Nucleotide Mixture Research Articles

A correctable decoding DNA sequencing with high accuracy and high throughput.

Eliminating errors in next-generation sequencing has proven to be challenging. Here we present a novel strategy for DNA sequencing, called correctable two-color fluorogenic DNA decoding sequencing, which can significantly improve sequencing accuracy and throughput by employing a dual-nucleotide addition combined with fluorogenic sequencing-by-synthesis (SBS) chemistry. This sequencing method involves introducing a mixture of natural nucleotide X, labeled unblocked nucleotide X', 3' blocked nucleotide Y*, and labeled 3' blocked nucleotide Y* into each reaction cycle. By cyclically interrogating a template twice with different nucleotide combinations, two sets of base-encoding are sequentially obtained, enabling accurate deduction of base sequence. We demonstrate the remarkable efficacy of this approach in detecting and correcting sequencing errors, achieving a theoretical error rate of 0.0005%, which is twice as accurate as Sanger sequencing. Furthermore, we show the capability to detect known mutation sites using information from only a single sequencing run. The correctable two-color fluorogenic DNA decoding sequencing approach should enable accurate identification of extremely rare genomic variations in diverse applications in biology and medicine.

Atomistic insights into the reentrant phase-transitions in polyuracil and polylysine mixtures.

The phase separation of protein and RNA mixtures underpins the assembly and regulation of numerous membraneless organelles in cells. The ubiquity of protein-RNA condensates in cellular regulatory processes is in part due to their sensitivity to RNA concentration, which affects their physical properties and stability. Recent experiments with poly-cationic peptide-RNA mixtures have revealed closed-loop phase diagrams featuring lower and upper critical solution temperatures. These diagrams indicate reentrant phase transitions shaped by biomolecular interactions and entropic forces such as solvent and ion reorganization. We employed atomistic simulations to study mixtures with various RNA-polylysine stoichiometries and temperatures to elucidate the microscopic driving forces behind reentrant phase transitions in protein-RNA mixtures. Our findings reveal an intricate interplay between hydration, ion condensation, and specific RNA-polylysine hydrogen bonding, resulting in distinct stoichiometry-dependent phase equilibria governing stabilities and structures of the condensate phase. Our simulations show that reentrant transitions are accompanied by desolvation around the phosphate groups of RNA, with increased contacts between phosphate and lysine side chains. In RNA-rich systems at lower temperatures, RNA molecules can form an extensive pi-stacking and hydrogen bond network, leading to percolation. In protein-rich systems, no such percolation-induced transitions are observed. Furthermore, we assessed the performance of three prominent water force fields-Optimal Point Charge (OPC), TIP4P-2005, and TIP4P-D-in capturing reentrant phase transitions. OPC provided a superior balance of interactions, enabling effective capture of reentrant transitions and accurate characterization of changes in solvent reorganization. This study offers atomistic insights into the nature of reentrant phase transitions using simple model peptide and nucleotide mixtures. We believe that our results are broadly applicable to larger classes of peptide-RNA mixtures exhibiting reentrant phase transitions.

The Zootechnical Performance, Health State Modulation, Morphology, and Intestinal Microbiome of Nile Tilapia Juveniles Fed with a Functional Blend of Immunostimulants Associated with a Diet High in Soybean Meal

The aim of this study was to evaluate the effect of supplementing feed with a functional mixture of immunomodulators, including β-glucans, nucleotides, ascorbic acid, and alpha-tocopherol, associated with a diet with lower levels of animal protein (11.5%) and higher levels of soybean meal (43.5%), on the zootechnical performance, health, hematological and immunological parameters, intestinal morphology, centesimal composition, and intestinal microbiome of juvenile Nile tilapia (initial weight 1.88 g ± 0.25 g, mean ± standard deviation). Two isocaloric and isoproteic diets (35% crude protein) were formulated, one with the inclusion of the immunostimulant functional mixture (40 kg·t−1), composed of 150 mg·kg−1 of nucleotides, 1000 mg·kg−1 of β-glucans, 1000 mg·kg−1 of ascorbic acid (vitamin C), and 20 mg·kg−1 of alpha-tocopherol (vitamin E), and another without. The combined supplementation of nucleotides, β-glucans, ascorbic acid, and alpha-tocopherol resulted in a 59.95% increase in final weight, 64% weight gain, 66% daily gain, a 21.31% decrease in feed conversion rate, and double the retention of body protein. Supplementation also improved intestinal morphology and modulated the intestinal microbiome, increasing Chao-1 diversity. Transmission electron microscopy confirmed that fish fed with both diets exhibited intact intestinal mucosal membranes. Supplementation did not alter the hematological and immunological parameters, suggesting that there was no overstimulation of the fish’s immune system. This work allows us to evaluate the effect of reducing the use of animal protein in the diets of fish, along with the effects of nucleotides, β-glucans, ascorbic acid, and alpha-tocopherol. Together, these compounds can provide fish with the necessary tools to achieve optimal health and growth.

Heat flows enrich prebiotic building blocks and enhance their reactivity

The emergence of biopolymer building blocks is a crucial step during the origins of life1–6. However, all known formation pathways rely on rare pure feedstocks and demand successive purification and mixing steps to suppress unwanted side reactions and enable high product yields. Here we show that heat flows through thin, crack-like geo-compartments could have provided a widely available yet selective mechanism that separates more than 50 prebiotically relevant building blocks from complex mixtures of amino acids, nucleobases, nucleotides, polyphosphates and 2-aminoazoles. Using measured thermophoretic properties7,8, we numerically model and experimentally prove the advantageous effect of geological networks of interconnected cracks9,10 that purify the previously mixed compounds, boosting their concentration ratios by up to three orders of magnitude. The importance for prebiotic chemistry is shown by the dimerization of glycine11,12, in which the selective purification of trimetaphosphate (TMP)13,14 increased reaction yields by five orders of magnitude. The observed effect is robust under various crack sizes, pH values, solvents and temperatures. Our results demonstrate how geologically driven non-equilibria could have explored highly parallelized reaction conditions to foster prebiotic chemistry.

Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations.

Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) initiation depends on interaction between viral 5'-leader RNA, RT and host tRNA3Lys. Therefore, we sought to identify co-evolutionary changes between the 5'-leader and RT in viruses developing RT-inhibitor resistance mutations. We sequenced 5'-leader positions 37-356 of paired plasma virus samples from 29 individuals developing the nucleoside RT inhibitor (NRTI)-resistance mutation M184V, 19 developing a non-nucleoside RT inhibitor (NNRTI)-resistance mutation and 32 untreated controls. 5'-Leader variants were defined as positions where ≥20 % of next-generation sequencing (NGS) reads differed from the HXB2 sequence. Emergent mutations were defined as nucleotides undergoing a ≥4-fold change in proportion between baseline and follow-up. Mixtures were defined as positions containing ≥2 nucleotides each present in ≥20 % of NGS reads. Among 80 baseline sequences, 87 positions (27.2 %) contained a variant; 52 contained a mixture. Position 201 was the only position more likely to develop a mutation in the M184V (9/29 vs 0/32; P=0.0006) or NNRTI-resistance (4/19 vs 0/32; P=0.02; Fisher's exact test) groups than the control group. Mixtures at positions 200 and 201 occurred in 45.0 and 28.8 %, respectively, of baseline samples. Because of the high proportion of mixtures at these positions, we analysed 5'-leader mixture frequencies in two additional datasets: five publications reporting 294 dideoxyterminator clonal GenBank sequences from 42 individuals and six National Center for Biotechnology Information (NCBI) BioProjects reporting NGS datasets from 295 individuals. These analyses demonstrated position 200 and 201 mixtures at proportions similar to those in our samples and at frequencies several times higher than at all other 5'-leader positions. Although we did not convincingly document co-evolutionary changes between RT and 5'-leader sequences, we identified a novel phenomenon, wherein positions 200 and 201 immediately downstream of the HIV-1 primer binding site exhibited an extraordinarily high likelihood of containing a nucleotide mixture. Possible explanations for the high mixture rates are that these positions are particularly error-prone or provide a viral fitness advantage.

Dietary Supplementation of a Mixture of Nucleotides, β-Glucan and Vitamins C and E Improved the Growth and Health Performance of Olive Flounder, Paralichthys olivaceus

A twelve-week feeding trial was conducted to investigate the effect of dietary supplementation of a functional immunostimulant mixture (FIM; nucleotides, β-glucan and vitamins C and E) on growth, feed utilization, innate immunity, digestive enzyme activity, hematological parameters, intestinal morphology and inflammatory gene expressions of olive flounder, Paralichthys olivaceus. A fish meal-based basal diet (control) was formulated, and three other diets were prepared by incorporating 0.5, 1.0 and 1.5% FIM into the basal diet (HB0.5, HB1.0 and HB1.5, respectively). Five replicate groups of fish (26.3 ± 0.1 g) were fed one of the experimental diets. Inclusion of 1.5% FIM in the diet significantly enhanced growth and feed utilization. Significantly higher plasma hemoglobin, hematocrit, total protein levels and lower plasma glucose level were observed in the HB1.5 group. Total immunoglobulin content, lysozyme, nitroblue tetrazolium, myeloperoxidase, superoxide dismutase, glutathione peroxidase and catalase activities and immune-related gene expressions of toll-like receptor and perforin were significantly increased at the highest inclusion level. FIM supplementation significantly increased villus height and goblet cell counts. Anti-inflammatory gene expressions were significantly upregulated at a 1.5% level. Dietary supplementation of 1.5% of FIM could improve growth and feed utilization, immune, hematological and intestinal histomorphological parameters of olive flounder.

A Mixture of Nucleosides and Nucleotides Increases Bone Marrow Cell and Peripheral Neutrophil Number in Mice Infected with Methicillin-Resistant Staphylococcus aureus

We studied the effects of a mixture of nucleosides and nucleotides on the peripheral neutrophil number and the proliferation of bone marrow cells in mice challenged with methicillin-resistant Staphylococcus aureus. BALB/c mice were fed a nucleotide-free 20% casein diet (control) or this diet supplemented with nucleosides and nucleotides orally (Expt. 1) or intraperitoneally (Expt. 2 and 3). On d 10, the mice were challenged intravenously with methicillin-resistant S. aureus (6.7 × 1012 colony forming units/L). In Expt. 1 and 2, numbers of total and differential counts of blood leucocytes were counted on d 0 (before), 1, 3 and 5 after the infection. In Expt. 3, 30 min before killing, bromodeoxyuridine (20 mg/kg), an analogue of thymidine, was administered intraperitoneally and its incorporation in the DNA synthetic phase of bone marrow cells was determined at 0 h (before), 3, 6 and 24 h after the infection. Mice fed the supplemented diet had higher (P < 0.05) leucocyte and neutrophil numbers on d 0 compared with the control group. The neutrophil numbers tended to be greater in the supplemented group at 1, 3 and 5 d after the infection. Intraperitoneal administration of nucleosides and nucleotides increased (P < 0.05) neutrophil numbers before and after the infection. Twenty-four h after the infection, incorporation of bromodeoxyuridine into the DNA synthetic phase of bone marrow cells in the group administered nucleosides and nucleotides was higher (P < 0.05) than in the control group. We conclude that, following methicillin-resistant S. aureus injection, intraperitoneal administration of a nucleoside-nucleotide mixture may stimulate bone marrow cell proliferation and increase the peripheral blood neutrophil numbers. Oral administration may elicit weaker effects.

Effect of feed enzymes and functional immunostimulants supplementation on growth performance and overall health of postlarvae and juvenile Pacific white shrimp, Penaeus vannamei, fed soybean‐based diets

AbstractSoybean meal (SBM) is widely used in shrimp feed agro‐industry as a fish meal (FM) replacement. However, high levels of SBM may compromise animal health as a result of nutrient imbalance. This study aimed to investigate the effects of feed enzyme combination (a mixture of 6‐phytase, serine protease, and endo‐1,3(4)‐β‐glucanase) and functional immunostimulant combination (a mixture of brewer's yeast, nucleotides, vitamin C, and vitamin E) in improving the overall health of Pacific white shrimp fed soybean‐based diet. Four diets were formulated with different amounts of SBM, FM, and poultry meal (PM): 0% SBM (with 25% FM and 12.6% PM), 30% SBM (with 12.5% FM and 5.7% PM), 30% SBM plus 0.045% feed enzymes, and 30% SBM plus 0.1% functional immunostimulants. The postlarvae were fed the test diets for 45 days. Then, the body weight, survival, FCR, Vibrio spp. count, and immune responses were analyzed. The resistance of shrimp to Vibrio parahaemolyticus infection was also evaluated. The results suggest that the diet with 30% SBM was deleterious to the shrimp's health. Feed enzymes and functional immunostimulant supplements improved overall performance, immune function, and resistance to V. parahaemolyticus infection of shrimp fed the diet containing 30% SBM compared with the 30% SBM diet without feed supplements.

Neuroprotective Actions of Different Exogenous Nucleotides in H2O2-Induced Cell Death in PC-12 Cells.

Exogenous nucleotides (NTs) are considered conditionally essential nutrients, and the brain cannot synthesize NTs de novo. Therefore, the external supplementation of exogenous NTs is of great significance for maintaining normal neuronal metabolism and function under certain conditions, such as brain aging. This study, therefore, sets out to assess the neuroprotective effect of four kinds of single exogenous NTs and a mixture of the NTs, and to elucidate the potential mechanism. A rat pheochromocytoma cell line PC-12 was treated with different concentrations of exogenous NTs after 4 h of exposure to 200 µM H2O2. We found that the exogenous NTs exerted significant neuroprotection through decreasing neuron apoptosis and DNA damage, ameliorating inflammation and mitochondrial dysfunction, promoting cell viability, and augmenting antioxidant activity, and that they tended to up-regulate the NAD+/SIRTI/PGC-1α pathway involved in mitochondrial biogenesis. Among the different NTs, the neuroprotective effect of AMP seemed to be more prominent, followed by the NT mixture, NMN, and CMP. AMP also exhibited the strongest antioxidant activity in H2O2-treated PC-12 cells. UMP was excellent at inhibiting neuronal inflammation and improving mitochondrial function, while GMP offered major advantages in stabilizing mitochondrial membrane potential. The mixture of NTs had a slightly better performance than NMN, especially in up-modulating the NAD+/SIRTI/PGC-1α pathway, which regulates mitochondrial biogenesis. These results suggest that antioxidant activity, anti-inflammatory activity, and protection of mitochondrial function are possible mechanisms of the neuroprotective actions of exogenous NTs, and that the optimization of the mixture ratio and the concentration of NTs may achieve a better outcome.

Dietary Fish Meal Level and a Package of Choline, β-Glucan, and Nucleotides Modulate Gut Function, Microbiota, and Health in Atlantic Salmon (Salmo salar, L.).

Steatosis and inflammation have been common gut symptoms in Atlantic salmon fed plant rich diets. Choline has recently been identified as essential for salmon in seawater, and β-glucan and nucleotides are frequently used to prevent inflammation. The study is aimed at documenting whether increased fishmeal (FM) levels (8 levels from 0 to 40%) and supplementation (Suppl) with a mixture of choline (3.0 g/kg), β-glucan (0.5 g/kg), and nucleotides (0.5 g/kg) might reduce the symptoms. Salmon (186 g) were fed for 62 days in 16 saltwater tanks before samples were taken from 12 fish per tank for observation of biochemical, molecular, metabolome, and microbiome indicators of function and health. Steatosis but no inflammation was observed. Lipid digestibility increased and steatosis decreased with increasing FM levels and supplementation, seemingly related to choline level. Blood metabolites confirmed this picture. Genes in intestinal tissue affected by FM levels are mainly involved in metabolic and structural functions. Only a few are immune genes. The supplement reduced these FM effects. In gut digesta, increasing FM levels increased microbial richness and diversity, and changed the composition, but only for unsupplemented diets. An average choline requirement of 3.5 g/kg was indicated for Atlantic salmon at the present life stage and under the present condition.

Maternal nucleotide supplementation improves the intestinal morphology and immune function in lipopolysaccharide-challenged newborn piglets.

This study aimed to evaluate the effects of maternal nucleotide (NT) supplementation on intestinal morphology and immune function in lipopolysaccharide-challenged newborn piglets. At 85 d gestation, 12 sows were selected and assigned to two groups: the CON group (basal diet, n = 6) and the NT group (basal diet with 1 g/kg NT mixture, n = 6). After parturition, newborn piglets were collected without suckling. Piglets from the CON group were intraperitoneally injected with sterile saline or lipopolysaccharide (LPS, 10 mg/kg body weight), and divided into the C-CON (n = 6) and C-LPS groups (n = 6). Piglets from the NT group received the same treatment and were divided into the N-CON (n = 6) and N-LPS groups (n = 6). The blood and small intestinal samples of piglets were collected 1 h after injection. The results showed that: (1) maternal NT supplementation increased the concentrations of serum complement C3 and C4 (P < 0.05), and suppressed the increase in serum hypersensitive C-reactive protein in LPS-challenged newborn piglets (P < 0.05); (2) maternal NT supplementation increased the villus height and the ratio of villus height to crypt depth in the duodenum of newborn piglets (P < 0.05) and inhibited the LPS-induced decrease in the villus height in the jejunum and ileum (P < 0.05). (3) The LPS-induced increased levels of interleukin-6 in the jejunum and tumor necrosis factor-α in the ileum of newborn piglets were suppressed by maternal NT supplementation (P < 0.05). (4) In the jejunum of newborn piglets, maternal NT supplementation inhibited the LPS-induced increase in toll-like receptor 4 (TLR4) mRNA and protein expression (P < 0.05) and the decrease of nuclear factor-κB inhibitor α (IκBα) protein expression (P < 0.05). In the ileum, piglets had a lower nuclear factor-κB (NFκB) mRNA expression in the NT groups than the CON groups (P < 0.05), and maternal NT supplementation suppressed the decrease of IκBα mRNA in LPS-treated piglets (P < 0.05). In conclusion, maternal NT supplementation could promote the intestinal development and immune function of newborn piglets, and may improve LPS-induced intestinal inflammatory responses via the TLR4/IκBα/NFκB pathway.

A Single Nucleotide Mixture Enhances the Antitumor Activity of Molecular-Targeted Drugs Against Hepatocellular Carcinoma.

New strategies for molecular-targeted drug therapy for advanced hepatocellular carcinoma (HCC) ignore the contribution of the nutritional status of patients and nutritional support to improve physical status and immunity. We aimed to elucidate the role of a single nucleotide mixture (SNM) in the anti-tumor therapy of HCC, and to explore the importance of a SNM as adjuvant therapy for HCC. Compared with a lipid emulsion (commonly used nutritional supplement for HCC patients), the SNM could not induce metabolic abnormalities in HCC cells (Warburg effect), and did not affect expression of metabolic abnormality-related factors in HCC cells. The SNM could also attenuate the lymphocyte injury induced by antitumor drugs in vitro and in vivo, and promote the recruitment and survival of lymphocytes in HCC tissues. Using HCC models in SCID (server combined immune-deficiency) mice or BalB/c mice, the SNM had anti-tumor activity, and could significantly upregulate the antitumor activity of molecular-targeted drugs (tyrosine-kinase inhibitors [TKI] and immune-checkpoint inhibitors [ICI]) against HCC. We employed research models in vivo and in vitro to reveal the anti-tumor activity of the SNM on HCC. Our findings expand understanding of the SNM and contribute to HCC (especially nutritional support) therapy.

Gut Health and Microbiota in Out-of-Season Atlantic Salmon (Salmo salar L.) Smolts Before and After Seawater Transfer Under Commercial Arctic Conditions: Modulation by Functional Feed Ingredients

Atlantic salmon (Salmo salarL.) undergo great alterations in physiology and gut microbiota composition throughout their life stages. This study assessed gut health and microbiota in out-of-season smolts before and after seawater transfer and modulatory effects of functional feed ingredients under commercial Arctic conditions. The fish were fed two series of diets, one without (Ref diet) and one with a mixture of functional ingredients (Test diet). Both diets varied in nutrient composition as required according to the developmental stage of the fish. For fish in freshwater, the mixture of functional ingredients contained nucleotides and immune stimulants, in seawater nucleotides, DHA, and EPA. Samples were collected four weeks before and four weeks after seawater transfer. Regardless of diet, seawater transfer (seawater compared to freshwater) significantly suppressed fish growth rate, condition factor, plasma nutrient levels, digesta bile acid concentrations, expression of genes related to gut immune functions (i.e., cytokines and T-cell markers), and increased intestinal microbial richness and diversity. Seawater transfer also reduced the symptoms of pyloric caeca lipid malabsorption with a corresponding decreasing effect on perilipin-2 (plin2) expression. In the gut microbiota of fish in freshwater, the unclassifiedRuminococcaceaefamily dominated strongly, accounting for about 85% of the total abundance, whereas in seawater the generaLactobacillusandPhotobacteriumwere the dominant taxa, accounting for about 90% of the total abundance. Multivariate association analysis showed that relative abundance of certain lactic acid bacteria (LAB) correlated positively with expression of important immune genes. Regarding the effects of functional feed ingredients, Test-fed fish in FW showed higher plasma cholesterol levels, and reduced symptoms of lipid malabsorption, suggesting that the mixture of nucleotides and immune stimulants enhanced digestive and absorptive capacity. However, the inclusion of nucleotides, DHA, and EPA affected the SW-fish only marginally. In conclusion, the outcomes of the present study highlight the great reductions in growth and impact on gut health biomarkers after seawater transfer, in this case observed under commercial Arctic conditions, and the promotion of metabolic capacity of Atlantic salmon fed functional ingredients in freshwater, which may shape future best-practices in salmon industry.

Comparison of five basal compositions of selective chocolate agar media for isolation of Taylorella equigenitalis

The gold standard method to isolate and identify Taylorella equigenitalis, the contagious agent of equine metritis, is the culture method according to the World Organisation for Animal Health Terrestrial Manual. No selective T. equigenitalis chocolate agar medium has been developed since the 1980s and the existing media show limited performances due to the fastidious nature of T. equigenitalis and the presence of interfering bacteria in the genital tract of equines. Here, the growth rates of 6 T. equigenitalis strains and 7 non-T. equigenitalis strains were compared on Timoney's selective medium formulated with 5 different basal agars (Columbia, Eugon, Blood, Mueller-Hinton and Tryptose Blood) provided by 2 to 4 suppliers per basal agar. The impact of glucose and/or Vitox supplementation was also investigated. Overall, the performance of selective T. equigenitalis media could be improved by substituting Eugon or Columbia agar with Blood, Mueller-Hinton or Tryptose Blood agar. It is nevertheless essential to validate the basal agar/supplier pair using a panel of T. equigenitalis strains. Furthermore, our findings confirm the need to supplement the selective media with a mixture of amino acids, nucleotides, and organic, mineral and vitamin compounds, translated here by Vitox supplementation.

Dietary Nucleotides Retard Oxidative Stress-Induced Senescence of Human Umbilical Vein Endothelial Cells.

Several lines of evidence suggest an inhibitory role of dietary nucleotides (NTs) against oxidative stress and inflammation, which promote senescence in age-associated cardiovascular diseases. We sought to test whether the dietary NTs could retard the hydrogen peroxide (H2O2)-induced senescence of human umbilical vein endothelial cells (HUVECs) and to elucidate the efficiency of different NTs as well as the potential mechanism. Senescence was induced in HUVECs by 4 h exposure to 200 µM H2O2 and was confirmed using senescence-associated-β-galactosidase staining (SA-β-gal), cell viability, and Western blot analyses of p16INK4A and p21Waf1/Cip1 after 24 h administration of growth medium. We find that NTs retards oxidative stress-induced HUVECs senescence, as shown by a lower percentage of SA-β-gal-positive cells, lower expression of p16INK4A, and p21Waf1/Cip1 as well as higher cell viability. GMP100 was the most excellent in delaying HUVECs senescence, which was followed by the NTs mixture, NMN, CMP50, and UMP50/100, while AMP retards HUVECs senescence by specifically reducing p15INK4b expression. NTs all have significant anti-inflammatory effects; AMP and CMP were more prominent in restoring mitochondrial function, GMP and CMP were more competent at eliminating ROS and MDA, while AMP and UMP were more efficient at enhancing antioxidant enzyme activity. The role of the NTs mixture in retarding HUVECs senescence is full-scaled. These results stated that the mechanisms of NTs retarding HUVECs senescence could be related to its antioxidant and anti-inflammation properties promoting cell proliferation and protecting mitochondrial function activities.

Microbiota in intestinal digesta of Atlantic salmon (Salmo salar), observed from late freshwater stage until one year in seawater, and effects of functional ingredients: a case study from a commercial sized research site in the Arctic region

BackgroundThe importance of the gut microbiota for health and wellbeing is well established for humans and some land animals. The gut microbiota is supposedly as important for fish, but existing knowledge has many gaps, in particular for fish in the Arctic areas. This study addressed the dynamics of Atlantic salmon digesta-associated gut microbiota assemblage and its associations with host responses from freshwater to seawater life stages under large-scale, commercial conditions in the Arctic region of Norway, and explored the effects of functional ingredients. The microbiota was characterized by 16S rRNA gene sequencing in distal intestinal digesta at four time points: 2 weeks before seawater transfer (in May, FW); 4 weeks after seawater transfer (in June, SW1); in November (SW2), and in April (SW3) the following year. Two series of diets were fed, varying throughout the observation time in nutrient composition according to the requirements of fish, one without (Ref diet), and the other with functional ingredients (Test diet). The functional ingredients, i.e. nucleotides, yeast cell walls, one prebiotic and essential fatty acids, were supplemented as single or mixtures based on the strategies from the feed company.ResultsOverall, the fish showed higher microbial richness and lactic acid bacteria (LAB) abundance after seawater transfer, while Simpson’s diversity decreased throughout the observation period. At SW1, the gut microbiota was slightly different from those at FW, and was dominated by the genera Lactobacillus and Photobacterium. As the fish progressed towards SW2 and SW3, the genera Lactobacillus and Mycoplasma became more prominent, with a corresponding decline in genus Photobacterium. The overall bacterial profiles at these time points showed a clear distinction from those at FW. A significant effect of functional ingredients (a mixture of nucleotides, yeast cell walls and essential fatty acids) was observed at SW2, where Test-fed fish showed lower microbial richness, Shannon’s diversity, and LAB abundance. The multivariate association analysis identified differentially abundant taxa, especially Megasphaera, to be significantly associated with gut immune and barrier gene expressions, and plasma nutrients.ConclusionsThe gut microbiota profile varied during the observation period, and the Mycoplasma became the dominating bacteria with time. Megasphaera abundance was associated with gut health and plasma nutrient biomarkers. Functional ingredients modulated the gut microbiota profile during an important ongrowing stage.

Gut immune functions and health in Atlantic salmon (Salmo salar) from late freshwater stage until one year in seawater and effects of functional ingredients: A case study from a commercial sized research site in the Arctic region

The present study was conducted to strengthen the knowledge on gut immune functions and health in Atlantic salmon under large scale, commercial conditions in the Arctic region of Norway. Two groups of fish were monitored, one fed a series of diets without functional ingredients (Ref) and the other diets with functional ingredients (Test). The nutritional composition of the two diet series varied in parallel according to the nutrient requirements of the fish during the observation time. The content of functional ingredients in the Test diets, i.e. nucleotides, yeast cell walls, a prebiotic and essential fatty acids, varied in accordance with a strategy developed by the feed company. The fish were observed at four sampling time points, the first (FW) in May 2016 two weeks before seawater transfer, the other three throughout the following seawater period until the fish reached a size of about 2 kg, i.e. in June, four weeks after seawater transfer (SW1); in November (SW2), and in April the following year (SW3). Gut health was assessed based on histopathological indicators of lipid malabsorption and gut inflammation, expression of gut immune, barrier and other health related genes, plasma biomarkers, somatic indices of intestinal sections, as well as biomarkers of digestive functions.Seawater transfer of the fish (SW1 compared to FW) caused a marked lowering of expression of genes related to immune and barrier functions in the distal intestine, i.e. cytokines (il1β, il10, tgfβ, ifnγ), T-cell markers (cd3γδ), myd88 and tight junction proteins (zo-1, claudin-15, claudin-25b), indicating suppressed immune and barrier functions. At SW2 and SW3, most of the immune biomarkers showed values similar to those observed at FW. The development of plasma cholesterol and triglyceride levels showed similar picture, with markedly lower levels after seawater transfer. Lipid malabsorption was observed in particular in fish from SW1 and SW2, as indicated by hyper-vacuolation of the pyloric caeca enterocytes with concurrently increased expression levels of plin2. Regarding effects of functional ingredients, significantly lower condition factor and plasma triglyceride level were observed for Test-fed fish at SW2, indicating a metabolic cost of use of a mixture of nucleotides, yeast cell walls and essential fatty acids. No clear effects of functional ingredients on expression of gut immune genes and other health indexes were observed through the observation period. The great, temporary lowering of expression of gut immune and barrier genes at SW1 is suggested to be an important factor underlying the increased vulnerability of the fish at this time point. Our findings regarding supplementation with functional ingredients raise questions whether some of these ingredients overall are beneficial or might come with a metabolic cost. Our results highlight the need for a better understanding of the cause and consequences of the suppression of gut immune functions of farmed Atlantic salmon just after seawater transfer, and the use of functional ingredients under commercial conditions.

Profiling DNA mutation patterns by SERS fingerprinting for supervised cancer classification

Profiling DNA mutation patterns for cancer classification plays an essential role in precision and personalized medicine. Conventional PCR-based mutation assay is limited by the extensive labour on target amplification. We herein create an amplification-free surface enhanced Raman spectroscopy (SERS) biochip which enables direct and simultaneous identification of multiple point mutations in tumor cells. Without pre-amplifying the target sequences, the SERS assay reads out the presence of cellular mutations through the interpretation of Raman fingerprints. The SERS sensor is integrated into a microfluidic chip, achieving one-step multiplex analysis within 40 min. Importantly, by combining SERS spectra encoding technique with supervised learning algorithm, a panel of nucleotide mixtures can be well distinguished according to their mutation profiles. We initially demonstrate an excellent levels of classification in samples from colorectal cancer and melanoma cell lines. For final clinical validation, the system performance is verified by classifying cancer patient samples, which shows an accuracy above 90%. Due to the simplicity and rapidness, the SERS biosensor is expected to become a promising tool for clinical point-of-care diagnosis towards precision medicine.

Hierarchical chirality expression of gemini surfactant aggregates via equilibrium between chiral nucleotide and nonchiral mono-anions.

The assembling behaviors of nonchiral dicationic amphiphilic molecules (gemini) in the presence of the mixture of chiral anionic nucleotides and nonchiral anions are investigated. We demonstrate that subtle balance of various physico-chemical parameters and the competition between chiral and nonchiral anions at the interface of gemini assemblies influences the expression of molecular chirality at the micrometer scale through the hierarchical molecular assembly.

An Optical Model for Quantitative Raman Microspectroscopy.

Raman spectroscopy is an invaluable technique for identifying compounds by the unique pattern of their molecular vibrations and is capable of quantifying the individual concentrations of those compounds provided that certain parameters about the sample and instrument are known. We demonstrate the development of an optical model to describe the intensity distribution of incident laser photons as they pass through the sample volume, determine the limitations of that volume that may be detected by the spectrometer optics, and account for light absorption by molecules within the sample in order to predict the total Raman intensity that would be obtained from a given, uniform sample such as an aqueous solution. We show that the interplay between the shape and divergence of the laser beam, the position of the focal plane, and the dimensions of the spectrometer slit are essential to explaining experimentally observed trends in deep ultraviolet Raman intensities obtained from both planar and volumetric samples, including highly oriented pyrolytic graphite and binary mixtures of organic nucleotides. This model offers the capability to predict detection limits for organic compounds in different matrices based on the parameters of the spectrometer, and to define the upper/lower limits within which concentration can be reliably determined from Raman intensity for such samples. We discuss the potential to quantify more complex samples, including as solid phase mixtures of organics and minerals, that are investigated by the unique instrument parameters of the Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) investigation on the upcoming Mars 2020 rover mission.