Dose–response evaluation of the standardized ileal digestible tryptophan : lysine ratio to maximize growth performance of growing-finishing gilts under commercial conditions

Environmental regulations as well as economic incentives have resulted in greater use of synthetic amino acids in swine diets. Tryptophan is typically the second limiting amino acid in corn-soybean meal-based diets. However, using corn-based co-products emphasizes the need to evaluate the pig’s response to increasing Trp concentrations. Therefore, the objective of these studies was to evaluate the dose–response to increasing standardized ileal digestible (SID) Trp : Lys on growth performance of growing-finishing gilts housed under large-scale commercial conditions. Dietary treatments consisted of SID Trp : Lys of 14.5%, 16.5%, 18.0%, 19.5%, 21.0%, 22.5% and 24.5%. The study was conducted in four experiments of 21 days of duration each, and used corn-soybean meal-based diets with 30% distillers dried grains with solubles. A total of 1166, 1099, 1132 and 975 gilts (PIC 337×1050, initially 29.9±2.0 kg, 55.5±4.8 kg, 71.2±3.4 kg and 106.2±3.1 kg BW, mean±SD) were used. Within each experiment, pens of gilts were blocked by BW and assigned to one of the seven dietary treatments and six pens per treatment with 20 to 28 gilts/pen. First, generalized linear mixed models were fit to data from each experiment to characterize performance. Next, data were modeled across experiments and fit competing dose–response linear and non-linear models and estimate SID Trp : Lys break points or maximums for performance. Competing models included broken-line linear (BLL), broken-line quadratic and quadratic polynomial (QP). For average daily gain (ADG), increasing the SID Trp : Lys increased growth rate in a quadratic manner (P<0.02) in all experiments except for Exp 2, for which the increase was linear (P<0.001). Increasing SID Trp : Lys increased (P<0.05) feed efficiency (G : F) quadratically in Exp 1, 3 and 4. For, ADG the QP was the best fitting dose–response model and the estimated maximum mean ADG was obtained at a 23.5% (95% confidence interval (CI): [22.7, 24.3%]) SID Trp : Lys. For maximum G : F, the BLL dose–response models had the best fit and estimated the SID Trp : Lys minimum to maximize G : F at 16.9 (95% CI: [16.0, 17.8%]). Thus, the estimated SID Trp : Lys for 30 to 125 kg gilts ranged from a minimum of 16.9% for maximum G : F to 23.5% for maximum ADG.     

Specificity of MLL1 and TET3 CXXC domains towards naturally occurring cytosine modifications

CXXC domains have traditionally been considered as CpG specific DNA binding domains that are repelled by cytosine modifications. This view has recently been challenged by the demonstration that CXXC domain of TET3 has relaxed sequence specificity and binds with the highest affinity to symmetric DNA duplex containing 5caCpG. Here, we present a comparative analysis of the MLL1-CXXC and TET3-CXXC sequence specificity and tolerance to cytosine modifications (5-methyl, 5-hydroxymethyl, 5-formyl, 5-carboxyl) in CpG and non-CpG context. For the first time, we take into consideration possible interference from cytosine bases elsewhere in the sequence. We show that despite similar overall structure, MLL1-CXXC has greater sequence and modification specificity than TET3-CXXC. MLL1-CXXC is specific only for CpG and does not tolerate any cytosine modifications. In contrast, TET3-CXXC does not require the CpG context of cytosine bases. Methyl-, formyl- and carboxyl-modifications are tolerated by TET3-CXXC, but only preceding G. Based on our and other data we propose a parsimonious model of MLL1-CXXC and TET3-CXXC DNA binding. This model explains why the binding of modified DNA duplexes by TET3-CXXC requires in some cases a register shift and is therefore context-dependent.     

Two‐domain analysis of JmjN‐JmjC and PHD‐JmjC lysine demethylases: Detecting an inter‐domain evolutionary stress

Residues at different positions of a multiple sequence alignment sometimes evolve together, due to a correlated structural or functional stress at these positions. Co‐evolution has thus been evidenced computationally in multiple proteins or protein domains. Here, we wish to study whether an evolutionary stress is exerted on a sequence alignment across protein domains, i.e., on longer sequence separations than within a single protein domain. JmjC‐containing lysine demethylases were chosen for analysis, as a follow‐up to previous studies; these proteins are important multidomain epigenetic regulators. In these proteins, the JmjC domain is responsible for the demethylase activity, and surrounding domains interact with histones, DNA or partner proteins. This family of enzymes was analyzed at the sequence level, in order to determine whether the sequence of JmjC‐domains was affected by the presence of a neighboring JmjN domain or PHD finger in the protein. Multiple positions within JmjC sequences were shown to have their residue distributions significantly altered by the presence of the second domain. Structural considerations confirmed the relevance of the analysis for JmjN‐JmjC proteins, while among PHD‐JmjC proteins, the length of the linker region could be correlated to the residues observed at the most affected positions. The correlation of domain architecture with residue types at certain positions, as well as that of overall architecture with protein function, is discussed. The present results thus evidence the existence of an across‐domain evolutionary stress in JmjC‐containing demethylases, and provide further insights into the overall domain architecture of JmjC domain‐containing proteins.     

Computational characterization of substrate and product specificities,and functionality of S‐adenosylmethionine binding pocket in histone lysine methyltransferases from Arabidopsis,rice and maize

Histone lysine methylation by histone lysine methyltransferases (HKMTs) has been implicated in regulation of gene expression. While significant progress has been made to understand the roles and mechanisms of animal HKMT functions, only a few plant HKMTs are functionally characterized. To unravel histone substrate specificity, degree of methylation and catalytic activity, we analyzed Arabidopsis Trithorax‐like protein (ATX), Su (var)3‐9 h omologs protein (SUVH), Su(var)3‐9 related protein (SUVR), ATXR5, ATXR6, and E(Z) HKMTs of Arabidopsis, maize and rice through sequence and structure comparison. We show that ATXs may exhibit methyltransferase specificity toward histone 3 lysine 4 (H3K4) and might catalyse the trimethylation. Our analyses also indicate that most SUVH proteins of Arabidopsis may bind histone H3 lysine 9 (H3K9). We also predict that SUVH7, SUVH8, SUVR1, SUVR3, ZmSET20 and ZmSET22 catalyse monomethylation or dimethylation of H3K9. Except for SDG728, which may trimethylate H3K9, all SUVH paralogs in rice may catalyse monomethylation or dimethylation. ZmSET11, ZmSET31, SDG713, SDG715, and SDG726 proteins are predicted to be catalytically inactive because of an incomplete S‐adenosylmethionine (SAM) binding pocket and a post‐SET domain. E(Z) homologs can trimethylate H3K27 substrate, which is similar to the Enhancer of Zeste homolog 2 of humans. Our comparative sequence analyses reveal that ATXR5 and ATXR6 lack motifs/domains required for protein‐protein interaction and polycomb repressive complex 2 complex formation. We propose that subtle variations of key residues at substrate or SAM binding pocket, around the catalytic pocket, or presence of pre‐SET and post‐SET domains in HKMTs of the aforementioned plant species lead to variations in class‐specific HKMT functions and further determine their substrate specificity, the degree of methylation and catalytic activity.     

Whole genome DNA methylation profiling of oral cancer in ethnic population of Meghalaya,North East India reveals novel genes

Oral Squamous Cell Carcinoma (OSCC) is a serious and one of the most common and highly aggressive malignancies. Epigenetic factors such as DNA methylation have been known to be implicated in a number of cancer etiologies. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome with special reference to the ethnic population of Meghalaya, North East India. The present study identifies 27,205 CpG sites and 3811 regions that are differentially methylated in oral cancer when compared to matched normal. 45 genes were found to be differentially methylated within the promoter region, of which 38 were hypermethylated and 7 hypomethylated. 14 of the hypermethylated genes were found to be similar to that of the TCGA-HNSCC study some of which are TSGs and few novel genes which may serve as candidate methylation biomarkers for OSCC in this poorly characterized ethnic group.     

FINE CHEMICAL STRUCTURE OF CARRAGEENAN FROM THE COMMERCIALLY CULTIVATED KAPPAPHYCUS STRIATUM (SACOL VARIETY) (SOLIERIACEAE,GIGARTINALES, RHODOPHYTA)1

The polysaccharide extracted from Kappaphycus striatum (Schmitz) Doty (sacol variety), a recently farmed eucheumoid seaweed, was characterized by Fourier transform infrared and NMR spectroscopy. The extract is composed mainly of 3‐linked β‐d ‐galactopyranosyl‐4‐sulfate residues alternating with 4‐linked 3,6‐anhydro‐α‐d ‐galactopyranosyl residues (κ‐carrageenan). Minor components include 3,6‐anhydrogalactopyranosyl‐2‐sulfate residues (ι‐carrageenan) and 6‐O‐methylgalactopyranosyl‐4‐sulfate residues (methylated carrageenan). The substitution pattern of carrageenan in the tribe Eucheumatoideae and the family Solieriaceae is revisited in terms of chemotaxonomic affiliation.     

Immobilization of cytochrome c on beaded poly(N-acrylylpyrrolidine)

In order to examine a procedure whereby the points of covalent attachment between the components of a protein-polymer conjugate could be determined, horse heart cytochrome c was attached to a beaded copolymer of N-acrylylpyrrolidine, N,N′-bis(acrylyl)-1,2-diaminoethane and N-acrylyl-1,6-aminohexane through a cleavable azo linkage. Studies of protein removed from this conjugate showed that attachment of the polymer to cytochrome occurred predominantly through single lysine residues on the protein surface; lysine-25 was tentatively identified as the residue most extensively utilized in this way. Protein was also linked to the polymer by two lysine residues and a significant amount of protein was irreversibly attached to the polymer under the reaction conditions used.     

Flavonoids from the external leaf resins of four hemizonia species (asteraceae)

The external leaf resins of four Hemizonia species afforded nine methylated flavonoids, including flavanones, flavones and flavonols. Besides the rare compounds 7-methyleriodictyol and 3,6,8-trimethoxy-5,7,3′,4′-tetrahydroxyflavone the new 6-methoxy-5,7,8,3′,4′-pentahydroxyflavone was isolated and identified by spectroscopic means.     

Ultraviolet inactivation and excision-repair in Bacillus subtilis. I. Construction and characterization of a transformable eightfold auxotrophic strain and two ultraviolet-sensitive derivatives

An eightfold auxotrophic strain of Bacillus subtilis was constructed. It was about equally well transformable for all markers. When this strain was used as recipient in transformation, single marker transformation frequencies of 0.5–2.0% were obtained. The markers were located relatively to each other using marker frequency analysis. Two UV-sensitive derivatives, equally well transformable as the parental multiple auxotroph, were isolated. One was highly sensitive to UV irradiation, was host cell reactivation-negative and did not show DNA breakdown or recovery of DNA synthesis after exposure to UV. Using UV-inactivated transforming DNA, this strain's transformability was strongly reduced as compared with both the UV-resistant parental strain and the other, moderately UV-sensitive, strain.     

Six new flavonoids from Citrus

Valencia orange (C. sinensis) and Robinson tangerine [(C. paradisi × C. reticulata) × (C. reticulata)] were examined for flavonoids. Thirteen flavonoids were isolated, six of which are new constituents of citrus peel. These are: 3,5,6,7,3′,4′-hexamethoxyflavone, 3,5,7,8,3′,4′-hexamethoxyflavone, 5-hydroxy-3,7,8,3′,4′-pentamethoxyflavone, 5-hydroxy-3,6,7,8,3′,4′-hexamethoxyflavone, 5,7,8,4′-tetramethoxyflavone and 5,7,8,3′,4′-pentamethoxyflavone. The latter three flavonoids are reported for the first time as natural products. A method is described for readily obtaining small quantities of 5,7,8,4′-tetramethoxy and 5,7,8,3′,4′-pentamethoxyflavones from their 5,6,7-trimethoxy analogs.