Evolution and expression of LEAFY genes in ferns and lycophytes.

BACKGROUND: The LEAFY (LFY) transcription factors are present in algae and across land plants. The available expression and functional data of these genes in embryophytes suggest that LFY genes control a plethora of processes including the first zygotic cell division in bryophytes, shoot cell divisions of the gametophyte and sporophyte in ferns, cone differentiation in gymnosperms and floral meristem identity in flowering plants. However, their putative plesiomorphic role in plant reproductive transition in vascular plants remains untested. RESULTS: We perform Maximum Likelihood (ML) phylogenetic analyses for the LFY gene lineage in embryophytes with expanded sampling in lycophytes and ferns. We recover the previously identified seed plant duplication that results in LEAFY and NEEDLY paralogs. In addition, we recover multiple species-specific duplications in ferns and lycophytes and large-scale duplications possibly correlated with the occurrence of whole genome duplication (WGD) events in Equisetales and Salviniales. To test putative roles in diverse ferns and lycophytes we perform LFY expression analyses in Adiantum raddianum, Equisetum giganteum and Selaginella moellendorffii. Our results show that LFY genes are active in vegetative and reproductive tissues, with higher expression in early fertile developmental stages and during sporangia differentiation. CONCLUSIONS: Our data point to previously unrecognized roles of LFY genes in sporangia differentiation in lycophytes and ferns and suggests that functions linked to reproductive structure development are not exclusive to seed plant LFY homologs.

GATA2 deficiency detected by newborn screening for SCID: A case report.

The early diagnosis and treatment of inborn errors of immunity (IEI) is crucial in reducing the morbidity and mortality due to these disorders. The institution of newborn screening (NBS) for the diagnosis of Severe Combined Immune Deficiency (SCID) has decreased the mortality of this disorder and led to the discovery of novel genetic defects that cause this disease. GATA2 deficiency is an autosomal dominant, pleiotropic disease with clinical manifestations that include bone marrow failure, monocyte and B cell deficiency, leukemia, pulmonary alveolar proteinosis and lymphedema. We present the case of an infant identified by newborn screening for SCID due to GATA2 deficiency.

Robbin C. Moran, Fern and Lycophyte Curator- an Appreciation.

To mark the commencement of his retirement as Nathaniel Lord Britton Curator of Botany, and appointment as Curator Emeritus at the New York Botanical Garden, we pay tribute to Robbin Moran and impact on the botanical community with a brief synopsis of his career. Naturalist, fern expert, adored teacher-it is difficult to adequately pay tribute to his accomplishments, and his impact on botany in a single article. Robbin has published four books, 13 monographs of neotropical fern clades, over 170 scientific papers, and dozens of popular articles. He has named 115 new species, five new genera, and one family of ferns. He is eponymized by seven new species and the genus Moranopteris. We recount his earliest days and academic trajectory to become a leading researcher and educator in pteridology. We highlight his major influences, scientific accomplishments, and outreach to the botanical community.

A target enrichment probe set for resolving the flagellate land plant tree of life.

PREMISE: New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. METHODS: We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages. RESULTS: Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. CONCLUSIONS: A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.

Understanding Suicide in Our Community through the Lens of the Pediatric ICU: An Epidemiological Review (2011-2017) of One Midwestern City in the US.

Suicide frequency has tripled for some pediatric age groups over the last decade, of which, serious attempts result in pediatric intensive care unit (PICU) admissions. We paired clinical, aggregate geospatial, and temporal demographics to understand local community variables to determine if epidemiological patterns emerge that associate with risk for PICU admission. Data were extracted at an urban, high-volume, quaternary care facility from January 2011 to December 2017 via ICD 10 codes associated with suicide. Clinical, socioeconomic, geographical, and temporal variables were reviewed. In total, 1036 patients over the age of 9 were included, of which n = 161 were PICU admissions. Females represented higher proportions of all suicide-related hospital admissions (67.9%). Looking at race/ethnicity, PICU admissions were largely Caucasian (83.2%); Blacks and Hispanics had lower odds of PICU admissions (OR: 0.49; 0.17, respectively). PICU-admitted patients were older (16.0 vs. 15.5; p = 0.0001), with lower basal metabolic index (23.0 vs. 22.0; p = 0.0013), and presented in summer months (OR: 1.51, p = 0.044). Time-series decomposition showed seasonal peaks in June and August. Local regions outside the city limits identified higher numbers of PICU admissions. PICUs serve discrete geographical regions and are a source of information, when paired with clinical geospatial/seasonal analyses, highlighting clinical and societal risk factors associated with PICU admissions.

Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii.

Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 h of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ.

Simple and Divided Leaves in Ferns: Exploring the Genetic Basis for Leaf Morphology Differences in the Genus Elaphoglossum (Dryopteridaceae).

Despite the implications leaves have for life, their origin and development remain debated. Analyses across ferns and seed plants are fundamental to address the conservation or independent origins of megaphyllous leaf developmental mechanisms. Class I KNOX expression studies have been used to understand leaf development and, in ferns, have only been conducted in species with divided leaves. We performed expression analyses of the Class I KNOX and Histone H4 genes throughout the development of leaf primordia in two simple-leaved and one divided-leaved fern taxa. We found Class I KNOX are expressed (1) throughout young and early developing leaves of simple and divided-leaved ferns, (2) later into leaf development of divided-leaved species compared to simple-leaved species, and (3) at the leaf primordium apex and margins. H4 expression is similar in young leaf primordia of simple and divided leaves. Persistent Class I KNOX expression at the margins of divided leaf primordia compared with simple leaf primordia indicates that temporal and spatial patterns of Class I KNOX expression correlate with different fern leaf morphologies. However, our results also indicate that Class I KNOX expression alone is not sufficient to promote divided leaf development in ferns. Class I KNOX patterns of expression in fern leaves support the conservation of an independently recruited developmental mechanism for leaf dissection in megaphylls, the shoot-like nature of fern leaves compared with seed plant leaves, and the critical role marginal meristems play in fern leaf development.

Class I KNOX Is Related to Determinacy during the Leaf Development of the Fern Mickelia scandens (Dryopteridaceae).

Unlike seed plants, ferns leaves are considered to be structures with delayed determinacy, with a leaf apical meristem similar to the shoot apical meristems. To better understand the meristematic organization during leaf development and determinacy control, we analyzed the cell divisions and expression of Class I KNOX genes in Mickelia scandens, a fern that produces larger leaves with more pinnae in its climbing form than in its terrestrial form. We performed anatomical, in situ hybridization, and qRT-PCR experiments with histone H4 (cell division marker) and Class I KNOX genes. We found that Class I KNOX genes are expressed in shoot apical meristems, leaf apical meristems, and pinnae primordia. During early development, cell divisions occur in the most distal regions of the analyzed structures, including pinnae, and are not restricted to apical cells. Fern leaves and pinnae bear apical meristems that may partially act as indeterminate shoots, supporting the hypothesis of homology between shoots and leaves. Class I KNOX expression is correlated with indeterminacy in the apex and leaf of ferns, suggesting a conserved function for these genes in euphyllophytes with compound leaves.

The Evolution of the KANADI Gene Family and Leaf Development in Lycophytes and Ferns.

Leaves constitute the main photosynthetic plant organ and even though their importance is not debated, the origin and development of leaves still is. The leaf developmental network has been elucidated for angiosperms, from genes controlling leaf initiation, to leaf polarity and shape. There are four KANADI (KAN) paralogs in Arabidopsis thaliana needed for organ polarity with KAN1 and KAN2 specifying abaxial leaf identity. Yet, studies of this gene lineage outside angiosperms are required to better understand the evolutionary patterns of leaf development and the role of KAN homologs. We studied the evolution of KAN genes across vascular plants and their expression by in situ hybridization in the fern, Equisetum hyemale and the lycophyte Selaginella moellendorffii. Our results show that the expression of KAN genes in leaves is similar between ferns and angiosperms. However, the expression patterns observed in the lycophyte S. moellendorffii are significantly different compared to all other vascular plants, suggesting that the KAN function in leaf polarity is likely only conserved across ferns, gymnosperms, and angiosperms. This study indicates that mechanisms for leaf development are different in lycophytes compared to other vascular plants.

Expression of the KNOTTED HOMEOBOX Genes in the Cactaceae Cambial Zone Suggests Their Involvement in Wood Development.

The vascular cambium is a lateral meristem that produces secondary xylem (i.e., wood) and phloem. Different Cactaceae species develop different types of secondary xylem; however, little is known about the mechanisms underlying wood formation in the Cactaceae. The KNOTTED HOMEOBOX (KNOX) gene family encodes transcription factors that regulate plant development. The role of class I KNOX genes in the regulation of the shoot apical meristem, inflorescence architecture, and secondary growth is established in a few model species, while the functions of class II KNOX genes are less well understood, although the Arabidopsis thaliana class II KNOX protein KNAT7 is known to regulate secondary cell wall biosynthesis. To explore the involvement of the KNOX genes in the enormous variability of wood in Cactaceae, we identified orthologous genes expressed in species with fibrous (Pereskia lychnidiflora and Pilosocereus alensis), non-fibrous (Ariocarpus retusus), and dimorphic (Ferocactus pilosus) wood. Both class I and class II KNOX genes were expressed in the cactus cambial zone, including one or two class I paralogs of KNAT1, as well as one or two class II paralogs of KNAT3-KNAT4-KNAT5. While the KNOX gene SHOOTMERISTEMLESS (STM) and its ortholog ARK1 are expressed during secondary growth in the Arabidopsis and Populus stem, respectively, we did not find STM orthologs in the Cactaceae cambial zone, which suggests possible differences in the vascular cambium genetic regulatory network in these species. Importantly, while two class II KNOX paralogs from the KNAT7 clade were expressed in the cambial zone of A. retusus and F. pilosus, we did not detect KNAT7 ortholog expression in the cambial zone of P. lychnidiflora. Differences in the transcriptional repressor activity of secondary cell wall biosynthesis by the KNAT7 orthologs could therefore explain the differences in wood development in the cactus species.

Challenging the paradigms of leaf evolution: Class III HD-Zips in ferns and lycophytes.

Despite the extraordinary significance leaves have for life on Earth, their origin and development remain vigorously debated. More than a century of paleobotanical, morphological, and phylogenetic research has still not resolved fundamental questions about leaves. Developmental genetic data are sparse in ferns, and comparative studies of lycophytes and seed plants have reached opposing conclusions on the conservation of a leaf developmental program. We performed phylogenetic and expression analyses of a leaf developmental regulator (Class III HD-Zip genes; C3HDZs) spanning lycophytes and ferns. We show that a duplication and neofunctionalization of C3HDZs probably occurred in the ancestor of euphyllophytes, and that there is a common leaf developmental mechanism conserved between ferns and seed plants. We show C3HDZ expression in lycophyte and fern sporangia and show that C3HDZs have conserved expression patterns during initiation of lateral primordia (leaves or sporangia). This expression is maintained throughout sporangium development in lycophytes and ferns and indicates an ancestral role of C3HDZs in sporangium development. We hypothesize that there is a deep homology of all leaves and that a sporangium-specific developmental program was coopted independently for the development of lycophyte and euphyllophyte leaves. This provides molecular genetic support for a paradigm shift in theories of lycophyte leaf evolution.

Obstrucción intestinal por semillas de Vasconcellea: reporte de tres casos y revisión de la literatura / Intestinal obstruction due to Vasconcellea seeds: Report of three cases and literature review / Obstrução intestinal por sementes de Vasconcellea: reporte de três casos e revisão da literatura

Vasconcellea spp., es una especie de papaya andina que crece en las áreas rurales cerca a Medellín, Colombia. Debido al agradable y dulce sabor de sus frutos, con frecuencia los niños ingieren accidentalmente sus semillas. Luego de la ingestión, las semillas se engranan en la luz del colon y obstruyen la salida de la materia fecal, lo que causa dolor y distensión abdominal, y favorece la translocación bacteriana. El diagnóstico se basa en la historia clínica y el tacto rectal. El tratamiento depende del grado de afectación local y sistémica e incluye la desimpactación del contenido rectal bajo anestesia general y lavados del colon con solución salina al 0,9%. En los casos más graves se ha requerido colostomía derivativa. En la literatura médica no existen reportes de obstrucción intestinal por semillas de Vasconcellea, posiblemente porque se han confundido con las del género Carica. En este artículo se describen tres casos tratados en servicios pediátricos de Medellín en los años 2012 y 2013; observamos que es una entidad poco sospechada, lo que lleva a un diagnóstico tardío con posibles consecuencias catastróficas. Es importante educar a la población para prevenir la ingestión de las semillas.

Vasconcellea spp., is a species of Andean papaya commonly cultivated in rural communities close to Medellín, Colombia. Due to the pleasant and sweet flavor of its fruits, children frequently ingest its seeds accidentally. After ingestion, the seeds are engaged in the colonic lumen and block the exit of stools, causing pain and bloating, and promoting bacterial translocation. Diagnosis is based on clinical history and rectal examination. Treatment depends on the degree of local and systemic involvement and includes disimpaction of rectal contents under general anesthesia and colonic washes with 0.9% saline solution. In severe cases derivative colostomy has been required. In the literature there are no reports of intestinal obstruction due to Vasconcellea seeds, possibly because it has been mistaken for seeds of the genus Carica. In this article, three cases treated at pediatric services in Medellín, Colombia, in 2012 and 2013 are described. We note that this is a rarely suspected disease, leading to late diagnosis and potential catastrophic consequences. It is important to educate people to prevent the ingestion of the seeds.

Vasconcellea spp., é uma espécie de mamão papaia andino que cresce nas áreas rurais perto a Medellín, Colômbia. Devido ao agradável e doce sabor de seus frutos, com frequência as crianças ingerem acidentalmente suas sementes. Depois da ingestão, as sementes se engrenam na luz do cólon e obstruem a saída da matéria fecal, o que causa dor e distensão abdominal, e favorece a translocação bacteriana. O diagnóstico se baseia na história clínica e o tato retal. O tratamento depende do grau de afetação local e sistémica e inclui a desimpactação do conteúdo retal sob anestesia geral e lavagens do cólon com solução salina a 0,9%. Nos casos mais graves foi necessário colostomia derivativa. Na literatura médica não existem reportes de obstrução intestinal por sementes de Vasconcellea, possivelmente porque se confundiram com as do gênero Carica. Neste artigo se descrevem três casos tratados em serviços pediátricos de Medellín nos anos 2012 e 2013; observamos que é uma entidade pouco suspeitada, o que leva a um diagnóstico tardio com possíveis consequências catastróficas. É importante educar à população para prevenir a ingestão das sementes.

Preparation of samples for leaf architecture studies, a method for mounting cleared leaves.

PREMISE OF THE STUDY: Several recent waves of interest in leaf architecture have shown an expanding range of approaches and applications across a number of disciplines. Despite this increased interest, examination of existing archives of cleared and mounted leaves shows that current methods for mounting, in particular, yield unsatisfactory results and deterioration of samples over relatively short periods. Although techniques for clearing and staining leaves are numerous, published techniques for mounting leaves are scarce. • METHODS AND RESULTS: Here we present a complete protocol and recommendations for clearing, staining, and imaging leaves, and, most importantly, a method to permanently mount cleared leaves. • CONCLUSIONS: The mounting protocol is faster than other methods, inexpensive, and straightforward; moreover, it yields clear and permanent samples that can easily be imaged, scanned, and stored. Specimens mounted with this method preserve well, with leaves that were mounted more than 35 years ago showing no signs of bubbling or discoloration.

The evolution, morphology, and development of fern leaves.

Leaves are lateral determinate structures formed in a predictable sequence (phyllotaxy) on the flanks of an indeterminate shoot apical meristem. The origin and evolution of leaves in vascular plants has been widely debated. Being the main conspicuous organ of nearly all vascular plants and often easy to recognize as such, it seems surprising that leaves have had multiple origins. For decades, morphologists, anatomists, paleobotanists, and systematists have contributed data to this debate. More recently, molecular genetic studies have provided insight into leaf evolution and development mainly within angiosperms and, to a lesser extent, lycophytes. There has been recent interest in extending leaf evolutionary developmental studies to other species and lineages, particularly in lycophytes and ferns. Therefore, a review of fern leaf morphology, evolution and development is timely. Here we discuss the theories of leaf evolution in ferns, morphology, and diversity of fern leaves, and experimental results of fern leaf development. We summarize what is known about the molecular genetics of fern leaf development and what future studies might tell us about the evolution of fern leaf development.