase of 0.8-1.5 psu. On the Great Bahama Bank, where smface waters are influenced by the North Atlantic subtropical gyre, δ18Ow increased by 0.3% during the last 200 years. Although a portion (~0.1%) of this shift may be an artifact of anthropogenically-driven changes in surface water ΣCO2, the remaining δl8Ow signal implies a 0.4 to 1 psu increase in salinity after 200 yr BP. The simplest explanation of the δ18Ow data is southward migration of the Atlantic Hadley circulation during the LIA. Scaling of the δ18Ow records to salinity using the modern low-latitude δ18Ow-S slope produces an unrealistic reversal in the salinity gradient between the two sites. Only if C180 w is scaled to salinity using a high-latitude δ18Ow-S slope can the records be reconciled. Changes in atmospheric 14C paralleled shifts in Dry Tortugas δ18Ow , suggesting that variable solar irradiance paced centennial-scale Hadley cell migration and changes in Florida Current salinity during the last millennium.I would also like to thank the National Science Foundation (NSF grant OCE-0096469) and WHOI Academic Programs for supporting this work

Priorities vs. Reality: A Task Analysis of Secondary School Principals in the State of Minnesota

Abstract “The principal’s role in delivering quality education has long been recognized as an important organizational characteristic of schools. How principals should perform their roles, however, has been the subject of debate” (Smith & Andrews, 1989, p. 21). Since the inception of the principalship, the role of the principal has encompassed all operations of their school. During the early 1900s principals were primarily managers of facilities. Principals were predominately male teachers who performed clerical administrative duties such as the school schedule, length of year, facility management etc. (Kafka, 2009). As the role of education in our society has grown, so has the principalship. Each decade has brought changes to public schools as the needs of society have changed. Schools grow and change, and at the head of each school is a principal who is responsible for this growth and change (Goodwin, Cunningham, & Eagle, 2005). During the 1950s and 1960s, our country went through turbulent times in the arenas of social change and global competition. Schools became the focus of change in order to help solve the inequities in society and to help us compete scientifically and economically on the world stage. By the 1970s, our educational systems ranking on the world stage started to suffer. Principals were directed to focus on instructional leadership in order to better prepare our students to compete globally. Rigorous education of children was prioritized as a means for America to better compete in the global society (Drake & Roe, 1994). “His cardinal function is the improvement of instruction, which will enhance the learning experiences of his students” (Melton, 1970, p. 2). Society has seen major changes over the past 100 years, socially and scientifically. Technology is now part of our schools and everyday experience. As society has evolved, so has public education and the role of the public school principal. Duties have been added to the principalship, nothing has been deleted. The management issues of previous decades still exist and the instructional leadership duties continue be expanded upon. With all the responsibilities of today’s principalship, what are the most important functions for principals to perform? There is continuous conflict within the definition of the principalship as instructional leader or building manager or both (Portin & Jianping, 1999). “The historical conflict between the instructional leadership role and managerial aspects of the principalship has had a major impact on the entire profession” (Richardson, 1991, p. 9). The purpose of this study is to determine those leadership tasks that consume the majority of Minnesota secondary school principals’ time. The study will examine Minnesota secondary school principals’ perceptions of those tasks they believe should consume the majority of their time. These perceptions will be compared to Minnesota secondary school principals’ reported time on job-related tasks. The study will ascertain whether or not Minnesota secondary school principals’ perceived priority tasks match actual time on task and if they spend more time providing instructional leadership or managerial leadership

Philosophia ancillans, hoc est processus pie philosophandi, ex suffragio atq[ue] indultu ampl: collegii philosoph. In inclyta almâ Aboensi, directore ... dn. m. Davide Lund, poeseos prof: regio ord. Pro gradu magisterii in philosophia indipiscendo, sobriis, sobriè propositu ab Henningo Fuldha, Tavastens: In auditorio maximo, die 16. Maji horisq[ue] svetis anni 1691.

Invokaatio: I.N.J.Dedikaatio: Johannes Gezelius, Jacobus Flachsenius.Gratulaatio: David Lund, Ericus Tammelinus.Painovuosi nimekkeestä.Arkit: 4 arkintunnuksetonta lehteä, A-D4

Florida Current surface temperature and salinity variability during the last millennium

Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography, 21 (2006): PA2009, doi:10.1029/2005PA001218.The salinity and temperature of the Florida Current are key parameters affecting the transport of heat into the North Atlantic, yet little is known about their variability on centennial time scales. Here we report replicated, high-resolution foraminiferal records of Florida Current surface hydrography for the last millennium from two coring sites, Dry Tortugas and the Great Bahama Bank. The oxygen isotopic composition of Florida Current surface water (δ18Ow) near Dry Tortugas increased 0.4‰ during the course of the Little Ice Age (LIA: ~1200-1850 A. D.), equivalent to a salinity increase of 0.8-1.5 psu. On the Great Bahama Bank, where surface waters are influenced by the North Atlantic subtropical gyre, δ18Ow increased by 0.3‰ during the last 200 years. Although a portion (~0.1‰) of this shift may be an artifact of anthropogenically-driven changes in surface water ΣCO2, the remaining δ18Ow signal implies a 0.4 to 1 psu increase in salinity after 200 yr BP. The simplest explanation of the δ18Ow data is southward migration of the Atlantic Hadley circulation during the LIA. Scaling of the δ18Ow records to salinity using the modern low-latitude δ18Ow-S slope produces an unrealistic reversal in the salinity gradient between the two sites. Only if δ18Ow is scaled to salinity using a high-latitude δ18Ow-S slope can the records be reconciled. Changes in atmospheric 14C paralleled shifts in Dry Tortugas δ18Ow, suggesting that variable solar irradiance paced centennialscale ITCZ migration and changes in Florida Current salinity during the last millennium.This work was supported by NSF grant OCE-0096469

The Ambivalence of Connexin43 Gap Peptides in Cardioprotection of the Isolated Heart against Ischemic Injury

The present study investigates infarct-reducing effects of blocking ischemia-induced opening of connexin43 hemichannels using peptides Gap19, Gap26 or Gap27. Cardioprotection by ischemic preconditioning (IPC) and Gap peptides was compared, and combined treatment was tested in isolated, perfused male rat hearts using function and infarct size after global ischemia, high-resolution respirometry of isolated mitochondrial and peptide binding kinetics as endpoints. The Gap peptides reduced infarct size significantly when given prior to ischemia plus at reperfusion (Gap19 76.2 ± 2.7, Gap26 72.9 ± 5.8 and Gap27 71.9 ± 5.8% of untreated control infarcts, mean ± SEM). Cardioprotection was lost when Gap26, but not Gap27 or Gap19, was combined with triggering IPC (IPC 73.4 ± 5.5, Gap19-IPC 60.9 ± 5.1, Gap26-IPC 109.6 ± 7.8, Gap27-IPC 56.3 ± 8.0% of untreated control infarct). Binding stability of peptide Gap26 to its specific extracellular loop sequence (EL2) of connexin43 was stronger than Gap27 to its corresponding loop EL1 (dissociation rate constant Kd 0.061 ± 0.004 vs. 0.0043 ± 0.0001 s−1 , mean ± SD). Mitochondria from IPC hearts showed slightly but significantly reduced respiratory control ratio (RCR). In vitro addition of Gap peptides did not significantly alter respiration. If transient hemichannel activity is part of the IPC triggering event, inhibition of IPC triggering stimuli might limit the use of cardioprotective Gap peptides