Publications by authors named "Laura L Klein"

14 Publications

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Characterizing 3D inflorescence architecture in grapevine using X-ray imaging and advanced morphometrics: implications for understanding cluster density.

J Exp Bot 2019 11;70(21):6261-6276

Donald Danforth Plant Science Center, St Louis, MO, USA.

Inflorescence architecture provides the scaffold on which flowers and fruits develop, and consequently is a primary trait under investigation in many crop systems. Yet the challenge remains to analyse these complex 3D branching structures with appropriate tools. High information content datasets are required to represent the actual structure and facilitate full analysis of both the geometric and the topological features relevant to phenotypic variation in order to clarify evolutionary and developmental inflorescence patterns. We combined advanced imaging (X-ray tomography) and computational approaches (topological and geometric data analysis and structural simulations) to comprehensively characterize grapevine inflorescence architecture (the rachis and all branches without berries) among 10 wild Vitis species. Clustering and correlation analyses revealed unexpected relationships, for example pedicel branch angles were largely independent of other traits. We identified multivariate traits that typified species, which allowed us to classify species with 78.3% accuracy, versus 10% by chance. Twelve traits had strong signals across phylogenetic clades, providing insight into the evolution of inflorescence architecture. We provide an advanced framework to quantify 3D inflorescence and other branched plant structures that can be used to tease apart subtle, heritable features for a better understanding of genetic and environmental effects on plant phenotypes.
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http://dx.doi.org/10.1093/jxb/erz394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859732PMC
November 2019

Rootstock effects on scion phenotypes in a 'Chambourcin' experimental vineyard.

Hortic Res 2019 1;6:64. Epub 2019 May 1.

2Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103-2010 USA.

Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we used the French-American hybrid grapevine 'Chambourcin' ( L.) as a model to explore the rootstock-scion relationship. We examined leaf shape, ion concentrations, and gene expression in 'Chambourcin' grown ungrafted as well as grafted to three different rootstocks ('SO4', '1103P' and '3309C') across 2 years and three different irrigation treatments. We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation. For ion concentrations, the primary source of variation identified was the position of a leaf in a shoot, although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions. Lastly, we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines. Thus, our work reveals the subtle and complex effect of grafting on 'Chambourcin' leaf morphology, ionomics, and gene expression.
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http://dx.doi.org/10.1038/s41438-019-0146-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6491602PMC
May 2019

Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace.

Front Plant Sci 2018 25;9:553. Epub 2018 Apr 25.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.

Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.
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http://dx.doi.org/10.3389/fpls.2018.00553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996898PMC
April 2018

High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections.

Am J Bot 2018 02 12;105(2):215-226. Epub 2018 Mar 12.

United States Department of Agriculture, Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY, 14425, USA.

Premise Of The Study: Grapes are one of the most economically important berry crops worldwide, with the vast majority of production derived from the domesticated Eurasian species Vitis vinifera. Expansion of production into new areas, development of new cultivars, and concerns about adapting grapevines for changing climates necessitate the use of wild grapevine species in breeding programs. Diversity within Vitis has long been a topic of study; however, questions remain regarding relationships between species. Furthermore, the identity of some living accessions is unclear.

Methods: This study generated 11,020 single nucleotide polymorphism (SNP) markers for more than 300 accessions in the USDA-ARS grape germplasm repository using genotyping-by-sequencing. Resulting data sets were used to reconstruct evolutionary relationships among several North American and Eurasian Vitis species, and to suggest taxonomic labels for previously unidentified and misidentified germplasm accessions based on genetic distance.

Key Results: Maximum likelihood analyses of SNP data support the monophyly of Vitis, subg. Vitis, a Eurasian subg. Vitis clade, and a North American subg. Vitis clade. Data delineate species groups within North America. In addition, analysis of genetic distance suggested taxonomic identities for 20 previously unidentified Vitis accessions and for 28 putatively misidentified accessions.

Conclusions: This work advances understanding of Vitis evolutionary relationships and provides the foundation for ongoing germplasm enhancement. It supports conservation and breeding efforts by contributing to a growing genetic framework for identifying novel genetic variation and for incorporating new, unsampled populations into the germplasm repository system.
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http://dx.doi.org/10.1002/ajb2.1033DOI Listing
February 2018

Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences.

Front Plant Sci 2017 9;8:900. Epub 2017 Jun 9.

Department of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute, National Land Survey of FinlandMasala, Finland.

The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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http://dx.doi.org/10.3389/fpls.2017.00900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465304PMC
June 2017

Digital Morphometrics of Two North American Grapevines (: Vitaceae) Quantifies Leaf Variation between Species, within Species, and among Individuals.

Front Plant Sci 2017 17;8:373. Epub 2017 Mar 17.

Department of Biology, Saint Louis University, St. LouisMO, USA; Science and Conservation Department, Missouri Botanical Garden, St. LouisMO, USA.

Recent studies have demonstrated that grapevine ( spp.) leaf shape can be quantified using digital approaches which indicate phylogenetic signal in leaf shape, discernible patterns of developmental context within single leaves, and signatures of local environmental conditions. Here, we extend this work by quantifying intra-individual, intraspecific, and interspecific variation in leaf morphology in accessions of North American and in a common environment. For each species at least four clonal replicates of multiple genotypes were grown in the Missouri Botanical Garden Kemper Center for Home Gardening. All leaves from a single shoot were harvested and scanned leaf images were used to conduct generalized Procrustes analysis, linear discriminant analysis, and elliptical Fourier analysis. Leaf shapes displayed genotype-specific signatures and species distinctions consistent with taxonomic classifications. Leaf shape variation within genotypes and among clones was the result of pest and pathogen-induced leaf damage that alters leaf morphology. Significant trends in leaf damage caused by disease and infestation were non-random with respect to leaf position on the shoot. Digital morphometrics is a powerful tool for assessing leaf shape variation among species, genotypes, and clones under common conditions and suggests biotic factors such as pests and pathogens as important drivers influencing leaf shape.
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http://dx.doi.org/10.3389/fpls.2017.00373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5355467PMC
March 2017

Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes.

Trends Plant Sci 2016 05 11;21(5):418-437. Epub 2015 Dec 11.

Saint Louis University, Department of Biology, 3507 Laclede Avenue, St. Louis, MO 63103-2010, USA; Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, MO 63110-2226, USA. Electronic address:

Grafting is an ancient agricultural practice that joins the root system (rootstock) of one plant to the shoot (scion) of another. It is most commonly employed in woody perennial crops to indirectly manipulate scion phenotype. While recent research has focused on scions, here we investigate rootstocks, the lesser-known half of the perennial crop equation. We review natural grafting, grafting in agriculture, rootstock diversity and domestication, and developing areas of rootstock research, including molecular interactions and rootstock microbiomes. With growing interest in perennial crops as valuable components of sustainable agriculture, rootstocks provide one mechanism by which to improve and expand woody perennial cultivation in a range of environmental conditions.
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http://dx.doi.org/10.1016/j.tplants.2015.11.008DOI Listing
May 2016

Latent developmental and evolutionary shapes embedded within the grapevine leaf.

New Phytol 2016 Apr 18;210(1):343-55. Epub 2015 Nov 18.

United States Department of Agriculture, Agriculture Research Service, Grape Genetics Research Unit, Geneva, NY, 14456, USA.

Across plants, leaves exhibit profound diversity in shape. As a single leaf expands, its shape is in constant flux. Plants may also produce leaves with different shapes at successive nodes. In addition, leaf shape varies among individuals, populations and species as a result of evolutionary processes and environmental influences. Because leaf shape can vary in many different ways, theoretically, the effects of distinct developmental and evolutionary processes are separable, even within the shape of a single leaf. Here, we measured the shapes of > 3200 leaves representing > 270 vines from wild relatives of domesticated grape (Vitis spp.) to determine whether leaf shapes attributable to genetics and development are separable from each other. We isolated latent shapes (multivariate signatures that vary independently from each other) embedded within the overall shape of leaves. These latent shapes can predict developmental stages independent from species identity and vice versa. Shapes predictive of development were then used to stage leaves from 1200 varieties of domesticated grape (Vitis vinifera), revealing that changes in timing underlie leaf shape diversity. Our results indicate that distinct latent shapes combine to produce a composite morphology in leaves, and that developmental and evolutionary contributions to shape vary independently from each other.
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http://dx.doi.org/10.1111/nph.13754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063178PMC
April 2016

A curious case of anti-D antibody titer.

J Midwifery Womens Health 2009 Nov-Dec;54(6):497-502

University of Colorado Denver, College of Nursing, Education 2 North, 13120 E. 19th St., Box C-288, Aurora, CO 80045, USA.

RhD alloimmunization remains a threat to 1% of the 10% of RhD-negative women in the United States who are giving birth to RhD-positive fetuses despite routine antenatal and postpartum administration of Rh(o)D immune globulin (RhIG). This report examines the clinical course of an RhD-negative woman who developed a high anti-D antibody titer during her pregnancy while carrying an RhD-positive female fetus yet had a negative antibody screen at the time she gave birth. Although she delivered a healthy newborn unaffected by hemolytic disease, subsequent pregnancies will be treated as though she is RhD alloimmunized. The discussion below includes possible causes for the abrupt rise in this woman's anti-D antibody titer, a review of the complex Rh system and cellular anamnestic response, and current fetal surveillance for hemolytic disease of the fetus and newborn.
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http://dx.doi.org/10.1016/j.jmwh.2009.08.006DOI Listing
January 2010

Shotgun proteomic analysis of vaginal fluid from women in late pregnancy.

Reprod Sci 2008 Apr;15(3):263-73

Department of Obstetrics and Gynecology, University of Colorado Denver Health Sciences Center, Aurora, CO 80045, USA.

Liquid chromatography and tandem mass spectrometry without prior fractionation (shotgun proteomics) were used to analyze vaginal fluid from patients admitted for signs and symptoms of preterm labor. The patients had an average age of 26.3 +/- 5.9 years, a gestational age of 30.5 +/- 2.5 weeks, and a median cervical dilation of 1 cm (range, 0-6 cm). None of the patients exhibited signs of vaginal infection at the time of enrollment. Shotgun proteomics yielded reproducible identifications (R = 0.973) of more than 40 proteins in vaginal fluid samples, such as plasma proteins, epithelial structural proteins, and several immunoregulatory proteins, including some that were previously linked to intra-amniotic infection. This initial characterization of the vaginal fluid proteome using a nonbiased, high-throughput technique yields reproducible results in late pregnancy. The presence of host defense proteins in vaginal fluid suggests that this technique may be useful for future study of inflammation-related preterm birth.
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http://dx.doi.org/10.1177/1933719107311189DOI Listing
April 2008

Detection of intra-amniotic infection in a rabbit model by proteomics-based amniotic fluid analysis.

Am J Obstet Gynecol 2005 Oct;193(4):1302-6

Department of Obstetrics and Gynecology, University of Colorado Health Sciences Center, Denver, CO, USA.

Objective: This study was undertaken to identify intra-amniotic infection caused by several different organisms in a rabbit model by using proteomics.

Study Design: Twenty infected and 18 uninfected amniotic fluid samples were subjected to proteomic analysis by surface-enhanced laser desorption ionization (SELDI-TOF, Ciphergen Biosystems, Fremont, Calif), 1- and 2-dimensional gel electrophoresis, and tandem mass spectrometry (MS/MS).

Results: Detailed SELDI-TOF spectra revealed a constitutive 4.0 kd peak in all animals. Infected samples also displayed a signature double peak at 3.6 kd. A SELDI-TOF signature profile for intra-amniotic infection predicted positive amniotic fluid and/or fetal cultures with a sensitivity of 90% and specificity of 83%. Similar proteomic profiles were obtained regardless of the infecting organism. The 3.6 kd peak appeared to contain rabbit calgranulin C and rabbit calcyclin, members of the S100 family of calcium binding proteins.

Conclusion: Amniotic fluid proteomic analysis was able to detect intra-amniotic infection in this experimental rabbit model. S100 proteins may be involved in the host inflammatory response to intra-amniotic infection.
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http://dx.doi.org/10.1016/j.ajog.2005.06.017DOI Listing
October 2005

Infection and preterm birth.

Obstet Gynecol Clin North Am 2005 Sep;32(3):397-410

Department of Obstetrics and Gynecology, University of Colorado Health Sciences Center, Denver, 80262, USA.

As many as 50% of spontaneous preterm births are infection-associated. Intrauterine infection leads to a maternal and fetal inflammatory cascade, which produces uterine contractions and may also result in long-term adverse outcomes, such as cerebral palsy. This article addresses the prevalence, microbiology, and management of intrauterine infection in the setting of preterm labor with intact membranes. It also outlines antepartum treatment of infections for the purpose of preventing preterm birth.
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http://dx.doi.org/10.1016/j.ogc.2005.03.001DOI Listing
September 2005

Use of microbial cultures and antibiotics in the prevention of infection-associated preterm birth.

Am J Obstet Gynecol 2004 Jun;190(6):1493-502

Department of Obstetrics and Gynecology, University of Colorado Health Sciences Center, Denver, USA.

Objective: The purpose of this study was to summarize recent evidence regarding infection-associated preterm birth and to make appropriate recommendations. Antepartum treatment of lower genital tract infection or bacterial colonization has been found to reduce the incidence of preterm birth in the case of asymptomatic bacteriuria and bacterial vaginosis in selected patients but has been proved to be ineffective for vaginal colonization with organisms such as Ureaplasma urealyticum and group B streptococcus.

Study Design: This is a clinical opinion based on a review of recent data related to 1) the association between lower genital tract infection and preterm birth and 2) antibiotic trials to prevent preterm birth.

Results: Antepartum treatment of lower genital tract infection or bacterial colonization has been found to reduce the incidence of preterm birth in the case of asymptomatic bacteriuria and bacterial vaginosis in selected patients, but has been proven to be ineffective for vaginal colonization with organisms such as Ureaplasma urealyticum and group B streptococcus. Large well-designed trials have shown that the routine administration of antibiotics to women with preterm labor and intact membranes is not beneficial; however, antibiotic regimens including macrolides are recommended for preterm premature rupture of the membranes.

Conclusion: Large well-designed trials have shown that the routine administration of antibiotics to women with preterm labor and intact membranes is not beneficial; however, antibiotic regimens that include macrolides are recommended for preterm premature rupture of the membranes.
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http://dx.doi.org/10.1016/j.ajog.2004.03.014DOI Listing
June 2004

Cardiac disease in pregnancy.

Obstet Gynecol Clin North Am 2004 Jun;31(2):429-59, viii

Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Colorado Health Sciences Center, Campus Box B-198 Campus Box B-198, 4200 East 9th Avenue, Denver, CO 80262, USA.

This article reviews the complications, management and prognosis of cardiac disease in pregnancy.
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http://dx.doi.org/10.1016/j.ogc.2004.03.001DOI Listing
June 2004
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