The amount of food ingested in a single meal by rainbow trout offered chopped herring, dry and wet diets

Two-year-old 1·5-kg rainbow trout were held in cages and conditioned by feeding either on low-fat chopped herring (H trout) or dry pellets (P trout) for 15 weeks. Their satiation amounts were then determined under standard conditions. On a wet weight basis H trout ate 2·5-3·5 times more food than P trout; this was sufficient to compensate for the high water content of herring and thereby maintain the dry matter intake. When P trout were offered herring (PH trout) they consumed more food than when offered dry pellets but not as much as H trout. Stomach capacity restricted the intake and their dry matter intake was reduced by c. 40%. When H trout were offered dry pellets (HP trout) they adjusted their intake immediately close to the level of P trout although their larger stomachs could have accommodated more than twice this volume of dry food. The return of appetite after a satiation meal was almost linear with time. Appetite increased at c. 556 mg g^-1 body weight h^-1 for H trout and at 142 mg g^-1 bw h^-1 for P trout. The return of appetite in PH trout was significantly slower (c. 370 mg g^-1 bw h^-1) than in H trout; the previous dietary history of the PH trout limited their capacity to process larger volumes of wet food in a single meal. Fish offered dry diet (P and HP trout) had similar rates of appetite return despite their previous feeding history suggesting that the property of the dry feed itself might limit meal size. The total gastric emptying time of diets of similar dry matter content (with and without large amounts of water) was similar, but the delay time before gastric emptying starts tended to be longer for dry diets. Dry pellets appear to impose a demand for water that prolongs the gastric delay. This water demand is met partly by drinking since the trout fed on dry pellets drank significantly more (436 ± 189 mg kg^-1 h^-1) than unfed and herring-fed trout which drank little or not at all (65 ± 113 and 70 ± 66 mg kg^-1 h^-1 respectively). Dietary water facilitated food processing and increased daily dry matter intake of trout when fed four times a day. When only one satiation meal per day was allowed, dietary water had no effect. It is concluded from this work that, in addition to gastric volume, a short-term limitation on the size of satiation meals in the rainbow trout is the availability of water to moisturize the food and thus to promote gastric digestion and emptying.     

Escherichia coli K-12 genes essential for the synthesis of c-type cytochromes and a third nitrate reductase located in the periplasm

The ' aeg46.5  ' operon was originally detected as an 'anaerobically expressed gene' located at minute 46.5 on the Escherichia coli linkage map. Subsequent results from the E. coli Genome Sequencing Project revealed that the ' aeg46.5  ' promoter was located in the centisome 49 (minute 47) region. Downstream from this promoter are 15 genes, seven of which are predicted to encode a periplasmic nitrate reductase and eight encode proteins homologous to proteins essential for cytochrome c assembly in other bacteria. All of these genes, together with the ' aeg46.5  ' promoter, have been subcloned on a 20 kb Eco RI fragment from Kohara phage 19D1. Evidence is presented that, as predicted, the region includes structural genes for two c -type cytochromes of mass 16 kDa and 24 kDa, which are transcribed from the previously described ' aeg46.5  ' promoter, and that the first seven genes encode a functional nitrate reductase. We, therefore, propose that they should be designated nap (nitrate reductase in the periplasm) genes. Plasmids encoding the entire 20 kb region, or only the downstream eight genes, complemented five mutations resulting in total absence of all five known c -type cytochromes in E. coli , providing biochemical evidence that these are ccm (for cytochrome c maturation) genes. The ccm region was transcribed both from the FNR-dependent, NarL- and NarP-regulated nap promoter (formerly the ' aeg46.5  ' promoter) and from constitutive or weakly regulated promoters apparently located within the downstream nap and ccm genes.     

Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod

Atlantic cod is composed of multiple migratory and stationary populations widely distributed in the North Atlantic Ocean. The Northeast Arctic cod (NEAC) population in the Barents Sea undertakes annual spawning migrations to the northern Norwegian coast. Although spawning occurs sympatrically with the stationary Norwegian coastal cod (NCC), phenotypic and genetic differences between NEAC and NCC are maintained. In this study, we resolve the enigma by revealing the mechanisms underlying these differences. Extended linkage disequilibrium (LD) and population divergence were demonstrated in a 17.4‐Mb region on linkage group 1 (LG1) based on genotypes of 494 SNPs from 192 parents of farmed families of NEAC, NCC or NEACxNCC crosses. Linkage analyses revealed two adjacent inversions within this region that repress meiotic recombination in NEACxNCC crosses. We identified a NEAC‐specific haplotype consisting of 186 SNPs that was fixed in NEAC sampled from the Barents Sea, but segregating under Hardy–Weinberg equilibrium in eight NCC stocks. Comparative genomic analyses determine the NEAC configuration of the inversions to be the derived state and date it to ~1.6–2.0 Mya. The haplotype block harbours 763 genes, including candidates regulating swim bladder pressure, haem synthesis and skeletal muscle organization conferring adaptation to long‐distance migrations and vertical movements down to large depths. Our results suggest that the migratory ecotype experiences strong directional selection for the two adjacent inversions on LG1. Despite interbreeding between NEAC and NCC, the inversions are maintaining genetic differentiation, and we hypothesize the co‐occurrence of multiple adaptive alleles forming a ‘supergene’ in the NEAC population.     

Imputation of missing covariate values in epigenome-wide analysis of DNA methylation data

DNA methylation is a widely studied epigenetic mechanism and alterations in methylation patterns may be involved in the development of common diseases. Unlike inherited changes in genetic sequence, variation in site-specific methylation varies by tissue, developmental stage, and disease status, and may be impacted by aging and exposure to environmental factors, such as diet or smoking. These non-genetic factors are typically included in epigenome-wide association studies (EWAS) because they may be confounding factors to the association between methylation and disease. However, missing values in these variables can lead to reduced sample size and decrease the statistical power of EWAS. We propose a site selection and multiple imputation (MI) method to impute missing covariate values and to perform association tests in EWAS. Then, we compare this method to an alternative projection-based method. Through simulations, we show that the MI-based method is slightly conservative, but provides consistent estimates for effect size. We also illustrate these methods with data from the Atherosclerosis Risk in Communities (ARIC) study to carry out an EWAS between methylation levels and smoking status, in which missing cell type compositions and white blood cell counts are imputed.     

Genetic Characterization of ExPEC-Like Virulence Plasmids among a Subset of NMEC

Neonatal Meningitis Escherichia coli (NMEC) is one of the most common causes of neonatal bacterial meningitis in the US and elsewhere resulting in mortality or neurologic deficits in survivors. Large plasmids have been shown experimentally to increase the virulence of NMEC in the rat model of neonatal meningitis. Here, 9 ExPEC-like plasmids were isolated from NMEC and sequenced to identify the core and accessory plasmid genes of ExPEC-like virulence plasmids in NMEC and create an expanded plasmid phylogeny. Results showed sequenced virulence plasmids carry a strongly conserved core of genes with predicted functions in five distinct categories including: virulence, metabolism, plasmid stability, mobile elements, and unknown genes. The major functions of virulence-associated and plasmid core genes serve to increase in vivo fitness by adding multiple iron uptake systems to the genetic repertoire to facilitate NMEC’s survival in the host’s low iron environment, and systems to enhance bacterial resistance to host innate immunity. Phylogenetic analysis based on these core plasmid genes showed that at least two lineages of ExPEC-like plasmids could be discerned. Further, virulence plasmids from Avian Pathogenic E. coli and NMEC plasmids could not be differentiated based solely on the genes of the core plasmid genome.     

Phenolic metabolites of Ceratocystis ulmi

The C₁₀ acid 2,4-dihydroxy-6-(1-hydroxyacetonyl) benzoic acid, together with the 6-acetonyl- and 6-pyruvyl-analogues, has been identified as a metabolic product of Ceratocystis ulmi, the causative agent of Dutch elm disease. In a comparison of aggressive “fluffy” and non-aggressive “waxy” strains of C. ulmi, the C₁₀ acids were produced more rapidly and in greater yield by the former group.     

Budding in the Dimorphic Fungus Phialophora dermatitidis

Ultrastructural comparisons of yeast and hyphal bud formation in Phialophora dermatitidis reveal that bud initiation is characterized by a blastic rupture of the outer portion of the yeast or hyphal wall and the emergence of a bud protuberance through the resulting opening. The wall of the emerging bud is continuous, with only an inner wall layer of the parental yeast or hypha. The outer, ruptured portion of the parental wall typically forms a collar around the constricted emergence region of the developing bud. The cytoplasm within the very young emerging bud invariably contains a small number of membrane-bound vesicles. The septum formed between the daughter bud and the parental yeast or hypha is a complete septum devoid of a septal pore, septal pore plug, or any associated Woronin bodies characteristic of simple septa of the moniliform or true hyphae. These observations suggest that yeast bud formation and lateral hyphal bud formation in the dimorphic fungus P. dermatitidis involve a growth process which occurs identically in both the yeast and mold phase of this human pathogenic organism.     

Functional and biochemical characterization of B-cell differentiation factor (BCDF) produced by an HTLV-I-transformed human T-cell clone and demonstration of specific binding of the factor to a BCDF responsive cell line

We have previously described YA2, a human T-cell clone that secretes B-cell differentiation factor (BCDF) but not B-cell growth factor (BCGF). The BCDFs secreted by YA2 and HTLV-I-transformed YA2 (TYA2) were functionally similar in their ability to stimulate Ig secretion by Staphylococcus aureus Cowan strain I-activated B cells and IgM secretion by SKW6.4 cells. In addition, they were biochemically similar with a MW of 30 kDa by high-performance liquid chromatography (HPLC) sieving, and a pI of 6.0-6.8 by isoelectric focusing. The BCDF activity was not blocked by antibodies to interleukin 2 and BCGF. BCDF was purified from TYA2 supernatant by sequential media protein immunoadsorption, flat bed isoelectric focusing, HPLC TSK 2000 sieving, and repeated immunoadsorption and was then iodinated. The iodinated material had functional BCDF activity and migrated to a single band at MW 30 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and at pI of 6.8 by polyacrylamide gel isoelectric focusing. 125I-BCDF purified in this manner bound specifically to a BCDF-responsive cell line and not to phytohemagglutinin-activated T cells. 125I binding to the BCDF-responsive cell line was competitively inhibitable by the addition of cold BCDF. Thus we have purified and characterized a factor with BCDF activity and demonstrated that this factor binds specifically to a BCDF-responsive cell line.     

Comparison of 3-isobutyl-1-methylxanthine-induced accumulation of putrescine in rat pancreas and liver

3-Isobutylmethylxanthine (IBMX), a potent phosphodiesterase inhibitor, causes accumulation of putrescine of same magnitude in rat pancreas and liver. IBMX produces increases of acetyl CoA: polyamine N'-acetyltransferase (PAT) and of ornithine decarboxylase (ODC) activities in both organs. However ODC activity is 300 times higher in liver than in pancreas. In the latter organ, there is a transient increase of N1-acetylspermidine, followed by a decrease of spermidine, alpha-Difluoromethylornithine (DFMO), a potent ODC inhibitor, impairs the accumulation of putrescine in liver but not in pancreas. These results suggest that in pancreas the accumulated putrescine is essentially formed from spermidine, via N1-acetylation and oxidation, while in liver it is formed from decarboxylation of ornithine. A possible involvement of cAMP in the stimulation of the polyamine interconversion pathway is discussed.