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.

<ol>
	<li>Chu, C. J., Jones, T. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Experience-dependent+structural+plasticity+in+cortex+heterotopic+to+focal+sensorimotor+cortical+damage.">Experience-dependent structural plasticity in cortex heterotopic to focal sensorimotor cortical damage.</a> Exp Neurol. 166, 403-414 (2000).</li><li>Emerick, A. J., Kartje, G. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Behavioral+recovery+and+anatomical+plasticity+in+adult+rats+after+cortical+lesion+and+treatment+with+monoclonal+antibody+IN-1.">Behavioral recovery and anatomical plasticity in adult rats after cortical lesion and treatment with monoclonal antibody IN-1.</a> Behav Brain Res. 152, 315-325 (2004).</li><li>Faraji, J., Metz, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sequential+bilateral+striatal+lesions+have+additive+effects+on+single+skilled+limb+use+in+rats.">Sequential bilateral striatal lesions have additive effects on single skilled limb use in rats.</a> Behav Brain Res. 177, 195-204 (2007).</li><li>Farr, T. D., Liu, L., Colwell, K. L., Whishaw, I. Q., Metz, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bilateral+alteration+in+stepping+pattern+after+unilateral+motor+cortex+injury:+a+new+test+strategy+for+analysis+of+skilled+limb+movements+in+neurological+mouse+models.">Bilateral alteration in stepping pattern after unilateral motor cortex injury: a new test strategy for analysis of skilled limb movements in neurological mouse models.</a> J Neurosci Methods. 153, 104-113 (2006).</li><li>Kleim, J. A., Barbay, S., Nudo, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+reorganization+of+the+rat+motor+cortex+following+motor+skill+learning.">Functional reorganization of the rat motor cortex following motor skill learning.</a> J Neurophysiol. 80, 3321-3325 (1998).</li><li>Merkler, D., Metz, G. A., Raineteau, O., Dietz, V., Schwab, M. E., Fouad, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Locomotor+recovery+in+spinal+cord-injured+rats+treated+with+an+antibody+neutralizing+the+myelin-associated+neurite+growth+inhibitor+Nogo-A.">Locomotor recovery in spinal cord-injured rats treated with an antibody neutralizing the myelin-associated neurite growth inhibitor Nogo-A.</a> J Neurosci. 21, 3665-3673 (2001).</li><li>McVea, D. A., Pearson, K. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stepping+of+the+forelegs+over+obstacles+establishes+long-lasting+memories+in+cats.">Stepping of the forelegs over obstacles establishes long-lasting memories in cats.</a> Curr Biol. 17, R621-R623 (2007).</li><li>Metz, G. A. S., Dietz, V., Schwab, M. E., Meent, H. v. a. n. d. e. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effects+of+unilateral+pyramidal+tract+section+on+hindlimb+motor+performance+in+the+rat.">The effects of unilateral pyramidal tract section on hindlimb motor performance in the rat.</a> Behav Brain Res. 95, 37-46 (1998).</li><li>Metz, G. A. S., Dietz, V., Schwab, M. E., Fouad, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient+testing+of+motor+function+in+spinal+cord+injured+rats.">Efficient testing of motor function in spinal cord injured rats.</a> Brain Res. 883, 165-177 (2000).</li><li>Metz, G. A., Whishaw, I. Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drug-induced+rotation+intensity+in+unilateral+dopamine-depleted+rats+is+not+correlated+with+end+point+or+qualitative+measures+of+forelimb+or+hindlimb+motor+performance.">Drug-induced rotation intensity in unilateral dopamine-depleted rats is not correlated with end point or qualitative measures of forelimb or hindlimb motor performance.</a> Neuroscience. 111, 325-336 (2002).</li><li>Miklyaeva, E. I., Castaneda, E., Whishaw, I. Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Skilled+reaching+deficits+in+unilateral+dopamine-depleted+rats:+impairments+in+movement+and+posture+and+compensatory+adjustments.">Skilled reaching deficits in unilateral dopamine-depleted rats: impairments in movement and posture and compensatory adjustments.</a> J Neurosci. 14, 7148-7158 (1994).</li><li>Muir, G. D., Whishaw, I. Q., Kolb, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Locomotion in The Behavior of the laboratory rat. , 150-161 (2005).</li><li>Muir, G. D., Whishaw, I. Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ground+reaction+forces+in+locomoting+hemi-parkinsonian+rats:+a+definitive+test+for+impairments+and+compensations.">Ground reaction forces in locomoting hemi-parkinsonian rats: a definitive test for impairments and compensations.</a> Exp Brain Res. 126, 307-314 (1999).</li><li>Muir, G. D., Whishaw, I. Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Red+nucleus+lesions+impair+overground+locomotion+in+rats:+a+kinetic+analysis.">Red nucleus lesions impair overground locomotion in rats: a kinetic analysis.</a> Eur J Neurosci. 12, 1113-1122 (2000).</li><li>Riek-Burchardt, M., Henrich-Noack, P., Metz, G. A., Reymann, K. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+chronic+sensorimotor+impairments+in+the+ladder+rung+walking+task+in+rats+with+endothelin-1-induced+mild+focal+ischemia.">Detection of chronic sensorimotor impairments in the ladder rung walking task in rats with endothelin-1-induced mild focal ischemia.</a> J Neurosci Methods. 137, 227-233 (2004).</li><li>Ploughman, M., Attwood, Z., White, N., Dor&#233;, J. J., Corbett, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Endurance+exercise+facilitates+relearning+of+forelimb+motor+skill+after+focal+ischemia.">Endurance exercise facilitates relearning of forelimb motor skill after focal ischemia.</a> Eur J Neurosci. 25, 3453-3460 (2007).</li><li>Thallmair, M., Metz, G. A. S., Z'Graggen, W. J., Kartje, G. L., Schwab, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+recovery+parallels+enhanced+plasticity+of+the+lesioned+adult+CNS+by+antibodies+to+neurite+growth+inhibitors.">Functional recovery parallels enhanced plasticity of the lesioned adult CNS by antibodies to neurite growth inhibitors.</a> Nature Neurosci. 1, 124-131 (1998).</li><li>Meyenburg, J. v. o. n., Brosamle, C., Metz, G. A., Schwab, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regeneration+and+sprouting+of+chronically+injured+corticospinal+tract+fibers+in+adult+rats+promoted+by+NT-3+and+the+mAb+IN-1,+which+neutralizes+myelin-associated+neurite+growth+inhibitors.">Regeneration and sprouting of chronically injured corticospinal tract fibers in adult rats promoted by NT-3 and the mAb IN-1, which neutralizes myelin-associated neurite growth inhibitors.</a> Exp Neurol. 154, 583-594 (1998).</li><li>Whishaw, I. Q., Coles, B. L., Pellis, S. M., Miklyaeva, E. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impairments+and+compensation+in+mouth+and+limb+use+in+free+feeding+after+unilateral+dopamine+depletions+in+a+rat+analog+of+human+Parkinson's+disease.">Impairments and compensation in mouth and limb use in free feeding after unilateral dopamine depletions in a rat analog of human Parkinson's disease.</a> Behav Brain Res. 84, 167-177 (1997a).</li><li>Whishaw, I. Q., Woodward, N. C., Miklyaeva, E., Pellis, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+limb+use+by+control+rats+and+unilateral+DA-depleted+rats+in+the+Montoya+staircase+test:+movements,+impairments+and+compensatory+strategies.">Analysis of limb use by control rats and unilateral DA-depleted rats in the Montoya staircase test: movements, impairments and compensatory strategies.</a> Behav Brain Res. 89, 167-177 (1997b).</li><li>Whishaw, I. Q., Gorny, B., Sarna, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Paw+and+limb+use+in+skilled+and+spontaneous+reaching+after+pyramidal+tract,+red+nucleus+and+combined+lesions+in+the+rat:+behavioral+and+anatomical+dissociations.">Paw and limb use in skilled and spontaneous reaching after pyramidal tract, red nucleus and combined lesions in the rat: behavioral and anatomical dissociations.</a> Behav Brain Res. 93, 167-183 (1998).</li><li>Z'Graggen, W. J., Metz, G. A. S., Kartje, G. L., Schwab, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+recovery+and+enhanced+ccrtico-fugal+plasticity+in+the+adult+rat+after+unilateral+pyramidal+tract+section+and+blockade+of+myelin-associated+neurite+growth+inhibitors.">Functional recovery and enhanced ccrtico-fugal plasticity in the adult rat after unilateral pyramidal tract section and blockade of myelin-associated neurite growth inhibitors.</a> J Neurosci. 18, 4744-4757 (1998).</li></ol>

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. Qua...

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 ...

the-ladder-rung-walking-task-scoring-system-its-practical

Research

JoVE Journal

Biology

25.8K 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.

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 ...

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 ...

Imaging Spatial Reorganization of a MAPK Signaling Pathway Using the Tobacco Transient Expression System

Visualization of dynamic signaling events in live cells has been a challenge. We expanded an established transient expression system, the biomolecular fluorescent complementation (BiFC) assay in tobacco epidermal cells, from testing protein-protein interaction to monitoring spatial distribution of signal transduction in plant cells. In this protocol, we used the BiFC assay to show that the interaction and the signaling between the Arabidopsis MAPKKK YODA and MAPK6 occur at the plasma membrane. When the scaffold protein BASL was co-expressed, the YODA-MAPK interaction redistributed and spatially co-polarized with CFP-BASL. This modified tobacco expression system allows for quick examination of signaling localization and dynamic changes (less than 4 days) and can accommodate multiple of fluorescent protein colors (at least three). We also presented detailed methods to quantify protein distribution (asymmetric spatial localization, or &#34;polarization&#34;) in tobacco cells. This advanced tobacco expression system has a potential to be used widely for quick testing of dynamic signaling events in live plant cells.

At the subcellular level, signaling events are dynamically modulated by developmental and environmental cues. Here we describe a protocol that employs the tobacco transient expression system to monitor dynamic protein-protein interaction and to disclose spatial organization of signal transduction in plant cells.

Visualization of dynamic signaling events in live cells has been a challenge. We expanded an established transient expression system, the biomolecular ...

Agrobacterium-Mediated Genetic Transformation, Transgenic Production, and Its Application for the Study of Male Reproductive Development in Rice

Male sterility is an important agronomic trait for hybrid seed production that is usually characterized by functional defects in male reproductive organs/gametes. Recent advances in CRISPR-Cas9 genome editing technology allow for high editing efficacy and timesaving knockout mutations of endogenous candidate genes at specific sites. Additionally, Agrobacterium-mediated genetic transformation of rice is also a key method for gene modification, which has been widely adopted by many public and private laboratories. In this study, we applied CRISPR-Cas9 genome editing tools and successfully generated three male sterile mutant lines by targeted genome editing of OsABCG15 in a japonica cultivar. We used a modified Agrobacterium-mediated rice transformation method that could provide excellent means of genetic emasculation for hybrid seed production in rice. Transgenic plants can be obtained within 2&#8211;3 months and homozygous transformants were screened by genotyping using PCR amplification and Sanger sequencing. Basic phenotypic characterization of the male sterile homozygous line was performed by microscopic observation of the rice male reproductive organs, pollen viability analysis by iodine potassium iodide (I2-KI) staining semi-thin cross-sectioning of developing anthers.

Agrobacterium-Mediated Genetic Transformation, Transgenic Production, and Its Application for the Study of Male Reproductive Development in Rice

This work describes the use of CRISPR-Cas9 genome editing technology to knockout endogenous gene OsABCG15 followed by a modified Agrobacterium-mediated transformation protocol to produce a stable male-sterile line in rice.