Tracking algorithms chase down pathogens

Understanding subcellular dynamic processes governing pathogenic mechanisms is a necessary step towards the development of new drugs and strategies against infectious diseases. Subcellular pathogenic mechanisms, such as viral invasion processes involve highly dynamic nanometric-scale objects and rapid molecular interactions that require the study of individual particle paths. Single-particle tracking methods allow visualizing and characterizing the dynamics of biological objects, and provide a straightforward and accurate means to understand subcellular processes. This review describes a number of particle-tracking methods in time-lapse microscopy sequences and provides examples of using such techniques to investigate mechanisms of host-pathogen interactions.     

Assessing Mitochondrial Movement Within Neurons: Manual Versus Automated Tracking Methods

Owing to the small size of mitochondria and the complexity of their motility patterns, mitochondrial tracking is technically challenging. Mitochondria are often tracked manually; however, this is time‐consuming and prone to measurement error. Here, we examined the suitability of four commercial and open‐source software alternatives for automated mitochondrial tracking in neurons compared with manual measurements. We show that all the automated tracking tools dramatically underestimated track length, mitochondrial displacement and movement duration, with reductions ranging from 45 to 77% of the values obtained manually. In contrast, mitochondrial velocity was generally overestimated. Only the number of motile mitochondria and their directionality were similar between strategies. Despite these discrepancies, we show that automated tools successfully detected transport alterations after applying an oxidant agent. Thus, automated methods appear to be suitable for assessing relative transport differences between experimental groups, but not for absolute quantification of mitochondrial dynamics. Although useful for objective and time‐efficient measurements of mitochondrial movements, results provided by automated methods should be interpreted with caution.      

Diatrack particle tracking software: Review of applications and performance evaluation

Object tracking is an instrumental tool supporting studies of cellular trafficking. There are three challenges in object tracking: the identification of targets; the precise determination of their position and boundaries; and the assembly of correct trajectories. This last challenge is particularly relevant when dealing with densely populated images with low signal‐to‐noise ratios—conditions that are often encountered in applications such as organelle tracking, virus particle tracking or single‐molecule imaging. We have developed a set of methods that can handle a wide variety of signal complexities. They are compiled into a free software package called Diatrack. Here we review its main features and utility in a range of applications, providing a survey of the dynamic imaging field together with recommendations for effective use. The performance of our framework is shown to compare favorably to a wide selection of custom‐developed algorithms, whether in terms of localization precision, processing speed or correctness of tracks.      

Use of passive radio frequency identification technologies to monitor nest usage in the northern carmine bee‐eater (Merops n. nubicus)

The use of radio frequency identification (RFID) technology is common in animal‐monitoring applications in the wild and in zoological and agricultural settings. RFID is used to track animals and to collect information about movements and other behaviors, as well as to automate or improve husbandry. Disney's Animal Kingdom® uses passive RFID technology to monitor nest usage by a breeding colony of northern carmine bee‐eaters. We implemented RFID technologies in various equipment configurations, initially deploying low‐frequency (LF) 125 kHz RFID and later changing to high‐frequency (HF) 13.56 MHz RFID technology, to monitor breeding behavior in the flock. We installed antennas connected to RFID readers at the entrances of nest tunnels to detect RFID transponders attached to leg bands as birds entered and exited tunnels. Both LF‐RFID and HF‐RFID systems allowed the characterization of nest visitation, including the timing of nest activity, breeding pair formation, identification of egg‐laying females, participation by nonresidents, and detection of nest disruptions. However, we collected a substantially larger volume of data using the increased bandwidth and polling speed inherent with HF‐RFID, which permitted tag capture of multiple birds simultaneously and resulted in fewer missed nest visits in comparison to LF‐RFID. Herein, we describe the evolution of the RFID setups used to monitor nest usage for more than 7 years, the types of data that can be gained using RFID at nests, and how we used these data to gain insights into carmine bee‐eater breeding behavior and improve husbandry.     

Tracking bio‐molecules in live cells using quantum dots

Single particle tracking (SPT) techniques were developed to explore bio‐molecules dynamics in live cells at single molecule sensitivity and nanometer spatial resolution. Recent developments in quantum dots (Qdots) surface coating and bio‐conjugation schemes have made them most suitable probes for live cell applications. Here we review recent advancements in using quantum dots as SPT probes for live cell experiments. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Simple and Direct Assembly of Kymographs from Movies Using KYMOMAKER

In tracking analysis, the movement of cargos by motor proteins in axons is often represented by a time‐space plot termed a ‘kymograph’. Manual creation of kymographs is time‐consuming and complicated for cell biologists. Therefore, we developed KYMOMAKER, a simple system that automatically creates a kymograph from a movie without generating multiple time‐dissected movie stacks. In addition, KYMOMAKER can automatically extract faint vesicle traces, and can thereby effectively analyze cargos expressed at low levels in axons. A filter can be applied to remove traces of non‐physiological movements and to extract meaningful traces of anterograde or retrograde cargo transport. For example, only cargos that move at a speed of >0.4 µm/second for a distance of >1 µm can be included. Another function of KYMOMAKER is to create a color kymograph in which the color of the trace varies according to the position of the fluorescent particle in the axis perpendicular to the long axis of the axon. Such positional information is completely lost in conventional kymographs. KYMOMAKER is an open access program that can be easily used to analyze vesicle transport in axons by cell biologists who do not have specific knowledge of bioimage informatics .      

Urine — a source for noninvasive genetic monitoring in wildlife

Noninvasive samples are of increasing importance to study wild populations. In this study, we investigate the applicability of urine samples as the sole source of DNA for routine noninvasive genetic monitoring of wildlife using wolves (Canis lupus) as an example. Within the scope of a long‐term wolf population survey, we collected during winter snow tracking in Bieszczady Mountains, Poland 41 urine samples considered as utilizable for genetic analyses. DNA concentration was determined by quantitative real‐time polymerase chain reaction (qPCR) and six microsatellite loci were genotyped in threefold repeated genotyping experiments to assess the reliability of genetic analyses of urine. DNA concentration of 33 urine samples was successfully quantified and of 14 samples, we obtained congruent results for all analysed loci and all repeated genotyping experiments. The gender of urine samples was identified with a Y‐chromosome‐linked marker. Considering the high discovery rate of urine in conjunction with its genotype reliability, our study confirms that urine is a valuable source in noninvasive genetic monitoring. Additionally, preselection of samples via qPCR proved to be a powerful tool contributing to a beneficial cost‐value ratio of genetic analyses by minimizing genotyping errors.     

Estimation of hurdle clearance parameters using a monocular human motion tracking method

This paper presents a method of monocular human motion tracking for estimation of hurdle clearance kinematic parameters. The analysis involved 10 image sequences of five hurdlers at various training levels. Recording of the sequences was carried out under simulated starting conditions of a 110 m hurdle race. The parameters were estimated using the particle swarm optimization algorithm and they are based on analysis of the images recorded with a 100 Hz camera. The proposed method does not involve using any special clothes, markers, inertial sensors, etc. As the quality criteria, the mean absolute error and mean relative error were used. The level of computed errors justifies the use of this method to estimate hurdle clearance parameters.     

A single cell tracking system in real-time

We describe here a novel real-time cell tracking system which can measure cell migration routes under cell culture condition. This system includes a mini incubator which controls temperature and CO₂ gas flow and a PDMS (polydimethylsiloxane) chip for chemotaxis measurement. The main differences from previous ones are real-timely long-term (?24 h) tracking for single cell quantitatively, simple and inexpensive constitution of optical parts for illumination and imaging, and compatible to commercial well plate. The tracking principle is to trace cell images for each 0.2 s by converting the live cell images to binary images of black and white. Migration results of HUVEC and NCI-H23 cells are obtained respectively using this system. The results are single cell path (x, y) during migration, cell size, migration distance, migration speed, real-time pictures and so on. This system is applicable to all kinds of researches related to cell migration such as cell angiogenesis, chemotaxis, and moreover cancer metastasis.     

Wettability of juvenile plumage as a major cause of mortality threatens endangered Barau's petrel

Seabirds spend most of their life at sea and have to possess a waterproof plumage to be able to sit on water for extended periods. We tracked juvenile Barau's petrels for the first time, when they leave their birth colony and found that half of the transmitters stopped soon after they first landed on the water off Réunion Island. We suspected from observation at sea that birds may have problems with the waterproofness of their plumage. Therefore during the next season we set up a simple protocol to assess waterproofness of the plumage of the birds just before they fledge. This protocol is based on the calculation of a wettability index expressed as the mass of water logged in the plumage after simulating the bird sitting on the sea surface. We found that at least one third of chicks ready to fledge gained more than 4 g of water in 20 s, indicating that plumage was not waterproof. Within a sample of birds having fledged and before reaching the sea surface, a similar proportion of birds had their plumage not waterproof. For the birds tracked, only those with an index indicating a waterproof plumage successfully dispersed after their first touch on the sea surface. We provide evidence of a possible major cause of mortality of juvenile seabirds that has not been described previously in wild seabirds, but could exist in other species. This issue may be a major cause of threat to the endangered Barau's petrel.     

Climate change vulnerability of forest biodiversity: climate and competition tracking of demographic rates

Forest responses to climate change will depend on demographic impacts in the context of competition. Current models used to predict species responses, termed climate envelope models (CEMs), are controversial, because (i) calibration and prediction are based on correlations in space (CIS) between species abundance and climate, rather than responses to climate change over time (COT), and (ii) they omit competition. To determine the relative importance of COT, CIS, and competition for light, we applied a longitudinal analysis of 27 000 individual trees over 6–18 years subjected to experimental and natural variation in risk factors. Sensitivities and climate and resource tracking identify which species are vulnerable to these risk factors and in what ways. Results show that responses to COT differ from those predicted based on CIS. The most important impact is the effect of spring temperature on fecundity, rather than any input variable on growth or survival. Of secondary importance is growing season moisture. Species in the genera Pinus, Ulmus, Magnolia, and Fagus are particularly vulnerable to climate variation. However, the effect of competition on growth and mortality risk exceeds the effects of climate variation in space or time for most species. Because sensitivities to COT and competition are larger than CIS, current models miss the most important effects. By directly comparing sensitivity to climate in time and space, together with competition, the approach identifies which species are sensitive to climate change and why, including the heretofore overlooked impact on fecundity.     

A review of potential techniques for identifying individual stoats (Mustela erminea) visiting control or monitoring stations

Abstract

We review ways of individually identifying stoats (Mustela erminea) and similar small mammals from visits to bait stations or to monitoring devices in the field. Tracking devices are the cheapest and most practical method currently available of measuring the presence of a particular species, but there has been little research on the recognition of individuals. Elongation of tracking tunnels, or using sooty plates rather than ink to record prints, may improve detectability of individual markings. Recording visits to bait stations or tracking tunnels from DNA sequencing of hair or skin samples is likely to be prohibitively expensive for many monitoring programmes. Identification of stoats visiting bait stations or tracking tunnels using electronic devices has great potential, but these techniques are impracticably expensive because stoats move over such large areas that individual receivers and data loggers would be needed for each bait station. Chemical bait markers such as rhodamine B may be the most suitable method for identifying which animals have used a particular bait station.     

Tracking sperm in three-dimensions

Sperm motility, crucial for fertilization, has been mostly studied in two dimensions (2D) by recording their swimming trajectories near a flat surface. However, spermatozoa swim in three-dimensions (3D) to find eggs, with their speed being the main impediment to track them under realistic conditions. Here, we describe a novel method allowing 3D tracking and analysis of the trajectories of multiple free-swimming sperm. The system uses a piezo-electric device displacing a large focal distance objective mounted on a microscope to acquire 70 image stacks per second, each stack composed of 60 images that span a depth of 100 μm. With this method, 3D paths of multiple sperm in the same field could be visualized simultaneously during 1 s . Within the same sample we found that surface-confined sperm swam 25% slower, produced 3-fold fewer circular revolutions per second, and had trajectories of 134% greater radius of curvature than those sperm swimming freely in 3D.     

A general algorithm for peak-tracking in multi-dimensional NMR experiments

We present an algorithmic method allowing automatic tracking of NMR peaks in a series of spectra. It consists in a two phase analysis. The first phase is a local modeling of the peak displacement between two consecutive experiments using distance matrices. Then, from the coefficients of these matrices, a value graph containing the a priori set of possible paths used by these peaks is generated. On this set, the minimization under constraint of the target function by a heuristic approach provides a solution to the peak-tracking problem. This approach has been named GAPT, standing for General Algorithm for NMR Peak Tracking. It has been validated in numerous simulations resembling those encountered in NMR spectroscopy. We show the robustness and limits of the method for situations with many peak-picking errors, and presenting a high local density of peaks. It is then applied to the case of a temperature study of the NMR spectrum of the Lipid Transfer Protein (LTP).     

Comparing motion capture cameras versus human observer monitoring of mammal movement through fence gaps: a case study from Kenya

Monitoring the movement and distribution of wildlife is a critical tool of an adaptive management framework for wildlife conservation. We installed motion‐triggered cameras to capture the movement of mammals through two purpose‐built migration gaps in an otherwise fenced conservancy in northern Kenya. We compared the results to data gathered over the same time period (1 Jan 2011–31 Dec 2012) by the human observers monitoring mammal tracks left at the same fence gaps in a sandy loam detection strip. The camera traps detected more crossing events, more species and more individuals of each species per crossing event than did the human track observers. We tested for volume detection differences between methods for the five most common species crossing each gap and found that all detection rates were heavily weighted towards the camera‐trap method. We review some of the discrepancies between the methods and conclude that although the camera traps record more data, the management of that data can be time‐consuming and ill‐suited to some time‐sensitive decision‐making. We also discuss the importance of daily track monitoring for adaptive management conservation and community security.     

Phototropism

Despite 100 years of research, involving many noted experimentalists, our understanding of the importance and mechanisms of phototropism is sadly incomplete. However, a renewed interest in the area has brought new minds and new approaches to the subject and there are encouraging signs of progress.     

Wildlife 3D multi-object tracking

The study of wildlife populations and species has gained increased relevance due to significant endangerment, loss of habitats and world climate change. Using camera traps for monitoring is a common method to estimate species diversity, occupancy and relative abundance. We present a 3D multi-object tracking method for wildlife camera trapping using RGB-D cameras. We infer precise three-dimensional pose estimations of individual animals (i.e. locations and orientations) and also three-dimensional estimations of their observed movements, including velocity estimations. More precisely, we achieved a scaled Average Multi-Object Tracking Accuracy (sAMOTA) of 88.43%. The code is available athttps://github.com/m-klasen/3D_wildlife_tracking.