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Pufferfish

Pufferfish, also known as blowfish or swellfish, are a group of marine and freshwater fish known for their ability to inflate their bodies when threatened.
These fascinating creatures belong to the order Tetraodontiformes and are found in tropical and subtropical waters around the world.
Pufferfish are characterized by their distinctive round, spiny bodies and their unique defense mechanism of inflating themselves with water or air to appear larger and deter predators.
They are highly sought after in some cuisines, but also contain a potent neurotoxin that can be fatal if not properly prepared.
Researchers are continually exploring the biology, behavior, and potential medicinal applications of these remarkable fish.
Whether you're studying pufferfish behavior, ecology, or pharmacology, PubCompare.ai can help you find the most accurate and reproducible protocols from the literature to enhace your pufferfish reserch.

Most cited protocols related to «Pufferfish»

Protein sequences for human, mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), pufferfish (Takifugu rubripes), zebrafish (Danio rerio) and fruitfly (Drosophila melanogaster) were retrieved from Ensembl (3 (link)). In addition, we obtained nematode (Caenorhabditis elegans and Caenorhabditis briggsae) proteins from WormBase (14 (link)), baker's yeast (Saccharomyces cerevisiae) proteins from SGD (15 (link)), fission yeast (Schizosaccharomyces pombe) proteins from GeneDB (16 (link)) and thale cress (Arabidopsis thaliana) proteins from TIGR (17 (link)). In addition to these fully sequenced species, TreeFam includes UniProt (18 (link)) proteins from animal species whose genomes have not been fully sequenced. Where multiple splice forms were available for a gene, all were downloaded, but just one splice form was chosen to represent the gene during the process of building a family (see ‘Constructing Phylogenetic Trees’ below). For TreeFam release 1.1, the Ensembl sequences were downloaded on 27th December 2004, and the other sequences in January 2005.
Publication 2005
Amino Acid Sequence Animals Arabidopsis thaliana Proteins Arabidopsis thalianas Caenorhabditis Caenorhabditis elegans Chickens Drosophila Drosophila melanogaster Genes Genome Homo sapiens link protein Mice, House Nematoda NR4A2 protein, human Proteins Pufferfish Rattus norvegicus Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins Schizosaccharomyces pombe Takifugu rubripes Zebrafish
The methods used in the early phases of the cohort have been described elsewhere (Barros et al., 1990 , 2001 (link); Victora et al., 1992 ). The study began as a perinatal health survey (Barros, 1986 ) including all 6,011 infants born in three maternity hospitals (accounting for 99.2% of all births in the city). The 5,914 live-born infants were weighed with regularly calibrated pediatric scales (Filizolla, Brazil) to the nearest 10g. Birth length was not recorded. Mothers were weighed and measured and answered a short questionnaire on socioeconomic, demographic, and health-related variables.
The cohort children were followed up at several points in time (Table 1). Initially, those born from January to April 1982 were targeted in the 1983 Follow-up Study through the addresses obtained during the hospital interview, when they were aged 8-16 months (mean age 11.3 months).
To calculate the proportion of children located in each follow-up visit, those known to have died were added to those examined. In 1983, 66 of the 1,919 children born from January to April 1982 were know to have died; added to the 1,457 whose mothers or caretakers were interviewed, these accounted for 79.3% of the children who were targeted. Address errors were the main reason for non-response. Non-response rates quoted in the present paper are slightly different from those presented in earlier publications (Barros et al., 1990 ), since they did not fully account for children who had died.
The subsequent phases included the 1984 Follow-up Study (January-April 1984), when the mean age was 19.4 months (range 12-29), and the 1986 Follow-up Study (December 1985-May 1986) (mean age 43.1 months; range 35-53). To minimize losses to follow-up, in each round the approximately 70,000 urban households were visited in search of children born in 1982. After the census was completed, children who still had not been located were searched for at their last known address. This approach resulted in locating 87.2% and 84.1% of the original cohort, respectively.
During each visit, the mother or caretaker answered pre-coded, standardized questionnaires (see Table 2 for a list of the main variables collected). Children were weighed with portable spring scales (CMS, United Kingdom) and were measured with locally made AHRTAG stadiometers (Barros & Victora, 1998 ). Standard weighing and measuring methods were used (Jelliffe, 1966 ), and the interviewers were extensively trained before fieldwork. Quality-control measures included repeating some 5% of the interviews and measurements by a fieldwork supervisor, standardization sessions, and double data entry.
Two sub-studies were also performed. The Psychomotor Development Study (Victora et al., 1990 ) was performed on a random sub-sample of 360 children born from January to April 1982 who had been seen at all follow-up visits. At the mean age of 4.5 years, they were tested with the Griffiths's scales in six areas of development (locomotor, personal-social, hearing and speech, eye-hand coordination, performance, and practical reasoning).
The Mortality Study entailed the identification of all deaths occurring among cohort children. All hospitals, cemeteries, civil records offices, and the Regional Secretariat of Health were regularly visited from 1982 to 1982 to detect deaths of children and adolescents belonging to the 1982 cohort; from 1987 onwards, it became clear that civil records offices were detecting all deaths, and thus other sources were no longer monitored. Causes of death were investigated by reviewing case notes from outpatient clinics and hospitals, in addition to interviewing family members and the attending physicians. During the interviews a full history of the events preceding the death was obtained with the help of a questionnaire based on that used during the Inter-American Investigation of Mortality in Childhood (Puffer & Serrano, 1973 ). Two independent referees assigned the causes of death using this information; in case of discordance a third senior referee made the final decision. Causes of death were coded according to the Portuguese edition of the International Classification of Diseases, 9th version (OMS, 1980 ). This study is still ongoing.
Publication 2003
Adolescent Child Childbirth Family Member Households Infant Interviewers Mothers Physicians Pufferfish Speech Vision
Seventeen new species have been added since TreeFam v1 (4 (link)). TreeFam v4 contains predicted protein sequences from the fully sequenced genomes of 25 animal species: human, chimpanzee, macaque, mouse, rat, cow, dog, opossum, chicken, frog, two pufferfish (Takifugu and Tetraodon), zebrafish, medaka, stickleback, sea squirts (Ciona intestinalis and C. savignyi), two fruit-flies (Drosophila melanogaster and D. pseudoobscura), two mosquitoes (Aedes aegypti and Anopheles gambiae), the flatworm Schistosoma mansoni, and the nematodes Caenorhabditis elegans, C. briggsae and C. remanei. In addition, four outgroup genomes are included: baker's yeast, fission yeast, rice and thale cress (Arabidopsis).
The C. briggsae and C. remanei proteins were downloaded from WormBase (16 (link)), D. pseudoobscura proteins from FlyBase (17 (link)), fission yeast and flatworm proteins from GeneDB (18 (link)), thale cress proteins from TIGR (19 (link)), rice proteins from the Beijing Genomics Institute (20 (link)) and the remaining sequences from Ensembl (15 (link)). In addition to these species, TreeFam includes UniProt (21 (link)) proteins from animal species whose genomes have not been fully sequenced. For TreeFam v4, all sequences were downloaded in October 2006.
Publication 2007
Aedes Amino Acid Sequence Animals Anopheles gambiae Arabidopsis Arabidopsis thaliana Proteins Arabidopsis thalianas Caenorhabditis elegans Chickens Ciona intestinalis citrate carrier Culicidae Didelphidae Drosophila Drosophila melanogaster Flatworms Genome Homo sapiens link protein Macaca Mice, House Nematoda Oryza sativa Oryzias latipes Pan troglodytes Proteins Pufferfish Rana Saccharomyces cerevisiae Schistosoma mansoni Schizosaccharomyces pombe Sea Squirts Sticklebacks Takifugu Zebrafish
Genome annotations were produced using the MAKER47 (link)–49 (link) genome annotation pipeline, which supports re-annotation using pre-existing gene models as input. Previous Petromyzon marinus gene models (WUGSC 7.0/petMar2 assembly)50 (link) were mapped against the new genome assembly into GFF3 format and were used as prior model input to MAKER for re-annotation. Snap51 (link) and Augustus52 (link),53 (link) were also used with MAKER and were trained using the pre-existing lamprey gene models. Additional input to MAKER included previously-published mRNA-seq reads derived from lamprey embryos and testes10 (link),12 (link),13 (link) and assembled using Trinity54 (link), as well as mRNA-seq reads (NexSeq 75–100 bp paired-end) were derived from whole embryos and dissected heads at Tahara stage 20, as well as dissected embryonic dorsal neural tubes at Tahara stage 18, 20 and 21. The following protein datasets were also used: Ciona intestinalis (sea squirt)55 (link), Lottia gigantea (limpet)56 (link), Nematostella vectensis (sea anemone)57 (link), Takifugu rubripes (pufferfish)58 (link), Branchiostoma floridae (lancelet)59 (link), Callorhinchus milii (elephant shark)60 (link), Xenopus tropicalis (western clawed frog)61 (link), Drosophila melanogaster (fruit fly)62 (link), Homo sapiens (human)63 (link),64 (link), Mus musculus (mouse)65 (link), Danio rerio (zebrafish)66 (link), Hydra magnipapillata67 (link), Trichoplax adhaerens68 (link), and the Uniprot/Swiss-Prot protein database69 (link),70 (link). Protein domains were identified in final gene models using the InterProScan domain identification pipeline71 (link)–73 (link), and putative gene functions were assigned using BLASTP74 (link) identified homology to the Uniprot/Swiss-Prot protein database.
Publication 2017
Branchiostoma floridae Ciona intestinalis Drosophila Drosophila melanogaster Elephants Embryo Genome Head Homo sapiens Hydra Lampreys Lancelets Mice, House Mus Operator, Genetic Petromyzon marinus Protein Domain Proteins Pufferfish RNA, Messenger Sea Anemones Sharks Takifugu rubripes Trichoplax Tube, Neural Urochordata Xenopus laevis Zebrafish
The latest build of genome assembly of zebrafish (Zv9) and pufferfish (tetNig2) were downloaded from UCSC Genome Browser (Kuhn et al. 2009 (link)). CAGE tags were mapped using Bowtie (Langmead et al. 2009 (link)), allowing a maximum of two mismatches and only uniquely mapping tags. Since the CAGE protocol often yields an additional G nucleotide at the 5′-end of the tag, we removed the starting G when mismatching G at the first position and removed tags with an additional mismatch at the second position (affecting 1%–2% of CAGE tags; see Supplemental Table 13). The remaining unique 5′-ends were regarded as CAGE tag-defined transcriptional start sites (CTSSs). The number of CAGE tags mapping to each CTSS across different samples was normalized as in Balwierz et al. (2009) (link) to obtain the normalized number of tags per million (tpm).
Publication 2013
CAGE1 protein, human CTSS protein, human Genome Nucleotides Pufferfish Transcription Initiation Site Zebrafish

Most recents protocols related to «Pufferfish»


Fishes (n = 192) were collected in early April 2021 at Orpheus Island, GBR (18°36’44.3”S 146°28’59.4”E). All were “healthy” in that they were intact with good colour and no visible signs of disease, stress, or wasting. The vast majority were adult individuals. These included sixty-one species across sixteen reef fish families: Gobiidae (gobies) (n = 30 species), Labridae (wrasses) (n = 6), Pomacentridae (damselfishes) (n = 5), Blenniidae (blennies) (n = 5), Acanthuridae (surgeonfishes) (n = 3), Apogonidae (cardinalfishes) (n = 2), Monacanthidae (filefishes) (n = 2), Tetraodontidae (pufferfishes) (n = 1), Pseudochromidae (dottybacks) (n = 1), Chaetodontidae (butterflyfishes) (n = 1), Atherinidae (silversides, hardyheads) (n = 1), Serranidae (groupers) (n = 1), Tripterygiidae (triplefin blennies) (n = 1), Muraenidae (moray eels) (n = 1), Bythitidae (brotulas) (n = 1), and Ophichthidae (snake eels) (n = 1) (Supplementary Table S1). We sampled one to twelve individuals per species (±2.7 SD) (Supplementary Table S1). Of these species, forty-three (thirty-two cryptobenthic reef fishes and eleven large reef fishes) (n = 148 individuals) were collected from a reef fish community within a 100-m2 sampling area (along the northern margin of Pioneer Bay). The other eighteen (seven cryptobenthic reef fishes and eleven large reef fishes) (n = 44 individuals) were collected from similar habitats (i.e. shallow fringing reefs) around Orpheus Island (Supplementary Table S1). Fishes within the focal sampling area were collected using an enclosed clove oil method, in which a small portion of the reef is enclosed within a fine net, and all fishes within the net were anaesthetized using clove oil (Ackerman and Bellwood 2002 (link)). Additional fish were collected using nets and/or dilute clove oil. All fish caught were placed either dissected (liver and gills) or whole in RNAlater and then transported to the lab on ice (Supplementary Table S1). Specimens were then stored at −80°C until RNA extraction.
Publication 2023
Adult Eels Fishes Gills Liver Oil, Clove Pufferfish Serranidae SLC6A2 protein, human Snakes
Following behavioral testing, one cohort of the Chat::Cre+ transgenic rats (N = 4 males, N = 4 females) were injected with an adeno‐associated viral vector (AAV) into the basal forebrain (BF) to induce enhanced yellow fluorescent protein (EYFP) expression in cholinergic neurons. Rats were anesthetized with isoflurane (5% for induction, 2.5% for maintenance, E‐Z Systems Palmer, PA) in oxygen, placed in a Kopf stereotaxic device (David Kopf Instruments, Tujunga CA), and body temperature was maintained using a homeothermic blanket (Harvard Apparatus, Holliston, MA). After administration of a local anesthetic (2% carbocaine, s.c.) at the incision site, the basal forebrain was targeted by drilling two holes through the skull using the following coordinates measured from Bregma with skull flat: A/P‐0.8, L/M+/− 2.4, DV ‐8.6‐8.8.46 Rats were injected bilaterally with 2 μl of rAAV5/Ef1a‐DIO‐EYFP (UNC Viral Vector Core; LOT AV4310L) using a 33‐gauge needle on a Neuros Hamilton syringe at a rate of 0.2 μl/min using a motorized injector (Stoelting QSI Stereotaxic injector Wood Dale, IL). Following injections, the viral vector was allowed to diffuse for 10 min before the needle was withdrawn. Nalbuphine (2 mg/kg, s.c.) was administered postoperatively for pain management, the diet was supplemented with bacon softies (Bio‐serve, Frenchtown, NJ) to maintain postoperative weight, and topical nitrofurazone powder (NFZ puffer, Neogen Corporation) was used for prevention of infection at the incision site. Animals were allowed 3 weeks of recovery prior to perfusion and euthanasia to determine the number of BF cholinergic neurons expressing eYFP using immunofluorescence for choline acetyltransferase (ChAT; described below).
Publication 2023
Adeno-Associated Virus Aftercare Animals BACON protocol Basal Forebrain Body Temperature Carbocaine Choline O-Acetyltransferase Cholinergic Neurons Cloning Vectors Cranium Diet Euthanasia Females Immunofluorescence Infection Isoflurane Local Anesthesia Males Management, Pain Medical Devices Nalbuphine Needles Nitrofurazone Oxygen Perfusion Powder Proteins Pufferfish Rats, Transgenic Rattus Syringes
Hemostatic factors were analyzed in citrate plasma samples collected after an overnight fast. Plasma samples were centrifuged (10 min. at 15°) immediately after collection and then aliquoted and stored at −80 °C. The separation of plasma from the other blood components was completed after 30 min. at the latest. The following hemostatic factors were analyzed: antithrombin III, D-dimers, factor VIII, fibrinogen, protein S, partial thromboplastin time (aPTT), quick value, and international normalized ratio (INR).
Antithrombin III (reference value: 83–118%) was determined by chromogenic activity assay (Innovance Antithrombin, SCS cleaner, Siemens Healthcare Diagnostics, Eschborn, Germany). D-dimers (reference value: <500 µg/dL) were measured by means of a particle-enhanced immunoturbidimetric assay (Innovance D-Dimer Kit, Siemens Healthcare Diagnostics). Factor VIII activity (reference value: 70–150%) was measured photometrically (coagulation factor VIII deficient plasma, Pathromtin SL, CaCl2, Siemens Healthcare Diagnostics), as well as quick value (reference value: 82–125%; Thromborel S, Siemens Healthcare Diagnostics), aPTT (reference value: 26–36 s; Pathromtin SL, CaCl Lösung, Actin FS, Siemens Healthcare Diagnostics), and protein S (reference value: men: 73–130%, women: 52–126%; Hemoclot protein S, OVB-Puffer, CaCl2, SCS Cleaner). Fibrinogen (reference value: 210–400 mg/dL) was measured photometrically and turbidimetrically (Multifibren U, Siemens Healthcare Diagnostics). INR (reference value: 0.9–1.15) was calculated from the prothrombin ratio (Thromborel S, Siemens Healthcare Diagnostics) by dividing the thromboplastin time of the subject by that of normal plasma squared with International Sensitivity Index (ISI) as defined by the World Health Organization [14 ]. Reference values of all hemostatic factors were taken from University Clinic Augsburg, while all other serum parameters were measured at the clinical laboratory of the University Hospital (Klinikum Großhadern) of the Ludwig-Maximilians University in Munich. Measurement procedures were performed and controlled by trained laboratory personnel according to standardized protocols.
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Publication 2023
Actins Activated Partial Thromboplastin Time antihemorrhagic factor Antithrombin III azo rubin S Biological Assay Blood Component Transfusion Citrates Clinical Laboratory Services Diagnosis Factor VIII fibrin fragment D Fibrinogen Hypersensitivity Immunoturbidimetric Assay International Normalized Ratio Laboratory Personnel Plasma Protein S Prothrombin Pufferfish Serum Thromboplastin Woman
Tissue from the pathological routine diagnostics was used for histological examination. To characterize the TIME, we chose CD4 (Ventana, anti-CD4 Rabbit Monoclonal Primary Antibody, Clone SP35, dilution: 1:200) and CD8 (Ventana, anti-CD8 Rabbit Monoclonal Primary Antibody, Clone SP57, dilution: 1:200) as marker for lymphocytes, CD68 (Dako Anti-Human CD68, Clone KP1, dilution: 1:200) as a pan marker for macrophages and CD163 (Novocastra, Lyophilized Mouse Monoclonal Antibody CD163, Clone 10D6, dilution: 1:100) as a marker for M2-macrophages. First, a new hematoxylin-eosin slide was prepared, and the tumor was identified (Figure 1A,B). All immunohistochemical stains were performed on tissue sections (4 µm thickness) prepared from formalin-fixed (4% neutral buffered formalin) paraffin-embedded tissue blocks. The procedure is part of the established routine diagnostic at our institute. Briefly, immunohistochemical staining was performed using a Roche Ventana Benchmark Ultra automated slide stainer (Ventana Medical Systems, Roche, France) with the OptiView DAB IHC Detection Kit (Roche, France). The first step of the automatic staining program includes deparaffinization and rehydrating the specimens. Then antigen retrieval was completed by heat treatment lasting for 32 min with Tris-EDTA Borat Puffer (pH 8–8.5). After incubation of the diluted primary antibodies, the nuclei were counterstained with hematoxylin.
All slides were scanned (3DHISTECH Ltd. Pannoramic slide scanner 250) and evaluated using a virtual microscopy software (3DHISTECH Ltd. Case Viewer Ver.2.2). To quantify lymphocytes, ten high power fields (HPF) were identified independently by two pathologists (A.M. & C.B.). The invasion front and tumor center were identified, and the positive cells were counted. The mean values were calculated. The CD68 reaction was used to visualize all macrophages. To evaluate the quantity of the macrophages, ten HPF of the invasion tumor front and intra-tumoral area were examined and the positive cells were counted. The mean value (confidence interval 95%) of macrophages within the tumor front and the intra-tumoral area was calculated. The macrophages were then characterized concerning their subpopulations. M2-macrophages were detected using CD163-antibody. The M2-macrophages were quantified, utilizing the same previously described procedure for quantifying CD68-positive macrophages. The number of M1-macrophages per HPF was calculated through the difference between CD68-positive-macrophages and CD163-positive-M2-macrophages.
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Publication 2023
Antibodies Antibodies, Anti-Idiotypic Antigens CD163 protein, human Cell Nucleus Cells Clone Cells Diagnosis Edetic Acid Eosin Formalin Hematoxylin Homo sapiens Immunoglobulins Lymphocyte Macrophage Microscopy Monoclonal Antibodies Mus Neoplasm Invasiveness Neoplasms Paraffin Pathologists Population Group Pufferfish Rabbits Technique, Dilution Tissues Tromethamine
Initially, NCH421k cells (6 × 105) and U-87 MG (5 × 105) were seeded in wells of six-well plate and incubated for 24 h. Next day, anti-vimentin (Nb79) nanobody was added to final concentration 100 μg/mL and incubated for 48 h. After incubation, cells were washed with PBS three times and treated with 50 μL of RIPA puffer (ThermoFisher, Waltham, MA, USA) together with Halt protease inhibitors (ThermoFisher) and phosphatase inhibitors (ThermoFisher) for 15 min to enable cell lysis. Afterward, samples were collected to a tube and centrifuged for 15 min at 13,000 rpm. Supernatant was transferred to new microcentrifuge tubes and concentration of each cell lysate was measured on Synergy H4 Hybrid Multi-Mode Microplate Reader (BioTek, Winooski, VT, USA) using BCA Protein Assay Kit (ThermoFisher Scientific). For Western blotting, 10 μg of each sample was separated using NuPAGE 4% to 12% Bis-Tris Mini Gels (Invitrogen) and transferred to an Immobilon-P Transfer Membrane (Milipore, Burlington, MA, USA). Membrane was then blocked with 5% milk in PBS for 1 h at room temperature, and incubated with primary antibodies overnight at 4 °C. The antibodies and their working dilutions (all from Cell Signaling Technology, Danvers, MA, USA) were 1:2000 rabbit anti-ZO-1 (cat. number: 8193), 1:2000 rabbit anti-beta-catenin (cat. number: 8480), 1:2000 rabbit anti-vimentin (cat. number: 5741), 1:2000 rabbit anti-ZEB1 (cat. number: 3396). The next day, membrane was incubated with 1:5000 secondary anti-rabbit antibodies IgG, HRP-linked Antibody (cat. number: 7074, Cell Signaling Technology) for 2 h at room temperature. As a loading control, we used GAPDH (0.05 μg/mL, cat. number G8795 Sigma Aldrich, St. Louis, MO, USA). Signals were detected using SuperSignal West Pico Chemiluminescent Substrate (Thermo Scientific) and Fujifilm LAS-4000 (Tokyo, Japan). The results were analysed with the Multi Gauge version 3.2 software (FUJIFILM Manufacturing Corp., Tokyo, Japan). All the whole western blot figures can be found in the Supplementary Materials.
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Publication 2023
anti-IgG Antibodies Biological Assay Bistris Cells CTNNB1 protein, human GAPDH protein, human Gels Hybrids Immobilon P Immunoglobulins inhibitors Milk, Cow's Phosphoric Monoester Hydrolases Protease Inhibitors Proteins Pufferfish Rabbits Radioimmunoprecipitation Assay Technique, Dilution Tissue, Membrane Vimentin Western Blotting

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More about "Pufferfish"

Pufferfish, also known as blowfish or swellfish, are a fascinating group of marine and freshwater fish known for their unique ability to inflate their bodies when threatened.
These remarkable creatures belong to the order Tetraodontiformes and are found in tropical and subtropical waters around the globe.
Characterized by their distinctive round, spiny bodies, pufferfish have developed a remarkable defense mechanism - they can inflate themselves with water or air to appear larger and deter predators.
This adaptation has made them highly sought-after in some cuisines, but it also means they contain a potent neurotoxin that can be fatal if not properly prepared.
Researchers are continually exploring the biology, behavior, and potential medicinal applications of these fascinating fish.
Tools like PubCompare.ai can help optimize pufferfish research by enabling users to find the most accurate and reproducible protocols from literature, preprints, and patents.
Leveraging AI-driven comparisons, this tool enhances the accuracy and reproducibility of pufferfish studies.
Whether you're studying pufferfish behavior, ecology, or pharmacology, techniques like the PcDNA3.1 expression vector, High-Capacity cDNA Reverse Transcription Kit, ATP Bioluminescence Assay Kit CLS II, and RNeasy Mini Kit can be invaluable in your research.
Uncovering the secrets of these unique creatures, from their uniqe defense mechanisms to their potential medicinal applications, could lead to groundbreaking discoveries.
So dive into the world of pufferfish research and let the power of PubCompare.ai guide you to the most accurate and reproducible protocols, enhancing your studies and contributing to our understanding of these remarkable fish.