DEVELOPMENTAL ANATOMY OF JUVENILE AND ADULT SHOOTS OF MARCGRAVIA RECTIFOLIA L

Marcgravia rectifolia L. is a dimorphic vine having distinct juvenile and adult shoots. The juvenile shoot is a climber characterized by an orthotropic growth habit, a flattened stem, adventitious roots, and ovate leaves. The adult shoot, on the other hand, possesses a plagiotropic growth habit, has a cylindrical stem, few or no adventitious roots, and lanceolate leaves. Both phases have distichous phyllotaxy, however the plastochron is shorter for the adult phase than for the juvenile. Internode elongation occurs earlier for adult shoots than for juvenile shoots. Cytological analyses show the flattened stem of the juvenile results from differential production of cells, especially in the pith region. On the other hand, internodes of the adult phase are longer than juvenile internodes, a result of more cells produced rather than longer cells. In juvenile stems a perivascular band of elongated fibers develops, while in adult stems this band consists of brachyosclereids. Both phases undergo secondary growth and have non-storied cambia. Cambial activity begins in the 6th internode of each phase. As secondary growth proceeds, the adult stem produces much more xylem than juvenile stems of the same age. Adventitious roots produced in the juvenile stem are located in vertical rows at the “corners” of flattened stems and are attachment structures aiding the climbing habit of this vine. Phase changes occur regularly in this species. The juvenile phase usually transforms into the adult, however the adult phase can spontaneously revert back into the juvenile phase. The anatomical features and the phase changes are discussed and compared to Hedera helix, a vine whose phase changes have been studied in some detail. It is suggested that the anatomical features of Marcgravia rectifolia L. including its phase changes, may provide an alternative system to study physiological changes similar to those done with Hedera helix.     

A QUANTITATIVE DESCRIPTION OF CORTISONE-INDUCED ALTERATIONS IN THE ULTRASTRUCTURE OF RAT LIVER PARENCHYMAL CELLS

A stereological comparison of the hepatic parenchymal cells from 125-g male rats given a daily injection for 6 days of either 5 mg of cortisone acetate or saline (controls) was carried out with both light and electron microscopy. Cortisone treatment results in an increase in average parenchymal cell cytoplasmic volume from 5100 to 5800 µ³ and a decrease in average nuclear diameter from 7.1 to 6.5 µ. The volume of the average mitochondrion is increased fourfold in midzonal and peripheral regions of hepatic lobules, and there is a decrease in the number of mitochondria per cell such that the total mitochondrial volume per cell remains approximately unchanged. The numbers of peroxisomes are reduced, while the numbers of lysosomes and lipid droplets are increased in all parts of the lobules. The average volume of glycogen is doubled in all cells. The areas of membranes of the smooth- and rough-surfaced endoplasmic reticulum are decreased to one-half and two-thirds of their control values, respectively. The effects of cortisone on these various structural elements is discussed with respect to steroid-related alterations in biochemical processes.     

The widespread occurrence of plant cytosomes resembling animal microbodies

Summary Single membrane bounded organelles characterized by a physical association with endoplasmic reticulum have been observed in a wide range of cell types and plant species including Gymnosperm, Angiosperm, Pteridophyte, and Thallophyte (algae and fungi) tissues. The morphological similarity between these organelles and animal microbodies suggests that they are cytological homologues. Plant microbodies were observed both with and without dense internal inclusions but unlike animal microbodies could not be shown to contain uricase. Plant microbody membranes are resistant to degenerative influences and remain associated with a small portion of endoplasmic reticulum even in isolated cell fractions.     

Study of model systems to test the potential function of Artemia group 1 late embryogenesis abundant (LEA) proteins

Embryos of the brine shrimp, Artemia franciscana, are genetically programmed to develop either ovoviparously or oviparously depending on environmental conditions. Shortly upon their release from the female, oviparous embryos enter diapause during which time they undergo major metabolic rate depression while simultaneously synthesize proteins that permit them to tolerate a wide range of stressful environmental events including prolonged periods of desiccation, freezing, and anoxia. Among the known stress-related proteins that accumulate in embryos entering diapause are the late embryogenesis abundant (LEA) proteins. This large group of intrinsically disordered proteins has been proposed to act as molecular shields or chaperones of macromolecules which are otherwise intolerant to harsh conditions associated with diapause. In this research, we used two model systems to study the potential function of the group 1 LEA proteins from Artemia. Expression of the Artemia group 1 gene (AfrLEA-1) in Escherichia coli inhibited growth in proportion to the number of 20-mer amino acid motifs expressed. As well, clones of E. coli, transformed with the AfrLEA-1 gene, expressed multiple bands of LEA proteins, either intrinsically or upon induction with isopropyl-β-thiogalactoside (IPTG), in a vector-specific manner. Expression of AfrLEA-1 in E. coli did not overcome the inhibitory effects of high concentrations of NaCl and KCl but modulated growth inhibition resulting from high concentrations of sorbitol in the growth medium. In contrast, expression of the AfrLEA-1 gene in Saccharomyces cerevisiae did not alter the growth kinetics or permit yeast to tolerate high concentrations of NaCl, KCl, or sorbitol. However, expression of AfrLEA-1 in yeast improved its tolerance to drying (desiccation) and freezing. Under our experimental conditions, both E. coli and S. cerevisiae appear to be potentially suitable hosts to study the function of Artemia group 1 LEA proteins under environmentally stressful conditions.

Electronic supplementary material

The online version of this article (doi:10.1007/s12192-015-0647-3) contains supplementary material, which is available to authorized users.     

Perturbation approaches for integral projection models

Perturbation analysis of population models is fundamental to elucidating mechanisms of population dynamics and examining scenarios of change. The use of integral projection models (IPMs) has increased in the last decade, and while many of the tools and approaches developed for matrix models remain relevant, the nature of IPMs expands the framework of perturbation analysis, with different approaches often requiring important considerations. This article provides a review of – and practical guide to – different perturbation approaches for IPMs, formalizes methodologies for perturbing IPM size transition probabilities, and highlights areas where researchers should be particularly careful and critical when conducting and interpreting perturbation analysis. I use a simulated dataset to compare five hierarchical perturbation approaches for IPMs found within 63 published studies, and apply a combination of approaches to the example of an invasive perennial plant. Other perturbation approaches for IPMs are also highlighted. Most perturbation analyses for IPMs to date have focused on the response of the asymptotic population growth rate (λ) to changes in elements of the discretized projection kernel and/or the growth– survival and reproduction– recruitment sub‐kernels. Perturbations to vital rate functions and regression predictions underlying these kernels provide mechanistic insight, but are less common and can require important considerations regarding the perturbation of size transitions separate from survival and the nature of the state variable (used to represent size). The second most common approach is more specific to IPMs and examines the influence of vital rate regression parameters, each of which can have broad influence on the population growth rate. Researchers using IPMs have many perturbation options available and should carefully consider which approach or combination of approaches is most applicable and interpretable for their specific questions.     

The Influence of Physical Habitat,Pyrethroids, and Metals on Benthic Community Condition in an Urban and Residential Stream in California

This study was designed to characterize benthic communities and physical habitat in both an urban (Kirker Creek) and residential (Pleasant Grove Creek) stream in California in late spring of 2006 and 2007. Concurrent water quality evaluations, physical sediment parameters, pyrethroids, bulk metals, and SEM/AVS ratios were also measured during both years of this study. The relationship of various benthic metrics to physical habitat metrics, pyrethroids, and metals was evaluated for each stream using stepwise multiple linear regressions with both years combined for each stream, as well as both years and both streams combined, to increase the statistical power for determining significant relationships. Physical habitat was determined to be poor in each stream during both years of sampling. More than 100 benthic taxa were reported annually for both streams based on 2006 and 2007 sampling. A significant result from the stepwise regression analysis combining data for 2 years across both streams is that when habitat metrics and to a lesser degree metals are considered in the statistical models pyrethroids do not display any significant relationships to the benthic metrics. In summary, it is apparent from this analysis that the health of benthic communities in both streams is primarily affected by habitat metrics.     

FogBank: a single cell segmentation across multiple cell lines and image modalities

Background

Many cell lines currently used in medical research, such as cancer cells or stem cells, grow in confluent sheets or colonies. The biology of individual cells provide valuable information, thus the separation of touching cells in these microscopy images is critical for counting, identification and measurement of individual cells. Over-segmentation of single cells continues to be a major problem for methods based on morphological watershed due to the high level of noise in microscopy cell images. There is a need for a new segmentation method that is robust over a wide variety of biological images and can accurately separate individual cells even in challenging datasets such as confluent sheets or colonies.

Results

We present a new automated segmentation method called FogBank that accurately separates cells when confluent and touching each other. This technique is successfully applied to phase contrast, bright field, fluorescence microscopy and binary images. The method is based on morphological watershed principles with two new features to improve accuracy and minimize over-segmentation.First, FogBank uses histogram binning to quantize pixel intensities which minimizes the image noise that causes over-segmentation. Second, FogBank uses a geodesic distance mask derived from raw images to detect the shapes of individual cells, in contrast to the more linear cell edges that other watershed-like algorithms produce.We evaluated the segmentation accuracy against manually segmented datasets using two metrics. FogBank achieved segmentation accuracy on the order of 0.75 (1 being a perfect match). We compared our method with other available segmentation techniques in term of achieved performance over the reference data sets. FogBank outperformed all related algorithms. The accuracy has also been visually verified on data sets with 14 cell lines across 3 imaging modalities leading to 876 segmentation evaluation images.

Conclusions

FogBank produces single cell segmentation from confluent cell sheets with high accuracy. It can be applied to microscopy images of multiple cell lines and a variety of imaging modalities. The code for the segmentation method is available as open-source and includes a Graphical User Interface for user friendly execution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0431-x) contains supplementary material, which is available to authorized users.     

High-throughput screening for developability during early-stage antibody discovery using self-interaction nanoparticle spectroscopy

The discovery of monoclonal antibodies (mAbs) that bind to a particular molecular target is now regarded a routine exercise. However, the successful development of mAbs that (1) express well, (2) elicit a desirable biological effect upon binding, and (3) remain soluble and display low viscosity at high concentrations is often far more challenging. Therefore, high throughput screening assays that assess self-association and aggregation early in the selection process are likely to yield mAbs with superior biophysical properties. Here, we report an improved version of affinity-capture self-interaction nanoparticle spectroscopy (AC-SINS) that is capable of screening large panels of antibodies for their propensity to self-associate. AC-SINS is based on concentrating mAbs from dilute solutions around gold nanoparticles pre-coated with polyclonal capture (e.g., anti-Fc) antibodies. Interactions between immobilized mAbs lead to reduced inter-particle distances and increased plasmon wavelengths (wavelengths of maximum absorbance), which can be readily measured by optical means. This method is attractive because it is compatible with dilute and unpurified mAb solutions that are typical during early antibody discovery. In addition, we have improved multiple aspects of this assay for increased throughput and reproducibility. A data set comprising over 400 mAbs suggests that our modified assay yields self-interaction measurements that are well-correlated with other lower throughput assays such as cross-interaction chromatography. We expect that the simplicity and throughput of our improved AC-SINS method will lead to improved selection of mAbs with excellent biophysical properties during early antibody discovery.