Quantitative determination of urea concentrations in cell culture medium.

Direct and indirect cost of urea excretion

Alanine is a major end product of metabolism by Giardia lamblia: a proton nuclear magnetic resonance study

Hydrogenosomes are organelles that produce ATP and hydrogen, and are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Although all of these organelles generate hydrogen, the hydrogenosomes from these organisms are structurally and metabolically quite different, just like mitochondria where large differences also exist. These differences have led to a continuing debate about the evolutionary origin of hydrogenosomes. Here we show that the hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis, which thrives in the hindgut of cockroaches, have retained a rudimentary genome encoding components of a mitochondrial electron transport chain. Phylogenetic analyses reveal that those proteins cluster with their homologues from aerobic ciliates. In addition, several nucleus-encoded components of the mitochondrial proteome, such as pyruvate dehydrogenase and complex II, were identified. The N. ovalis hydrogenosome is sensitive to inhibitors of mitochondrial complex I and produces succinate as a major metabolic end product--biochemical traits typical of anaerobic mitochondria. The production of hydrogen, together with the presence of a genome encoding respiratory chain components, and biochemical features characteristic of anaerobic mitochondria, identify the N. ovalis organelle as a missing link between mitochondria and hydrogenosomes.

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Uric acid is the end product of purine metabolism in some species including man and not in others. In birds and reptiles for example, it is the final metabolite of protein as well as purine degradation. In those organisms in which uric acid is not the terminal excretory product of purine metabolism, the molecule is oxidized to allantoin by the enzyme, urate: O2-oxidoreductase, also called urate oxidase or uricase (Fig. 1). This enzyme which opens the six-membered ring in the purine molecule, is found in various microorganisms, plants, and the livers and kidneys of most animals. In mammals allantoin is generally the major end product of purine metabolism, but in nonmammalian species there is further metabolism of allantoin. Amphibia and te-leost fishes convert allantoin to allantoic acid through the action of the enzyme, allantoinase. The latter opens the five-membered purine ring. Nonteleost fishes contain the enzyme allantoicase which breaks down allantoic acid into urea and glyoxylic acid. Finally, some invertebrates are known to convert urea to ammonia and carbon dioxide through the action of urease.

A comprehensive study was performed on 25 bacterial clinical isolates originally identified as Corynebacterium xerosis. Three reference strains of C. xerosis were also included in the study. On the basis of a variety of phenotypic characteristics tested, all strains could be divided into two separate clusters: reference strains ATCC 373 (the type strain of C. xerosis) and ATCC 7711 showed yellow-pigmented, dry, rough colonies, fermented 5-keto-gluconate, exhibited strong leucine arylamidase and alpha-glucosidase activities, produced lactate as the major end product of glucose metabolism, were susceptible to most of the 19 antimicrobial agents tested, and showed an inhibition zone around disks containing the vibriocidal compound O/129. In contrast, the remaining 26 strains including reference strain NCTC 7243 as well as all clinical isolates formed white-grayish, dry, slightly rough colonies, did not ferment 5-keto-gluconate, exhibited only weak leucine arylamidase and no alpha-glucosidase activity, produced large amounts of propionic acid as the end product of glucose metabolism, and were resistant to most antimicrobial agents tested, including O/129. Chemotaxonomic (cellular fatty acids, mycolic acids, and G+C content) and molecular genetic (16S rRNA gene sequence) investigations revealed that the strains of the second cluster unambiguously belonged to the species C. amycolatum. Our data suggest that most strains reported in the literature as C. xerosis are probably misidentified and correspond to C. amycolatum.

Background: Chorioamnionitis is one of the important causes of preterm labor. Preterm labor with chorioamnionitis is associated with oxidative stress. We reported that 4-hydroxy-2-nonenal (4-HNE), a major end product of oxidative fatty acid metabolism, is accumulated in the placenta with chorioamnionitis. The aim of this study was to confirm the effect of 4-HNE on cyclooxygenase-2 (COX-2) and prostaglandin (PG) induction in the uterine myometrial tissues. We also examined the effect of N-acetylcysteine (NAC) on 4-HNE-induced COX-2 expression. Methods: Uterine myometrial tissues were obtained from 5 patients. One of them underwent elective cesarean section without labor, and 4 of them underwent hysterectomy because of placental previa or atonic bleeding. We stimulated the uterine myometrial tissues with 4-HNE. In addition, the tissues were pretreated with NAC before 4-HNE treatment. The expression of COX-2 mRNA was observed by real-time PCR. PGE2 and prostacyclin release into the supernatants of the tissue cultures was measured by ELISA. Results: 4-HNE induced the COX-2 mRNA expression and PGE2 production in the uterine myometrial tissue culture in a dose-dependent and time-dependent manner. NAC inhibited 4-HNE-induced COX-2 expression. Conclusion: 4-HNE may play an important role in preterm labor. NAC might be protective against preterm labor under oxidative stress.

Strep'to.ha.lo.ba.cil'lus. Gr. masc. adj. streptos , pliant, bent; Gr. masc. n. hals (gen. halos ), salt; L. masc. n. bacillus , stick, a small rod; N.L. masc. n. Streptohalobacillus , a pliant salt‐loving rod. Firmicutes / Bacilli / Bacillales / Bacillaceae / Streptohalobacillus Cells are straight to slightly curved rods which occur singly, in pairs, or in chains. Endospores are not observed. Gram‐stain‐positive. The cell‐wall peptidoglycan type is A1γ, with meso ‐diaminopimelic acid as the diagnostic diamino acid. Motile by means of peritrichous flagella. Streptohalobacillus is a facultatively anaerobic chemoheterotroph. Moderately halophilic and halotolerant. Growth can occur in the absence of sugars. Acetate, ethanol, and lactic acid are major metabolic end products from glucose following anaerobic fermentation. Oxidase‐positive but catalase‐negative. Nitrate is reduced to nitrite. The major isoprenoid quinone is MK‐6. The predominant cellular fatty acids are C 16:0 , anteiso‐C 13:0 , and anteiso‐C 15:0 . Phylogenetically, the genus is a member of the family Bacillaceae and related most closely to Halolactibacillus species. The type species is Streptohalobacillus salinus . Isolated from a saline soil of Qaidam Basin, China. DNA G + C content (mol%) : 36.2 ( T m ). Type species : Streptohalobacillus salinus Wang et al. 2011 VP .

Strains LMG 27428(T) and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428(T) and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734(T). Strain LMG 27428(T) could be distinguished from S. pleomorphus ATCC 29734(T) based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734(T). The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428(T) and LMG 27427. Strain LMG 27428(T) ( =DSM 26963(T)) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( =DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756(T) =ATCC 29734(T) =DSM 20574(T)). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983(T) (94.4% 16S rRNA gene sequence similarity to strain LMG 27428(T)) and Eubacterium biforme DSM 3989(T) (92.7% 16S rRNA gene sequence similarity to strain LMG 27428(T)). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983(T) =ATCC 27803(T) =JCM 10261(T) and that of Holdemanella biformis is DSM 3989(T) =ATCC 27806(T) =CCUG 28091(T).

An.ae.ro.coc'cus. Gr. prep. an without; Gr. n. aer air; Gr. masc. n. kokkos berry, coccus; N.L. masc. n. Anaerococcus anaerobic coccus. Firmicutes / “Clostridia” / Clostridiales / Incertae Sedis ‐ Family I / Anaerococcus Cocci, occurring in pairs, tetrads, irregular masses or chains. Gram‐stain‐positive. Nonmotile. Nonsporeforming. Strictly anaerobic. Metabolize peptones and amino acids; the major metabolic end products are butyric acid, lactic acid and small amounts of propionic and succinic acids. Most species are able to ferment several carbohydrates, but are weakly fermentative. Glucose, fructose, sucrose and lactose are major sugars fermented. Most species do not produce indole. The position 1, position 3, and interpeptide bride of peptidoglycan are glycine or alanine, l ‐lysine, and d ‐glutamic acid or d ‐aspartic acid. Major cellular fatty acid are C 18:1 , C 16:1 , C 18 , and C 16 (Ezaki et al., 1983; O'Leary and Wilkinson, 1988). Members of the genus are typically isolated from the human vagina and various purulent secretions. DNA G+C content (mol%) : 30–35. Type species : Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki, Kawamura, Li, Li, Zhao and Shu 2001b, 1526 VP .

Isolation and characterization of a phenol-degrading, sulfate-reducing bacterium from swine manure

Determination of urea with special emphasis on biosensors: A review

An obligately anaerobic, Gram-positive, non-motile, coccus-shaped bacterial strain designated AGMB00490T was isolated from swine faeces. 16S rRNA gene sequence-based phylogenetic analysis indicated that the isolate belongs to the genus Peptoniphilus and that the most closely related species is Peptoniphilus gorbachii WAL 10418T (=KCTC 5947T, 97.22 % 16S rRNA gene sequence similarity). Whole genome sequence analysis determined that the DNA G+C content of strain AGMB00490T was 31.2 mol% and moreover that the genome size and numbers of tRNA and rRNA genes were 2 129 517 bp, 34 and 10, respectively. Strain AGMB00490T was negative for oxidase and urease; positive for catalase, indole production, arginine arylamidase, leucine arylamidase, tyrosine arylamidase and histidine arylamidase; and weakly positive for phenylalanine arylamidase and glycine arylamidase. The major cellular fatty acids (>10 %) of the isolate were determined to be C16 : 0 and C18 : 1 ω9c. Strain AGMB00490T produced acetic acid as a major end product of metabolism. Accordingly, phylogenetic, physiologic and chemotaxonomic analyses revealed that strain AGMB00490T represents a novel species for which the name Peptoniphilus faecalis sp. nov. is proposed. The type strain is AGMB00490T (=KCTC 15944T=NBRC 114159T).

An obligately anaerobic, non-motile, Gram-negative and rod-shaped strain (AGMB03916T) was isolated from faeces of a 2-week-old piglet raised at the National Institute of Animal Science in Wanju, Republic of Korea. Growth of strain AGMB03916T occurred at 30-45 °C (optimum, 37 °C), at pH 6-9 (optimum, pH 8) and in the presence of 0.5-1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence analyses, strain AGMB03916T was closely related to two validly published species of the genus Phocaeicola, Phocaeicola plebeius and Phocaeicola coprocola. The 16S rRNA gene sequence similarity of strain AGMB03916T compared to P. plebeius M12T (=KCTC 5793T) and P. coprocola M16T (=KCTC 5443T) were 96.3 and 95.0 %, respectively. The genomic DNA G+C content of strain AGMB03916T was 46.4 mol%. The average nucleotide identity values between strain AGMB03916T and the reference strains were 74.9-78.5 %. Cells were able to utilize d-glucose, lactose, sucrose, maltose, salicin, aesculin hydrolysis, cellobiose and raffinose. The major end product of metabolism was acetate. The major cellular fatty acids (>10 %) of the isolate were iso-C15 : 0, anteiso-C15 : 0, C16 : 0, C16 : 0 3-OH and summed feature 11 (iso-C17 : 0 3-OH and/or C18 : 2 DMA). On the basis of the genotypic, biochemical, chemotaxonomic, phenotypic and phylogenetic data, strain AGMB03916T represents a novel species of the genus Phocaeicola, for which the name Phocaeicola faecicola sp. nov. is proposed. The type strain is AGMB03916T (=KCTC 25014T=GDMCC 1.2574T).

Determination of Uric Acid in Avian Excreta by the Use of Uricase and Differential Spectrophotometry