Automated analysis of living cells through the quantitative use of automated phase contrast microscopy

A simplified theory of image formation in phase contrast microscopy is presented. It is shown that the phase shift induced in light (related to the refractive index) by the observed object can be reconstructed, point by point, from the phase-contrast digitally sampled image through an appropriate algorithm. This allows one to make quantitative observations on unstained, living cells.     

Light and transmission electron microscopical studies and amino acid analysis of the metacercarial cyst of Zygocotyle lunata (Trematoda).

Light microscopical studies indicated that the cyst of Zygocotyle lunata consists of outer, inner and ventral cyst walls. Transmission electron microscopical studies showed that the outer cyst and the ventral cyst each consist of two layers. The inner cyst is lamellated and contains a specialized ventral region designated the ventral lid. Amino acid analysis of cyst walls showed only trace amounts of cysteine, indicating that disulphide bonds are not used to stabilize the inner cyst of Z. lunata.     

Protein Production and Crystallization at the Joint Center for Structural Genomics

By definition, structural genomics centers must be able to address a large number of diverse protein targets. The methods developed should permit parallel and cost-effective processing while allowing for the diverse nature of proteins. Our approach to this problem is a multi-tiered effort where targets are characterized and categorized by behavior and processed in parallel by appropriate methods. The Joint Center for Structural Genomics (JCSG) has applied this tactic to create a fully integrated and scaleable structure determination pipeline. Highlights of the development of the current pipeline for protein production and crystallization are presented here.     

InsectDirectTM System: Rapid, High-level Protein Expression and Purification from Insect Cells

A fundamental challenge in high-throughput (HT) expression screening is to rapidly identify the appropriate expression system for many targets in parallel. Known or unknown open reading frames (ORFs) are typically amplified by PCR and then cloned into a variety of vectors, producing recombinants used to direct target protein expression in Escherichia coli, insect cells, mammalian cells, or yeast. To facilitate rapid expression and purification in Spodoptera insect cells (Sf9), we developed transient expression vectors that include an enterokinase cleavage site immediately upstream of a ligation-independent cloning site (Ek/LIC). We also developed a high-efficiency insect cell transfection reagent, and automation-compatible fusion protein purification system for insect cells to facilitate expression screening and protein production. Positive clones identified from the small-scale screening were subjected to a larger scale production. Using this InsectDirect^TM approach, we successfully expressed milligram quantities of different human proteins including heat shock proteins, phospholipases, and protein kinases.     

Solution structure of the ubiquitin-conjugating enzyme UbcH5B

The ubiquitination pathway is the main pathway for protein degradation in eukaryotic cells. The attachment of ubiquitin to a substrate protein is catalyzed by three types of enzymes, namely a ubiquitin activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3). Here, the structure of the human ubiquitin-conjugating enzyme (E2) UbcH5B has been solved by a combination of homology modeling, NMR relaxation data and automated NOE assignments. Comparison to E2 structures solved previously by X-ray crystallography or NMR shows in all cases the same compact fold, but differences are observed in the orientation of both N and C-terminal alpha-helices. The N-terminal helix that is involved in binding to ubiquitin ligases (E3) displays a different position, which could have consequences for precise E2-E3 recognition. In addition, multiple conformations of the side-chain of Asn77 are found in solution, which contrasts the single hydrogen-bonded conformation in the crystal structures of E2 enzymes. The possible implication of this conformational freedom of Asn77 for its catalytic function is discussed.     

The Relationship Between Daytime and Nighttime Food Intake in an Obese Night-Eater

Some obese individuals consume food during awakenings from nighttime sleep. Three studies were conducted on a 28-year-old morbidly obese male with chronic sleeping complaints and insignificant weight loss, despite self-reported daily caloric restriction: I. For 3 mo, the subject recorded food intake for 24-h periods. Mean daytime intake was 1286 kcal ± 386 (SD), and mean nighttime intake was 1036 kcal ± 487 (SD). Caloric values of daytime and nighttime intake were negatively correlated, r = ?0.22, df= 82, p<.05. II. Seven consecutive 24-h food intake recordings were obtained with an automated formula dispenser when the subject was an inpatient on a metabolic ward and received ad libitum formula as his sole food source. Mean daytime intake was 1245 ± 662 (SD), and mean nighttime intake was 231 ± 236 (SD). There was a non-significant negative correlation between daytime and nighttime intake, r = -0.32, df = 5, NS. III. The subject underwent polysomnographic studies on 2 non-consecutive nights, following the administration of either a low (600 kcal) or high (1800 kcal) daytime caloric condition. The subject, upon awakening from nighttime sleep, could eat from a platter of sandwich quarters placed at his bedside. The addition of 1200 kcal to daytime intake decreased nighttime intake by 654 kcal, or by 55% of the additional calories delivered during the day. The three studies (I, II, and III) show that daytime food intake can be negatively correlated with nighttime intake, and that daytime intake can influence nighttime intake in a documented obese night-eater.     

Do seasonal patterns of rat snake (Pantherophis obsoletus) and black racer (Coluber constrictor) activity predict avian nest predation?

Avian nest success often varies seasonally and because predation is the primary cause of nest failure, seasonal variation in predator activity has been hypothesized to explain seasonal variation in nest success. Despite the fact that nest predator communities are often diverse, recent evidence from studies of snakes that are nest predators has lent some support to the link between snake activity and nest predation. However, the strength of the relationship has varied among studies. Explaining this variation is difficult, because none of these studies directly identified nest predators, the link between predator activity and nest survival was inferred. To address this knowledge gap, we examined seasonal variation in daily survival rates of 463 bird nests (of 17 bird species) and used cameras to document predator identity at 137 nests. We simultaneously quantified seasonal activity patterns of two local snake species (N = 30 individuals) using manual (2136 snake locations) and automated (89,165 movements detected) radiotelemetry. Rat snakes (Pantherophis obsoletus), the dominant snake predator at the site (~28% of observed nest predations), were most active in late May and early June, a pattern reported elsewhere for this species. When analyzing all monitored nests, we found no link between nest predation and seasonal activity of rat snakes. When analyzing only nests with known predator identities (filmed nests), however, we found that rat snakes were more likely to prey on nests during periods when they were moving the greatest distances. Similarly, analyses of all monitored nests indicated that nest survival was not linked to racer activity patterns, but racer‐specific predation (N = 17 nests) of filmed nests was higher when racers were moving the greatest distances. Our results suggest that the activity of predators may be associated with higher predation rates by those predators, but that those effects can be difficult to detect when nest predator communities are diverse and predator identities are not known. Additionally, our results suggest that hand‐tracking of snakes provides a reliable indicator of predator activity that may be more indicative of foraging behavior than movement frequency provided by automated telemetry systems.     

Development of an automated method of detecting stereotyped feeding events in multisensor data from tagged rorqual whales

The introduction of animal‐borne, multisensor tags has opened up many opportunities for ecological research, making previously inaccessible species and behaviors observable. The advancement of tag technology and the increasingly widespread use of bio‐logging tags are leading to large volumes of sometimes extremely detailed data. With the increasing quantity and duration of tag deployments, a set of tools needs to be developed to aid in facilitating and standardizing the analysis of movement sensor data. Here, we developed an observation‐based decision tree method to detect feeding events in data from multisensor movement tags attached to fin whales (Balaenoptera physalus). Fin whales exhibit an energetically costly and kinematically complex foraging behavior called lunge feeding, an intermittent ram filtration mechanism. Using this automated system, we identified feeding lunges in 19 fin whales tagged with multisensor tags, during a total of over 100 h of continuously sampled data. Using movement sensor and hydrophone data, the automated lunge detector correctly identified an average of 92.8% of all lunges, with a false‐positive rate of 9.5%. The strong performance of our automated feeding detector demonstrates an effective, straightforward method of activity identification in animal‐borne movement tag data. Our method employs a detection algorithm that utilizes a hierarchy of simple thresholds based on knowledge of observed features of feeding behavior, a technique that is readily modifiable to fit a variety of species and behaviors. Using automated methods to detect behavioral events in tag records will significantly decrease data analysis time and aid in standardizing analysis methods, crucial objectives with the rapidly increasing quantity and variety of on‐animal tag data. Furthermore, our results have implications for next‐generation tag design, especially long‐term tags that can be outfitted with on‐board processing algorithms that automatically detect kinematic events and transmit ethograms via acoustic or satellite telemetry.     

A new automated technique for measuring respiration in soil samples

An automated 36 place valve to provide continuous soil respiration measurements was constructed. The valve is fully computer controlled and can sample and purge the soil atmosphere as frequently as every 75 minutes. The concentrations, automatically measured by the valve, are essentially identical to those measured manually by gas chromatography in the concentration range of 0.1 to 1% CO₂, and are kept in this range by adjusting the mass of soil and the sampling frequency. Data are transferred automatically to a computer spreadsheet program for data handling and plotting on either a rate or cumulative basis. The system has proved reliable over many thousands of analyses and has made detailed analysis of microbial activity on a continuous basis possible.