Biology subjects

Lee, J. M.

Publications and source records attributed to Lee, J. M..

6 recordsLinked to original sources

bioRxiv2018

Chlamydia muridarum infection differentially changes smooth muscle contractility and responses to prostaglandins in uterus and cervix

Chlamydia trachomatis infection is a primary cause of reproductive tract diseases including chronic pelvic pain and infertility. Previous studies showed that this infection alters physiological activities in mouse oviducts. Whether this occurs in the uterus and cervix has never been investigated. This study characterized the physiological activity of the uterus and the cervix in a Chlamydia muridarum (Cmu) mouse model of reproductive tract infection. Uterine or cervix smooth muscle contractility, responses to oxytocin or prostaglandins (PGF2 and PGE2) and mRNA expression of oxytocin and PG receptors were assessed 14 days post infection. Cmu infection did not affect the contractions of the uterine horn but significantly decreased the contraction amplitude of the cervix. Cmu infection did not alter the responses of uterine horn or cervix to oxytocin, however PGF2 induced contractions of the uterine horn, but not the cervix, were significantly increased following Cmu infection. PGE2 contraction amplitude in both the uterine horn and cervix was unaffected by Cmu infection. An upregulation of Ptgfr and a down-regulation of Ptegr4 mRNA expression was observed in the uterine horn following Cmu infection. These results indicate that Cmu infection alters contractility and prostaglandin signalling in the female reproductive tract but the effects are localised to specific regions.

physiology↗

bioRxiv2018

Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants

Human influenza virus rapidly accumulates mutations in its major surface protein hemagglutinin (HA). The evolutionary success of influenza virus lineages depends on how these mutations affect HAs functionality and antigenicity. Here we experimentally measure the effects on viral growth in cell culture of all single amino-acid mutations to the HA from a recent human H3N2 influenza virus strain. We show that mutations that are measured to be more favorable for viral growth are enriched in evolutionarily successful H3N2 viral lineages relative to mutations that are measured to be less favorable for viral growth. Therefore, despite the well-known caveats about cell-culture measurements of viral fitness, such measurements can still be informative for understanding evolution in nature. We also compare our measurements for H3 HA to similar data previously generated for a distantly related H1 HA, and find substantial differences in which amino acids are preferred at many sites. For instance, the H3 HA has less disparity in mutational tolerance between the head and stalk domains than the H1 HA. Overall, our work suggests that experimental measurements of mutational effects can be leveraged to help understand the evolutionary fates of viral lineages in nature -- but only when the measurements are made on a viral strain similar to the ones being studied in nature.\n\nSignificance StatementA key goal in the study of influenza virus evolution is to forecast which viral strains will persist and which ones will die out. Here we experimentally measure the effects of all amino-acid mutations to the hemagglutinin protein from a human H3N2 influenza strain on viral growth in cell culture. We show that these measurements have utility for distinguishing among viral strains that do and do not succeed in nature. Overall, our work suggests that new high-throughput experimental approaches may be useful for understanding virus evolution in nature.

evolutionary biology↗

bioRxiv2017

Quantifying the ease of viral escape from broad and narrow antibodies to influenza hemagglutinin

Influenza virus can completely escape most antibodies with single mutations. However, rare antibodies broadly neutralize many viral strains. It is unclear how easily influenza virus might escape such antibodies if it was under strong pressure to do so. Here we map all single amino-acid mutations that increase resistance to broad antibodies targeting an H1 hemagglutinin. Crucially, our approach not only identifies antigenic mutations but also quantifies their effect sizes. All antibodies select mutations, but the effect sizes vary widely. The virus can escape a broad antibody that targets residues in hemagglutinins receptor-binding site the same way it escapes narrow strain-specific antibodies: via single mutations with huge effects. In contrast, broad antibodies targeting hemagglutinins stalk only select mutations with small effects. Therefore, among the antibodies we have examined, breadth is an imperfect indicator of the potential for viral escape via single mutations. Broadly neutralizing antibodies targeting the H1 hemagglutinin stalk are quantifiably harder to escape than the other antibodies tested here.

microbiology↗

bioRxiv2017

Uncovering Medical Insights from Vast Amounts of Biomedical Data in Clinical Case Reports

Clinical case reports (CCRs) have a time-honored tradition in serving as an important means of sharing clinical experiences on patients presenting with atypical disease phenotypes or receiving new therapies. However, the huge amount of accumulated case reports are isolated, unstructured, and heterogeneous clinical data, posing a great challenge to clinicians and researchers in mining relevant information through existing indexing tools. In this investigation, in order to render CCRs more findable, accessible, interoperable, and reusable (FAIR) by the biomedical community, we created a resource platform, including the construction of a test dataset consisting of 1000 CCRs spanning 14 disease phenotypes, a standardized metadata template and metrics, and a set of computational tools to automatically retrieve relevant medical information and to analyze all published PubMed clinical case reports with respect to trends in publication journals, citations impact, MeSH Terms, drug use, distributions of patient demographics, and relationships with other case reports and databases. Our standardized metadata template and CCR test dataset may be valuable resources to advance medical science and improve patient care for researchers who are using machine learning approaches with a high-quality dataset to train and validate their algorithms. In the future, our analytical tools may be applied towards other large clinical data sources as well.

bioinformatics↗

bioRxiv2017

Electroencephalographic markers of brain development during sevoflurane anesthesia in children aged 0 to 3 years old

The general anesthetic sevoflurane acts on GABAergic-interneurons to generate stereotyped oscillations that relate fundamentally to neural circuit architecture. Each year, millions of children require general anesthesia, providing an experiment of nature that allows characterization of the developmental trajectory of GABAergic-inhibitory circuits in the human brain. We used multichannel electroencephalograph recordings in 91 children 0-40 months old. We mapped spatial power and coherence across the cortex. During sevoflurane exposure: (1) slow-delta oscillations are present in all ages; (2) theta and alpha oscillations emerge around 4 months; (3) alpha oscillations increase in power from 4 to 10 months; (4) frontal alpha oscillation predominance emerge at ~6 months; (5) frontal slow oscillations are coherent in the first 6 months of age only; and (6) frontal alpha oscillations become coherent around 10 months and persist in older ages. Our results suggest key developmental milestones are visible in the functional activity of sevoflurane-stimulated GABAergic circuits.

neuroscience↗

bioRxiv2017

Multiple reference genome sequences of hot pepper reveal the massive evolution of plant disease resistance genes by retroduplication

Transposable elements (TEs) provide major evolutionary forces leading to new genome structure and species diversification. However, the role of TEs in the expansion of disease resistance gene families has been unexplored in plants. Here, we report high-quality de novo genomes for two peppers (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum). Dynamic genome rearrangements involving translocations among chromosome 3, 5 and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs exhibited great abundance across the angiosperms, with most cases lineage-specific and thus recent events. Our study revealed that retroduplication has played key roles in the emergence of new disease-resistance genes in plants.

plant biology↗