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FasParser: a package for manipulating sequence data
Yan-Bo Sun
ZOOLOGICAL RESEARCH    2017, 38 (2): 110-112.   DOI: 10.24272/j.issn.2095-8137.2017.017
Abstract ( 247 )   PDF (526KB) (891)

A computer software package called ‘FasParser’ was developed for manipulating sequence data. It can be used on personal computers to perform series of analyses, including counting and viewing differences between two sequences at both DNA and codon levels, identifying overlapping regions between two alignments, sorting of sequences according to their IDs or lengths, concatenating sequences of multiple loci for a particular set of samples, translating nucleotide sequences to amino acids, and constructing alignments in several different formats, as well as some extracting and filtrating of data for a particular FASTA file. Majority of these functions can be run in a batch mode, which is very useful for analyzing large data sets. This package can be used by a broad audience, and is designed for researchers that do not have programming experience in sequence analyses. The GUI version of FasParser can be downloaded from https://github.com/Sun-Yanbo/FasParser, free of charge.

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The role of wildlife (wild birds) in the global transmission of antimicrobial resistance genes
Jing Wang, Zhen-Bao Ma, Zhen-Ling Zeng, Xue-Wen Yang, Ying Huang, Jian-Hua Liu
ZOOLOGICAL RESEARCH    2017, 38 (2): 55-80.   DOI: 10.24272/j.issn.2095-8137.2017.003
Abstract ( 202 )   PDF (2143KB) (722)

Antimicrobial resistance is an urgent global health challenge in human and veterinary medicine. Wild animals are not directly exposed to clinically relevant antibiotics; however, antibacterial resistance in wild animals has been increasingly reported worldwide in parallel to the situation in human and veterinary medicine. This underlies the complexity of bacterial resistance in wild animals and the possible interspecies transmission between humans, domestic animals, the environment, and wildlife. This review summarizes the current data on expanded-spectrum β-lactamase (ESBL), AmpC β-lactamase, carbapenemase, and colistin resistance genes in Enterobacteriaceae isolates of wildlife origin. The aim of this review is to better understand the important role of wild animals as reservoirs and vectors in the global dissemination of crucial clinical antibacterial resistance. In this regard, continued surveillance is urgently needed worldwide.

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Contents
Zoological Research    2017, 38 (2): 55-114.   DOI:
Abstract ( 91 )   PDF (14308KB) (662)
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A new species of the genus Amolops (Anura: Ranidae) from high-altitude Sichuan, southwestern China, with a discussion on the taxonomic status of Amolops kangtingensis
Liang Fei, Chang-Yuan Ye, Yu-Fan Wang, Ke Jiang
ZOOLOGICAL RESEARCH    2017, 38 (3): 138-145.   DOI: 10.24272/j.issn.2095-8137.2017.022
GCH1 plays a role in the high-altitude adaptation of Tibetans
Yong-Bo Guo, Yao-Xi He, Chao-Ying Cui, Ouzhuluobu, Baimakangzhuo, Duojizhuoma, Dejiquzong, Bianba, Yi Peng, Cai-juan Bai, Gonggalanzi, Yong-Yue Pan, Qula, Kangmin, Cirenyangji, Baimayangji, Wei Guo, Yangla, Hui Zhang, Xiao-Ming Zhang, Wang-Shan Zheng, Shu-Hua Xu, Hua Chen, Sheng-Guo Zhao, Yuan Cai, Shi-Ming Liu, Tian-Yi Wu, Xue-Bin Qi, Bing Su
ZOOLOGICAL RESEARCH    2017, 38 (3): 155-162.   DOI: 10.24272/j.issn.2095-8137.2017.037
Abstract ( 67 )   PDF (1868KB) (309)

Tibetans are well adapted to high-altitude hypoxia. Previous genome-wide scans have reported many candidate genes for this adaptation, but only a few have been studied. Here we report on a hypoxia gene (GCH1, GTP-cyclohydrolase I), involved in maintaining nitric oxide synthetase (NOS) function and normal blood pressure, that harbors many potentially adaptive variants in Tibetans. We resequenced an 80.8 kb fragment covering the entire gene region of GCH1 in 50 unrelated Tibetans. Combined with previously published data, we demonstrated many GCH1 variants showing deep divergence between highlander Tibetans and lowlander Han Chinese. Neutrality tests confirmed a signal of positive Darwinian selection on GCH1 in Tibetans. Moreover, association analysis indicated that the Tibetan version of GCH1 was significantly associated with multiple physiological traits in Tibetans, including blood nitric oxide concentration, blood oxygen saturation, and hemoglobin concentration. Taken together, we propose that GCH1 plays a role in the genetic adaptation of Tibetans to high altitude hypoxia.

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EP300 contributes to high-altitude adaptation in Tibetans by regulating nitric oxide production
Wang-Shan Zheng, Yao-Xi He, Chao-Ying Cui, Ouzhuluobu, Dejiquzong, Yi Peng, Cai-Juan Bai, Duojizhuoma, Gonggalanzi, Bianba, Baimakangzhuo, Yong-Yue Pan, Qula, Kangmin, Cirenyangji, Baimayangji, Wei Guo, Yangla, Hui Zhang, Xiao-Ming Zhang, Yong-Bo Guo, Shu-Hua Xu, Hua Chen, Sheng-Guo Zhao, Yuan Cai, Shi-Ming Liu, Tian-Yi Wu, Xue-Bin Qi, Bing Su
ZOOLOGICAL RESEARCH    2017, 38 (3): 163-170.   DOI: 10.24272/j.issn.2095-8137.2017.036
Abstract ( 60 )   PDF (498KB) (253)

The genetic adaptation of Tibetans to high altitude hypoxia likely involves a group of genes in the hypoxic pathway, as suggested by earlier studies. To test the adaptive role of the previously reported candidate gene EP300 (histone acetyltransferase p300), we conducted resequencing of a 108.9 kb gene region of EP300 in 80 unrelated Tibetans. The allele-frequency and haplotype-based neutrality tests detected signals of positive Darwinian selection on EP300 in Tibetans, with a group of variants showing allelic divergence between Tibetans and lowland reference populations, including Han Chinese, Europeans, and Africans. Functional prediction suggested the involvement of multiple EP300 variants in gene expression regulation. More importantly, genetic association tests in 226 Tibetans indicated significant correlation of the adaptive EP300 variants with blood nitric oxide (NO) concentration. Collectively, we propose that EP300 harbors adaptive variants in Tibetans, which might contribute to high-altitude adaptation through regulating NO production.

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Creating animal models, why not use the Chinese tree shrew (Tupaia belangeri chinensis)?
Yong-Gang Yao
Zoological Research    2017, 38 (3): 118-126.   DOI: 10.24272/j.issn.2095-8137.2017.032
Abstract ( 54 )   PDF (541KB) (319)

The Chinese tree shrew (Tupaia belangeri chinensis), a squirrel-like and rat-sized mammal, has a wide distribution in Southeast Asia, South and Southwest China and has many unique characteristics that make it suitable for use as an experimental animal. There have been many studies using the tree shrew (Tupaia belangeri) aimed at increasing our understanding of fundamental biological mechanisms and for the modeling of human diseases and therapeutic responses. The recent release of a publicly available annotated genome sequence of the Chinese tree shrew and its genome database (www.treeshrewdb.org) has offered a solid base from which it is possible to elucidate the basic biological properties and create animal models using this species. The extensive characterization of key factors and signaling pathways in the immune and nervous systems has shown that tree shrews possess both conserved and unique features relative to primates. Hitherto, the tree shrew has been successfully used to create animal models for myopia, depression, breast cancer, alcohol-induced or non-alcoholic fatty liver diseases, herpes simplex virus type 1 (HSV-1) and hepatitis C virus (HCV) infections, to name a few. The recent successful genetic manipulation of the tree shrew has opened a new avenue for the wider usage of this animal in biomedical research. In this opinion paper, I attempt to summarize the recent research advances that have used the Chinese tree shrew, with a focus on the new knowledge obtained by using the biological properties identified using the tree shrew genome, a proposal for the genome-based approach for creating animal models, and the genetic manipulation of the tree shrew. With more studies using this species and the application of cutting-edge gene editing techniques, the tree shrew will continue to be under the spot light as a viable animal model for investigating the basis of many different human diseases.

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Dynamic changes in DNA demethylation in the tree shrew (Tupaia belangeri chinensis) brain during postnatal development and aging
Shu Wei, Hai-Rong Hua, Qian-Quan Chen, Ying Zhang, Fei Chen, Shu-Qing Li, Fan Li, Jia-Li Li
ZOOLOGICAL RESEARCH    2017, 38 (2): 96-102.   DOI: 10.24272/j.issn.2095-8137.2017.013
Abstract ( 54 )   PDF (2497KB) (443)

Brain development and aging are associated with alterations in multiple epigenetic systems, including DNA methylation and demethylation patterns. Here, we observed that the levels of the 5-hydroxymethylcytosine (5hmC) ten-eleven translocation (TET) enzyme-mediated active DNA demethylation products were dynamically changed and involved in postnatal brain development and aging in tree shrews (Tupaia belangeri chinensis). The levels of 5hmC in multiple anatomic structures showed a gradual increase throughout postnatal development, whereas a significant decrease in 5hmC was found in several brain regions in aged tree shrews, including in the prefrontal cortex and hippocampus, but not the cerebellum. Active changes in Tet mRNA levels indicated that TET2 and TET3 predominantly contributed to the changes in 5hmC levels. Our findings provide new insight into the dynamic changes in 5hmC levels in tree shrew brains during postnatal development and aging processes.

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Comparative study of the transfection efficiency of commonly used viral vectors in rhesus monkey (Macaca mulatta) brains
Shi-Hao Wu, Zhi-Xing Liao, Joshua D. Rizak, Na Zheng, Lin-Heng Zhang, Hen Tang, Xiao-Bin He, Yang Wu, Xia-Ping He, Mei-Feng Yang, Zheng-Hui Li, Dong-Dong Qin, Xin-Tian Hu
ZOOLOGICAL RESEARCH    2017, 38 (2): 88-95.   DOI: 10.24272/j.issn.2095-8137.2017.015
Abstract ( 48 )   PDF (1959KB) (540)

Viral vector transfection systems are among the simplest of biological agents with the ability to transfer genes into the central nervous system. In brain research, a series of powerful and novel gene editing technologies are based on these systems. Although many viral vectors are used in rodents, their full application has been limited in non-human primates. To identify viral vectors that can stably and effectively express exogenous genes within non-human primates, eleven commonly used recombinant adeno-associated viral and lentiviral vectors, each carrying a gene to express green or red fluorescence, were injected into the parietal cortex of four rhesus monkeys. The expression of fluorescent cells was used to quantify transfection efficiency. Histological results revealed that recombinant adeno-associated viral vectors, especially the serotype 2/9 coupled with the cytomegalovirus, human synapsin I, or Ca2+/calmodulin-dependent protein kinase II promoters, and lentiviral vector coupled with the human ubiquitin C promoter, induced higher expression of fluorescent cells, representing high transfection efficiency. This is the first comparison of transfection efficiencies of different viral vectors carrying different promoters and serotypes in non-human primates (NHPs). These results can be used as an aid to select optimal vectors to transfer exogenous genes into the central nervous system of non-human primates.

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Tree shrew (Tupaia belangeri) as a novel laboratory disease animal model
Ji Xiao, Rong Liu, Ce-Shi Chen
Zoological Research    2017, 38 (3): 127-137.   DOI: 10.24272/j.issn.2095-8137.2017.033
Abstract ( 48 )   HTML   PDF (224KB) (381)

The tree shrew (Tupaia belangeri) is a promising laboratory animal that possesses a closer genetic relationship to primates than to rodents. In addition, advantages such as small size, easy breeding, and rapid reproduction make the tree shrew an ideal subject for the study of human disease. Numerous tree shrew disease models have been generated in biological and medical studies in recent years. Here we summarize current tree shrew disease models, including models of infectious diseases, cancers, depressive disorders, drug addiction, myopia, metabolic diseases, and immune-related diseases. With the success of tree shrew transgenic technology, this species will be increasingly used in biological and medical studies in the future.

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Reconsidering the distribution of gray wolves
Greger Larson
ZOOLOGICAL RESEARCH    2017, 38 (3): 115-116.   DOI: 10.24272/j.issn.2095-8137.2017.021
Abstract ( 41 )   PDF (106KB) (317)
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Food restriction affects maternal investment but not neonate phenotypes in a viviparous lizard
Yang Wang, Zhi-Gao Zeng, Liang Ma, Shu-Ran Li, Wei-Guo Du
ZOOLOGICAL RESEARCH    2017, 38 (2): 81-87.   DOI: 10.24272/j.issn.2095-8137.2017.011
Abstract ( 40 )   PDF (217KB) (2560)

Food availability significantly affects an animal's energy metabolism, and thus its phenotype, survival, and reproduction. Maternal and offspring responses to food conditions are critical for understanding population dynamics and life-history evolution of a species. In this study, we conducted food manipulation experiments in field enclosures to identify the effect of food restriction on female reproductive traits and postpartum body condition, as well as on hatchling phenotypes, in a lacertid viviparous lizard from the Inner Mongolian desert steppe of China. Females under low-food availability treatment (LFT) had poorer immune function and body condition compared with those under high-food availability treatment (HFT). The food availability treatments significantly affected the litter size and litter mass of the females, but not their gestation period in captivity or brood success, or the body size, sprint speed, and sex ratio of the neonates. Females from the LFT group had smaller litter sizes and, therefore, lower litter mass than those from the HFT group. These results suggest that female racerunners facing food restriction lay fewer offspring with unchanged body size and locomotor performance, and incur a cost in the form of poor postpartum body condition and immune function. The flexibility of maternal responses to variable food availability represents an important life strategy that could enhance the resistance of lizards to unpredictable environmental change.

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Characterization of cyclophilin D in freshwater pearl mussel (Hyriopsis schlegelii)
Xiu-Xiu Liu, Cheng-Yuan Wang, Chun Luo, Jun-Qing Sheng, Di Wu, Bei-Juan Hu, Jun-Hua Wang, Yi-Jiang Hong
ZOOLOGICAL RESEARCH    2017, 38 (2): 103-109.   DOI: 10.24272/j.issn.2095-8137.2017.018
Abstract ( 38 )   PDF (668KB) (381)

Cyclophilin D (referred to as HsCypD) was obtained from the freshwater pearl mussel (Hyriopsis schlegelii). The full-length cDNA was 2 671 bp, encoding a protein consisting of 367 amino acids. HsCypD was determined to be a hydrophilic intracellular protein with 10 phosphorylation sites and four tetratricopeptide repeat (TPR) domains, but no signal peptide. The core sequence region YKGCIFHRIIKDFMVQGG is highly conserved in vertebrates and invertebrates. Phylogenetic tree analysis indicated that CypD from all species had a common origin, and HsCypD had the closest phylogenetic relationship with CypD from Lottia gigantea. The constitutive mRNA expression levels of HsCypD exhibited tissue-specific patterns, with the highest level detected in the intestines, followed by the gonads, and the lowest expression found in the hemocytes.

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Pulmonary immune cells and inflammatory cytokine dysregulation are associated with mortality of IL-1R1-/-mice infected with influenza virus (H1N1)
Lei Guo, Yan-Cui Wang, Jun-Jie Mei, Ruo-Tong Ning, Jing-Jing Wang, Jia-Qi Li, Xi Wang, Hui-Wen Zheng, Hai-Tao Fan, Long-Ding Liu
ZOOLOGICAL RESEARCH    2017, 38 (3): 146-154.   DOI: 10.24272/j.issn.2095-8137.2017.035
Abstract ( 34 )   PDF (3292KB) (215)

Respirovirus infection can cause viral pneumonia and acute lung injury (ALI). The interleukin-1 (IL-1) family consists of proinflammatory cytokines that play essential roles in regulating immune and inflammatory responses in vivo. IL-1 signaling is associated with protection against respiratory influenza virus infection by mediation of the pulmonary anti-viral immune response and inflammation. We analyzed the infiltration lung immune leukocytes and cytokines that contribute to inflammatory lung pathology and mortality of fatal H1N1 virus-infected IL-1 receptor 1 (IL-1R1) deficient mice. Results showed that early innate immune cells and cytokine/chemokine dysregulation were observed with significantly decreased neutrophil infiltration and IL-6, TNF-α, G-CSF, KC, and MIP-2 cytokine levels in the bronchoalveolar lavage fluid of infected IL-1R1-/- mice in comparison with that of wild type infected mice. The adaptive immune response against the H1N1 virus in IL-1R1-/- mice was impaired with downregulated anti-viral Th1 cell, CD8+ cell, and antibody functions, which contributes to attenuated viral clearance. Histological analysis revealed reduced lung inflammation during early infection but severe lung pathology in late infection in IL-1R1-/- mice compared with that in WT infected mice. Moreover, the infected IL-1R1-/- mice showed markedly reduced neutrophil generation in bone marrow and neutrophil recruitment to the inflamed lung. Together, these results suggest that IL-1 signaling is associated with pulmonary anti-influenza immune response and inflammatory lung injury, particularly via the influence on neutrophil mobilization and inflammatory cytokine/chemokine production.

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Genes for the high life: New genetic variants point to positive selection for high altitude hypoxia in Tibetans
Nina G. Jablonski
ZOOLOGICAL RESEARCH    2017, 38 (3): 117-117.   DOI: 10.24272/j.issn.2095-8137.2017.031
Abstract ( 28 )   PDF (90KB) (270)
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Contents
Zoological Research    2017, 38 (3): 115-170.   DOI:
Abstract ( 25 )   PDF (72637KB) (345)
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Call for papers of the special issue on Animal Models and Infectious Diseases
ZOOLOGICAL RESEARCH    2017, 38 (2): 0-0.   DOI:
Abstract ( 17 )   PDF (380KB) (163)
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Author guidelines for submitting manuscripts to Zoological Research
ZOOLOGICAL RESEARCH    2017, 38 (2): 113-114.   DOI:
Abstract ( 9 )   PDF (93KB) (172)
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Contents
Zoological Research    2017, 38 (4): 171-212.   DOI:
Abstract ( 1 )   PDF (30540KB) (115)
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Overview of the improvement of the ring-stage survival assay-a novel phenotypic assay for the detection of artemisinin-resistant Plasmodium falciparum
Jie Zhang, Guo-Hua Feng, Chun-Yan Zou, Pin-Can Su, Huai-E Liu, Zhao-Qing Yang
Zoological Research    2017, 38 (6): 317-320.   DOI: 10.24272/j.issn.2095-8137.2017.075
Abstract ( 1 )   PDF (250KB) (87)
Artemisinin resistance in Plasmodium falciparum threatens the remarkable efficacy of artemisinin-based combination therapies worldwide. Thus, greater insight into the resistance mechanism using monitoring tools is essential. The ring-stage survival assay is used for phenotyping artemisinin-resistance or decreased artemisinin sensitivity. Here, we review the progress of this measurement assay and explore its limitations and potential applications.
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Myanmarorchestia victoria sp. nov. (Crustacea, Amphipoda, Talitridae), a new species of landhopper from the high altitude forests in Myanmar
Ya-Mi Zheng, Zhong-E Hou
Zoological Research    2017, 38 (5): 281-290.   DOI: 10.24272/j.issn.2095-8137.2017.067
A new species of sisorid catfish of the genus Exostoma from the Salween drainage, Yunnan, China
Xiao-Yong Chen, William J. Poly, David Catania, Wan-Sheng Jiang
Zoological Research    2017, 38 (5): 291-299.   DOI: 10.24272/j.issn.2095-8137.2017.065
Obituary: Professor Colin Groves (1942–2017)
Zoological Research    2017, 38 (6): 320-320.   DOI:
Abstract ( 0 )   PDF (84KB) (36)
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Contents
Zoological Research    2017, 38 (5): 213-316.   DOI:
Abstract ( 0 )   PDF (62931KB) (53)
 
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Models and detection of spontaneous recurrent seizures in laboratory rodents
Bin Gu, Katherine A. Dalton
Zoological Research    2017, 38 (4): 171-179.   DOI: 10.24272/j.issn.2095-8137.2017.042
Abstract ( 0 )   PDF (933KB) (184)
Epilepsy, characterized by spontaneous recurrent seizures (SRS), is a serious and common neurological disorder afflicting an estimated 1% of the population worldwide. Animal experiments, especially those utilizing small laboratory rodents, remain essential to understanding the fundamental mechanisms underlying epilepsy and to prevent, diagnose, and treat this disease. While much attention has been focused on epileptogenesis in animal models of epilepsy, there is little discussion on SRS, the hallmark of epilepsy. This is in part due to the technical difficulties of rigorous SRS detection. In this review, we comprehensively summarize both genetic and acquired models of SRS and discuss the methodology used to monitor and detect SRS in mice and rats.
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Five newly recorded Cyprinid fish (Teleostei: Cypriniformes) in Myanmar
Tao Qin, Zhi-Ying Chen, Lu-Lu Xu, Paing Zaw, Yunn Mi Mi Kyaw, Kyaw Win Maung, Xiao-Yong Chen
Zoological Research    2017, 38 (5): 300-309.   DOI: 10.24272/j.issn.2095-8137.2017.063
Contents
Zoological Research    2017, 38 (6): 317-458.   DOI:
Abstract ( 0 )   PDF (25831KB) (24)
 
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Complete mitochondrial genome of the leaf muntjac (Muntiacus putaoensis) and phylogenetics of the genus Muntiacus
Guo-Gang Li, Ming-Xia Zhang, Kyaw Swa, Kyaw-Win Maung, Rui-Chang Quan
Zoological Research    2017, 38 (5): 310-316.   DOI: 10.24272/j.issn.2095-8137.2017.058
Establishment of basal cell carcinoma animal model in Chinese tree shrew (Tupaia belangeri chinensis)
Li-Ping Jiang, Qiu-Shuo Shen, Cui-Ping Yang, Yong-Bin Chen
Zoological Research    2017, 38 (4): 180-190.   DOI: 10.24272/j.issn.2095-8137.2017.045
Abstract ( 0 )   PDF (3980KB) (128)
Basal cell carcinoma (BCC) is the most common skin cancer worldwide, with incidence rates continuing to increase. Ultraviolet radiation is the major environmental risk factor and dysregulation of the Hedgehog (Hh) signaling pathway has been identified in most BCCs. The treatment of locally advanced and metastatic BBCs is still a challenge and requires a better animal model than the widely used rodents for drug development and testing. Chinese tree shrews (Tupaia belangeri chinensis) are closely related to primates, bearing many physiological and biochemical advantages over rodents for characterizing human diseases. Here, we successfully established a Chinese tree shrew BCC model by infecting tail skins with lentiviral SmoA1, an active form of Smoothened (Smo) used to constitutively activate the Hh signaling pathway. The pathological characteristics were verified by immunohistochemical analysis. Interestingly, BCC progress was greatly enhanced by the combined usage of lentiviral SmoA1 and shRNA targeting Chinese tree shrew p53. This work provides a useful animal model for further BCC studies and future drug discoveries.
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Regeneration of adhesive tail pad scales in the New Zealand gecko (Hoplodactylus maculatus)(Reptilia;Squamata;Lacertilia) can serve as an experimental model to analyze setal formation in lizards generally
Lorenzo Alibardi, Victor Benno Meyer-Rochow
Zoological Research    2017, 38 (4): 191-197.   DOI: 10.24272/j.issn.2095-8137.2017.046
Abstract ( 0 )   PDF (10901KB) (76)
During the regeneration of the tail in the arboreal New Zealand gecko (Hoplodactylus maculatus) a new set of tail scales, modified into pads bearing setae 5-20 μm long, is also regenerated. Stages of the formation of these specialized scales from epidermal pegs that invaginate the dermis of the regenerating tail are described on the basis of light and electron microscopic images. Within the pegs a differentiating clear layer interfaces with the spinulae and setae of the Oberhäutchen according to a process similar to that described for the digital pads. A layer of clear cytoplasm surrounds the growing tiny setae and eventually cornifies around them and their spatular ends, later leaving the new setae freestanding on the epidermal surface. The fresh adhesive pads help the gecko to maintain the prehensile function of its regenerated tail as together with the axial skeleton (made of a cylinder of elastic cartilage) the pads allow the regenerated tail to curl around twigs and small branches just like the original tail. The regeneration of caudal adhesive pads represents an ideal system to study the cellular processes that determine setal formation under normal or experimental manipulation as the progressive phases of the formation of the setae can be sequentially analyzed.
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