Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data

In biomedical applications, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multivariate responses of a panel of markers such as from a signaling network. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While computational methods can identify cell populations in individual samples, without the ability to automatically match them across samples, it is difficult to compare and characterize the populations in typical experiments, such as those responding to various stimulations or distinctive of particular patients or time-points, especially when there are many samples. Joint Clustering and Matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate probability distribution. Simultaneously, JCM fits a random-effects model to construct an overall batch template – used for registering populations across samples, and classifying new samples. By tackling systems-level variation, JCM supports practical biomedical applications involving large cohorts. Software for fitting the JCM models have been implemented in an R package EMMIX-JCM, available from http://www.maths.uq.edu.au/~gjm/mix_soft/EMMIX-JCM/.     

Genetic diversity of naturalized cacao (<Emphasis Type="Italic">Theobroma cacao</Emphasis> L.) in Puerto Rico

Identification of genetically diverse cacao with disease resistance, high productivity, and desirable organoleptic traits is vitally important to the agricultural crop’s long-term sustainability. Environmental changes, pests, and diseases as well as nation’s sovereign property rights have led to a decrease in accessibility and exchange of germplasm of interest. Having been introduced during colonial times, naturalized cacao in Puerto Rico could serve as an unexplored source of genetic diversity in improvement programs. An island-wide survey was carried out to identify naturalized trees and to determine their genetic associations to reference cacao accessions. Samples were genotyped with Expressed Sequence Tag-derived single nucleotide polymorphism (SNP) markers. Principal coordinate, cluster, and population structure analysis using the genotype data for both local and reference samples assigned individuals into five distinct genetic backgrounds: Criollo, Trinitario, Amelonado, Upper Amazon Forastero (UAF), and Nacional. Puerto Rican cacao fit into four (Criollo, Trinitario, Amelonado and UAF) of the five genetic backgrounds, being mainly composed of individuals of Criollo ancestry. Based on historical evidence, cacao of Criollo background was probably brought to Puerto Rico from Venezuela and/or Central America during colonial times. Trinitario, Amelonado, and UAF genetic backgrounds are most likely products of more modern introductions. Genotyping cacao in Puerto Rico provides information on the history and possible origin of the naturalized trees on the island. In addition, the assessment has allowed the targeting of material for incorporation and long-term conservation filling gaps in the existing collection and providing new germplasm to be evaluated for agronomic performance.     

Copying out our ABCs: the role of gene redundancy in interpreting genetic hierarchies.

The complete sequence of the Arabidopsis genome is scheduled to be determined by the end of the year 2000. While this goal could prove to be something of a moving target (the estimated size of the genome has grown from 120 Mb to 130 Mb over the last year1), it is clear that the majority of genes required for higher plant growth, reproduction and development will have been described within this time frame. Some of the implications of this landmark achievement are already becoming clear, even though less than a half of the genome has been sequenced.     

Modelling phytoplankton dynamics in lakes and reservoirs: the problem of in-situ growth rates

During the Surface Water Acidification Programme, ahydrochemical plot study was carried out at thepristine Høylandet study site during 1986–89. Theplot soils were acidic iron podzols (sensuKubiena), with a significant content of secondaryaluminium (Al), forming a potential major source oftoxic Al in streams and lakes. Rain and mist inputscontain small amounts of anthropogenic sulphate, withammonium inputs being enhanced during the summermonths. Vegetation canopy interactions, includingsorption and leaching, change input water chemistrybefore it reaches the soil, in which organicinteractions increase, especially during the summer.Amphibole in the soil parent material is probablyresponsible for the large mineral weathering ratedetermined and this source of base cations, alliedwith the small anthropogenic inputs, results in Alconcentrations in the streamwater being small incomparison with impacted sites.     

Floral homeotic gene expression defines developmental arrest stages inBrassica oleracea L. vars.botrytis anditalica

Brassica oleracea L. vars.italica (broccoli) andbotrytis (cauliflower) both undergo developmental arrests which result in heading phenotypes. We characterized these arrested tissues at the morphological and molecular levels, and defined the developmental changes that ensue after arrest has been broken. We found that the order of floral organ initiation and the positions of resulting floral organ primordia in this species differed in some respects from that ofArabidopsis, which is a member of the same family, Brassicaceae. We also cloned homologs of theArabidopsis floral homeotic genesAPETALA1 (AP1) andAPETALA3 (AP3) fromB. oleracea and characterized their expression patterns. We found that theAP1 homolog was expressed in some of the meristems of arrest-stage cauliflower, providing evidence that this tissue is florally determined. In broccoli, both the API andAP3 homologs were expressed. However, the spatial pattern of expression of the broccoliAP1 homolog differed from that ofArabidopsis. In addition, we identified a homolog of theCAULIFLOWER (CAL) gene,BoiCAL, from broccoli. The predicted amino acid sequence indicated that theBoiCAL gene product does not contain the mutation thought to be responsible for the early arrest exhibited in cauliflower (Kempin et al. 1995), but contains other changes that might play a role in the broccoli heading phenotype.The GenBank accession numbers for the sequences reported here are: U67451 (Boi2AP1); U67452 (Boi2AP1); U67453 (Boi1AP3); U67455 (Boi2AP3); U67456 (BobAP3); and U67454 (BoiCAL)     

Class II tassel seed mutations provide evidence for multiple types of inflorescence meristems in maize (Poaceae)

The tassel seed mutations ts4 and Ts6 of maize cause irregular branching in its inflorescences, tassels, and ears, in addition to feminization of the tassel due to the failure to abort pistils. A comparison of the development of mutant and wild-type tassels and ears using scanning electron microscopy reveals that at least four reproductive meristem types can be identified in maize: the inflorescence meristem, the spikelet pair meristem, the spikelet meristem, and the floret meristem. ts4 and Ts6 mutations affect the fate of specific reproductive meristems in both tassels and ears. ts4 mutants fail to form spikelet meristems from spikelet pair meristems. Ts6 mutants are delayed in the conversion of certain spikelet meristems into floret meristems. Once floret meristems are established in both of these mutants, they form florets that appear normal but fail to undergo pistil abortion in the tassel. The abnormal branching associated with each mutant is suppressed at the base of ears, permitting the formation of normal, fertile spikelets. The classification of the different types of reproductive meristems will be useful in interpretation of gene expression patterns in maize. It also provides a framework for understanding meristem functions that can be varied to diversify inflorescence architectures in the Gramineae.     

Regulation of extent of vegetative development of the maize shoot meristem

In maize plants ( Zea mays L.), the extent of vegetative development in the shoot is precisely regulated such that the apical meristem produces a predictable number of leaves before converting to tassel development. In previous experiments using shoot apex culture, we showed that the developmental program that limits vegetative development in maize is not intrinsic to the shoot apical meristem. Rather, the meristem receives information from elsewhere in the plant and responds by either continuing leaf initiation or becoming determined for determinate growth and forming an inflorescence, the tassel. Here we examine leaf primordia as potential sources for that information using shoot apex culture. Our results show that the presence of the four to six youngest leaf primordia on the shoot apex is sufficient to provide such information. The ability to reset shoot development by meristem culture also allows us to examine the basis for expression of a specific phenotype at a particular developmental stage. We found that the mutation hcf106 , which is typically expressed only during seedling stages, is not re-expressed when the shoot morphogically has regained a juvenile phase.     

High-Dimensional Analysis of Acute Myeloid Leukemia Reveals Phenotypic Changes in Persistent Cells during Induction Therapy

The plasticity of AML drives poor clinical outcomes and confounds its longitudinal detection. However, the immediate impact of treatment on the leukemic and non-leukemic cells of the bone marrow and blood remains relatively understudied. Here, we conducted a pilot study of high dimensional longitudinal monitoring of immunophenotype in AML. To characterize changes in cell phenotype before, during, and immediately after induction treatment, we developed a 27-antibody panel for mass cytometry focused on surface diagnostic markers and applied it to 46 samples of blood or bone marrow tissue collected over time from 5 AML patients. Central goals were to determine whether changes in AML phenotype would be captured effectively by cytomic tools and to implement methods for describing the evolving phenotypes of AML cell subsets. Mass cytometry data were analyzed using established computational techniques. Within this pilot study, longitudinal immune monitoring with mass cytometry revealed fundamental changes in leukemia phenotypes that occurred over time during and after induction in the refractory disease setting. Persisting AML blasts became more phenotypically distinct from stem and progenitor cells due to expression of novel marker patterns that differed from pre-treatment AML cells and from all cell types observed in healthy bone marrow. This pilot study of single cell immune monitoring in AML represents a powerful tool for precision characterization and targeting of resistant disease.