Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion.

Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have recently expanded in the space of thousands of years, rather than the millions of years as previously thought, a finding that dramatically changes our understanding of this pathogen's history. Finally, at a time when almost every pathogen is becoming increasingly resistant to antimicrobials, we show that there is no evidence of circulating genomic resistance in C. trachomatis

Post-transcriptional modifications in the small subunit ribosomal RNA from Thermotoga maritima, including presence of a novel modified cytidine

Post-transcriptional modifications of RNA are nearly ubiquitous in the principal RNAs involved in translation. However, in the case of rRNA the functional roles of modification are far less established than for tRNA, and are subject to less knowledge in terms of specific nucleoside identities and their sequence locations. Post-transcriptional modifications have been studied in the SSU rRNA from Thermotoga maritima (optimal growth 80°C), one of the most deeply branched organisms in the Eubacterial phylogenetic tree. A total of 10 different modified nucleosides were found, the greatest number reported for bacterial SSU rRNA, occupying a net of ∼14 sequence sites, compared with a similar number of sites recently reported for Thermus thermophilus and 11 for Escherichia coli. The relatively large number of modifications in Thermotoga offers modest support for the notion that thermophile rRNAs are more extensively modified than those from mesophiles. Seven of the Thermotoga modified sites are identical (location and identity) to those in E. coli. An unusual derivative of cytidine was found, designated N-330 (M (r) 330.117), and was sequenced to position 1404 in the decoding region of the rRNA. It was unexpectedly found to be identical to an earlier reported nucleoside of unknown structure at the same location in the SSU RNA of the archaeal mesophile Haloferax volcanii

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.

The use of whole-genome sequencing as a tool for the study of infectious bacteria is of growing clinical interest. Chlamydia trachomatis is responsible for sexually transmitted infections and the blinding disease trachoma, which affect hundreds of millions of people worldwide. Recombination is widespread within the genome of C. trachomatis, thus whole-genome sequencing is necessary to understand the evolution, diversity, and epidemiology of this pathogen. Culture of C. trachomatis has, until now, been a prerequisite to obtain DNA for whole-genome sequencing; however, as C. trachomatis is an obligate intracellular pathogen, this procedure is technically demanding and time consuming. Discarded clinical samples represent a large resource for sequencing the genomes of pathogens, yet clinical swabs frequently contain very low levels of C. trachomatis DNA and large amounts of contaminating microbial and human DNA. To determine whether it is possible to obtain whole-genome sequences from bacteria without the need for culture, we have devised an approach that combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification. Using IMS-MDA in conjunction with high-throughput multiplexed Illumina sequencing, we have produced the first whole bacterial genome sequences direct from clinical samples. We also show that this method can be used to generate genome data from nonviable archived samples. This method will prove a useful tool in answering questions relating to the biology of many difficult-to-culture or fastidious bacteria of clinical concern

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

The use of whole-genome sequencing as a tool for the study of infectious bacteria is of growing clinical interest. Chlamydia trachomatis is responsible for sexually transmitted infections and the blinding disease trachoma, which affect hundreds of millions of people worldwide. Recombination is widespread within the genome of C. trachomatis, thus whole-genome sequencing is necessary to understand the evolution, diversity, and epidemiology of this pathogen. Culture of C. trachomatis has, until now, been a prerequisite to obtain DNA for whole-genome sequencing; however, as C. trachomatis is an obligate intracellular pathogen, this procedure is technically demanding and time consuming. Discarded clinical samples represent a large resource for sequencing the genomes of pathogens, yet clinical swabs frequently contain very low levels of C. trachomatis DNA and large amounts of contaminating microbial and human DNA. To determine whether it is possible to obtain whole-genome sequences from bacteria without the need for culture, we have devised an approach that combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification. Using IMS-MDA in conjunction with high-throughput multiplexed Illumina sequencing, we have produced the first whole bacterial genome sequences direct from clinical samples. We also show that this method can be used to generate genome data from nonviable archived samples. This method will prove a useful tool in answering questions relating to the biology of many difficult-to-culture or fastidious bacteria of clinical concern

The Brain-Dead Organ Donor

Addressing all aspects of brain death and thoroughly detailing how a potential organ donor should be maintained to ensure maximum use of the organs and cells, The Brain-Dead Organ Donor: Pathophysiology and Management is a landmark addition to the literature. This first-of-its-kind, multidisciplinary volume will be of interest to a large section of the medical community. The first section of the book reviews the historical, medical, legal, and ethical aspects of brain death. That is followed by two chapters on the pathophysiology of brain death as investigated in small and large animal models. This includes a review of the many hormonal changes, including the neuroendocrine- adrenergic ‘storm’, that takes place during and following the induction of brain death, and how they impact metabolism. The next section of the book reviews various effects of brain death, namely its impact on thyroid function, the inflammatory response that develops, and those relating to innate immunity. The chapters relating to assessment and management of potential organ donors will be of interest to a very large group of transplant surgeons and physicians as well as critical care and neurocritical care physicians and nurses. Neurologists, endocrinologists, neurosurgeons, and pathologists will also be interested, especially in the more basic science sections on various aspects of brain-death and hormonal therapy. Organ procurement organizations and transplant coordinators worldwide will also be interested in this title. Other chapters will be of interest to medical historians, medico-legal experts, and ethicists.CONTENIDO: Introduction, Dimitri Novitzky, David K. C. Cooper, Pages 1-6 -- Historical Aspects of the Diagnosis of Death, Félix Bacigalupo, Daniela A. Huerta Fernández, Pages 7-11 -- The Determination of Brain Death, Curtis M. Keller, Boris Chulpayev, Michael Hoffmann, Pages 13-19 -- Legal Aspects of Brain Death and Organ Donorship, Ricky T. Munoz, Mark D. Fox, Pages 21-35 -- Ethical Issues in Organ Donation from Brain-Dead Donors, Mark D. Fox, Ricky T. Munoz, Pages 37-53 -- Pathophysiology of Brain Death in Small Animal Models, Bernhard Floerchinger, Nicholas L. Tilney, Stefan G. Tullius, Pages 55-64 -- Pathophysiology of Brain Death and Effects of Hormonal Therapy in Large Animal Models, Dimitri Novitzky, Winston N. Wicomb, David K. C. Cooper, Pages 65-90 -- The Efficacy of Thyroid Hormone Therapy in Brain-Dead Heart Donors: A Review of Thyroid Function in Health and Disease, Lawrence E. Shapiro, Tatiana Baron, Pages 91-105 -- The Inflammatory Response to Brain Death, Anne Barklin, Christine Lodberg Hvas, Else Toennesen, Pages 107-119 -- The Influence of Brain Death and Intensive Care Management on Donor Organs: Assessment of Inflammatory Markers, Wayel Jassem, Susan V. Fuggle, Pages 121-129 -- Brain Death-Induced Inflammation: Possible Role of the Cholinergic Anti-inflammatory Pathway, Simone Hoeger, Benito A. Yard, Pages 131-138 -- Innate Immunity and Injury During Brain Death: Opportunities for Intervention, Marc A. Seelen, Henri G. D. Leuvenink, Rutger J. Ploeg, Pages 139-145 -- Selection of the Brain-Dead Potential Organ Donor, Kadiyala V. Ravindra, Keri E. Lunsford, Paul C. Kuo, Pages 147-154 -- Infectious Disease Aspects of the Brain-Dead Potential Organ Donor, Nicole M. Theodoropoulos, Michael G. Ison, Pages 155-176 -- Malignancy in the Brain-Dead Organ Donor, Michael A. Nalesnik, Ron Shapiro, Michael G. Ison, Pages 177-189 -- Early Clinical Experience of Hormonal Therapy in the Brain-Dead Potential Organ Donor, Dimitri Novitzky, Burcin Ekser, David K. C. Cooper, Pages 191-207 -- Assessment, Monitoring, and Management of Brain-Dead Potential Organ Donors in the USA, Demetrios Demetriades, Lydia Lam, Pages 209-216 -- Assessment, Monitoring, and Management of Brain-Dead Potential Organ Donors in Europe, Gabriel J. Echeverri, Bruno G. Gridelli, Pages 217-235 -- Assessment, Monitoring, and Management of Brain-Dead Potential Organ Donors in Australia, Peter S. Macdonald, Anders E. M. Aneman, Deepak Bhonagiri, Daryl A. Jones, Gerry O’Callaghan, Helen I. Opdam et al., Pages 237-249 -- Management of the Brain-Dead Organ Donor: Perspectives of the Transplant Coordinator, Nicole T. Farina, David K. C. Cooper, Pages 251-261 -- Surgical Aspects of Thoracic and Abdominal Organ Procurement from Brain-Dead Donors, Michael J. Anstadt, Paul C. Kuo, Kadiyala V. Ravindra, Pages 263-281 -- Impact of Brain Death on Storage of the Heart, Winston N. Wicomb, David K. C. Cooper, Pages 283-288 -- Impact of Brain Death on Abdominal Organs and Allograft Preservation Strategies, Coney Bae, Anthony Watkins, Scot D. Henry, James V. Guarrera, Pages 289-298 -- Functional Repair of Brain Death-Induced Injury, Henri G. D. Leuvenink, Marc A. Seelen, Rutger J. Ploeg, Pages 299-310 -- Functional Repair of Brain Death-Injured Donor Lungs, Jonathan C. Yeung, Marcelo Cypel, Shaf Keshavjee, Pages 311-320 -- Thyroid Hormone Therapy to the Recipient of a Heart from a Brain-Dead Donor, Dimitri Novitzky, David K. C. Cooper, Pages 321-331 -- Current and Potential Future Trends in the Management of the Brain-Dead Organ Donor, Octavio E. Pajaro, James K. Kirklin, Pages 333-341 -- Maximizing Utilization of the Potential Deceased Donor: The Challenge Continues,Eliezer Katz,Pages 343-35

Ventral Striatal Noradrenergic Mechanisms Contribute to Sensorimotor Gating Deficits Induced by Amphetamine

The psychotomimetic drug -amphetamine (AMPH), disrupts prepulse inhibition (PPI) of the startle response, an operational measure of sensorimotor gating that is deficient in schizophrenia patients. Historically, this effect has been attributed to dopaminergic substrates; however, AMPH also increases norepinephrine (NE) levels, and enhancement of central NE transmission has been shown recently to disrupt PPI. This study examined the extent to which NE might participate in AMPH-induced disruptions of PPI and increases in locomotor activity, another classic behavioral effect of AMPH, by determining whether antagonism of postsynaptic NE receptors blocked these effects. Separate groups of male Sprague–Dawley rats received either the α1 receptor antagonist, prazosin (0, 0.3, 1 mg/kg), or the β receptor antagonist timolol (0, 3, 10 mg/kg) before administration of AMPH (0 or 1 mg/kg) before testing for PPI or locomotor activity. As an initial exploration of the anatomical substrates underlying possible α1 receptor-mediated effects on AMPH-induced PPI deficits, the α1 receptor antagonist terazosin (0 or 40 μg/0.5 μl) was microinfused into the nucleus accumbens shell (NAccSh) in conjunction with systemic AMPH administration before startle testing in a separate experiment. Prazosin, but not timolol, blocked AMPH-induced hyperactivity; both drugs reversed AMPH-induced PPI deficits without altering baseline startle responses. Interestingly, AMPH-induced PPI deficits also were partially blocked by terazosin in NAccSh. Thus, behavioral sequelae of AMPH (PPI disruption and hyperactivity) may be mediated in part by NE receptors, with α1 receptors in NAccSh possibly having an important role in the sensorimotor gating deficits induced by this psychotomimetic drug