Blood phenylalanine reduction reverses gene expression changes observed in a mouse model of phenylketonuria

Phenylketonuria (PKU) is a genetic deficiency of phenylalanine hydroxylase (PAH) in liver resulting in blood phenylalanine (Phe) elevation and neurotoxicity. A pegylated phenylalanine ammonia lyase (PEG-PAL) metabolizing Phe into cinnamic acid was recently approved as treatment for PKU patients. A potentially one-time rAAV-based delivery of PAH gene into liver to convert Phe into tyrosine (Tyr), a normal way of Phe metabolism, has now also entered the clinic. To understand differences between these two Phe lowering strategies, we evaluated PAH and PAL expression in livers of PAHenu2 mice on brain and liver functions. Both lowered brain Phe and increased neurotransmitter levels and corrected animal behavior. However, PAL delivery required dose optimization, did not elevate brain Tyr levels and resulted in an immune response. The effect of hyperphenylalanemia on liver functions in PKU mice was assessed by transcriptome and proteomic analyses. We observed an elevation in Cyp4a10/14 proteins involved in lipid metabolism and upregulation of genes involved in cholesterol biosynthesis. Majority of the gene expression changes were corrected by PAH and PAL delivery though the role of these changes in PKU pathology is currently unclear. Taken together, here we show that blood Phe lowering strategy using PAH or PAL corrects both brain pathology as well as previously unknown lipid metabolism associated pathway changes in liver.

Gulosibacter sediminis sp. nov., isolated from Indian Ocean marine sediment

A novel Gram-stain-positive, catalase-positive, oxidase-negative, aerobic, non-motile, rod-shaped bacterium, designated strain YIM M12148T, was isolated from a marine sediment sample collected from the Indian Ocean. The strain grew optimally at 28 °C, pH 8.0 and in the presence of 1–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M12148T belongs to the genus Gulosibacter , with the highest sequence similarity to Gulosibacter faecalis NBRC 15706T (96.12 %). The cell-wall sugars of strain YIM M12148T were rhamnose, ribose, glucose and mannose. The predominant isoprenoid quinones were MK-8 and MK-9. The polar lipids consisted of major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and one unknown lipid. Major fatty acids (>5 % of the total) of the novel isolate were anteiso-C15 : 0, iso-C15 : 0, iso-C13 : 0 and anteiso-C13 : 0. The genomic DNA G+C content of strain YIM M12148T was 67.15 mol%. On the basis of genotypic and phenotypic data, it is apparent that strain YIM M12148T represents a novel species of the genus Gulosibacter , for which the name Gulosibacter sediminis sp. nov. is proposed. The type strain is YIM M12148T (=KCTC 29660T=DSM 29154T).

Evidence of a molecular boundary lubricant at snakeskin surfaces

During slithering locomotion the ventral scales at a snake's belly are in direct mechanical interaction with the environment, while the dorsal scales provide optical camouflage and thermoregulation. Recent work has demonstrated that compared to dorsal scales, ventral scales provide improved lubrication and wear protection. While biomechanic adaption of snake motion is of growing interest in the fields of material science and robotics, the mechanism for how ventral scales influence the friction between the snake and substrate, at the molecular level, is unknown. In this study, we characterize the outermost surface of snake scales using sum frequency generation (SFG) spectra and near-edge X-ray absorption fine structure (NEXAFS) images collected from recently shed California kingsnake ( Lampropeltis californiae ) epidermis. SFG's nonlinear optical selection rules provide information about the outermost surface of materials; NEXAFS takes advantage of the shallow escape depth of the electrons to probe the molecular structure of surfaces. Our analysis of the data revealed the existence of a previously unknown lipid coating on both the ventral and dorsal scales. Additionally, the molecular structure of this lipid coating closely aligns to the biological function: lipids on ventral scales form a highly ordered layer which provides both lubrication and wear protection at the snake's ventral surface.

Formosa haliotis sp. nov., a brown-alga-degrading bacterium isolated from the gut of the abalone Haliotis gigantea

Four brown-alga-degrading, Gram-stain-negative, aerobic, non-flagellated, gliding and rod-shaped bacteria, designated LMG 28520T, LMG 28521, LMG 28522 and LMG 28523, were isolated from the gut of the abalone Haliotis gigantea obtained in Japan. The four isolates had identical random amplified polymorphic DNA patterns and grew optimally at 25 °C, at pH 6.0–9.0 and in the presence of 1.0–4.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences placed the isolates in the genus Formosa with Formosa algae and Formosa arctica as closest neighbours. LMG 28520T and LMG 28522 showed 100 % DNA–DNA relatedness to each other, 16–17 % towards F. algae LMG 28216T and 17–20 % towards F. arctica LMG 28318T; they could be differentiated phenotypically from these established species. The predominant fatty acids of isolates LMG 28520T and LMG 28522 were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 1 G and iso-C15 : 0. Isolate LMG 28520T contained menaquinone-6 (MK-6) as the major respiratory quinone and phosphatidylethanolamine, two unknown aminolipids and an unknown lipid as the major polar lipids. The DNA G+C content was 34.4 mol% for LMG 28520T and 35.5 mol% for LMG 28522. On the basis of their phylogenetic and genetic distinctiveness, and differential phenotypic properties, the four isolates are considered to represent a novel species of the genus Formosa, for which the name Formosa haliotis sp. nov. is proposed. The type strain is LMG 28520T ( = NBRC 111189T).

Kocuria dechangensis sp. nov., an actinobacterium isolated from saline and alkaline soils

A Gram-stain positive, strictly aerobic, non-motile and coccus-shaped actinobacterium, designated strain NEAU-ST5-33T, was isolated from saline and alkaline soils in Dechang Township, Zhaodong City, PR China. It formed beige-yellow colonies and grew at NaCl concentrations of 0–5 % (w/v) (optimum 0 %), at pH 6.0–9.0 (optimum pH 7.0) and over a temperature range of 4–50 °C (optimum 35 °C). Based on 16S rRNA gene sequence analysis, strain NEAU-ST5-33T was phylogenetically closely related to the type strains of species of the genus Kocuria, Kocuria polaris CMS 76orT, Kocuria rosea DSM 20447T, Kocuria turfanensis HO-9042T, Kocuria aegyptia YIM 70003T, Kocuria himachalensis K07-05T and Kocuria flava HO-9041T, with respective sequence similarities of 98.8 %, 98.8 %, 98.3 %, 98.1 %, 98.1 % and 97.9 %. DNA–DNA hybridization relatedness values of strain NEAU-ST5-33T with type strains of the closely related species ranged from 54 ± 1 % to 34 ± 1 %. The DNA G+C content was 61.2 mol%. The major fatty acids (>5 %) were C15 : 0 anteiso, C15 : 0 iso and C16 : 1ω7c and/or C16 : 1ω6c. The major menaquinone detected was MK-8 (H2), and the polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unknown aminolipid and one unknown lipid. On the basis of the genotypic, chemotaxonomic and phenotypic data, we propose that strain NEAU-ST5-33T represents a novel species of the genus Kocuria, with the name Kocuria dechangensis sp. nov. The type strain is NEAU-ST5-33T ( = CGMCC 1.12187T = DSM 25872T).

Longimonas halophila gen. nov., sp. nov., isolated from a marine solar saltern

A bacterial strain, designated SYD6T, was isolated from a marine solar saltern on the coast of Weihai, Shandong Province, PR China. Cells of strain SYD6T were rod-shaped, red, and approximately 5.0–9.0 μm in length and 0.4–0.6 μm in width. The strain was Gram-stain-negative, facultatively anaerobic, heterotrophic, catalase-positive and oxidase-negative. Growth occurred in 4–25 % (w/v) NaCl [with 2–15 % (w/v) MgCl2.6H2O also present], at 20–50 °C and pH 6.5–8.5. Optimal growth was observed at 37–42 °C, pH 7.5–8.0, with 6–8 % (w/v) NaCl [with 2–4 % (w/v) MgCl2.6H2O]. Nitrate was not reduced. Glucose, sucrose, maltose, fructose and ribose stimulated growth, but not glycerol, xylose or mannitol. The G+C content of the genomic DNA was 61.5 mol% (HPLC). The sole methyl naphthoquinone was MK-7 and the predominant cellular fatty acids (>10 %) were iso-C15 : 0 2-OH/C16 : 1ω7c, iso-C16 : 0, C18 : 1ω7c/C18 : 1ω6c and C18 : 1ω7c. The predominant polar lipids were phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and an unknown lipid. Phylogenetic analysis, based on 16S rRNA gene sequences, demonstrated that strain SYD6T was affiliated with the phylum Bacteroidetes. The most closely related neighbours were species of the genus Salisaeta and strain SYD6T had a 16S rRNA gene sequence similarity of 91.97 % with Salisaeta longa DSM 21114T. On the basis of these phenotypic and phylogenetic data, strain SYD6T represents a novel species of a new genus of the family Rhodothermaceae, for which the name Longimonas halophila gen. nov., sp. nov. is proposed. The type strain of the type species is SYD6T ( = CICC 10838T = KCTC 42399T).

Paenibacillus susongensis sp. nov., a mineral-weathering bacterium

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterial strain, designated M327T, was isolated from the weathered surfaces of rock (mica schist) from Susong, Anhui Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M327T belonged to the genus Paenibacillus and was related most closely to Paenibacillus terrigena A35T (98.6 % similarity) and Paenibacillus selenitireducens ES3-24T (98.3 %). Strain M327T contained meso-diaminopimelic acid in the cell wall and MK-7 as the major menaquinone. The main fatty acids of strain M327T were anteiso-C15 : 0 and iso-C16 : 0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown aminophospholipids and an unknown lipid. The total DNA G+C content of strain M327T was 48.6 mol%. Based on the low level of DNA–DNA relatedness (ranging from 26.6 to 33.1 %) to these type strains of species of the genus Paenibacillus and unique phenotypic characteristics, it is suggested that strain M327T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus susongensis sp. nov. is proposed. The type strain is M327T ( = CCTCC AB 2014058T = LMG 28236T = JCM 19951T).

Gryllotalpicola soli sp. nov., isolated from soil

A novel Gram-stain-positive, short rod-shaped, non-flagellated and mesophilic strain, KIS12-7T, isolated from a soil sample collected from Daecheong-Island in Ongjin County, Republic of Korea, was studied using a polyphasic approach. Phylogenetic trees based on the 16S rRNA gene sequence revealed that the novel strain was a member of the genus Gryllotalpicola , showing more than 97.0 % sequence similarity with Gryllotalpicola daejeonensis RU-04T (98.0 %), Gryllotalpicola koreensis RU-16T (97.7 %) and Gryllotalpicola kribbensis PU-02T (97.3 %). However, DNA–DNA relatedness values demonstrated that strain KIS12-7T could be clearly distinguished from closely related species of the genus Gryllotalpicola . The cell-wall peptidoglycan of strain KIS12-7T was of the type B2 and the acyl type was acetyl. The predominant menaquinones were MK-11 and MK-10. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown phosphoglycolipid, one unknown glycolipid, one unknown phospholipid and one unknown lipid. The G+C content of the genomic DNA was 72.1 mol%. On the basis of the evidence presented, strain KIS12-7T is a representative of a novel species of the genus Gryllotalpicola , and the name Gryllotalpicola soli sp. nov. is proposed; the type strain is KIS12-7T ( = DSM 27182T = KACC 17302T = NBRC 109659T).

Thermomonas carbonis sp. nov., isolated from the soil of a coal mine

Strain GZ436T was Gram-stain-negative, aerobic, non-motile, rod-shaped and isolated from the soil of a coal mine. 16S rRNA gene phylogenetic analysis showed that this strain clustered with Thermomonas brevis LMG 21746T (97.5 %), Thermomonas haemolytica A50-7-3T (96.3 %), Thermomonas koreensis KCTC 12540T (96.4 %), Thermomonas hydrothermalis SGM-6T (95.5 %) and Thermomonas fusca LMG 21737T (95.1 %). The major isoprenoid quinone was Q-8. The DNA G+C content was 67 mol%. Strain GZ436T contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unknown aminophospholipid, an unknown phospholipid and an unknown lipid as the major polar lipids. The predominant cellular fatty acids (>5 %) were iso-C15 : 0, iso-C11 : 0, iso-C11 : 0 3-OH, iso-C17 : 1ω9c, C16 : 0 and summed feature 3. The DNA–DNA relatedness value between strain GZ436T and T. brevis LMG 21746T was 54±0.4 %. According to phenotypic and phylogenetic characteristics, strain GZ436T represents a novel species of the genus Thermomonas , for which the name Thermomonas carbonis sp. nov. is proposed. The type strain is GZ436T ( = CCTCC AB 2013364T = KCTC 42013T).