The rockefeller university

Streptococcus pyogenes is a human commensal and a bacterial pathogen responsible for a wide variety of human diseases differing in symptoms, severity, and tissue tropism. The completed genome sequences of >37 strains of S. pyogenes, representing diverse disease-causing serotypes, have been published. The greatest genetic variation among these strains is attributed to numerous integrated prophage and prophage-like elements, encoding several virulence factors. A comparison of isogenic strains, differing in prophage content, would reveal the effects of these elements on streptococcal pathogenesis. However, curing strains of prophage is often difficult and sometimes unattainable. We have applied a novel counter-selection approach to identify rare S. pyogenes mutants spontaneously cured of select prophage. To accomplish this, we first inserted a two-gene cassette containing a gene for kanamycin resistance (Kan(R)) and the rpsL wild-type gene, responsible for dominant streptomycin sensitivity (Sm-S), into a targeted prophage on the chromosome of a streptomycin resistant (Sm-R) mutant of S. pyogenes strain SF370. We then applied antibiotic counter-selection for the re-establishment of the Kan(S)/Sm-R phenotype to select for isolates cured of targeted prophage. This methodology allowed for the precise selection of spontaneous phage loss and restoration of the natural phage attB attachment sites for all four prophage-like elements in this S. pyogenes chromosome. Overall, 15 mutants were constructed that encompassed every permutation of phage knockout as well as a mutant strain, named CEM1 Delta phi, completely cured of all bacteriophage elements (a similar to 10% loss of the genome); the only reported S. pyogenes strain free of prophage-like elements. We compared CEM1 Delta phi to the WT strain by analyzing differences in secreted DNase activity, as well as lytic and lysogenic potential. These mutant strains should allow for the direct examination of bacteriophage relationships within S. pyogenes and further elucidate how the presence of prophage may affect overall streptococcal survival, pathogenicity, and evolution.

There is almost unanimity that modern medicine should be evidence based. In this context, lack of prospectively randomized clinical trials (RCTs) is widely lamented in reproductive medicine. Some leading voices, indeed, increasingly suggest that only RCT-based clinical conclusions should be integrated into clinical practice, since lower levels of evidence are inadequate. We have argued that reproductive medicine requires special considerations because, like clinical oncology, fertility treatments (especially in older women) are time dependent. Unlike clinical oncology, reproductive medicine, however, does not receive substantial financial research support from government or industry and, at least in the United States, has, therefore, to be primarily funded via patient revenues. Given a 50% chance of receiving placebo, infertility patients are, understandably, reluctant to fund their own RCTs. We here selectively review this subject, contrasting opposing opinions recently published in the literature by a prominent reproductive scientist and one of the world's leading experts on evidence-based medicine. Placing these recent publications into the evolving context of infertility practice, as also addressed in this journal in recent publications, we conclude that objective reasons explain why relatively few RCTs are performed in reproductive medicine and predict that this will not change in the foreseeable future. Reproductive medicine, therefore, has to find ways to develop satisfactory clinical evidence in other ways, satisfying patients' rights to easy access to potentially beneficial medical treatments with low costs and low risks. The RCTs should be reserved for relatively high risk and/or high cost treatments.

Little is known about the molecular similarities and differences between neurons in the ventral (vSt) and dorsal striatum (dSt) and their physiological implications. In the vSt, serotonin [5-Hydroxy-tryptamine (5-HT)] modulates mood control and pleasure response, whereas in the dSt, 5-HT regulates motor behavior. Here we show that, in mice, 5-HT depolarizes cholinergic interneurons (ChIs) of the dSt whereas hyperpolarizing ChIs from the vSt by acting on different 5-HT receptor isoforms. In the vSt, 5-HT1A (a postsynaptic receptor) and 5-HT1B (a presynaptic receptor) are highly expressed, and synergistically inhibit the excitability of ChIs. The inhibitory modulation by 5-HT1B, but not that by 5-HT1A, is mediated by p11, a protein associated with major depressive disorder. Specific deletion of 5-HT1B from cholinergic neurons results in impaired inhibition of ACh release in the vSt and in anhedonic-like behavior.

Proteolytic cleavage of the amyloid-beta protein precursor (A beta PP) ecretases leads to extracellular release of amyloid-beta (A beta) peptides. Increased production of A beta(42) over A beta(40) and aggregation into oligomers and plaques constitute an Alzheimer's disease (AD) hallmark. Identifying products of the 'human chemical exposome' (HCE) able to induce A beta(42) production may be a key to understanding some of the initiating causes of AD and to generate non-genetic, chemically-induced AD animal models. A cell model was used to screen HCE libraries for A beta(42) inducers. Out of 3500+ compounds, six triazine herbicides were found that induced a beta- and gamma-secretases-dependent, 2-10 fold increase in the production of extracellular A beta(42) in various cell lines, primary neuronal cells, and neurons differentiated from human-induced pluripotent stem cells (iPSCs). Immunoprecipitation/mass spectrometry analyses show enhanced production of A beta peptides cleaved at positions 42/43, and reduced production of peptides cleaved at positions 38 and lower, a characteristic of AD. Neurons derived from iPSCs obtained from a familialAD(FAD) patient (A beta PP K724N) produced more A beta(42) versus A beta(40) than neurons derived from healthy controls iPSCs (A beta PP WT). Triazines enhanced A beta(42) production in both control and AD iPSCs-derived neurons. Triazines also shifted the cleavage pattern of alcadein alpha, another gamma-secretase substrate, suggesting a direct effect of triazines on gamma-secretase activity. In conclusion, several widely used triazines enhance the production of toxic, aggregation prone A beta(42)/A beta(43) amyloids, suggesting the possible existence of environmental "Alzheimerogens" which may contribute to the initiation and propagation of the amyloidogenic process in late-onset AD.

Protective immunoglobulin A (IgA) responses to oral antigens are usually orchestrated by gut dendritic cells (DCs). Here, we show that lung CD103(+) and CD24(+)CD11b(+) DCs induced IgA class-switch recombination (CSR) by activating B cells through T cell-dependent or -independent pathways. Compared with lung DCs (LDC), lung CD64(+) macrophages had decreased expression of B cell activation genes and induced significantly less IgA production. Microbial stimuli, acting through Toll-like receptors, induced transforming growth factor-beta (TGF-beta) production by LDCs and exerted a profound influence on LDC-mediated IgA CSR. After intranasal immunization with inactive cholera toxin (CT), LDCs stimulated retinoic acid-dependent up-regulation of alpha 4 beta 7 and CCR9 gut-homing receptors on local IgA-expressing B cells. Migration of these B cells to the gut resulted in IgA-mediated protection against an oral challenge with active CT. However, in germ-free mice, the levels of LDC-induced, CT-specific IgA in the gut are significantly reduced. Herein, we demonstrate an unexpected role of the microbiota in modulating the protective efficacy of intranasal vaccination through their effect on the IgA class-switching function of LDCs.

DNA combing allows the investigation of DNA replication on genomic single DNA molecules, but the lengths that can be analysed have been restricted to molecules of 200-500 kb. We have improved the DNA combing procedure so that DNA molecules can be analysed up to the length of entire chromosomes in fission yeast and up to 12 Mb fragments in human cells. Combing multi-Mb-scale DNA molecules revealed previously undetected origin clusters in fission yeast and shows that in human cells replication origins fire stochastically forming clusters of fired origins with an average size of 370 kb. We estimate that a single human cell forms around 3200 clusters at mid S-phase and fires approximately 100,000 origins to complete genome duplication. The procedure presented here will be adaptable to other organisms and experimental conditions.

Objective To investigate subjective experiences and patterns of engagement with a novel electronic tool for facilitating reflection and problem solving for individuals with type 2 diabetes, Mobile Diabetes Detective (MoDD). Methods In this qualitative study, researchers conducted semi-structured interviews with individuals from economically disadvantaged communities and ethnic minorities who are participating in a randomized controlled trial of MoDD. The transcripts of the interviews were analyzed using inductive thematic analysis; usage logs were analyzed to determine how actively the study participants used MoDD. Results Fifteen participants in the MoDD randomized controlled trial were recruited for the qualitative interviews. Usage log analysis showed that, on average, during the 4 weeks of the study, the study participants logged into MoDD twice per week, reported 120 blood glucose readings, and set two behavioral goals. The qualitative interviews suggested that individuals used MoDD to follow the steps of the problem-solving process, from identifying problematic blood glucose patterns, to exploring behavioral triggers contributing to these patterns, to selecting alternative behaviors, to implementing these behaviors while monitoring for improvements in glycemic control. Discussion This qualitative study suggested that informatics interventions for reflection and problem solving can provide structured scaffolding for facilitating these processes by guiding users through the different steps of the problem-solving process and by providing them with context-sensitive evidence and practice-based knowledge related to diabetes self-management on each of those steps. Conclusion This qualitative study suggested that MoDD was perceived as a useful tool in engaging individuals in self-monitoring, reflection, and problem solving.

The eukaryotic replisome is a multiprotein machine that contains DNA polymerases, sliding clamps, helicase, and primase along with several factors that participate in cell cycle and checkpoint control. The detailed structure of the 11-subunit CMG helicase (Cdc45/Mcm2-7/GINS) has been solved recently by cryoEM single-particle 3D reconstruction and reveals pumpjack motions that imply an unexpected mechanism of DNA translocation. CMG is also the organizing center of the replisome. Recent in vitro reconstitution of leading and lagging strand DNA synthesis has enabled structural analysis of the replisome. By building the replisome in stages from pure proteins, single-particle EM studies have identified the overall architecture of the eukaryotic replisome. Suprisingly leading and lagging strand polymerases bind to opposite faces of the CMG helicase, unlike the long-held view that DNA polymerases are located in back of the helicase to act on the unwound strands.

Non-fibrillar soluble oligomeric forms of amyloid-beta peptide (oA beta) and tau proteins are likely to play a major role in Alzheimer's disease (AD). The prevailing hypothesis on the disease etiopathogenesis is that oA beta initiates tau pathology that slowly spreads throughout the medial temporal cortex and neocortices independently of A beta, eventually leading to memory loss. Here we show that a brief exposure to extracellular recombinant human tau oligomers (oTau), but not monomers, produces an impairment of long-term potentiation (LTP) and memory, independent of the presence of high oA beta levels. The impairment is immediate as it raises as soon as 20 min after exposure to the oligomers. These effects are reproduced either by oTau extracted from AD human specimens, or naturally produced in mice overexpressing human tau. Finally, we found that oTau could also act in combination with oA beta to produce these effects, as sub-toxic doses of the two peptides combined lead to LTP and memory impairment. These findings provide a novel view of the effects of tau and A beta on memory loss, offering new therapeutic opportunities in the therapy of AD and other neurodegenerative diseases associated with A beta and tau pathology.

Characterizing the dynamic behavior of nucleosomes in the central nervous system is vital to our understanding of brain-specific chromatin-templated processes and their roles in transcriptional plasticity. Histone turnover-the complete loss of old, and replacement by new, nucleosomal histones-is one such phenomenon that has recently been shown to be critical for cell-type-specific transcription in brain, synaptic plasticity, and cognition. Such revelations that histones, long believed to static proteins in postmitotic cells, are highly dynamic in neurons were only possible owing to significant advances in analytical chemistry-based techniques, which now provide a platform for investigations of histone dynamics in both healthy and diseased tissues. Here, we discuss both past and present proteomic methods (eg, mass spectrometry, human "bomb pulse labeling") for investigating histone turnover in brain with the hope that such information may stimulate future investigations of both adaptive and aberrant forms of "neuroepigenetic" plasticity.