This research was supported by grants from the Medical Research Council, the Natural Sciences and Engineering Research Council of Canada, and the Canadian Stroke Network. GAM was also supported by the Alberta Heritage Foundation for Medical Research.

Ladder rung walking test apparatus
The horizontal ladder rung walking test apparatus consisted of side walls made of clear Plexiglas and metal rungs (3 mm diameter), which could be inserted to create a floor with a minimum distance of 1 cm between rungs (see Fig. 1; Metz and Whishaw, 2003). The side walls were 1 m long and 19 cm high measured from the height of the rungs. The ladder was elevated 30 cm above the ground with a neutral start cage and a refuge (home cage) at the end. Because animals were habituated during training, the elevation of the apparatus was unlikely to cause anxiety. The width of the alley was adjusted to the size of the animal, so that it was about 1 cm wider than an animal to prevent the animal from turning around.
The difficulty of the task was modified by varying the position of the metal rungs. A regular pattern of the rungs allowed the animals to learn the pattern over several training sessions and to anticipate the position of the rungs (Fig. 1, Pattern A). An irregular pattern that was changed from trial to trial prevented the animal from learning the pattern (Fig. 1, Pattern B). For the regular arrangement, the rungs were spaced at 2 cm intervals. For the irregular pattern, the distance of the rungs varied systematically from 1 to 5 cm. Five templates of irregular rung patterns were used, so that the same patterns were applied to all animals to standardize the difficulty of the test and enhance comparability of the outcome (see results).
Videorecording
A camera (Canovision, Canon Inc.) was positioned at a slight ventral angle, so positions of all four limbs could be recorded simultaneously. The shutter speed was set at 500 - 2000 s. The videorecordings were analyzed using frame-by-frame analysis at 30 f/sec.
Behavioral training and test analysis
The animals were trained to cross the ladder from a neutral cage to reach their home cage, so the home cage with littermates provided the positive reinforcement for walking. All animals crossed the ladder in the same direction. No further reinforcement was given to motivate the animals to cross the ladder. All animals were trained and tested five times per session.
Foot fault scoring
The qualitative evaluation of forelimb and hindlimb placement was performed using a foot fault scoring system as described earlier (Metz and Whishaw, 2003). Analysis was made by inspection of the video recordings frame-by-frame. Only consecutive steps of each limb were analyzed. Therefore, the last step before a gait interruption, such as a stop or a foot fault, and the first step after an interruption were not scored. The last stepping cycle performed at the end of the ladder was also excluded from scoring. Limb placement was scored in terms of limb placement on a rung and limb protrusion between rungs when a miss occurred.
The types of foot or paw placement on the rungs were rated using a 7-category scale (see Fig. 2). Foot or paw placement on the rung was rated according to their position and errors that occurred in placement accuracy.
(0) Total miss. 0 points were given when the limb completely missed a rung, i.e. did not touch it, and a fall occurred. A fall was defined as a limb deeply falling in-between rungs and body posture and balance were disturbed. (1) Deep slip. The limb was initially placed on a rung, then slipped off when weight-bearing and caused a fall. (2) Slight slip. The limb was placed on a rung, slipped off when weight bearing, but did not result in a fall nor interrupt the gait cycle. In this case, the animal was able to maintain balance and continue a coordinated gait. (3) Replacement. The limb was placed on a rung, but before it was weight bearing it was quickly lifted and placed on another rung. (4) Correction. The limb aimed for one rung, but was then placed on another rung without touching the first one. Alternatively, a score of 4 was recorded if a limb was placed on a rung and was quickly repositioned while remaining on the same rung. (5) Partial placement. The limb was placed on a rung with either wrist or digits of the forelimb or heel or toes of the hindlimb. (6) Correct placement. The midportion of the palm of a limb was placed on the rung with full weight support.
When different errors occurred at the same time, the lowest of the scores was recorded. For instance, if a foot was first placed on a rung and then placed on another one in the same step (score 3), and then slipped and fell in-between rungs (score 1), a score of 1 was recorded. When a fall occurred, only the limb initiating the error was rated and none of the other limbs was scored until the animal had repositioned all limbs. Error scores of five trials were averaged for analysis.
Foot placement accuracy analysis (number of errors)
The number of errors in each crossing was counted. Errors were determined based on the foot fault scoring system. An error was defined as each limb placement that received a score of 0, 1 or 2 points, i.e. an error represents any kind of foot slip or total miss. The number of errors and the number of steps was recorded for each limb separately. From these data, the mean number of errors per step was calculated and averaged for five trials. The second quantitative parameter analyzed was the average time needed to cross the entire length of the ladder task. Time measurement started after the animal was placed on the ladder and began walking the entire length of it. The time an animal spent in a stop was not included in the measurement.
Forepaw digit score
The forepaw digit score was recorded when the paw was placed correctly with its midportion on a rung (i.e. score 6 in the foot fault scoring system). The degree to which the digits of the forepaw could be flexed around a rung was rated in a three-point scale (Fig. 2). The score was applied to the position with the maximum weight support, i.e. the forelimb was positioned vertically on a rung. The scores were given as follows: (0) Digits closed in an approximate 90-degree angle. (1) Digits closed in an approximate 45 degree angle. (2) Digits completely flexed around the rung. Scores of five steps were averaged and used for analysis.
Figure legends
<img src="/files/ftp_upload/old/1204_2009_1_20_6/Fig 1 Grid.png" alt="figure 1" /> 
Fig 1. The skilled ladder rung walking test apparatus in the frontolateral view, with the specific measurements of the apparatus indicated. Two different rung patterns were used in the present study: Pattern A, regular rung arrangement, Pattern B, irregular rung arrangement. The irregular rung arrangement varied between consecutive trials.
<img src="/files/ftp_upload/old/1204_2009_1_20_7/Fig 2 (angle lines).png" alt="figure 2" />
Fig. 2. Representative photographs illustrating the three categories of the digit score. Note the angle of the digits in relation to the forelimb when in full weight support.

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We have nothing to disclose.

The present study introduces the ladder rung walking task as a new test to assess skilled walking, limb placement and limb co-ordination. The ladder rung walking task allows discrimination between subtle disturbances of motor function by combining qualitative and quantitative analysis of skilled walking. The video analysis procedure can be used for a more descriptive account of impairments, and the simple rating scale described in this paper reveals any errors in limb placement and digit flexion when grasping a rung. Qualitative analyses counting the number of footfall errors made and the time needed to cross the apparatus. These measures allow an efficient and valid examination of foot placement accuracy and digit use.
There are a number of tests of walking, including tests of rotorod walking, beam walking, cylinder test, and gait analysis, and ground reaction force analysis (Muir, 2005). Each of these tests can usefully fragment limb placement for behavioral analysis. There are a number of strength for the present testing protocol, however. First, the test allows spontaneous walking to be examined, because the animals require no food or water deprivation for motivation. Second, stepping across the rungs requires precise foot placement and grasping, allowing for analysis of both stepping and grasping. Most importantly, the present test provides a challenge to ongoing locomotion because the spacing of the rungs is varied. The variation can be used to challenge ongoing walking and/or memory of the stepping patterns (McVea and Pearson,2007).
The strength of the ladder rung walking test is that it is sufficiently challenging to reveal subtle chronic impairments in both fore- and hindlimb use and unmask impairments that require forebrain control. In the irregular rung condition of the task, animals are not capable of anticipating the rung location and learning a specific gait pattern. Consequently, each step requires adjustment in paw placement, stride length, and in distribution of body weight. While normal animals are able to adjust to an irregular rung pattern within a few trials, this ability is limited in animals with motor system lesion. The irregular rung arrangement also requires that the animals adapt their regular limb co-ordination to changing rung distances. In order to adapt limb co-ordination, animals have to control their weight support to quickly correct for any limb placement error. After a unilateral lesion, animals partially compensate for placement mistakes by using the intact limbs for weight support. Consequently, the ladder rung walking test can measure compensation by revealing foot placement errors on the intact side.
The rung walking test has been shown to be sensitive to chronic movement deficits after adult and neonate lesions to the motor system, including rat models of stroke (Emerick and Kartje, 2004; Rieck-Burchardt et al., 2004; Farr et al., 2006; Ploughman et al., 2007), Parkinson&rsquo;s disease (Metz and Whishaw, 2002; Faraji and Metz, 2007), and spinal cord injury (Z&rsquo;Graggen et al., 1998; Merkler et al., 2000). Furthermore, the ladder rung walking task detects changes in fine motor performance induced by physiological variables such as mild stress (Metz) and even changes in diet (Smith and Metz, 2005). In addition to rat models, the task is also useful for studying skilled walking in mice (Farr et al., 2006). Caution using this test needs to be used if severe spinal cord lesions are tested (Metz et al., 2000), as the rung walking task requires that animals are able to perform weight-bearing steps.
There is substantial evidence that animals with motor system lesion are able to compensate for lesion-induced deficits in skilled movements (Whishaw et al., 1997a,b, 1998; Miklyaeva et al., 1994; Kleim et al., 1998; Chu and Jones, 2000). Nevertheless, severe impairments may still be present. For example, animals with dopaminergic or red nucleus lesions recover the ability to walk on smooth surfaces or narrow beams, but measures of ground reaction forces reveal that their impairment is chronic (Muir and Whishaw, 1999, 2000). Because it reveals even subtle remaining motor deficits and compensatory adjustments, the rung walking test is a valuable tool for assessing loss and recovery of function due to brain or spinal cord injury, and the benefit of treatment approaches.

the ladder rung walking task: a scoring system and its practical application.

Progress in the development of animal models for/stroke, spinal cord injury, and other neurodegenerative disease requires tests of high sensitivity to elaborate distinct aspects of motor function and to determine even subtle loss of movement capacity. To enhance efficacy and resolution of testing, tests should permit qualitative and quantitative measures of motor function and be sensitive to changes in performance during recovery periods. The present study describes a new task to assess skilled walking in the rat to measure both forelimb and hindlimb function at the same time. Animals are required to walk along a horizontal ladder on which the spacing of the rungs is variable and is periodically changed. Changes in rung spacing prevent animals from learning the absolute and relative location of the rungs and so minimize the ability of the animals to compensate for impairments through learning. In addition, changing the spacing between the rungs allows the test to be used repeatedly in long-term studies. Methods are described for both quantitative and qualitative description of both fore- and hindlimb performance, including limb placing, stepping, co-ordination. Furthermore, use of compensatory strategies is indicated by missteps or compensatory steps in response to another limb&#x2019;s misplacement. 

Watch this Scientific Journal Video about The Ladder Rung Walking Task: A Scoring System and its Practical Application. at JoVE.com

The Ladder Rung Walking Task: A Scoring System and its Practical Application.

The ladder rung walking task is a new test to assess skilled walking and measure both forelimb and hindlimb placing, stepping, and inter-limb co-ordination.

Progress in the development of animal models for/stroke, spinal cord injury, and other neurodegenerative disease requires tests of high sensitivity to ...

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25.9K Views.  University of Lethbridge. The ladder rung walking task is a new test to assess skilled walking and measure both forelimb and hindlimb placing, stepping, and inter-limb co-ordination.

Video: The Ladder Rung Walking Task: A Scoring System and its Practical Application.

Induction and Clinical Scoring of Chronic-Relapsing Experimental Autoimmune Encephalomyelitis

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) that commonly affects young adults. It is characterized by demyelination and glial scaring in areas disseminated in the brain and spinal cord. These lesions alter nerve conduction and induce the disabling neurological deficits that vary with the location of the demyelinated plaques in the CNS (e.g. paraparesis, paralysis, blindness, incontinence).
Experimental autoimmune encephalomyelitis (EAE) is a model for MS. EAE was first induced accidentally in humans during vaccination against rabies, using viruses grown on rabbit spinal cords. Residues of spinal injected with the inactivated virus induced the CNS disease. Following these observations, a first model of EAE was described in non-human primates immunized with a CNS homogenate by Rivers and Schwenther in 1935. EAE has since been generated in a variety of species and can follow different courses depending on the species/strain and immunizing antigen used. For example, immunizing Lewis rats with myelin basic protein in emulsion with adjuvant induces an acute model of EAE, while the same antigen induces a chronic disease in guinea pigs.
The EAE model described here is induced by immunizing DA rats against DA rat spinal cord in emulsion in complete Freund's adjuvant. Rats develop an ascending flaccid paralysis within 7-14 days post-immunization. Clinical signs follow a relapsing-remitting course over several weeks. Pathology shows large immune infiltrates in the CNS and demyelination plaques. Special considerations for taking care for animals with EAE are described at the end of the video.

This video demonstrates the induction and clinical scoring of an animal model of multiple sclerosis: chronic-relapsing experimental autoimmune encephalomyelitis in DA rats. The disease, induced by immunizing rats with an emulsion containing whole rat spinal cord and complete Freund's adjuvant, presents clinical signs resembling the human disease.

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) that commonly affects young adults. It is characterized by ...

Use of Rotorod as a Method for the Qualitative Analysis of Walking in Rat

High speed videoanalysis of the details of movement can provide a source of information about qualitative aspects of walking movements. When walking on a rotorod, animals remain in approximately the same place making repetitive movements of stepping. Thus the task provides a rich source of information on the details of foot stepping movements. Subjects were hemi-Parkinson analogue rats, produced by injection of 6-hydroxydopamine (6-OHDA) into the right nigrostriatal bundle to deplete nigrostriatal dopamine (DA). The present report provides a video analysis illustration of animals previously were filmed from frontal, lateral, and posterior views as they walked (15). Rating scales and frame-by-frame replay of the video records of stepping behavior indicated that the hemi-Parkinson rats were chronically impaired in posture and limb use contralateral to the DA-depletion. The contralateral limbs participated less in initiating and sustaining propulsion than the ipsilateral limbs. These deficits secondary to unilateral DA-depletion show that the rotorod provides a use task for the analysis of stepping movements.

The rotorod test is used to assess motor status in the walking movement of hemi-Parkinson analogue rats.

High speed videoanalysis of the details of movement can provide a source of information about qualitative aspects of walking movements. When walking on a ...

Lens Transplantation in Zebrafish and its Application in the Analysis of Eye Mutants

The lens plays an important role in the development of the optic cup[1,2]. Using the zebrafish as a model organism, questions regarding lens development can be addressed. The zebrafish is useful for genetic studies due to several advantageous characteristics, including small size, high fecundity, short lifecycle, and ease of care. Lens development occurs rapidly in zebrafish. By 72 hpf, the zebrafish lens is functionally mature [3]. Abundant genetic and molecular resources are available to support research in zebrafish. In addition, the similarity of the zebrafish eye to those of other vertebrates provides basis for its use as an excellent animal model of human defects[4-7]. Several zebrafish mutants exhibit lens abnormalities, including high levels of cell death, which in some cases leads to a complete degeneration of lens tissues [8]. To determine whether lens abnormalities are due to intrinsic causes or to defective interactions with the surrounding tissues, transplantation of a mutant lens into a wild-type eye is performed. Using fire-polished metal needles, mutant or wild-type lenses are carefully dissected from the donor animal, and transferred into the host. To distinguish wild-type and mutant tissues, a transgenic line is used as the donor. This line expresses membrane-bound GFP in all tissues, including the lens. This transplantation technique is an essential tool in the studies of zebrafish lens mutants.

Lens development involves interactions with other tissues. Several zebrafish eye mutants are characterized by an abnormally small lens size. Here we demonstrate a lens transplantation experiment to determine whether this phenotype is due to intrinsic causes or defective interactions with tissues that surround the lens.

The lens plays an important role in the development of the optic cup[1,2]. Using the zebrafish as a model organism, questions regarding lens development ...

Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects

Measuring fruit morphology and color traits of vegetable and fruit crops in an objective and reproducible way is important for detailed phenotypic analyses of these traits. Tomato Analyzer (TA) is a software program that measures 37 attributes related to two-dimensional shape in a semi-automatic and reproducible manner1,2. Many of these attributes, such as angles at the distal and proximal ends of the fruit and areas of indentation, are difficult to quantify manually. The attributes are organized in ten categories within the software: Basic Measurement, Fruit Shape Index, Blockiness, Homogeneity, Proximal Fruit End Shape, Distal Fruit End Shape, Asymmetry, Internal Eccentricity, Latitudinal Section and Morphometrics. The last category requires neither prior knowledge nor predetermined notions of the shape attributes, so morphometric analysis offers an unbiased option that may be better adapted to high-throughput analyses than attribute analysis. TA also offers the Color Test application that was designed to collect color measurements from scanned images and allow scanning devices to be calibrated using color standards3. 
TA provides several options to export and analyze shape attribute, morphometric, and color data. The data may be exported to an excel file in batch mode (more than 100 images at one time) or exported as individual images. The user can choose between output that displays the average for each attribute for the objects in each image (including standard deviation), or an output that displays the attribute values for each object on the image. TA has been a valuable and effective tool for indentifying and confirming tomato fruit shape Quantitative Trait Loci (QTL), as well as performing in-depth analyses of the effect of key fruit shape genes on plant morphology. Also, TA can be used to objectively classify fruit into various shape categories. Lastly, fruit shape and color traits in other plant species as well as other plant organs such as leaves and seeds can be evaluated with TA.

Tomato Analyzer (TA) quantifies attributes of two dimensional shapes and color in a reproducible and accurate manner. A step-by-step procedure for obtaining high quality digitalized images of tomato fruit, morphological and color analyses of these images and several applications using the data generated through this software are described.

Measuring fruit morphology and color traits of vegetable and fruit crops in an objective and reproducible way is important for detailed phenotypic ...

Visualization of Caenorhabditis elegans Cuticular Structures Using the Lipophilic Vital Dye DiI

The cuticle of C. elegans is a highly resistant structure that surrounds the exterior of the animal1-4. The cuticle not only protects the animal from the environment, but also determines body shape and plays a role in motility4-6. Several layers secreted by epidermal cells comprise the cuticle, including an outermost lipid layer7.
Circumferential ridges in the cuticle called annuli pattern the length of the animal and are present during all stages of development8. Alae are longitudinal ridges that are present during specific stages of development, including L1, dauer, and adult stages2,9. Mutations in genes that affect cuticular collagen organization can alter cuticular structure and animal body morphology5,6,10,11. While cuticular imaging using compound microscopy with DIC optics is possible, current methods that highlight cuticular structures include fluorescent transgene expression12, antibody staining13, and electron microscopy1. Labeled wheat germ agglutinin (WGA) has also been used to visualize cuticular glycoproteins, but is limited in resolving finer cuticular structures14. Staining of cuticular surface using fluorescent dye has been observed, but never characterized in detail15. We present a method to visualize cuticle in live C. elegans using the red fluorescent lipophilic dye DiI (1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate), which is commonly used in C. elegans to visualize environmentally exposed neurons. This optimized protocol for DiI staining is a simple, robust method for high resolution fluorescent visualization of annuli, alae, vulva, male tail, and hermaphrodite tail spike in C. elegans.

Visualization of Caenorhabditis elegans Cuticular Structures Using the Lipophilic Vital Dye DiI

We present a method to visualize cuticle in live C. elegans using the red fluorescent lipophilic dye DiI (1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate), which is commonly used in C. elegans to visualize environmentally exposed neurons. With this optimized protocol, alae and annular cuticular structures are stained by DiI and observed using compound microscopy.

The cuticle of C. elegans is a highly resistant structure that surrounds the exterior of the animal1-4. The cuticle not only protects the animal from the ...

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

C. elegans has proven to be a valuable model system for the discovery and functional characterization of many genes and gene pathways1. More sophisticated tools and resources for studies in this system are facilitating continued discovery of genes with more subtle phenotypes or roles. 
Here we present a generalized protocol we adapted for identifying C. elegans genes with postembryonic phenotypes of interest using RNAi2. This procedure is easily modified to assay the phenotype of choice, whether by light or fluorescence optics on a dissecting or compound microscope. This screening protocol capitalizes on the physical assets of the organism and molecular tools the C. elegans research community has produced. As an example, we demonstrate the use of an integrated transgene that expresses a fluorescent product in an RNAi screen to identify genes required for the normal localization of this product in late stage larvae and adults. First, we used a commercially available genomic RNAi library with full-length cDNA inserts. This library facilitates the rapid identification of multiple candidates by RNAi reduction of the candidate gene product. Second, we generated an integrated transgene that expresses our fluorecently tagged protein of interest in an RNAi-sensitive background. Third, by exposing hatched animals to RNAi, this screen permits identification of gene products that have a vital embryonic role that would otherwise mask a post-embryonic role in regulating the protein of interest. Lastly, this screen uses a compound microscope equipped for single cell resolution.

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

We describe a sensitized method to identify postembryonic regulators of protein expression and localization in C. elegans using an RNAi-based genomic screen and an integrated transgene that expresses a functional, fluorescently tagged protein.

C. elegans has proven to be a valuable model system for the discovery and functional characterization of many genes and gene pathways1. More sophisticated ...

A Fluorescence-based Exonuclease Assay to Characterize DmWRNexo, Orthologue of Human Progeroid WRN Exonuclease, and Its Application to Other Nucleases

WRN exonuclease is involved in resolving DNA damage that occurs either during DNA replication or following exposure to endogenous or exogenous genotoxins. It is likely to play a role in preventing accumulation of recombinogenic intermediates that would otherwise accumulate at transiently stalled replication forks, consistent with a hyper-recombinant phenotype of cells lacking WRN. In humans, the exonuclease domain comprises an N-terminal portion of a much larger protein that also possesses helicase activity, together with additional sites important for DNA and protein interaction. By contrast, in Drosophila, the exonuclease activity of WRN (DmWRNexo) is encoded by a distinct genetic locus from the presumptive helicase, allowing biochemical (and genetic) dissection of the role of the exonuclease activity in genome stability mechanisms. Here, we demonstrate a fluorescent method to determine WRN exonuclease activity using purified recombinant DmWRNexo and end-labeled fluorescent oligonucleotides. This system allows greater reproducibility than radioactive assays as the substrate oligonucleotides remain stable for months, and provides a safer and relatively rapid method for detailed analysis of nuclease activity, permitting determination of nuclease polarity, processivity, and substrate preferences.

Exonucleases play critical roles in ensuring genome stability. Loss of WRN exonuclease function results in premature aging. Studying substrates and other requirements of the nuclease in vitro can help elucidate its role in vivo. Here we demonstrate a rapid and reproducible fluorescence-based assay to measure its nuclease activity.

WRN exonuclease is involved in resolving DNA damage that occurs either during DNA replication or following exposure to endogenous or exogenous genotoxins. ...

A Practical Guide to Phylogenetics for Nonexperts

Many researchers, across incredibly diverse foci, are applying phylogenetics to their research question(s). However, many researchers are new to this topic and so it presents inherent problems. Here we compile a practical introduction to phylogenetics for nonexperts.&#160;We outline in a step-by-step manner, a pipeline for generating reliable phylogenies from gene sequence datasets. We begin with a user-guide for similarity search tools via online interfaces as well as local executables. Next, we explore programs for generating multiple sequence alignments followed by protocols for using software to determine best-fit models of evolution. We then outline protocols for reconstructing phylogenetic relationships via maximum likelihood and Bayesian criteria&#160;and finally describe tools for visualizing phylogenetic trees. While this is not by any means an exhaustive description of phylogenetic approaches, it does provide the reader with practical starting information on key software applications commonly utilized by phylogeneticists. The vision for this article would be that it could serve as a practical training tool for researchers embarking on phylogenetic studies&#160;and also serve as an educational resource that could be incorporated into a classroom or teaching-lab.

Here we describe a step-by-step pipeline for generating reliable phylogenies from nucleotide or amino acid sequence datasets. This guide aims to serve researchers or students new to phylogenetic analysis.&#160;

Many researchers, across incredibly diverse foci, are applying phylogenetics to their research question(s). However, many researchers are new to this ...

Design and Analysis of Temperature Preference Behavior and its Circadian Rhythm in Drosophila

The circadian clock regulates many aspects of life, including sleep, locomotor activity, and body temperature (BTR) rhythms1,2. We recently identified a novel Drosophila circadian output, called the temperature preference rhythm (TPR), in which the preferred temperature in flies rises during the day and falls during the night 3. Surprisingly, the TPR and locomotor activity are controlled through distinct circadian neurons3. Drosophila locomotor activity is a well&#160;known circadian behavioral output and has provided strong contributions to the discovery of many conserved mammalian circadian clock genes and mechanisms4. Therefore, understanding TPR will lead to the identification of hitherto unknown molecular and cellular circadian mechanisms. Here, we describe how to perform and analyze the TPR assay. This technique not only allows for dissecting the molecular and neural mechanisms of TPR, but also provides new insights into the fundamental mechanisms of the brain functions that integrate different environmental signals and regulate animal behaviors. Furthermore, our recently published data suggest that the fly TPR shares features with the mammalian BTR3. Drosophila are ectotherms, in which the body temperature is typically behaviorally regulated. Therefore, TPR is a strategy used to generate a rhythmic body temperature in these flies5-8. We believe that further exploration of Drosophila TPR will facilitate the characterization of the mechanisms underlying body temperature control in animals.

Design and Analysis of Temperature Preference Behavior and its Circadian Rhythm in Drosophila

We recently identified a novel Drosophila circadian output, temperature preference rhythm (TPR), in which the preferred temperature in flies rises during the day and falls during the night. TPR is regulated independently from another circadian output, locomotor activity. Here&#160;we describe the design and analysis of TPR in Drosophila.

The circadian clock regulates many aspects of life, including sleep, locomotor activity, and body temperature (BTR) rhythms1,2. We recently identified a ...

Reconstruction of 3-Dimensional Histology Volume and its Application to Study Mouse Mammary Glands

Histology volume reconstruction facilitates the study of 3D shape and volume change of an organ at the level of macrostructures made up of cells. It can also be used to investigate and validate novel techniques and algorithms in volumetric medical imaging and therapies. Creating 3D high-resolution atlases of different organs1,2,3 is another application of histology volume reconstruction. This provides a resource for investigating tissue structures and the spatial relationship between various cellular features. We present an image registration approach for histology volume reconstruction, which uses a set of optical blockface images. The reconstructed histology volume represents a reliable shape of the processed specimen with no propagated post-processing registration error. The Hematoxylin and Eosin (H&#38;E) stained sections of two mouse mammary glands were registered to their corresponding blockface images using boundary points extracted from the edges of the specimen in histology and blockface images. The accuracy of the registration was visually evaluated. The alignment of the macrostructures of the mammary glands was also visually assessed at high resolution.
This study delineates the different steps of this image registration pipeline, ranging from excision of the mammary gland through to 3D histology volume reconstruction. While 2D histology images reveal the structural differences between pairs of sections, 3D histology volume provides the ability to visualize the differences in shape and volume of the mammary glands.

We present an image registration approach for 3-dimensional (3D) histology volume reconstruction, which facilitates the study of the changes of an organ at the level of macrostructures made up of cells . Using this approach, we studied the 3D changes between wild-type and Igfbp7-null mammary glands.

Histology volume reconstruction facilitates the study of 3D shape and volume change of an organ at the level of macrostructures made up of cells. It can ...

The Ladder Rung Walking Task: A Scoring System and its Practical Application.

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Induction and Clinical Scoring of Chronic-Relapsing Experimental Autoimmune Encephalomyelitis

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Lens Transplantation in Zebrafish and its Application in the Analysis of Eye Mutants

Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects

Visualization of Caenorhabditis elegans Cuticular Structures Using the Lipophilic Vital Dye DiI

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

A Fluorescence-based Exonuclease Assay to Characterize DmWRNexo, Orthologue of Human Progeroid WRN Exonuclease, and Its Application to Other Nucleases

A Practical Guide to Phylogenetics for Nonexperts

Design and Analysis of Temperature Preference Behavior and its Circadian Rhythm in Drosophila

Reconstruction of 3-Dimensional Histology Volume and its Application to Study Mouse Mammary Glands