Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection. By analysing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions

Genome sequencing reveals Zika virus diversity and spread in the Americas

Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests

The parallel evolution of competency‐based education in medical and higher education

Competency‐Based Education (CBE) programs have developed differently within higher education and medical education systems, yet both systems face challenges when bridging the gap between theory and practice. Both medicine and higher education face the challenge of adapting CBE programs for learners who begin the program with different configurations of knowledge and skillsets and learn at different rates. Additional challenges include, but are not limited to standard setting, time variability within programs for student learning, defining competencies, and training faculty to develop and assess CBE programs. This article argues there is much higher education programs can learn about defining competencies, assessing performance, and curriculum design by understanding how CBE is implemented in medical education. We also provide an overview of how CBE in medical education (CBE‐ME) has evolved compared to CBE in higher education (CBE‐HE), including examples of how medical education has addressed defining competency issues, assessing competence, and standard setting.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/168320/1/cbe21234_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/168320/2/cbe21234.pd

Consent Attitudes, Aggression, & Gender on Perceptions of Sexual Assault

Two decades of research have shown that compared to their Caucasian peers, African American students experience more severe punishments during their K-12 school years. We examined adult perceptions of a school altercation, varying the age and race of the children. We hypothesized that the African American child would be perceived more negatively than the Hispanic child, and the Caucasian child would be perceived more positively than both minority children. Participants (n = 114) were randomly assigned to one of three conditions. All three conditions described a fight between two boys and then between two adolescents. The only element that varied between the conditions was whether the accused student was African American, Caucasian, or Hispanic. Participants provided their perceptions of the situation and the students involved. Participants then responded to scales to measure aggression, impulsivity, and stereotyped thinking. Contrary to our hypothesis, our participants viewed the accused Caucasian child and adolescent more negatively than their peers and felt the accused African American child was likely to have been provoked. This change from previous research may reflect a recent societal focus on racial inequality. In fact, our participants, across race and gender, showed very low levels of stereotypical thinking. We also found that adults who reported more anger, hostility, and impulsivity were more frustrated by and less confident about how to interpret the altercation. School staff members with these characteristics may be more vulnerable to making emotional decisions rather than those in the best interest of the students

Consent Attitudes, Aggression, & Gender on Perceptions of Sexual Assault

Perceptions of sexual assault are heavily dependent on commonly held, but often false, beliefs. For example, most adults believe incautious behavior makes a victim more responsible for assault. We hypothesized that gender, aggression levels, consent attitudes, and empathy levels would be significant predictors of how individuals perceive sexual assault scenarios. Participants were 82 adults with a mean age of 20.46 (SD = 2.66). The majority were women (72%) and Caucasian (54%). Participants were randomly assigned to read a scenario where a young adult was sexually assaulted by two offenders. The gender of the victim and the offenders were altered across the four versions to be male/males, male/females, female/males, and female/females. Participants provided their perceptions of the assault, their views of consent, empathy levels, and aggression levels. Results revealed that adults adhered to rape myth beliefs by evaluating accused men more harshly than accused women. Adults who felt negatively about sexual consent were more likely to blame the victim, and aggressive individuals experienced more of this negativity. Women were more sympathetic toward all victims than were men, and also felt more in control over sexual consent. Compared to Caucasians, African American adults appeared to be concerned about false blame and reported that it is too easy to unfairly accuse someone of sexual assault in our society. These perceptions may reflect African Americans’ personal feelings of societal vulnerability. Our findings suggest that perceptions of sexual assault may reflect the perceiver as much as the situation being perceived

Targeting the Maladaptive Effects of Binge Drinking on Circadian Gene Expression

Previous studies (1) support a role of circadian genes in regulating alcohol intake, and (2) reveal that harmful alcohol use alters circadian rhythms. However, there is minimal knowledge of the effects of chronic alcohol processes on rhythmic circadian gene expression across brain regions important for circadian biology and alcohol intake. Therefore, the present study sought to test the effects of chronic binge-like drinking on diurnal circadian gene expression patterns in the master circadian pacemaker (SCN), the ventral tegmental area (VTA), and the nucleus accumbens (NAc) in High Drinking in the Dark-1 (HDID-1) mice, a unique genetic risk model for drinking to intoxication. Consistent with earlier findings, we found that 8 weeks of binge-like drinking reduced the amplitude of several core circadian clock genes in the NAc and SCN, but not the VTA. To better inform the use of circadian-relevant pharmacotherapies in reducing harmful drinking and ameliorating alcohol’s effects on circadian gene expression, we tested whether the casein kinase-1 inhibitor, PF-67046, or the phosphodiesterase type-4 (an upstream regulator of circadian signalling) inhibitor, apremilast, would reduce binge-like intake and mitigate circadian gene suppression. PF-67046 did not reduce intake but did have circadian gene effects. In contrast, apremilast reduced drinking, but had no effect on circadian expression patterns

Trypanosoma cruzi - Derived Sugar Epitopes - Synthesis and Immunology

The protozoan parasite Trypanosoma cruzi is the causative agent of Chagas disease. As of today no effective vaccine has been developed for it. Certain developmental stages of T.cruzi express cell surface oligosaccharides with terminal alpha-galactosyl and rhamnosyl residues, which are believed to be highly immunogenic in humans. The exact structures and sizes of these epitopes are still unknown. Our quest is to shine light on the chemical structures of immunogenic alpha-Gal and alpha-Rha containing mono-, di-, and trisaccharides that are conjugated to a keyhole limpet hemocyanin (KLH) carrier protein through a combination of chemical synthesis and immunological studies. The compounds synthesized were screened for their ability to be recognized by Chagasic antibodies in an enzyme-linked immunosorbent assay (ELISA). The best recognized sugar-KLH conjugates were used to immunize alpha-1,3 Gal T-KO mice, which do not express cell surface proteins with terminal alpha-galactosides, and are therefore a suitable model for humans. We have successfully synthesized and conjugated a library of nine saccharides with terminal alpha-galactosyl or rhamnosyl moieties, which elicit various levels of antibody production in mice. Upon challenge of the immunized mice with lethal doses of live T. cruzi, prolonged survival was observed when compared to the control group. The work presented here has implications for the development of a carbohydrate-based vaccine for Chagas disease

Anti-diabetic effects of GLP1 analogs are mediated by thermogenic interleukin-6 signaling in adipocytes.

Mechanisms underlying anti-diabetic effects of GLP1 analogs remain incompletely understood. We observed that in prediabetic humans exenatide treatment acutely induces interleukin-6 (IL-6) secretion by monocytes and IL-6 in systemic circulation. We hypothesized that GLP1 analogs signal through IL-6 in adipose tissue (AT) and used the mouse model to test if IL-6 receptor (IL-6R) signaling underlies the effects of the GLP1-IL-6 axis. We show that liraglutide transiently increases IL-6 in mouse circulation and IL-6R signaling in AT. Metronomic liraglutide treatment resulted in AT browning and thermogenesis linked with STAT3 activation. IL-6-blocking antibody treatment inhibited STAT3 activation in AT and suppressed liraglutide-induced increase in thermogenesis and glucose utilization. We show that adipose IL-6R knockout mice still display liraglutide-induced weight loss but lack thermogenic adipocyte browning and metabolism activation. We conclude that the anti-diabetic effects of GLP1 analogs are mediated by transient upregulation of IL-6, which activates canonical IL-6R signaling and thermogenesis

Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes

Abstract Background Mitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods. Results With the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~ 80–90%) with mean coverage ~ 1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes. Conclusions This method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once

Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes.

BackgroundMitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods.ResultsWith the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~ 80-90%) with mean coverage ~ 1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes.ConclusionsThis method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once