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"Scanlon, Michael"
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A mystery in Gabba Land
Muno and his friends follow clues to solve the mystery and find Muno's missing hat.
Book
Plant stem-cell organization and differentiation at single-cell resolution
Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing (scRNA-seq) to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem-cell organizing center subtending these cells. In addition, trajectory inference was used to trace the gene expression changes that accompany cell differentiation, revealing that ectopic expression of KNOTTED1 (KN1) accelerates cell differentiation and promotes development of the sheathing maize leaf base. These single-cell transcriptomic analyses of the shoot apex yield insight into the processes of stem-cell function and cell-fate acquisition in the maize seedling and provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis at the cellular level.
Journal Article
On the mechanisms of development in monocot and eudicot leaves
Comparisons of concepts in monocot and eudicot leaf development are presented, with attention to the morphologies and mechanisms separating these angiosperm lineages. Monocot and eudicot leaves are distinguished by the differential elaborations of upper and lower leaf zones, the formation of sheathing/nonsheathing leaf bases and vasculature patterning. We propose that monocot and eudicot leaves undergo expansion of mediolateral domains at different times in ontogeny, directly impacting features such as venation and leaf bases. Furthermore, lineage-specific mechanisms in compound leaf development are discussed. Although models for the homologies of enigmatic tissues, such as ligules and stipules, are proposed, tests of these hypotheses are rare. Likewise, comparisons of stomatal development are limited to Arabidopsis and a few grasses. Future studies may investigate correlations in the ontogenies of parallel venation and linear stomatal files in monocots, and the reticulate patterning of veins and dispersed stoma in eudicots. Although many fundamental mechanisms of leaf development are shared in eudicots and monocots, variations in the timing, degree and duration of these ontogenetic events may contribute to key differences in morphology. We anticipate that the incorporation of an ever-expanding number of sequenced genomes will enrich our understanding of the developmental mechanisms generating eudicot and monocot leaves.
Journal Article
Multiplexed transcriptomic analyzes of the plant embryonic hourglass
Zoologists have adduced morphological convergence among embryonic stages of closely related taxa, which has been called the phylotypic stage of embryogenesis. Transcriptomic analyzes reveal an hourglass pattern of gene expression during plant and animal embryogenesis, characterized by the accumulation of evolutionarily older and conserved transcripts during mid-embryogenesis, whereas younger less-conserved transcripts predominate at earlier and later embryonic stages. In contrast, comparisons of embryonic gene expression among different animal phyla describe an inverse hourglass pattern, where expression is correlated during early and late stages but not during mid-embryo development. Here, multiplexed spatial-transcriptomic analyzes is used to investigate embryogenesis and homology in maize, which has grass-specific morphology. A set of shared, co-expressed genes is identified during initiation of maize embryonic organs, replete for ancient/conserved genes manifesting an hourglass pattern during mid-embryogenesis. Transcriptomic comparisons of maize and
Arabidopsis
embryogenesis with that of the moss
Physcomitrium patens
identify an inverse hourglass pattern across plant phyla, as in animals. The data suggest that the phylotypic stages in plants and animals are characterized by expression of ancient and conserved genes during histogenesis, organization of embryonic axes, and initial morphogenesis. We propose a mechanism for gene evolution during the innovation of morphological novelty.
Multiplexed transcriptomic analyzes show that mid-embryogenesis features the accumulation of ancient and sequence-conserved transcripts in an hourglass pattern, during initial histogenesis and organization of the body plan in diverse plants.
Journal Article
Universal screening for SARS-CoV-2 infection among pregnant women at Elmhurst Hospital Center, Queens, New York
Universal screening for SARS-CoV-2 infection on Labor and Delivery (L&D) units is a critical strategy to manage patient and health worker safety, especially in a vulnerable high-prevalence community. We describe the results of a SARS-CoV-2 universal screening program at the L&D Unit at Elmhurst Hospital in Queens, NY, a 545-bed public hospital serving a diverse, largely immigrant and low-income patient population and an epicenter of the global pandemic.
We conducted a retrospective cross-sectional study. All pregnant women admitted to the L&D Unit of Elmhurst Hospital from March 29, 2020 to April 22, 2020 were included for analysis. The primary outcomes of the study were: (1) SARS-CoV-2 positivity among universally screened pregnant women, stratified by demographic characteristics, maternal comorbidities, and delivery outcomes; and (2) Symptomatic or asymptomatic presentation at the time of testing among SARS-CoV-2 positive women. A total of 126 obstetric patients were screened for SARS-CoV-2 between March 29 and April 22. Of these, 37% were positive. Of the women who tested positive, 72% were asymptomatic at the time of testing. Patients who tested positive for SARS-CoV-2 were more likely to be of Hispanic ethnicity (unadjusted difference 24.4 percentage points, CI 7.9, 41.0) and report their primary language as Spanish (unadjusted difference 32.9 percentage points, CI 15.8, 49.9) than patients who tested negative.
In this retrospective cross-sectional study of data from a universal SARS-Cov-2 screening program implemented in the L&D unit of a safety-net hospital in Queens, New York, we found over one-third of pregnant women testing positive, the majority of those asymptomatic. The rationale for universal screening at the L&D Unit at Elmhurst Hospital was to ensure safety of patients and staff during an acute surge in SARS-Cov-2 infections through appropriate identification and isolation of pregnant women with positive test results. Women were roomed by their SARS-CoV-2 status given increasing space limitations. In addition, postpartum counseling was tailored to infection status. We quickly established discharge counseling and follow-up protocols tailored to their specific social needs. The experience at Elmhurst Hospital is instructive for other L&D units serving vulnerable populations and for pandemic preparedness.
Journal Article
Cytokinin–CLAVATA cross-talk is an ancient mechanism regulating shoot meristem homeostasis in land plants
Plant shoots grow from stem cells within shoot apical meristems (SAMs), which produce lateral organs while maintaining the stem cell pool. In the model flowering plant Arabidopsis, the CLAVATA (CLV) pathway functions antagonistically with cytokinin signaling to control the size of the multicellular SAM via negative regulation of the stem cell organizer WUSCHEL (WUS). Although comprising just a single cell, the SAM of the model moss Physcomitrium patens (formerly Physcomitrella patens) performs equivalent functions during stem cell maintenance and organogenesis, despite the absence of WUS-mediated stem cell organization. Our previous work showed that the stem cell–delimiting function of the receptors CLAVATA1 (CLV1) and RECEPTOR-LIKE PROTEIN KINASE2 (RPK2) is conserved in the moss P. patens. Here, we use P. patens to assess whether CLV–cytokinin cross-talk is also an evolutionarily conserved feature of stem cell regulation. Application of cytokinin produces ectopic stem cell phenotypes similar to Ppclv1a, Ppclv1b, and Pprpk2 mutants. Surprisingly, cytokinin receptor mutants also form ectopic stem cells in the absence of cytokinin signaling. Through modeling, we identified regulatory network architectures that recapitulated the stem cell phenotypes of Ppclv1a, Ppclv1b, and Pprpk2 mutants, cytokinin application, cytokinin receptor mutations, and higher-order combinations of these perturbations. These models predict that PpCLV1 and PpRPK2 act through separate pathways wherein PpCLV1 represses cytokinin-mediated stem cell initiation, and PpRPK2 inhibits this process via a separate, cytokinin-independent pathway. Our analysis suggests that cross-talk between CLV1 and cytokinin signaling is an evolutionarily conserved feature of SAM homeostasis that preceded the role ofWUS in stem cell organization.
Journal Article
Constructing functional cuticles
Prior work has examined cuticle function, composition and ultrastructure in many plant species, but much remains to be learned about how these features are related. This study aims to elucidate relationships between these features via analysis of cuticle development in adult maize (Zea mays L.) leaves, while also providing the most comprehensive investigation to date of the composition and ultrastructure of adult leaf cuticles in this important crop plant.
We examined water permeability, wax and cutin composition via gas chromatography, and ultrastructure via transmission electron microscopy, along the developmental gradient of partially expanded adult maize leaves, and analysed the relationships between these features.
The water barrier property of the adult maize leaf cuticle is acquired at the cessation of cell expansion. Wax types and chain lengths accumulate asynchronously over the course of development, while overall wax load does not vary. Cutin begins to accumulate prior to establishment of the water barrier and continues thereafter. Ultrastructurally, pavement cell cuticles consist of an epicuticular layer, and a thin cuticle proper that acquires an inner, osmiophilic layer during development.
Cuticular waxes of the adult maize leaf are dominated by alkanes and alkyl esters. Unexpectedly, these are localized mainly in the epicuticular layer. Establishment of the water barrier during development coincides with a switch from alkanes to esters as the major wax type, and the emergence of an osmiophilic (likely cutin-rich) layer of the cuticle proper. Thus, alkyl esters and the deposition of the cutin polyester are implicated as key components of the water barrier property of adult maize leaf cuticles.
Journal Article
Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing
Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN) http://solgenomics.net. Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments.
Journal Article
A Cross-Sectional Study of Disclosure of HIV Status to Children and Adolescents in Western Kenya
Disclosure of HIV status to children is essential for disease management but is not well characterized in resource-limited settings. This study aimed to describe the prevalence of disclosure and associated factors among a cohort of HIV-infected children and adolescents in Kenya.
We conducted a cross-sectional study, randomly sampling HIV-infected children ages 6-14 years attending 4 HIV clinics in western Kenya. Data were collected from questionnaires administered by clinicians to children and their caregivers, supplemented with chart review. Descriptive statistics and disclosure prevalence were calculated. Univariate analyses and multivariate logistic regression were performed to assess the association between disclosure and key child-level demographic, clinical and psychosocial characteristics.
Among 792 caregiver-child dyads, mean age of the children was 9.7 years (SD = 2.6) and 51% were female. Prevalence of disclosure was 26% and varied significantly by age; while 62% of 14-year-olds knew their status, only 42% of 11-year-olds and 21% of 8-year-olds knew. In multivariate regression, older age (OR 1.49, 95%CI 1.35-1.63), taking antiretroviral drugs (OR 2.27, 95%CI 1.29-3.97), and caregiver-reported depression symptoms (OR 2.63, 95%CI 1.12-6.20) were significantly associated with knowing one's status. Treatment site was associated with disclosure for children attending one of the rural clinics compared to the urban clinic (OR 3.44, 95%CI 1.75-6.76).
Few HIV-infected children in Kenya know their HIV status. The likelihood of disclosure is associated with clinical and psychosocial factors. More data are needed on the process of disclosure and its impact on children.
Journal Article
WOX4 Promotes Procambial Development
Plant shoot organs arise from initial cells that are recruited from meristematic tissues. Previous studies have shown that members of the WUSCHEL-related HOMEOBOX (WOX) gene family function to organize various initial cell populations during plant development. The function of the WOX4 gene is previously undescribed in any plant species. Comparative analyses of WOX4 transcription and function are presented in Arabidopsis (Arabidopsis thaliana), a simple-leafed plant with collateral vasculature, and in tomato (Solanum lycopersicum), a dissected-leafed species with bicollateral venation. WOX4 is transcribed in the developing vascular bundles of root and shoot lateral organs in both Arabidopsis and tomato. RNA interference-induced down-regulation of WOX4 in Arabidopsis generated small plants whose vascular bundles accumulated undifferentiated ground tissue and exhibited severe reductions in differentiated xylem and phloem. In situ hybridization analyses of Atwox4-RNA interference plants revealed delayed and reduced expression of both the phloem developmental marker ALTERED PHLOEM1 and HOMEOBOX GENE8, a marker of the vascular procambium. Overexpression of SlWOX4 correlated with overproliferation of xylem and phloem in transgenic tomato seedlings. The cumulative data suggest that the conserved WOX4 function is to promote differentiation and/or maintenance of the vascular procambium, the initial cells of the developing vasculature.
Journal Article