The largest database of trusted experimental protocols
> Living Beings > Fish > Catfishes, Channel

Catfishes, Channel

Catfishes, Channel are a group of freshwater fish belonging to the order Siluriformes.
These fish are characterized by their elongated, cylindrical bodies, and distinctive whisker-like barbels around the mouth, which give them a unique appearance.
Channel Catfish are native to the rivers and lakes of North America and are highly valued for their edible flesh and sportfishing qualities.
They are known for their adaptability to a wide range of habitats and their ability to thrive in both natural and man-made environments.
This MeSH term provides a concise overview of the key characteristics and distribution of Catfishes, Channle, which are an important component of aquatic ecosystems and a popular target for recreational anglers.

Most cited protocols related to «Catfishes, Channel»

The completeness of the genome-sequence assembly was assessed by aligning the assembly of the 167X independently generated genomic sequences from 150 individuals to the reference genome assembly using MUMmer3.23 (http://mummer.sourceforge.net/) with default settings. The short reads from the 150 individuals were assembled using ABySS60 (link). In addition to genome sequence alignments, the number of genes included in the sequence assembly was used as a parameter for assessing the completeness. Channel catfish genes were compared with those of 12 teleost species whose whole genome has been sequenced (Supplementary Table 6). Protein-coding genes of these species were retrieved from Ensembl (version 78), with exception of the genes of Cynoglossus semilaevis (Cse_v1.0), which were retrieved from NCBI. For genes with multiple splicing variants, the longest variant was used. Only genes encoding proteins of >30 amino acids were used in the analysis. First, all proteins from the channel catfish and the 12 other species were combined in an all-versus-all BLASTP comparison with maximal e-value of 1e−5. Clusters of orthologous groups among these 13 species were identified using SiLiX (ref. 61 (link)) with minimum identity of 30% and minimal sequence overlap of 50%. Comparison of gene content was conducted using BLASTP analysis with a maximal e-value of 1e−5. The predicted protein sequences of channel catfish were queried against protein sequences of each of the 12 teleost species, separately. If all members of an orthologous group of catfish proteins had no match in a given species, then the gene was deemed present in channel catfish (Catfish+) but absent from the species under comparison. Similarly, the ‘Catfish−' genes were identified through reciprocal BLASTP comparisons of protein sequences of the other 12 species against channel catfish. Because the zebrafish genome has been considered ‘complete', a similar analysis was conducted to generate ‘Zebrafish+' and ‘Zebrafish−' genes for comparison. The correctness/accuracy of the sequence assembly was assessed by comparing SNP marker positions on the genetic map versus those on the genomic sequence scaffolds using positions determined as above with MUMmer. In addition, the mate-paired BES that aligned within a single scaffold were used to assess assembly accuracy.
Full text: Click here
Publication 2016
Amino Acids Amino Acid Sequence Catfishes, Channel Chromosome Mapping Gene Products, Protein Genes Genome Proteins Sequence Alignment Siluriformes Zebrafish
The starting point for this in silico analysis were the sequences for the two known salmon DNA transposons SALT1 [Genbank:L22865] [19 (link)] and Tss [Genbank:L12207] [18 (link)], as well as an analysis of the sequence of the T-cell receptor alpha locus of Salmo salar by RepeatMasker [46 ]. These two transposons as well as the RepeatMasker data were used to find faint similarities which were used in turn to find a larger number of each family in approximately 3 Mbp of sequence. The Dotter program [47 (link)] was used extensively to find regions of similar sequence, which were extracted and stored in an SQL database. The length of the transposon sequences was determined by identifying the inverted terminal repeat sequences where possible. Sequence alignments were performed with ClustalW [48 (link)] and phylogenetic trees generated with MEGA3.1 [49 (link)] using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), pairwise deletion, and a p-distance model. The entire alignment of the sequences was used in the phylogenetic reconstruction. Our salmon EST database was searched for the presence of sequences that are similar to the DNA transposon sequences that we found in salmon.
The following DNA sequences and BAC clones were used in this analysis. The Salmo salar TCRα locus [30 (link)], the major histocompatibility loci MHC class 1a and 1b [29 ], the growth hormone and interleukin loci (manuscripts in preparation), and zoneadhesin-like genes [Genbank:AY785950] and the Oncorhynchus mykiss sequences for the metallothionein gene [GENBANK:DQ156151], MHC1a [Genbank:AB162342] and MHC1b loci [Genbank:AB162343], and the IgH.A locus [Genbank:AY872256]. Genbank sequence entries were used in this study from a variety of other organisms (table 2): Oncorhynchus mykiss, Ictalurus punctatus, Esox lucius, Cyprinus carpio, Salvelinus namaycush, Salvelinus confluentus, Salvelinus fontinalis, Tanichthys albonus, Carassius auratus, Astatotilapia burtoni, Oryzias latipes, Petromyzon marinus, Danio rerio, Xenopus tropicalis, Xenopus laevis, Rana pipens, and Polypterus bichir. Sequences from Schistosoma japonicum EST Genbank data were found for transposon families as follows: DTSsa1 [Genbank:AY915112, AY809993], DTSsa2 [Genbank:AY816058, AY834394], DTSsa3 [Genbank:AY124772], DTSsa4 [Genbank:AY812589, AY915240], DTSsa5 [Genbank:AY813498], DTSsa6 [Genbank:AY813020], DTSsa7 [Genbank:AY813225, AY915121], SSTN1 [Genbank:AY809988, AY815476, AY915835], Tss [Genbank:AY915400, AY915891], and SALT1 [Genbank:AY223470, AY915102].
Representative sequences from all new families have been deposited in GenBank under accession numbers EF685954EF685960, EF685962EF685963, and EF685966EF685967.
Full text: Click here
Publication 2007
Catfishes, Channel Clone Cells Cyprinus carpio Deletion Mutation DNA Transposons Esox lucius Genes Goldfish Growth Hormone Interleukins Inverted Terminal Repeat Jumping Genes Metallothionein Oncorhynchus mykiss Oryzias latipes Petromyzon marinus Rana Salmo salar Salvelinus Schistosoma japonicum Sequence Alignment Sequence Analysis Syncope T Cell Receptor alpha Chain Genes Xenopus laevis Zebrafish
Demographic history was reconstructed based on a Hidden Markov Model (HMM) approach using PSMC30 (link). Briefly, the genomic sequences generated from each diploid channel catfish were aligned to the channel catfish reference assembly using BWA mem (version 0.7.12-r1039) with default settings. The consensus sequences were called using SAMtools (version 0.1.19). The ‘fq2psmcfa' tool was used to create the input file for PSMC modelling, with the option -q20. The consensus sequences were divided into non-overlapping 100 bp bins, with a bin scored as heterozygous if there was a heterozygote in the bin, otherwise it was scored as homozygous. The resultant bin sequences were used as the input for the PSMC estimates using ‘psmc' with the options -N25 -t15 -r5 -p ‘4+25*2+4+6'. The reconstructed population history was plotted using ‘psmc_plot.pl' with the options -u 2.5e-08 -g 7. Because plotting the results required input of generation time (-g 7) and mutation rate (-u 2.5e-08), generation time was calculated as: g=a+[s/(1-s)], where s is the expected adult survival rate which is recorded as 80% in channel catfish, and a is the sexual maturation age that is 3-year for channel catfish. Therefore, the generation time used in this PSMC model was determined as: g=3+[0.80/(1-0.80)]=7. The mutation rate was set following the rate described in a previous study in medaka64 (link).
Full text: Click here
Publication 2016
Adult BP 100 Catfishes, Channel Consensus Sequence Diploidy Genome Heterozygote Homozygote Sexual Maturation
A doubled haploid channel catfish individual17 (link) was used as template for sequencing. Genomic DNA was isolated from blood cells. Genomic DNA was sheared with a HydroShear instrument (Digilab, Inc., Marlborough, MA) using the regular chamber and set at shear code 13 for 20 cycles for 3-kb fragments and shear code 16 for 20 cycles for 8-kb fragments. Fragments were separated by field inversion agarose gel electrophoresis, isolated with a Whatman Elutrap elution system, and concentrated in a Microcon-50 (EMD Millipore, Billerica, MA). For fosmid library production, genomic DNA was sheared in the large chamber at shear code 15 for 30 cycles and purified as above, and the DNA was cloned into the pCC2FOS vector (Epicentre, Madison, WI) using the CopyControl HTP Fosmid Library Production Kit.
For Illumina sequencing, an Illumina TruSeq PCR-Free LT library was produced from Covaris-sheared genomic DNA of 400-bp and sequenced on the NextSeq500 platform. An Illumina Mate Pair Library Prep Kit was used to produce 3-kb and 8-kb fragment libraries, and these fragments were sequenced on an Illumina GAIIx and HiSeq platform, respectively. Paired-end sequences were produced from pooled fosmids, and sequenced on the Illumina GAIIx platform. Pacific Biosciences long read sequence was produced from 8–10 kb genomic DNA fragments with C2 chemistry (Expression Analysis, Durham, NC). The sequences were error-corrected using the pacbioToCA algorithm within Whole Genome Shotgun assembler v7.0 (ref. 55 (link)).
Full text: Click here
Publication 2016
Blood Cells BP 400 Catfishes, Channel Cloning Vectors DNA Library Field Inversion Gel Electrophoresis Genome Sepharose
Total RNA was isolated from the skin tissues of channel catfish and common carp using the RNeasy Plus Universal Kit (Qiagen, CA) according to the manufacturer's instructions. Raw sequencing reads were filtered for base quality ≥15 and read length ≥30 bp. The de novo assembly was produced using Trinity (version r2012-06-08)68 (link). The assembled contigs for each species were used as queries against the NCBI Non-Redundant protein database using BLASTX with maximum e-value of 1e−5, and only the best match was annotated for each contig.
Interspecific comparative skin transcriptome analyses between common carp (scaled) and channel catfish (scaleless) were conducted using TBLASTX with a E-value cutoff of 1e−5 with the following steps: (1) The carp skin transcriptome and the channel catfish skin transcriptome were de novo assembled, separately; (2) The carp skin transcriptome was annotated by BLASTX analysis against the non-redundant database; (3) A list of unique protein-coding transcripts from the common carp skin transcriptome were compiled and queried against the channel catfish skin transcriptome; (4) For carp contigs with no matches to the channel catfish transcriptome assembly but with matches to the non-redundant database, the sequences of each best match were retrieved from the non-redundant database and used to query the channel catfish skin transcriptome assembly. Those carp transcripts that remained unidentified were annotated as genes that were expressed in the carp skin but not expressed in the channel catfish skin.
Full text: Click here
Publication 2016
Catfishes, Channel Cyprinus carpio Gene Expression Profiling Genes Skin Staphylococcal Protein A Tissues Transcriptome

Most recents protocols related to «Catfishes, Channel»

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2023
Bicarbonate, Sodium BLOOD Catfishes, Channel Cell Lines Cells Clone Cells Culture Media Freezing Glutamine Hybridomas lymphoprep MS-222 Mus Serum Siluriformes Spleen Tissues Veins
The lotus root polyphenol extract (LRPE) was extracted from rhizome knots according to Zhu, Li, He, Thirumdas, Montesano and Barba [12 (link)]. Following that, the crude extract solution was loaded onto the AB-8 macroporous resin (0.3–1.25 mm particle size, Macklin, Shanghai, China) for purification as described by Wu, et al. [19 (link)]. The rhizome knot was purchased from a local market (Wuhan, China). The concentration of total polyphenol in LRPE determined by the method of Zhu, Li, He, Thirumdas, Montesano and Barba [12 (link)] was 68.73 mg/100 mg. The ascorbic acid (AA) (99.7%) was purchased from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China). The lotus seedpod procyanidins (LSPC) (50%) were provided by College of Food Science and Technology, Huazhong Agricultural University. The grape seed extract (GSE) (95%) was obtained from Tianjin Jianfeng Natural Products Research and Development Co., Ltd. (Tianjin, China).
Fresh and alive channel catfish, each 3 ± 0.2 kg, were purchased from a local market (Wuhan, China). All channel catfish were transported using water tanks to the laboratory with 30 min. The fish head, bone, viscera and skin were immediately removed. The back muscles of the fish were cut into approximately 2 cm thick and approximately 20 g fillets and then randomly separated into five groups: a CK group treated with sterile distilled water and four other treatment groups including AA, GSE, LSPC and LRPE at a concentration of 2 g/L. The concentration of each treatment group was determined according to the results of previous studies. Each solution was prepared just before use and precooled to 4 °C. Fillets were immersed in each treatment group for 10 min at room temperature before being drained thoroughly. The fillets were then placed in food packaging boxes at a cold storage temperature (4 ℃) and were collected at random for analysis at 0, 1, 3, 5, 7, 9, and 11 days.
Full text: Click here
Publication 2023
Ascorbic Acid Bones Catfishes, Channel Cold Temperature Complex Extracts Fishes Grape Seed Extract Head Lotus Muscle, Back Natural Products Plant Roots Polyphenols Procyanidins Resins, Plant Rhizome Skin Sterility, Reproductive Viscera
The consensus sequence of the lever arm of Myo19 was created by aligning full-length sequences of Myo19 from 55 organisms spanning vertebrata from humans to channel catfish (Ictalurus punctatus). Sequence IDs (amino acids in parentheses) were Q96H55 (764–834), Q5SV80 (764–834), A0A6P5QGB4 (764–834), A0A6J0DWE2 (761–831), I3ML92 (764–834), H0V2S3 (757–827), A0A1S3EZK3 (764–834), H2QCR4 (764–834), A0A2R9AXU1 (764–834), G3QY42 (764–834), A0A2K5WEM0 (763–833), A0A5F7ZMQ5 (784–854), A0A096P509 (764–834), A0A2K5NMX7 (764–834), A0A2K5IBB4 (764–834), A0A2K5DPV4 (764–834), F7BED0 (764–834), A0A2K6ELK8 (758–828), G3T3X5 (766–836), A0A6P4U2Y4 (783–853), A0A6J1XC86 (783–853), M3WFE8 (764–834), A0A6I9IYC4 (770–840), A0A384CFN0 (785–855), A0A3Q7WJX5 (796–866), A0A452SCT8 (764–834), G1LNM4 (764–834), A0A2Y9I8J8 (763–833), A0A3Q7NUK0 (763–833), A0A3Q7SA51 (760–830), G3MZU4 (747–817), A0A6P5DIZ3 (747–817), A0A6P7EIM7 (747–817), A0A452G219 (747–817), A0A2Y9LFM9 (758–828), A0A2U4C652 (758–828), A0A6J0AY11 (760–830), G1PM65 (764–834), A0A6P3RBN3 (760–830), A0A6J2MD46 (760–830), F7CK88 (765–835), A0A1S3W3P6 (760–830), G1SEC2 (759–829), A0A6P5KPB5 (765–835), A0A3Q2TZU2 (765–835), 0A1V4K263 (765–835), H0ZCE2 (765–834), A0A6I9HN03 (765–835), A0A6J0HRI7 (765–835), A0A091IJ51 (774–844), A0A6P7P858 (757–827), A0A6J2R2M5 (766–836), H2M6S2 (755–825), A0A1S3RN45 (766–836), and A0A2D0QDW7 (774–844). The sequence logo (Fig. 1A) was generated using online WebLOGO software (weblogo.berkeley.edu).
Full text: Click here
Publication 2023
Amino Acids Catfishes, Channel Consensus Sequence Homo sapiens Vertebrates
Pituitary glands were obtained from two fish farms. The first is located in São João da Boa Vista (São Paulo), and the processed material was used for studies regarding ag-LH and ag-FSH [16 (link)] and detection of a first partial region (~200 bp, “seq1”) of ag-GH, utilizing primer #1 and #2 (Table 1). Initially, the design of the two primers was based on conserved regions of the GH gene from three different fish species: Anguilla anguilla, Cyprinus carpio, and Ictalurus punctatus, available in GenBank under the accession numbers AY148493.1, M27000.1, and NM_001200245.1, respectively. For the selection of the species in this study, data previously obtained by our research group were used [16 (link),17 (link)]. These GH sequences were aligned and the region that presented the closest profile for the three species was chosen as a safe region for the design of the primers used in this first step. The second pituitary collection was from Canabrava do Norte, Mato Grosso State, within the facilities of the Raça fish farm, collaborating with our project. The animals weighed 15–40 kg and the collected pituitary glands were 70–100 mg. These were stored in 1 mL of RNALater™ (ThermoFisher Scientific, Waltham, MA, USA), and transported to our laboratory in São Paulo in dry ice.
Full text: Click here
Publication 2023
Anguilla Animals Catfishes, Channel Cyprinus carpio Dry Ice Fishes Genes Oligonucleotide Primers Pituitary Gland
To investigate the evolutionary relationships of Elovl genes in the Eleutheronema genus, the sequences of Elovl genes from E. tetradactylum and E. rhadinum were subjected to phylogenetic analysis and compared with the 106 publicly available Elovl genes of other organisms, including Homo sapiens, Mus musculus, Danio rerio, Oreochromis niloticus, Oncorhynchus mykiss, Oryzias latipes, Takifugu rubripes, Gadus morhua, Sander lucioperca, Salmo salar, Cyprinus carpio, Lepisosteus oculatus, Ictalurus punctatus, Tachysurus fulvidraco, Coregonus clupeaformis, and Ictalurus punctatus. All reference sequences were aligned by the ClustalW program in MEGAX with the default parameter29 (link), and the phylogenetic tree was constructed using the maximum like-hood method with 1000 replicates. The optimal protein substitution model for evolution of Elovl genes was the JTT model with gamma distribution, which was chosen based on the results using the option provided in MEGAX.
Full text: Click here
Publication 2023
Biological Evolution Catfishes, Channel Cyprinus carpio Evolution, Molecular Gadus morhua Gamma Rays Genes Homo sapiens Mice, House Oncorhynchus mykiss Oreochromis niloticus Oryzias latipes Proteins Salmo salar Takifugu rubripes Zebrafish

Top products related to «Catfishes, Channel»

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.
Sourced in United States, China, Japan, Italy, Germany, United Kingdom, Switzerland, France, Canada, Netherlands, Australia, Belgium, India
The Microplate reader is a laboratory instrument used to measure the absorbance or fluorescence of samples in a microplate format. It can be used to conduct various assays, such as enzyme-linked immunosorbent assays (ELISA), cell-based assays, and other biochemical analyses. The core function of the Microplate reader is to precisely quantify the optical properties of the samples in a multi-well microplate.
Sourced in China
The TMB kit is a laboratory product designed for the detection and quantification of horseradish peroxidase (HRP) activity in enzyme-linked immunosorbent assay (ELISA) applications. The kit provides a ready-to-use solution that enables the colorimetric measurement of HRP-mediated substrate conversion, which is commonly used as a signal amplification step in ELISA protocols.
Sourced in United States, China, United Kingdom, Germany, Australia, Japan, Canada, Italy, France, Switzerland, New Zealand, Brazil, Belgium, India, Spain, Israel, Austria, Poland, Ireland, Sweden, Macao, Netherlands, Denmark, Cameroon, Singapore, Portugal, Argentina, Holy See (Vatican City State), Morocco, Uruguay, Mexico, Thailand, Sao Tome and Principe, Hungary, Panama, Hong Kong, Norway, United Arab Emirates, Czechia, Russian Federation, Chile, Moldova, Republic of, Gabon, Palestine, State of, Saudi Arabia, Senegal
Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
Sourced in France
Montanide™ ISA763 A VG is a laboratory equipment product. It is an oil-based adjuvant for use in the formulation of vaccines.
Sourced in Germany, Japan
The PET32a is a laboratory instrument designed for positron emission tomography (PET) imaging. It is a core component of PET scanning systems used in medical research and diagnostics. The PET32a captures and processes data from PET scans, providing essential functionality for PET imaging applications.
Sourced in China, Japan
The PMD19-T simple is a compact and efficient desktop centrifuge designed for general laboratory use. It features a user-friendly interface and a versatile rotor that can accommodate various tube sizes. The core function of the PMD19-T simple is to separate different components within a liquid sample through controlled centrifugal force.
Sourced in United States, Germany, United Kingdom, France, China, Switzerland, Sao Tome and Principe, Spain, Ireland, India, Italy, Japan, Brazil, Australia, Canada, Macao, Czechia, New Zealand, Belgium, Cameroon, Austria, Israel, Norway, Denmark, Netherlands
Ampicillin is a broad-spectrum antibiotic used in laboratory settings. It is a penicillin-based compound effective against a variety of gram-positive and gram-negative bacteria. Ampicillin functions by inhibiting cell wall synthesis, leading to bacterial cell lysis and death.
Sourced in United States, Germany, China, Switzerland, Poland, United Kingdom, Japan
Synergy HTX is a multi-mode microplate reader designed for high-throughput screening and cell-based assays. It features advanced optics and detection technologies to enable rapid and accurate measurements of absorbance, fluorescence, and luminescence signals.
Sourced in United States
The Quantum Studio 6 flex is a real-time PCR system designed for gene expression and genotyping analysis. It features a 6-channel optical system and supports multiple sample formats, including 96-well plates, 8-tube strips, and individual tubes. The system provides precise temperature control and uniform thermal cycling for reliable and reproducible results.

More about "Catfishes, Channel"

Catfish, Channel Catfish, Ictalurus punctatus, Freshwater Fish, Siluriformes, Barbels, Aquatic Ecosystems, Recreational Angling, Fish Farming, Aquaculture, Feeding Behavior, Habitat, MS-222 (Tricaine Methanesulfonate), Microplate Readers, TMB (Tetramethylbenzidine) Kits, Fetal Bovine Serum (FBS), Montanide™ ISA763 A VG, PET32a Expression Vector, pMD19-T Simple Vector, Ampicillin, Synergy HTX Multi-Mode Microplate Reader, Quantum Studio 6 Flex Real-Time PCR System.
Channel catfish are a highly adaptable and widely-distributed group of freshwater fish in the order Siluriformes.
Characterized by their cylindrical bodies and distinctive whisker-like barbels, these catfish are native to the rivers and lakes of North America and are prized for their edibility and sportfishing appeal.
They thrive in a variety of natural and man-made aquatic environments, making them an important component of aquatic ecosystems.
Research on channel catfish often involves the use of specialized equipment and reagents such as MS-222 for anesthesia, microplate readers for assays, TMB kits for colorimetric detection, FBS for cell culture, Montanide™ adjuvants for immunization, and expression vectors like PET32a and pMD19-T for genetic studies.
Additionally, tools like the Synergy HTX multi-mode plate reader and Quantum Studio 6 Flex real-time PCR system are commonly used in channel catfish research.
These fish continue to be a valuable resource for both commercial aquaculture and recreational fishing, with ongoing scientific investigation into their biology, behavior, and potential applications.