Micro-computed tomography (micro-CT or microtomography) is a non-destructive imaging technique using X-rays which allows the digitisation of an object in three dimensions. The ability of micro-CT imaging to visualise both internal and external features of an object, without destroying the specimen, makes the technique ideal for the digitisation of valuable natural history collections. This handbook serves as a comprehensive guide to laboratory micro-CT imaging of different types of natural history specimens, including zoological, botanical, palaeontological and geological samples. The basic principles of the micro-CT technology are presented, as well as protocols, tips and tricks and use cases for each type of natural history specimen. Finally, data management protocols and a comprehensive list of institutions with micro-CT facilities, micro-CT manufacturers and relative software are included.
In this manuscript we present a focus stacking system, composed of commercial photographic equipment. The system is inexpensive compared to high-end commercial focus stacking solutions. We tested this system and compared the results with several different software packages (CombineZP, Auto-Montage, Helicon Focus and Zerene Stacker). We tested our final stacked picture with a picture obtained from two high-end focus stacking solutions: a Leica MZ16A with DFC500 and a Leica Z6APO with DFC290. Zerene Stacker and Helicon Focus both provided satisfactory results. However, Zerene Stacker gives the user more possibilities in terms of control of the software, batch processing and retouching. The outcome of the test on high-end solutions demonstrates that our approach performs better in several ways. The resolution of the tested extended focus pictures is much higher than those from the Leica systems. The flash lighting inside the Ikea closet creates an evenly illuminated picture, without struggling with filters, diffusers, etc. The largest benefit is the price of the set-up which is approximately € 3,000, which is 8 and 10 times less than the LeicaZ6APO and LeicaMZ16A set-up respectively. Overall, this enables institutions to purchase multiple solutions or to start digitising the type collection on a large scale even with a small budget.
Within populations, individual animals may vary considerably in morphology and ecology. The degree to which variation in morphology is related to ecological variation within a population remains largely unexplored. We investigated whether variation in body size and shape among sexes and age classes of the lizard Podarcis melisellensis translates in differential whole-animal performance (sprint speed, bite force), escape and prey attack behaviour in the field, microhabitat use and diet. Male and female adult lizards differed significantly in body size and head and limb proportions. These morphological differences were reflected in differences in bite strength, but not in sprint speed. Accordingly, field measurements of escape behaviour and prey attack speed did not differ between the sexes, but males ate larger, harder and faster prey than females. In addition to differences in body size, juveniles diverged from adults in relative limb and head dimensions. These shape differences may explain the relatively high sprint and bite capacities of juvenile lizards. Ontogenetic variation in morphology and performance is strongly reflected in the behaviour and ecology in the field, with juveniles differing from adults in aspects of their microhabitat use, escape behaviour and diet. . It is tempting to ascribe these ecological differences directly to sexual or ontogenetic differences in body size or shape, but theoretical developments in ecological morphology and empirical observations suggest that the relationship deserves closer inspection.In the spirit of Arnold's (1983) seminal contribution to ecological morphology, prudent assessments of the relationship between the morphology and the ecology of males and females, or juveniles and adults, requires measurements of whole-animal performance. These measurements will indicate whether the morphological variation observed is functionally and ecologically relevant, i.e. translates into differential performance. For instance, does sexual dimorphism in head size actually contribute to differences in bite performance? This is not self-evident, especially not when structures relevant in a survival context (e.g. aiding feeding or locomotion) are at the same time under sexual selection. Sexual selection for larger heads could, for example, theoretically increase head size in males without affecting muscle mass (Herrel Aguirre LF, Herrel A, Van Damme R, Mathyssen E. 2003. The implications of food hardness for diet in bats. Functional Ecology 17: 201-212. Arnold SJ. 1983. Morphology, performance and fitness. American Zoologist 23: 347-361. Bauwens D, Thoen C. 1981. Escape tactics and vulnerability to predation associated with reproduction in the lizard Lacerta vivipara. Journal of Animal Ecology 50: 733-743. Bonine KE, Garland T Jr. 1999. Sprint performance of phrynosomatid lizards, measured on a high-speed treadmill, correlates with hindlimb length. Journal of Zoology, London 248: 255-265. Bonnet X, Ineich I, Shine R. 2005. Terrestrial locomotion in sea snakes: the effects of sex and...
In recent years, the general understanding of the cell proliferation and cell cycle control has increased considerably (Inzé, 2005). The phosphorylation cascade that moves the cell cycle on is understood quite well, but the regulation of cell cycle-dependent gene expression is still to be elucidated. In the eukaryotic cell cycle there are two active phases -DNA synthesis or S-phase, and segregation of chromosomes or M-phase -preceded by the regulatory gap phases, G1 and G2, respectively. G1/S and G2/M transitions are controlled by cyclin-dependent serine/threonine kinases (CDKs) which are key regulators of the cell cycle. CDK activities are controlled by various mechanisms including phosphorylation, dephosphorylation, and binding of regulatory cyclin subunits. Usually, the expression pattern of CDKs is constitutive throughout the cell cycle, meanwhile the periodic expression of cyclins provides the characteristic cell cycle phase-specific timing of CDK activities (Morgan, 1997). However, plants contain a unique class of CDKs (Btype CDKs) with periodic gene expression and elevated protein accumulation at G2/Mphases (Fobert et al., 1996; Segers et al., 1996; Magyar et al., 1997;Umeda et al., 1999;Sorrell et al., 2001; Menges and Murray, 2002). The alfalfa (Medicago sativa) Cdc2MsD, and Cdc2MsF (according to recent nomenclature Medsa;CDKB1;1 and Medsa;CDKB2;1 respectively; Joubès et al., 2000) belong into this plant-specific CDK class (Magyar et al., 1997).The transcriptional regulation of cell cycle phase-specific genes may involve several mechanisms based on multiple regulatory elements within the promoter regions of the genes. In the case of the mitotic B-type cyclin genes of Catharantus roseus (Catro;CycB1;1/CYM promoter) (Ito et al., 1998; and Nicotiana sylvestris (Nicsy;CycB1;1) (Tréhin et al., 1997;, cis-acting promoter elements were sufficient to insure cell cycle-dependent expression in a heterologous promoter context. The most important cis-elements which are involved in the regulation of the timing of the B-type cyclin transcription are AGACCGTTG in the CYM promoter region designated as the Mphase-specific activator sequence (MSA) (Ito et al., 1998), and ACAAACGGTAA in the Nicsy;CycB1;1 promoter (Tréhin et al., 1999). Although the consensus sequence is highly similar between the two elements, yet different Myb transcription factors are supposed to bind them (Tréhin et al., 1999;Ito et al., 2001;Ito, 2005). The regulation of G2-to-M-phase transition has special significance considering plant development because it is linked to the synthesis of the new cell wall and the possibility of endoreduplication. Endoreduplication involves repetitive chromosomal DNA replications without intervening mitosis or cytokinesis, leading to increased ploidy (Larkins et al., 2001; Boudolf et al., 2004b). The switch between mitotic chromosome segregation and endoreduplication programs is of major relevance in plant development including cell size determination and endosperm formation (Grafi and Larkins, 1995).Controlling of...
We tested five 3D digitization systems and one method of 2D+ recording on one object: a human skull from the Royal Belgian Institute of Natural Sciences collection (RBINS). We chose a skull because it has both simple and complex structures and different materials such as bone and enamel within the same object.The results obtained with the different technologies were compared for 3D shape accuracy, texture quality, digitization and processing time and finally price.Our results show that the structured light scanner provided the best results to record external structures, CT was found to be the best to record internal structures and is also the best for recording reflecting material such as enamel. Photogrammetry is a very good compromise between portability, price and quality. RTI is a method of 2D+ recording and is a complementary technique, using the same equipment than photogrammetry, which can capture small morphological features that are not easily digitized with the 3D techniques.
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