> Living Beings > Fish > Lampreys

Lampreys

Lampreys are a group of jawless, eel-like vertebrates that have been the subject of extensive research.
Thesse ancient, fascinating creatures possess a unique anatomy and physiology, making them an invaluable model organism for understanding the evolution of vertebrates.
PubCompare.ai's innovative AI-driven comparison tool empowers researchers to quickly locate the most accurate and reproducible protocols from publications, preprints, and patents, revolutionizing the study of lampreys and enhancing the quality and reliability of related research.

Most cited protocols related to «Lampreys»

Lamprey Genome Assembly and Hox Cluster Analysis

The lamprey genome assembly has been deposited under GenBank accession AEFG01. Improved assemblies for Hox clusters have been deposited under GenBank accessions JQ706314–JQ706327. Transcript sequencing data have been deposited under GenBank Short Read Archive accessions SRX109761.3, SRX109762.3, SRX109764.3, SRX109765.3, SRX109766.3, SRX109767.3, SRX109768.3, SRX109769.3, SRX109770.3, SRX110023.2, SRX110024.2, SRX110025.2, SRX110026.2, SRX110027.2, SRX110028.2, SRX110029.2, SRX110030.2, SRX110031.2, SRX110032.2, SRX110033.2, SRX110034.2 and SRX110035.2. Additional information is provided in Supplementary Table 5.

Smith J.J., Kuraku S., Holt C., Sauka-Spengler T., Jiang N., Campbell M.S., Yandell M.D., Manousaki T., Meyer A., Bloom O.E., Morgan J.R., Buxbaum J.D., Sachidanandam R., Sims C., Garruss A.S., Cook M., Krumlauf R., Wiedemann L.M., Sower S.A., Decatur W.A., Hall J.A., Amemiya C.T., Saha N.R., Buckley K.M., Rast J.P., Das S., Hirano M., McCurley N., Guo P., Rohner N., Tabin C.J., Piccinelli P., Elgar G., Ruffier M., Aken B.L., Searle S.M., Muffato M., Pignatelli M., Herrero J., Jones M., Brown C.T., Chung-Davidson Y.W., Nanlohy K.G., Libants S.V., Yeh C.Y., McCauley D.W., Langeland J.A., Pancer Z., Fritzsch B., de Jong P.J., Zhu B., Fulton L.L., Theising B., Flicek P., Bronner M.E., Warren W.C., Clifton S.W., Wilson R.K, & Li W. (2013). Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nature genetics, 45(4), 415-421e2.

Publication 2013

Genome Lampreys

Identification and Classification of OR-like Genes

Here, “OR-like genes” include amphioxus OR genes and Type 1
and Type 2 genes in vertebrates, though some Type 2 genes are suggested to be
non-OR genes (see Results). The method for identifying OR-like genes is
essentially the same as that described in a previous paper (Niimura and Nei 2007 (link)) but was slightly
modified. TBlastN (Altschul et al. 1997 (link))
searches were conducted against genome sequences of 14 nonmammalian chordate
species using known OR genes as queries. The query genes included an OR-like
gene from amphioxus (GenBank accession number, AB182635; Satoh 2005 (link)) and two OR genes from river lampreys
(AJ012708 and AJ012709; Freitag et al.
1999) as well as zebra fish, fugu, western clawed frog, chicken, mouse,
and human OR genes that had been previously identified (Niimura and Nei 2003 (link), 2005a (link), 2005b (link)). From the
sequences detected by the TBlastN searches, functional OR genes were identified
by the method in Niimura and Nei
(2007). To identify Type 2 genes from mammalian genomes, TBlastN searches
were conducted against the platypus, opossum, cow, dog, mouse, rat, macaque,
chimpanzee, and human genome sequences using nonmammalian Type 2 genes
identified in this study as queries. Because Type 2 genes and amphioxus OR genes
are more diverse than mammalian OR genes, I conducted TBlastN searches
iteratively using functional Type 2 genes and amphioxus OR genes identified
above as queries and confirmed that no new genes were detected. The functional
genes identified were classified into groups α–λ
on the basis of phylogenetic trees (see Results).
Truncated genes and pseudogenes were detected by conducting TBlastN searches
against the genome sequences with the cutoff E value of 1
× 10⁻²⁰ using the functional OR-like genes
identified above as queries (for details, see Niimura and Nei 2007 (link)). The truncated genes and pseudogenes were
classified into groups α–λ in the following way.
Suppose that, for a given sequence A (a truncated gene or a pseudogene), a query
(functional) gene B showed the lowest E value among all
queries. In this case, the sequence A was assigned to the group to which the
gene B belongs. Amino acid sequences of all OR-like genes identified in this
study are available in supplementary data sets 1 and 2 (Supplementary Material online). The names of genes that belong
to each group are provided in supplementary data set 3 (Supplementary Material online).

, & Niimura Y. (2009). On the Origin and Evolution of Vertebrate Olfactory Receptor Genes: Comparative Genome Analysis Among 23 Chordate Species. Genome Biology and Evolution, 1, 34-44.

Publication 2009

Amino Acid Sequence Chickens Chordata Didelphidae Genes Genome Genome, Human Homo sapiens Lampreys Lancelets Macaca Mammals Mice, Laboratory Pan troglodytes Platypus, Duckbilled Pseudogenes Rivers Takifugu Vertebrates Xenopus laevis Zebrafish

Phylogenetic Analysis of Sea Lamprey Hox Genes

Phylogenetic analysis was performed on Hox paralog groups with 4 or more members in sea lamprey: groups 4, 8, 9, 11 and 13. For each paralog group, predicted Sea lamprey Hox protein sequences were aligned against homologs from other vertebrate species and amphioxus, retrieved from Genbank. Our approach was informed by the experiences detailed by Kuraku et al^{89 (link)}, Qiu et al^{90 (link)}, Mehta et al^{17 (link)} and Manousaki et al⁹¹. In selecting jawed vertebrate taxa for these analyses, we avoided teleost fish and Xenopus laevis as these lineages have undergone additional genome duplication events, which can lead to their co-orthologous genes/proteins being more derived than those from non-duplicated lineages. Thus, we opted for Elephant shark (C. milii) and coelacanth (L. menadoensis) as Chondrichthian and ‘basal’ Sarcopterygian representatives respectively, both of which having slowly evolving protein-coding genes and well characterized Hox gene complements^{92 (link),93 (link)}. Urochordates are the sister group of vertebrates but the divergent nature of their Hox genes led us to favor the cephalochordate amphioxus as a source for outgroup sequences in our analyses. We chose to perform protein alignments rather than DNA alignments due to the high coding GC content in lamprey, which can result in artifactual clustering of lamprey genes in DNA trees. Nevertheless, the unique pattern of amino-acid composition in lamprey proteins is an unavoidable complicating factor that impinges on their phylogenetic analysis and can lead to artifactual clustering of lamprey proteins, as described in Qiu et al^{90 (link)}. The MEGA7^{41 (link)} software suite was used for sequence alignment, best-fit substitution model evaluation and phylogeny reconstruction. Protein alignments were performed with full available length protein sequences using MUSCLE^{41 (link)}. Best-fit substitution models were evaluated and chosen for each alignment. Maximum likelihood, neighbor joining and maximum parsimony approaches were used for phylogenetic analysis, with 100 bootstrap replicates generated for node support. For each method, all positions in the alignment containing gaps and missing data were eliminated.

Smith J.J., Timoshevskaya N., Ye C., Holt C., Keinath M.C., Parker H.J., Cook M.E., Hess J.E., Narum S.R., Lamanna F., Kaessmann H., Timoshevskiy V.A., Waterbury C.K., Saraceno C., Wiedemann L.M., Robb S.M., Baker C., Eichler E.E., Hockman D., Sauka-Spengler T., Yandell M., Krumlauf R., Elgar G, & Amemiya C.T. (2018). The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature genetics, 50(2), 270-277.

Publication 2017

Amino Acids Amino Acid Sequence Elephants Fishes Gene Products, Protein Genes Genes, Homeobox Genome Lampreys Lancelets Petromyzon marinus Proteins Sequence Alignment Sequence Analysis Sharks Trees Urochordata Vertebrates Xenopus laevis

Comparative Genomics Reveals Conserved Synteny

Analyses of conserved synteny were performed as previously described^{4 (link)}. Briefly, predicted protein sequences from the lamprey genome were aligned to proteins from Gar (LepOcu1: GCA_000242695.1) and Chicken (Galgal4: GCA_000002315.2) genome assemblies^{79 (link)}. All alignments with bitscore ≥100 and ≥90% of the best match (within a species) were considered putative orthologs of each lamprey, chicken or gar gene. Groups of orthologs were filtered to remove those with more than 6 members in any given species. Enrichment of orthologs on chromosomes or chromosomal segments was assessed using χ² tests, incorporating Yates’ correction for continuity and Bonferroni corrections for multiple testing as previously described^{4 (link)}.

Publication 2017

Amino Acid Sequence Chickens Chromosomes Conserved Synteny Genes Genome Lampreys Proteins

Pairwise Genome Alignments with FDR Filtering

Our pipeline starts with pairwise alignments to the Zv9/danRer7 zebrafish genome assembly using the following genomes that broadly sample ∼450 My of vertebrate evolution: medaka (oryLat2), tetraodon (tetNig2), fugu (v5) (36 (link)), (fr3, http://www.fugu-sg.org/), stickleback (gasAcu1), lamprey (petMar1), cow (bosTau4), dog (canFam2), horse (equCab2), chicken (galGal3), human (hg19), elephant (loxAfr3), mouse (mm9), opossum (monDom5), platypus (ornAna1) and frog (xenTro2) (Figure 2, Steps 1 and 2). We built pairwise alignments to zebrafish using lastz (37 (link)) with the HoxD55 scoring matrix and sensitive parameter settings: H = 2000, Y = 3000, L = 3000 and K = 2000. The pairwise alignments were built using genomes that were hard-masked for repeats using UCSC Table Browser’s RepMask and Simple Repeats tracks (28 (link)).
Although sensitive alignment parameters are necessary to detect homologies between diverged sequences, they also produce dubious alignments. Therefore, we subsequently quality filtered the lastz alignments using threshold values determined by FDR calculations. Specifically, we created two randomized genomes obtained by di-nucleotide shuffling every entire zebrafish chromosome (global shuffling) as well as di-nucleotide shuffling 100-bp sliding windows in every zebrafish chromosome (local shuffling). The position and size of all assembly gaps was preserved in both cases. Then, we aligned both shuffled genomes against the real genome of stickleback, fugu, tetraodon, medaka and lamprey and estimated the FDR as the number of bases in the shuffled genome that align (false positives) divided by the number of bases in the real genome that align (true positives and false positives). We kept a local alignment if a sliding window of size ≥30 bp has ≥60% sequence identity and ≥1.8 bits entropy. These parameters give an FDR between 0.13 and 0.3 for global shuffling and an FDR between 0.15 and 0.34 for local shuffling (Supplementary Table S1) and were subsequently used for all real pairwise alignments. Here, sequence identity is calculated as the number of matches over the alignment length. Entropy is calculated as

This entropy filter excludes unmasked tandem repeats or regions of low-sequence complexity that typically yield non-orthologous alignments with high-sequence identity but where only a subset of the four DNA bases predominately aligns.

Hiller M., Agarwal S., Notwell J.H., Parikh R., Guturu H., Wenger A.M, & Bejerano G. (2013). Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish. Nucleic Acids Research, 41(15), e151.

Publication 2013

Biological Evolution BP 100 Chickens Chromosomes Didelphidae DNA, A-Form Elephants Entropy Equus caballus Genome Homo sapiens Lampreys Mice, House Nucleotides Oryzias latipes Platypus, Duckbilled Rana Sequence Alignment Sticklebacks Takifugu Tandem Repeat Sequences Vertebrates Zebrafish

Most recents protocols related to «Lampreys»

Rac1 Inhibitor Effects on Lamprey Epidermis

Lampreys treated with the Rac1 inhibitor were cultured using the same above-described approach. The working solution was prepared using DMSO, PEG300 and Tween-80 according to the manufacturer’s instructions (Shanghai Yuanye Biological, Shanghai, China). Subsequently, 1.8 mL of physiological salt solution was added, and the samples were stored at −20 °C. The above-described method was used to damage the epidermis of the lampreys, and before damage, the lampreys were injected with the inhibitor before damage at a low (15 mg/kg) or high concentration (50 mg/kg) or with the carrier control (DMSO, PEG300, Tween-80); the inhibitor was injected subcutaneously every other day. The damaged tissues were collected after 2 and 7 days for staining.

Li S., Zhao Z., Li Q., Li J, & Pang Y. (2023). Lamprey Wound Healing and Regenerative Effects: The Collaborative Efforts of Diverse Drivers. International Journal of Molecular Sciences, 24(4), 3213.

Full text: Click here

Publication 2023

Biopharmaceuticals Epidermis Lampreys physiology polyethylene glycol 300 Sodium Chloride Sulfoxide, Dimethyl Tissues Tween 80

Epidermal Regeneration in Lampreys

Adult lampreys (Lethenteron reissneri, body length: 15 cm ± 1 cm) were obtained from Huanren Manchu Autonomous County, Benxi, Liaoning Province, China. The lampreys were then maintained in an aquarium at 4 °C. All lamprey handling and experimental procedures were approved by the Animal Welfare and Research Ethics Committee of the Institute of Dalian Medical University. For the epidermal regeneration challenge, adult lampreys (N = 30) were divided randomly into five groups: no wound (CTL), 0 days after damage (Dam 0 d), 2 days after damage (Dam 2 d), 7 days after damage (Dam 7 d), 14 days after damage (Dam 14 d), and 21 days after damage (Dam 21 d). After anesthetization with 0.05% MS-222 (tricaine methanesulfonate, Sigma–Aldrich, E10521, St. Louis, MO, USA), the body surface was scraped using a sterilized scalpel to create a wound bed (1.5 cm × 0.5 cm) until no more mucoid tissue could be scraped. The whole process was performed gently to minimize damage to the dermis. For full-thickness damage, a scalpel with only a 5-mm blade exposed was used to make a 0.5-cm-long wound on the side of the lamprey parallel to the body. Images were captured with a zoom stereo microscope (SMZ1500, Nikon, Japan).

Full text: Click here

Publication 2023

Adult Dermis Epidermis Ethics Committees, Research Human Body Lampreys methanesulfonate Microscopy MS-222 Regeneration Tissues tricaine Wounds

Lamprey Cell Proliferation Analysis

EdU-injected lampreys were cultured under the same conditions, and 50 mg/kg EdU (Beyotime, Shanghai, China) was injected intraperitoneally at the indicated time points and detected according to the manufacturer’s protocols. After another injection 24 h later, at Dam 7 d, samples were collected and stained. EdU incorporation was evaluated using the Click-it EdU imaging technique.

Full text: Click here

Publication 2023

Lampreys

Histological Analysis of Skin Regeneration

Intact and regenerating skin samples were harvested, fixed in Bouin’s solution and embedded in paraffin wax. The paraffin-embedded tissues were sectioned to a thickness of approximately 4 µm and stained with hematoxylin and eosin (H&E), Masson’s trichrome (Sangon Biotech, Shanghai, China) [33 (link)] and PAS (Periodic Acid Schiff, Solarbio, G1281, Beijing, China)-AB (Alcian blue, Sangon Biotech, Shanghai, China) [69 (link)]. In brief, the slices were hydrated with xylene and a series of graded ethanol solutions and stained (aniline blue instead of light green). For the sampling of subcutaneous adipose tissue, the dermis was removed, and the muscle layer was removed after 1 or 2 days of epidermal damage in juvenile lamprey and stained using the method described above. The integrity of the skin structure and the types of cells were examined under a microscope.

Full text: Click here

Publication 2023

Alcian Blue aniline blue Bladder Detrusor Muscle Cells Dermis Eosin Epidermis Ethanol Lampreys Methyl Green Microscopy Paraffin Periodic Acid Skin Subcutaneous Fat Tissues Xylene

Freshwater Lamprey Collection from Chernaya River

Four adult males of L. fluviatilis (LF-01, LF-02, LF-03, and LF-04) were caught in the Chernaya River near the Karshevo village (Pudozhsky District, Karelia, Russia). The Chernaya River belongs to the Onega Lake basin. The studied lamprey is a freshwater potamodromous form of L. fluviatilis from the eastern part of the species’ area.

Matveevsky S., Tropin N., Kucheryavyy A, & Kolomiets O. (2023). The First Analysis of Synaptonemal Complexes in Jawless Vertebrates: Chromosome Synapsis and Transcription Reactivation at Meiotic Prophase I in the Lamprey Lampetra fluviatilis (Petromyzontiformes, Cyclostomata). Life, 13(2), 501.

Full text: Click here

Publication 2023

Adult Lampreys L Forms Males Rivers

Top products related to «Lampreys»

Ms 222 by Merck Group

Sourced in United States, Germany, Spain, China, United Kingdom, Sao Tome and Principe, France, Denmark, Italy, Canada, Japan, Macao, Belgium, Switzerland, Sweden, Australia

MS-222 is a chemical compound commonly used as a fish anesthetic in research and aquaculture settings. It is a white, crystalline powder that can be dissolved in water to create a sedative solution for fish. The primary function of MS-222 is to temporarily immobilize fish, allowing for safe handling, examination, or other procedures to be performed. This product is widely used in the scientific community to facilitate the study and care of various fish species.

Superscript 3 by Thermo Fisher Scientific

Sourced in United States, Germany, United Kingdom, Japan, Australia, Canada, France, China, Netherlands, Spain, Lithuania, Switzerland, Belgium, Italy

Superscript III is a reverse transcriptase enzyme produced by Thermo Fisher Scientific. It is designed for cDNA synthesis from RNA templates during the process of reverse transcription.

Pgem t easy vector by Promega

Sourced in United States, China, Germany, United Kingdom, Japan, France, Italy, Australia, Switzerland, Spain, Israel, Canada

The pGEM-T Easy Vector is a high-copy-number plasmid designed for cloning and sequencing of PCR products. It provides a simple, efficient method for the insertion and analysis of PCR amplified DNA fragments.

Lipofectamine 3000 by Thermo Fisher Scientific

Sourced in United States, China, Germany, Japan, United Kingdom, France, Canada, Italy, Australia, Switzerland, Denmark, Spain, Singapore, Belgium, Lithuania, Israel, Sweden, Austria, Moldova, Republic of, Greece, Azerbaijan, Finland

Lipofectamine 3000 is a transfection reagent used for the efficient delivery of nucleic acids, such as plasmid DNA, siRNA, and mRNA, into a variety of mammalian cell types. It facilitates the entry of these molecules into the cells, enabling their expression or silencing.

Lsm 780 by Zeiss

Sourced in Germany, United States, Japan, France, China, Canada, United Kingdom, Switzerland, Singapore, Italy, Panama, India

The LSM 780 is a laser scanning microscope developed by Zeiss. It is designed for high-resolution imaging and analysis of biological samples. The instrument utilizes advanced confocal technology to provide detailed, three-dimensional images of specimens.

Gelfoam by Pfizer

Sourced in United States, Belgium, Japan

Gelfoam is a sterile, absorbable gelatin sponge that is used as a hemostatic agent. It is designed to provide temporary control of bleeding from small blood vessels.

Dnase 1 by Qiagen

Sourced in Germany, United States, United Kingdom, Canada, France, Japan, Italy, Netherlands, Spain, China, Sweden, Australia, Switzerland

DNase I is a laboratory enzyme used to degrade DNA. It catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, effectively fragmenting DNA molecules.

Axiocam hrc camera by Zeiss

Sourced in Germany, United Kingdom, France, Japan, United States, Canada

The AxioCam HRc is a high-resolution digital camera designed for microscopy applications. It features a 12.6-megapixel CMOS sensor capable of capturing high-quality images with a resolution of 4096 x 3072 pixels. The camera is designed to provide accurate color reproduction and fast data transfer rates, making it suitable for a variety of microscopy techniques.

Rnaiso reagent by Takara Bio

Sourced in Japan, China, United States

RNAiso reagent is a total RNA isolation solution developed by Takara Bio. It is designed to effectively extract and purify high-quality total RNA from a variety of biological samples.

Pcdna3 by Thermo Fisher Scientific

Sourced in United States, China, United Kingdom, Germany, Japan, Canada, France, Sweden, Netherlands, Italy, Portugal, Spain, Australia, Denmark

The PcDNA3.1 is a plasmid vector used for the expression of recombinant proteins in mammalian cells. It contains a powerful human cytomegalovirus (CMV) promoter, which drives high-level expression of the inserted gene. The vector also includes a neomycin resistance gene for selection of stable transfectants.

What are the unique features of Lampreys that make them an invaluable model organism?

Lampreys possess a distinct anatomy and physiology that make them a fascinating subject of research. As jawless, eel-like vertebrates, they provide insights into the evolution of vertebrates and the development of key organ systems. Their unique features, such as a cartilaginous skeleton, a simple nervous system, and a distinctive feeding mechanism, offer researchers an invaluable model for understanding the fundamental principles of vertebrate biology.

How can PubCompare.ai help researchers studying Lampreys?

PubCompare.ai's AI-driven comparison tool revolutionizes the way researchers study Lampreys. By quickly screening protocol literature, the platform helps identify the most accurate and reproducible methods, enabling researchers to choose the best options for their specific research goals. The platform's analysis can highlight key differences in protocol effectiveness, allowing researchers to enhance the quality and reliability of their Lamprey-related studies.

What are the different variations or types of Lampreys, and how do they differ?

Lampreys are a diverse group of species, with over 40 known varieties. Some key differences include their size, habitat, and feeding preferences. For example, the Sea Lamprey is a larger, parasitic species that attaches to and feeds on other fish, while the Brook Lamprey is a smaller, non-parasitic species that lives in freshwater streams. Understanding these variations is crucial for researchers to select the most appropriate Lamprey model for their investigations.

What are some specific applications of Lamprey research?

Lampreys have been invaluable in advancing our understanding of vertebrate evolution and biology. Their simple nervous system, for instance, has provided insights into the development of the spinal cord and brain. Additionally, Lamprey research has contributed to the study of regeneration, as these creatures possess remarkable abilities to regrow damaged tissues and organs. Furthemore, Lampreys have been used to explore the evolution of the immune system and the development of blood-clotting mechanisms.

How can researchers overcome common usage challenges when working with Lampreys?

One of the key challenges in Lamprey research is ensuring the reproducibility and accuracy of experimental protocols. This is where PubCompare.ai can be particularly helpful. The platform's AI-driven analysis can identify the most effective protocols, highlighting critical insights that help researchers choose the best methods for their specific needs. This not only saves time and resources, but also enhances the reliability and quality of Lamprey-related studies, overcoming common usage challenges faced by researchers.

More about "Lampreys"

Lampreys are a fascinating group of jawless, eel-like vertebrates that have been the subject of extensive scientific research.
These ancient creatures, also known as cyclostomes or agnathans, possess a unique anatomy and physiology that make them an invaluable model organism for understanding the evolution of vertebrates.
PubCompare.ai's innovative AI-driven comparison tool empowers researchers to quickly locate the most accurate and reproducilble protocols from publications, preprints, and patents.
This revolutionary platform helps enhance the quality and reliability of lamprey research by enabling scientists to identify the best methods and techniques.
Lampreys are often utilized in studies involving MS-222 (tricaine methanesulfonate) as an anesthetic, Superscript III for cDNA synthesis, the pGEM-T Easy vector for cloning, and Lipofectamine 3000 for transfection.
Imaging techniques such as LSM 780 confocal microscopy and AxioCam HRc camera are commonly employed.
Researchers may also use Gelfoam for tissue implantation, DNase I for DNA digestion, and RNAiso reagent for RNA extraction.
The PcDNA3.1 expression vector is another valuable tool in lamprey research, allowing for the study of gene expression and function.
By leveraging these advanced techniques and technologies, scientists can delve deeper into the fascinating world of lampreys, uncovering new insights into vertebrate evolution and development.