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Morphometric measurements are subjective and used to assess the carcass development and quantitatively measure the muscular distribution in the carcass with estimates of its conformation. In the present study there were not significative differences observed for these parameters or for carcass compactness index (CCI), inferring that the use of cactus pear silage as well as intermittent water supply combined or alone did not alter animal growth and/or carcass conformation, maintaining the muscle pattern achieved by the control diet (usual) and demonstrating body and carcass uniformity. Since animals used in this study were homogeneous and had similar age and body performance, as indicated by the carcass morphometric measurements and by the difference between the empty carcass and hot carcass weights, which resulted in the sum of head + limb with an average of 8.2 ± 0.13 kg between treatments, giving an idea that the animals were similar in chronological age, since the allometric growth of the body occurs from the extremities to the interior of the body.The significant difference between treatments with inclusion of cactus pear silage for hot carcass yield (HCY) and cold carcass yield (CCY) may be related to the weight of the full gastrointestinal tract, which showed higher values for animals fed with a higher proportion of Tifton 85 grass hay in the diet (0% CPS). Increasing the NDF content of the diet reduces the passage rate of digesta, and the emptying of the gastrointestinal tract (GT) that cause a distension of the rumen-reticulum and increase the weight of the gastrointestinal tract, resulting in lower HCY and consequently lower CCY. While the diets with inclusion of CPS increase NFC content, such as pectin, which have higher rates of rumen degradability and, higher rates of passage7,8,9.Measurements and evaluations carried out on the carcass, such as the carcass compactness index and loin eye area (LEA), are parameters that quantitatively measure the muscle distribution in the carcass, an edible part of greater financial return, which indicates the conformation of these animals3, while the body condition score (BCS) and the measure C, which are highly correlated, measure the distribution of fat on the carcass, giving an idea of the carcass finish, in which the higher these variables, the greater the proportion of fat that allows for less water loss due to carcass cooling10. These variables in the present study were also not influenced by the levels of cactus pear silage and water restrictions, presenting an overall mean of 0.17 kg/cm, 7.68 cm, 2.42 points and 0.7 mm respectively, and consequently did not influence the losses due to cooling, which presented an average loss of 1.48%.The main cuts of the goat carcass are the neck, leg, shoulder, loin, and rib. Their economic values differ, and their proportions become an important index to evaluate the carcass quality9. The cuts of greatest importance and commercial values are the leg and the loin, called noble cuts because they present greater yield and muscle tenderness, being interesting that they present a good proportion in the carcass, for providing greater edible tissue content, mainly muscle.Carcasses with similar weight tend to have equivalent proportions of cuts, as they exhibit isogonic growth. As the cold carcass weight (CCW) and the conformation of the animals were similar, with similar morphometric measurements, they had a direct relationship in the absence of an effect on commercial cuts.The commercial value of the carcass, whether through carcass yield and/or the proportions of the cuts, is also linked to tissue composition, thus the dissection of the leg represents an estimate of measuring the tissue composition of the carcass, in which is sought a greater proportion of muscle, intermediate proportion of fat and less bone in carcasses11. In this way, diets with cactus pear silage and the different levels of intermittent water supply resulted in the constancy in the amount of muscle, fat, and bone in legs of goats. The similarity in muscle proportion is related to the lack of effects on slaughter weight and CCW, as the weight of muscles is highly correlated to carcass weight. The average muscle yield was above 60% in all treatments, confirming that the animals showed good efficiency to the diets and adapted well to the water supply levels. Although the diets with cactus silage had high amounts of metabolizable energy (ME) and no difference in DM intake, the energy input was similar that not influencing carcass weights and carcass compactness index. That is, it did not influence muscle deposition in the carcass, probably due to synchronicity of energy and protein.As for the weight and proportion of bone tissue, it is believed that because this is a tissue with early development in relation to muscle and fat2, diets in the final stages of growth (average of 8 months) would hardly change their participation in the tissue composition, where the relationship of this tissue with the others is usually only increased when there are changes in the proportion of muscle and/or fat.Water restriction, as long as it is moderate and acute, mainly affects the loss of body water and not tissues, which does not cause deleterious effects on animal productivity and growth.The muscle:fat ratio indicates the state of leg fattening, while the muscle:bone ratio estimates the carcass muscularity, both being attributes of quality3. The similarity previously reported in the weight of fat, bone and muscle corroborates that these relationships also do not have differences. The same occurs for the leg muscularity index (LMI), due to the weight of the five muscles used to determine the index and the length of the femur which had been similar between the animals.Nevertheless, when considering fat as a percentage of participation in leg weight, it is possible to observe that the intermittency in water supply in both intervals (24 and 48 h) reduced the proportion of fat in the leg. Although in this research, the water supply levels did not affect the daily intake of dry matter from animals, with average intake of 650.67 g/kg DM, ranging from 599 to 682 g/kg DM between treatments7, during days of water deprivation, fat mobilization for energy availability may occur, possibly offsetting water stress and influencing not only feed intake, on these days of deprivation but also affecting energy metabolism, which results in the mobilization of energy reserves2.When the physicochemical composition of the meat was evaluated, it was observed that the diets and water supply levels probably did not affect the reserves of muscle glycogen during the pre-slaughter management as can be seen through pHinitial and pHfinal. The pHinitial right after slaughter should be close to neutrality, as well as in the live animal, indicating that the animal did not suffer from stress during the pre-slaughter period. The pHfinal, on the other hand, is expected to show a considerable variation, between 5.55 and 6.2 for goat meat; and due be inversely proportional to the concentration of muscle glycogen at the time of slaughter, that is, a more intense expenditure of glycogen stores results in less lactic acid production and higher pHfinal10,12,13. In this research, the pHfinal had an average of 5.74, a pH higher than the isoelectric point of muscle proteins (5.2–5.3). This result is favorable, since it is above the neutral charge and presenting an excessive negative charge that provides the repulsion of filaments, which allows water molecules to bind and improve the organoleptic characteristics of the meat, through succulence and texture of meat13 evaluated by cooking loss, moisture, and shear force, principally. The cooking loss (CL), moisture and shear force (SF) were within the values recommended (20–35% CL, moisture above 70% and SF up to 44.13 Newton (N) for goat meat) to classify the meat as soft and tender14. Statistically, interactions were found between the supply of silage and intermittent water supply, in which goats on a diet without cactus pear silage and without intermittent water supply showed higher values of cooking losses and shear force.Higher concentrations of collagen content and/or greater activities of calpastatin (which inhibit the action of calpains), as well as larger fascicles and greater number of fibers present in each muscle fascicle, as was visually observed in the meat of the animals in this research, can lead to reductions in meat tenderness15. Because goat carcasses are generally small, with low marbling degree and a thin layer of subcutaneous fat, there is rapid heat dissipation at the beginning of the post-mortem period, which can lead to cold shortening, muscle hardening, and less tender meats16.pHfinal of the meat has a high correlation with color parameters (L*—lightness, a*—redness, b*—yellowness and Chroma), as the pHfinal can affect the reaction of myoglobin to oxymyoglobin. The b* index in meat, on the other hand, may be related to the concentration of fat and/or the presence of carotenoids in the diet which can be affected by forage preservation processes, such as silage and hay, which significantly reduces by up to 80% carotenoids levels13. It is believed that the carotenoid concentrations in the diet of this study were similar between treatments and consequently in values of b* of meat. Values of a* and Chroma directly depend on the content and state of the heme pigments in the muscle, due to the chemical state of iron (Fe), playing an important role in meat color10. These parameters showed no significant difference between treatments, however, higher values of a* and Chroma in meat are desired, as a result of the increase in oxymyoglobin and decrease in metmyoglobin that provides the meat’s “bloom”. According to Dawson et al.17, the minimum critical value for meat luminosity (L*) is 34. Lower values of L are related to elevating pHfinal, which results in the high concentration of metmyoglobin, making the meat darker, which causes rejection by consumers for associating dark meat to as old meat.The meat’s presentation and more precisely its color is an important factor that can influence a consumer’s purchase decision, as it gives us the idea of freshness and meat’ quality. The L* and a* color parameters are the most representative for these characteristics18. Although in our research it did not have a significant effect on the color parameters, we can indicate that the meat obtained in this research would be well accepted by consumers, because Hopkins19 suggests that consumers will consider meat color acceptable when the L* value is equal to or exceeds 34, and a* value below 19 or equal to or exceeds 9.5 according to Khliji et al.18. In the present study, all values for L* remained above this aforementioned threshold and the values of a* remained within these values which suggests that meats from all diets and water supply levels had an acceptable color for consumers.When evaluating the chemical composition of meat, no significant differences were observed between treatments, except for the ash content, that remained above the average values found in the literature, which is 0.99–1.10%16. It is believed that because cactus pear is a rich source of Ca, Mg, K and with increasing level of cactus pear silage in the diet31, these minerals were consumed in larger amounts, which could have resulted in a higher proportion of minerals in the meat of animals that received 42% cactus pear silage.The lipid fatty acid profile in meat has a major impact on sensory properties and nutritional quality, influencing acceptance and health for consumers20,21. Intermittent water supply, cactus pear silage, and interaction between water supply and cactus pear silage did not influence most fatty acids present in the Longissimus lumborum muscle of the animals under study, except only a few saturated fatty acids e.g. docosanoic acid (C22:0), tricosanoic acid (C23:0), BCFA, anteiso-tridecanoic acid (C13:0 anteiso) and anteiso-pentadecanoic acid (C15:0 anteiso).Biohydrogenation of ruminal bacteria results in a circumstantial variety of fatty acids (FA), which will be absorbed in the intestine and later incorporated into the meat of goats. In addition to the diet and the biohydrogenation, the meat lipid profile can vary due to de novo synthesis, desaturation, duration of the feeding period and differences in pathways of various FA by the animal organism22.A high concentration of saturated fatty acids present in meat is not desirable, as there is evidence that saturated fatty acids, mainly C16:0, as well as myristic (C14:0) and lauric (C12:0) increase the blood cholesterol and low-density lipoproteins (LDL) concentration, due to interferences with hepatic LDL receptors23, however, in the studied treatments, there were no significant differences for these fatty acids. On the other hand, C18:0 has no impact on cholesterol levels, due to being poorly digested and easily desaturated to C18:1 by Δ9-desaturase24, present in the cell endoplasmic reticulum. This fatty acid is not harmful to health and is considered the only desirable SFA. As the levels of C18:0 in diets tend to be minimal, their main origin is the biohydrogenation of PUFA and de novo syntheses in diets with a high energy pattern25.In addition to carrying out the biohydrogenation process, ruminal bacteria synthesize a series of FA, mainly those of odd and branched chain, that comprise mainly the lipids of the bacterial membrane26,27, to maintain membrane fluidity. Linear odd-chains fatty acids are formed when propionyl-CoA, instead of acetyl-CoA, is used as a de novo synthesis initiator25. On the other hand, iso and anteiso FA are synthesized by the precursors branched-chain amino acids (valine, leucine, and isoleucine) and their corresponding branched- short-chain carboxylic acids (isobutyric, isovaleric and 2-methyl butyric acids)28.There is an increasing interest to study odd-and branched-chain fatty acids (OBCFAs) from animal products, mainly in milk due to its higher concentration compared to meat. Researchers reported that several OBCFAs have potential health benefits in humans29 as improved gut health30 and presenting anti-cancer activity31, as well as improve the sensory characteristics of the meat, providing a greater sensation of tenderness and juiciness, because BCFA content are associated with a less consistent fat in meat from lambs due to its lower melting point and its chain structure32.The FAs profile in the ruminal bacteria is largely composed by OBCFAs (C15:0; anteiso C15:0; iso C15:0; C17:0; iso C17:0; C17:1 and anteiso C17:0) in the bacteria membrane lipids24. Thus, the higher concentration of OBCFAs might be the result of the difference in the rumen bacterial populations induced by variation in the dietary carbohydrate, that is, a higher concentration of cellulolytic bacteria in relation to amylolytic bacteria, due to the high neutral detergent fiber (NDF) content in the diet with 0% cactus forage silage. It is also known that amylolytic bacteria produce more linear odd chain and anteiso FAs than iso FAs, whereas cellulolytic bacteria produce more iso FAs28,32. As the Tifton 85 grass hay-based diet had the highest neutral detergent fiber corrected for ash and protein (NDFap) and starch content (highest % of ground corn), the meat of those animals had higher concentrations of anteiso C15:0 and anteiso C13:0 compared to animals fed diets with the inclusion of cactus pear silage, also influencing the total sum of branched chain fatty acids.Although levels of intermittent water supply have generated punctual changes in tricosanoic acid (C23:0) SFA, the same was not observed for MUFA and PUFA, due to changes in the rumen environment, promoted by water restrictions, which were not sufficient to circumstantially modify biohydrogenation, resulting in similarities in concentrations of unsaturated fatty acids in goat meat.The animals subjected to 24 h of intermittent water supply (IWS) presented the highest concentration of C23:0 in relation to other treatments, which is interesting because it is involved in the synthesis of ceramide and reduces the risk of diabetes in humans33.The cactus pear has high non-fibrous carbohydrate (NFC) content (mainly pectin), having 59.5% high and medium rumen degradation carbohydrates which provide a higher production rate and removal of short-chain fatty acids and changes in rumen bacterial populations34. The inclusion of CPS resulted in a higher passage rate of digesta, affected biohydrogenation, and resulted in the escape of intermediate fatty acids isomers that are absorbed in the small intestine. Consequently, there was changing composition of fatty acids in the muscle of these animals, with a significant effect being observed only in the cis-13 C18:1. Furthermore, diets with high proportions of cactus pear silage (CPS), such as 42% CPS diet, can decrease ruminal pH and affect the final stages of biohydrogenation, resulting in the escape of intermediate fatty acids isomers, that are absorbed in the small intestine, which can explain the similarity of the C20:1 in 42% CPS diet from the Tifton hay-based diet, with differences between goat meat from 21% CPS diet and Tifton hay-based diet.Oleic acid (c9-C18:1) was the MUFA with the highest participation in the lipid profile of goat meat, which is interesting because it has a hypocholesterolemic effect, being a desirable fatty acid (DFA) for not reducing the serum high density lipoproteins (HDL) levels and thus prevent cardiovascular disease by reducing LDL levels35. The high concentrations of c9-C18:1 in ruminant meat come from the food intake, the effect of biohydrogenation, and mainly of the high activity of Δ9-desaturase, necessary for animal biosynthesis through desaturation of C18:0 to c9-C18:127. This fatty acid in the lipid profile of red meat varies between 30 and 43%36, confirming that the meat in the present study had a good concentration of this fatty acid.Much of unsaturated fatty acids, which have 18 carbons or 16 carbons, are largely converted to C18:0 and C16:0 through biohydrogenation, and when this process is not 100% completed, in addition to the PUFA that pass through this process intact, some product intermediates are formed, reaching the duodenum and are absorbed by the animal, in which significant amounts of cis and trans-monounsaturated, such as vaccenic fatty acid (t11-C18:1), reach the duodenum and are absorbed, later composing the muscle tissue22.The literature indicates that the precursor of conjugated linoleic acid (CLA) in the meat of animals is trans vaccenic acid (t11-C18:1), so the enzyme ∆9-desaturase, besides acting in the conversion of stearic into oleic fatty acid, also converts the trans-vaccenic acid to its corresponding CLA isomer, c9t11-C18:236. This pathway is more expressive in the mammary gland, and as the concentration of vaccenic acid (t11-C18:1) was not different, the concentration of CLA was not affected by the supply of silage and intermittent water supply, in the same way, that there are also no differences in the activity of ∆9-desaturase. Nevertheless, it is worth noting that in the human adipose tissue there is also the presence of ∆9-desaturase, and therefore, increased intake of vaccenic fatty acid could have the same beneficial effects associated with the intake of CLA, where the dietary vaccenic fatty acid shows 19–30% conversion rate37.Tifton hay is a natural source of n-3 fatty acids, mainly C18:3 n-3 with up to 20% participation in the lipid profile2, allowing a certain part of these PUFAs to be absorbed and increased in the tissue muscle, with 10 to 30% PUFAs in the diet generally escaping from biohydrogenation.Linoleic fatty acid (c9c12 C18:2) and α-linolenic acid (C18:3 n-3) are essential fatty acids for humans, that serve as precursors of the n-3 and n-6 pathways, distinct families, but synthesized by some of the same enzymes (∆4-desaturase, ∆5-desaturase, and ∆6-desaturase)25. Arachidonic fatty acid (C20:4 n-6) comes from elongation and desaturation of linoleic acid, where its concentrations, even close to that of its precursor, may indicate that there was a high activity of ∆6-desaturase (desaturation to γ-linolenic), elongase (elongation of γ-linolenic to dihomo-gamma-linolenic) and ∆5-desaturase. This fatty acid was influenced by the diets, presenting lower concentrations in the meat of animals fed the 42% cactus pear silage when compared to the Tifton hay diet (0% cactus pear silage).A higher concentration of long-chain PUFA n-3, docosahexaenoic (C22:6 n-3), was observed in the muscle of animals fed on Tifton hay. This was probably due to the high concentration of C18:3 n-3, precursor of C22:6 n-3, that the hay presents in relation to the cactus pear silage.The ratios and proportions of fatty acids are used to determine nutritional and nutraceutical values of the product or diet, and mainly, to indicate the cholesterolemic potential4. It is interesting that the n-6/n-3 ratio is low due to the pro-inflammatory properties of n-6; it is recommended to decrease its intake to assist in disease prevention38, while n-3 fatty acids are anti-inflammatory, antithrombotic, antiarrhythmic and reduce blood lipids, with vasodilating properties, being interesting that they present a higher proportion24. n-6 fatty acids tend to have a higher percentage in meat, and this directly influences the formation of n-3 isomers, since linoleic acid, when in excess, can reduce the synthesis of linolenic acid metabolites. The percentage of FA in one group can interfere with the metabolism of the other, reducing its incorporation into tissue lipids and altering its general biological effects38. Therefore, it is not recommended that the n-6/n-3 ratio be kept above 5 or 639, demonstrating that the averages of the current research remained acceptable.In relation to atherogenicity index (AI) and thrombogenicity index (TI), Ulbricht and Southgate39 proposed that sheep meat should have values of up to 1.0 and 1.58, respectively, and the lower the values for these indices in the lipid fraction, the greater the prevention of early stages of cardiovascular diseases. In the present study, the general averages observed were 0.29 for the AI, and 0.81 for the TI, although there were no significant differences, all treatments are within the recommended range, despite having been used as comparative standard to sheep, due to the absence of the proposed standard for goat meat.The h:H ratio did not differ for diets and water supply levels, but had an average of 1.90, below the reference value for meat products, which is 2.0. Values above 2.0 are recommended and favorable40, as it indicates a higher proportion of hypocholesterolemic fatty acids, that are beneficial to human health.The ∆9-desaturase enzyme that acts on both the mammary gland and adipose tissue, responsible for the transformation of SFA into unsaturated fatty acids (UFA), as well as in the endogenous conversion of CLA37 did not differ between treatments. On the other hand, the elongase showed less activity. Probably there was a greater “de novo” synthesis which resulted in a greater accumulation of palmitic fatty acid, and a reduction in the activity of the elongase enzyme.The crossbred goats demonstrated to present efficient mechanisms for adapting to water restrictions, especially when receiving feed with higher water content, such as cactus pear silage, being able to replace Tifton hay with 42% cactus pear silage in the diet for goats in confinement without negatively affecting the carcass traits and meat quality. Because, although these animals have shown some differences in the indices of tenderness and juiciness of their meats, however, all presented values of juiciness and tenderness compatible with meat extremely appreciated by the consumer market, and even goat meat showing some fatty acids with different concentrations induced by the supply of silage and water intermittence, the final lipid profile was appropriate to the health of consumers, observed by the absence of differences in the total concentrations of PUFA and in the main nutraceutical parameters (DFA, n-6/n-3; h:H; AI and TI).These results are relevant, indicating that goat feedlots in regions with low water availability may adopt strategies of lesser demand for drinking water and considerable concentrations of cactus pear silage in the diet, can reduce production costs without considerably affecting the product to be marketed, and therefore, provide higher profitability of the system. More

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Sequence analysisProtein sequence searches were conducted in the GenBank nr database with BLASTP42 using default parameters, including automatically adjusting parameters for short input sequences (Table S1). Conserved domain searches were run against the GenBank Conserved Domain Database (CDD)43. Sequence alignments were conducted in CLC Main Workbench 20.0.4 (Qiagen) with the fast alignment algorithm, gap open cost = 10, and gap extension cost = 1. Biochemical properties of the fish putative thiaminase I protein sequences were predicted with the Create Sequence Statistics function in CLC Main Workbench 20.0.4 (Qiagen, Hilden, Germany). The molecular weights were calculated from the sum of the amino acids in the sequence, and the isoelectric points (pIs) were calculated from the pKa values for the individual amino acids in the sequence.Bacteria culturePure cultures of P. thiaminolyticus strain 818822 were cultured at 37 °C in Terrific Broth (MO BIO Laboratories, Carlsbad, CA) in either a shaking incubator or in a beveled flask with a stir bar and were harvested after 48–80 h of culture. Upon harvest, cultures were processed immediately or frozen whole in 50 mL Falcon tubes at − 80 °C. Fresh or thawed cultures were spun at 14,000×g, and culture supernatant was concentrated using Amicon-ultra 10 kDa molecular weight cut-off (MWCO) filters (EMD Millipore, Billerica, MA).The zebrafish and alewife candidate thiaminase I genes were cloned and overexpressed in E. coli to determine whether they produced functional thiaminases. The recombinant thiaminase I gene from P. thiaminolyticus was overexpressed in E. coli as a positive control. Candidate and control genes were synthesized (Integrated DNA Technologies, Inc., Coralville, Iowa) and placed into the pET52b vector (EMD Millipore). Insert sequences are provided in Supplementary Figs. S10–S13. The empty pET52b vector was used as a negative control. The plasmid was transformed into E. coli (Rosetta 2(DE3)pLysS Singles Competent Cells, EMD Millipore) according to the manufacturer’s instructions, and expression of candidate genes was induced by the addition of IPTG. Cells were lysed in 1X BugBuster (Millipore) according to the manufacturer’s instructions in the presence of benzonase nuclease, and soluble and insoluble fractions were separated by centrifugation.Tissue collectionsAdult common carp were captured from Lake Erie using short-set gill nets. Adult alewife and quagga mussels (Dreissena bugensis) were collected from Sturgeon Bay, Lake Michigan using bottom trawls. Fish collections were completed during July 2007. Sex of sampled fish was not identified. Upon collection, unanesthetized animals were immediately euthanized by flash freezing between slabs of dry ice and stored at − 80 °C. Fish were harvested by the Great Lakes Science Center, U.S. Geological Survey (USGS). Laboratory use of frozen animal tissues and wild type and recombinant bacteria was in accordance with institutional guidelines and biosafety procedures at Oregon State University and USGS. Animal care and use procedures were approved by the Great Lakes Science Center, USGS. All USGS sampling and handling of fish during research are carried out in accordance with guidelines for the care and use of fishes by the American Fisheries Society44. All methods are reported in accordance with applicable ARRIVE guidelines (https://arriveguidelines.org). Zebrafish from OSU’s zebrafish facility were anesthetized and euthanized by overdose with waterborne 200 ppm ethyl 3-aminobenzoate methanesulfonate (MS-222, Sigma-Aldrich, St. Louis, MO) following protocols approved by the OSU Animal Institutional Care and Use Committee and were frozen at − 80 °C after euthanization. Gills, liver, spleen, and the intestinal tract were dissected, and gill tissue was homogenized separately from liver, spleen, and gut, which were homogenized together and designated “viscera.” Homogenization and protein preparation procedures were the same as that for alewife. Zebrafish from Columbia Environmental Research Center (CERC), USGS cultures were anesthetized and euthanized by overdose with 200 ppm ethyl 3-aminobenzoate methanesulfonate (MS-222, Sigma-Aldrich, St. Louis, MO) in water following protocols approved by CERC Institutional Animal Care and Use Committee (IACUC). Whole fish (0.2–0.6 g) were homogenized in 10 mL cold phosphate buffer, pH 6.5. Whole common carp and alewife were thawed until they could just be dissected. Preliminary trial extractions on alewife stomach and intestines, spleen, and gills revealed similar results and revealed that gills and spleen tissue produced the cleanest protein preparations. Therefore, subsequent extractions for common carp and alewife used gill tissue. Samples were pooled from 3 to 5 individual fish, haphazardly chosen from the sampled fish without exclusions. Quagga mussels were thawed just sufficiently to be husked from their shell and were used whole. Researchers were aware of the species and tissue designation of each sample throughout the experiments. Animal tissues were placed in ice-cold (4 °C) beakers containing cold extraction buffer (16 mM K3HPO4, 84 mM KH2PO4, 100 mM NaCl, pH 6.5 with 1 mM DTT, 2 mM EDTA, 3 mM Pepstatin, 1X Protease inhibitor cocktail (Sigma), and 1 mM AEBSF). All extractions were carried out at 4 °C in pre-chilled glassware. Samples were mechanically homogenized using a rotor–stator tissue grinder. Samples were stirred gently for several hours to overnight at 4 °C, centrifuged at 14,000×g to remove debris, and strained through cheesecloth to remove any insoluble lipids. Extracts were then subjected to 30–75% ammonium sulfate precipitation. Pellets from the precipitation were resuspended in buffer (83 mM KH2PO4, 17 mM K2HPO4, and 100 mM NaCl), centrifuged to remove any remaining debris, and stored in 30% glycerol at − 20 °C.Protein electrophoresisNative PAGE was run using either pre-cast TGX gels (BioRad, Hercules, California) of varying percentage (7.5% to 12% or 8–16% gradient gels) or on hand-cast gels (TGX FastCast, BioRad) made according to the manufacturer’s instructions.Blue-native PAGE was used to estimate the mass of thiaminases in their native conformation. Blue-native PAGE45 gels were run using the NativePage Novex Bis–Tris system (Life Technologies) or hand-cast equivalents46. Light blue cathode buffer was used to facilitate visualization of the activity stain.Standard denaturing SDS-PAGE was used to estimate the molecular mass of thiaminases after denaturation. Denaturing SDS-PAGE was run using one of three relatively equivalent methods: pre-cast TGX gels (BioRad) according to the manufacturer’s instructions, hand-cast Tris–HCl gels using standard Laemmli chemistry47 with an operating pH of approximately 9.5, or hand-cast Bis–Tris gels (MOPS buffer) with an operating pH of approximately 7. For all denaturing and non-denaturing SDS-PAGE applications, standard Laemmli sample buffer was used, and samples were heated to 75 °C for 15 min to facilitate denaturation followed by brief centrifugation to eliminate any precipitated debris.Non-denaturing PAGE was used as an alternative to denaturing PAGE for the common carp thiaminase that could not be renatured (i.e., activity could not be recovered) following a denaturing SDS-PAGE. Non-denaturing PAGE was conducted using any of the three aforementioned gel chemistries with SDS-containing running buffers including reductant (DTT), but samples were not heated prior to application to the gel. Samples for non-denaturing PAGE were allowed to incubate in sample buffer at room temperature for 30 min prior to gel loading. This preserves the charge-shift induced by SDS but does not result in protein denaturation, facilitating in-gel analysis of thiaminase I activity after separation.To visualize proteins following electrophoresis, gels were stained with Coomassie stain (CBR-250 at 1 g/L in methanol/acetic acid/water (4:5:1) and destained with methanol/acetic acid/water (1.7:1:11.5). Mini-gels were run on BioRad’s mini-protean gel rigs. Midi-gels (16 cm length) were run on Hoefer’s SE660, and large-format gels (32 cm length) were run on a BioRad’s Protean Slab Cell. Mini-gels were generally run at room temperature, and midi- and large-format gels were run at 4 °C. Blue-native PAGE was always run at 4 °C.Two-dimensional electrophoresis (2DE) separated proteins in the first dimension based on pI and in the second dimension based on mass (either native or denatured). 2DE was performed by combining in-gel IEF with either denaturing SDS-PAGE, non-denaturing SDS-PAGE, or native PAGE. IPG strips were incubated in TRIS-buffered equilibration solution48 either with 6 M urea, SDS, and iodacetamide (denaturing) or without urea, SDS, and iodacetamide (non-denaturing) for 20 min. Low melting point agarose was used to solidify IGP strips in place. Agarose was cooled to just above the gelling temperature, as hot agarose inactivated thiaminase I activity.Isoelectric focusingIsoelectric focusing (IEF) was conducted both in-gel and in-liquid. In-gel IEF was conducted in immobilized pH gradient (IPG) strips using a Multifor II (GE Healthcare Life Sciences). Prior to rehydration, all protein preparations were desalted in low-salt (~ 5 to 10 mM) sodium or potassium phosphate buffer (pH 6.5) using 10 kDA MWCO filters. All samples were applied using sample volumes and protein concentrations recommended by the manufacturer. For standard denaturing in-gel IEF, rehydration solution consisted of 8 M urea, 2% CHAPS, 2% IPG buffer of the appropriate pH-range, 1% bromophenol blue, and 18 mM DTT. The IEF was conducted at maximum of 2 mA total current and 5 W total power, with an EPS3500 XL power supply in gradient mode. Voltage gradients were based on standard protocols recommended by the manufacturer. In-gel IEF was also performed under native conditions to allow thiaminase I activity staining of IPG strips. Protocols were essentially the same as those for denaturing conditions, with the following exceptions: (1) urea was eliminated and the CHAPS concentration was reduced to 0.5% in the rehydration solution; (2) rehydration was conducted at 14 °C; and (3) the water in the cooling tray was cooled to 4 °C.In-liquid IEF was conducted using a Rotofor (BioRad) according to the manufacturer’s instructions. Non-denaturing in-liquid IEF was also conducted using a focusing solution including no urea, 2% pH 3–10 biolyte, 0.5% CHAPS, 20% glycerol, and 5 mM DTT. The addition of glycerol helped retain activity but also increased focusing times. The Rotofor was run at a constant 15 W with a maximum current of 20 mA and voltage set for a maximum of 2000 V. Samples containing 8 M urea were cooled to 14 °C during focusing to avoid urea precipitation, whereas samples lacking urea were cooled to 4 °C during focusing. Protein extracts in salt solutions greater than 10 mM were desalted directly in focusing solution using a 10 kDA MWCO filter. Focusing runs were allowed to proceed until the voltage stabilized and fractions were harvested with the needle array and vacuum pump. Ampholytes were removed by addition of NaCl to 1 M and then samples were desalted into phosphate buffer using a 10kD MWCO filter.Thiaminase I activity measurementsFor quantitative measurements of thiaminase I activity, we conducted a radiometric assay at CERC as previously described49. Zebrafish homogenates were diluted 1:8, 1:16, or 1:32 in cold phosphate buffer, pH 6.5. Two replicates per dilution were assayed. Activity was calculated from the greatest dilution that gave activity within the linear range of the assay and was reported as pmol thiamine consumed per g tissue (wet weight) per minute (pmol/g/min).Thiaminase I activity stainingAfter electrophoresis, gels were stained for thiaminase I activity using a previously described diazo-coupling reaction19,50. Briefly, gels were washed 3 times in water, twice in 25 mM sodium phosphate buffer with 1 mM DTT, and once in 25 mM sodium phosphate buffer without DTT. Gels were then incubated in 0.89 mM thiamine-HCl and co-substrate (1.45 mM pyridoxine, 24 mM nicotinic acid, or 20 mM pyridine) in 25 mM sodium phosphate buffer for 10 min. Gels were briefly rinsed in water and placed in a lidded container and incubated at 37 °C for 30 min to allow thiamine degradation by any thiaminases in the gel. The diazo stain19,50 was then applied to detect remaining thiamine in the gel for five minutes with gentle agitation. Stained gels were rinsed with water and photographed, and further stained with Coomassie to visualize proteins. More

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