Morphological and phylogenetic analyses reveal two new Penicillium species isolated from the ancient Great Wall loess in Beijing, China.

Introduction: Penicillium species exhibit a broad distribution in nature and play a crucial role in human and ecological environments. Methods: Two Penicillium species isolated from the ancient Great Wall loess in the Mentougou District of Beijing, China, were identified and described as new species, namely, Penicillium acidogenicum and P. floccosum, based on morphological characteristics and phylogenetic analyses of multiple genes including ITS, BenA, CaM, and RPB2 genes. Results: Phylogenetic analyses showed that both novel species formed a distinctive lineage and that they were most closely related to P. chrzaszczii and P. osmophilum, respectively. Discussion: Penicillium acidogenicum is characterized by biverticillate conidiophores that produce globose conidia and is distinguished from similar species by its capacity to grow on CYA at 30°C. Penicillium floccosum is typically recognized by its restricted growth and floccose colony texture. The description of these two new species provided additional knowledge and new insights into the ecology and distribution of Penicillium.

Copper(II) Can Kinetically Trap Arctic and Italian Amyloid-ß40 as Toxic Oligomers, Mimicking Cu(II) Binding to Wild-Type Amyloid-ß42: Implications for Familial Alzheimer's Disease.

The self-association of amyloid-ß (Aß) peptide into neurotoxic oligomers is believed to be central to Alzheimer's disease (AD). Copper is known to impact Aß assembly, while disrupted copper homeostasis impacts phenotype in Alzheimer's models. Here we show the presence of substoichiometric Cu(II) has very different impacts on the assembly of Aß40 and Aß42 isoforms. Globally fitting microscopic rate constants for fibril assembly indicates copper will accelerate fibril formation of Aß40 by increasing primary nucleation, while seeding experiments confirm that elongation and secondary nucleation rates are unaffected by Cu(II). In marked contrast, Cu(II) traps Aß42 as prefibrillar oligomers and curvilinear protofibrils. Remarkably, the Cu(II) addition to preformed Aß42 fibrils causes the disassembly of fibrils back to protofibrils and oligomers. The very different behaviors of the two Aß isoforms are centered around differences in their fibril structures, as highlighted by studies of C-terminally amidated Aß42. Arctic and Italian familiar mutations also support a key role for fibril structure in the interplay of Cu(II) with Aß40/42 isoforms. The Cu(II) dependent switch in behavior between nonpathogenic Aß40 wild-type and Aß40 Arctic or Italian mutants suggests heightened neurotoxicity may be linked to the impact of physiological Cu(II), which traps these familial mutants as oligomers and curvilinear protofibrils, which cause membrane permeability and Ca(II) cellular influx.

Thiopseudomonas acetoxidans sp. nov., an aerobic acetic and butyric acids oxidizer isolated from anaerobic fermentation liquid of food waste.

A Gram-stain-negative, oxidase-negative, rod-shaped, motile, facultatively anaerobic bacterial strain, designated as CY1220T, was isolated from an anaerobic fermentation liquid of food waste treatment plant. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain CY1220T belongs to the genus Thiopseudomonas, with the highest sequence similarity to Thiopseudomonas alkaliphila B4199T (95.91%), followed by Thiopseudomonas denitrificans X2T (95.56%). The genomic DNA G + C content of strain CY1220T was 48.6 mol%. The average nucleotide identity values and digital DNA-DNA hybridization values between strain CY1220T and the type species of T. alkaliphila and T. denitrificans were in the range of 70.8-71.6% and 19.2-20.0%, respectively, below the thresholds for species delineation. The strain was able to grow utilizing acetic acid and butyric acid (AABA) as the sole carbon source in aerobic conditions. Genomic analysis predicted that the strain could synthesize vitamin B12 and ectoine. The predominant cellular fatty acids were C18:1 ω7c and/or C18:1 ω6c, C16:0, C16:1 ω7c and/or C16:1 ω6c and C12:0. The polar lipids comprised diphosphatidylglycerol, unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol, and phospholipid. Q-8 (2.1%) and Q-9 (97.9%) were detected as the respiratory quinones. Based on its phenotypic, genotypic and genomic characteristics, strain CY1220T represents a novel species in the genus Thiopseudomonas, for which the name Thiopseudomonas acetoxidans sp. nov. is proposed. The type strain is CY1220T (= GDMCC 1.3503 T = JCM 35747 T).

Polyphase taxonomy and genome analysis reveal the adaptability of Luteolibacter rhizosphaerae sp. nov. to the rhizosphere soil of Ulmus pumila L.

A Gram-stain-negative, rod-shaped, non-flagellated, pale-yellow bacterium, designated GHJ8T, was isolated from the rhizosphere soil of Ulmus pumila L., Shanxi Province, China. Growth occurred at 20-37 °C (optimum, 28 °C), pH 6.0-11.0 (optimum, pH 8.0), and 0-1% NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GHJ8T was related to members of the genus Luteolibacter, and close to Luteolibacter flavescens GKXT (98.5%), Luteolibacter luteus G-1-1-1T (97.3%), Luteolibacter arcticus MC 3726T (97.2%), and Luteolibacter marinus NBU1238T (96.0%). The genome size of strain GHJ8T was 6.2 Mbp, with a G + C content of 62.5%. Genomic mining revealed that the strain contained antibiotic resistance genes and secondary metabolic gene clusters, indicating that it had adaptation mechanisms to environmental stress. Comparative genomic analyses clearly separated strain GHJ8T from the recognized species of the genus Luteolibacter based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below the thresholds for species delineation. The major cellular fatty acids were iso-C14:0 (30.8%), C16:1 ω9c (23.0%), C16:0 (17.3%), and C14:0 (13.4%). The quinone system was composed of the major menaquinones MK-8, MK-9, and MK-10, and the principal polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, an unidentified glycolipid, two unidentified phospholipids, and three unidentified lipids. Based on its phenotypic and genotypic properties and phylogenetic inference, strain GHJ8T is a novel species of the genus Luteolibacter, for which the name Luteolibacter rhizosphaerae sp. nov. is proposed. The type strain is GHJ8T (= GDMCC 1.2160T = KCTC 82452T = JCM 34400T).

Alcanivorax quisquiliarum sp. nov., isolated from anaerobic fermentation liquid of food waste by high-throughput cultivation.

Strain CY1518T was isolated from an anaerobic fermentation liquid of food waste treatment plant in Beijing, PR China, and characterized to assess its taxonomy. Cells of CY1518T were Gram-stain-negative, oxidase-negative, catalase-positive and ellipsoidal. Growth occurred at 20-42 °C (optimum, 37 °C), pH 6.0-10.0 (optimum, pH 8) and with 0-6.0 % (w/v) NaCl (optimum, 1.5%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CY1518T belongs to the genus Alcanivorax, with the highest sequence similarity to Alcanivorax pacificus W11-5T (95.97 %), followed by Alcanivorax indicus SW127T (95.08%). The similarity between strain CY1518T and other strains of Alcanivorax was less than 95 %. The genomic DNA G+C content of strain CY1518T was 60.88 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain CY1518T and the closely related taxa A. pacificus W11-5T and A. indicus SW127T were 77.61, 78.03 and 21.2 % and 74.15, 70.02 and 19.3%, respectively. The strain was able to use d-serine, Tween 40 and some organic acid compounds for growth. The polar lipids comprised aminophospholipid, diphosphatidylglycerol, glycolipid, an unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol and phospholipid. The principal fatty acids (>5 %) were C19 : 0 cyclo ω8c (36.3%), C16 : 0 (32.3%), C12 : 0 3-OH (8.3%) and C12 : 0 (7.6%). Based on its phenotypic, genotypic and genomic characteristics, strain CY1518T represents a novel species in the genus Alcanivorax, for which the name Alcanivorax quisquiliarum sp. nov. is proposed. The type strain is CY1518T (=GDMCC 1.2918T=JCM 35120T).

Development of an efficient method for separation and purification of cordycepin from liquid fermentation of Cordyceps militaris and analysis of cordycepin antitumor activity.

Cordycepin (3 '-deoxyadenosine) is the main active component of Cordyceps militaris, which is a chemical marker for quality detection of Cordyceps militaris and has important medicinal development value. Existing methods for obtaining cordycepin are complex and costly. In this study, an economical and simple method for separation and purification of cordycepin from Cordyceps militaris fermentation liquid through physical crystallization was explored. First, lyophilized powdered fermentation liquid (LPFL) and pure methanol (1 g/100 mL, w/v) were mixed, and then repeatedly dissolved and crystallized until the precipitation was white. Purified product was obtained by freeze-drying the precipitate. The substance was determined to be cordycepin by high performance liquid chromatography, mass spectrometry and infrared spectroscopy, and the purity was 94.26%. Compared with the existing methods, this method is simple and low cost. In addition, the functional activity of cordycepin was determined by in vitro test. The results exhibited that cordycepin caused death and morphological changes in human colon cancer Caco-2 cells, and significantly inhibited the proliferation of Caco-2 cells, with a half-maximal inhibitory concentration (IC50) of 107.2 µg/mL. Cordycepin could induce early apoptosis of Caco-2 and caused cell cycle arrest in the G2 phase. Caco-2 cell apoptosis and cell cycle arrest showed dose dependence to cordycepin over a certain range. These results improved cordycepin purification method, provided insights into the mechanism of cordycepin in cancer inhibition, and would provide important reference for further development and clinical application of cordycepin.

Cross-seeding of WT amyloid-ß with Arctic but not Italian familial mutants accelerates fibril formation in Alzheimer's disease.

Alzheimer's disease (AD) involves the neurotoxic self-assembly of a 40 and 42 residue peptide, Amyloid-ß (Aß). Inherited early-onset AD can be caused by single point mutations within the Aß sequence, including Arctic (E22G) and Italian (E22K) familial mutants. These mutations are heterozygous, resulting in an equal proportion of the WT and mutant Aß isoform expression. It is therefore important to understand how these mixtures of Aß isoforms interact with each other and influence the kinetics and morphology of their assembly into oligomers and fibrils. Using small amounts of nucleating fibril seeds, here, we systematically monitored the kinetics of fibril formation, comparing self-seeding with cross-seeding behavior of a range of isoform mixtures of Aß42 and Aß40. We confirm that Aß40(WT) does not readily cross-seed Aß42(WT) fibril formation. In contrast, fibril formation of Aß40(Arctic) is hugely accelerated by Aß42(WT) fibrils, causing an eight-fold reduction in the lag-time to fibrillization. We propose that cross-seeding between the more abundant Aß40(Arctic) and Aß42(WT) may be important for driving early-onset AD and will propagate fibril morphology as indicated by fibril twist periodicity. This kinetic behavior is not emulated by the Italian mutant, where minimal cross-seeding is observed. In addition, we studied the cross-seeding behavior of a C-terminal-amidated Aß42 analog to probe the coulombic charge interplay between Glu22/Asp23/Lys28 and the C-terminal carboxylate. Overall, these studies highlight the role of cross-seeding between WT and mutant Aß40/42 isoforms, which can impact the rate and structure of fibril assembly.

Roseococcus pinisoli sp. nov., lacking pufL and pufM bacteriochlorophyll a: synthesizing genes.

A Gram-stain-negative, cocci-to-oval-shaped bacterial strain, designated XZZS9T, was isolated from the rhizosphere soil of Pinus sylvestris var. mongolica and characterized taxonomically using a polyphasic approach. Growth occurred at 20-35 °C (optimum, 28 °C), pH 6.0-11.0 (optimum, pH 7.0), and in 0-1% NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain XZZS9T was related to members of the genus Roseococcus, with the highest sequence identity to Roseococcus microcysteis NIBR12T (96.9%). The major cellular fatty acids (> 5% of the total) were C18:1 ω7c and C19:0 cyclo ω8c. The major isoprenoid quinone was Q-9 and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified glycophospholipid, and an unidentified phospholipid. Genome sequencing revealed that had a genome size of 4.79 Mbp with a G + C content of 69.5%. Comparative genomic analyses clearly separated strain XZZS9T from the known species of the genus Roseococcus based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below the thresholds for species delineation. Genome annotations did not find pufL and pufM genes in strain XZZS9T, suggesting a possible lack of photosynthetic reaction. Based on genotypic and phenotypic characteristics, strain XZZS9T represents a novel species of the genus Roseococcus, for which we propose the name Roseococcus pinisoli sp. nov. The type strain is XZZS9T (= KCTC 82435T = JCM 34402T = GDMCC 1.2158T).

Sphingomonas quercus sp. nov., Isolated from Rhizosphere Soil of Quercus mongolica.

Strain XMGL2T, isolated from rhizosphere soil of Quercus mongolica in China, was characterized using a polyphasic taxonomic approach. Cells were Gram-negative, aerobic, non-spore-forming, and rod-shaped. Growth occurred at 20-37 °C (optimum, 28 °C), pH 5.0-10.0 (optimum, pH 6.0), and with 0-1% NaCl (optimum, 1%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XMGL2T was related to members of the genus Sphingomonas and had the highest 16S rRNA gene sequence identity to Sphingomonas oleivorans FW-11 T (96.4%). The average nucleotide identity and digital DNA-DNA hybridization values between strain XMGL2T and the closely related taxa Sphingomonas oleivorans FW-11 T and Sphingomonas fennica K101T were 75.3/19.8% and 75.8/20.2%, respectively. The major cellular fatty acids were C18:1 ω7c, C14:0 2-OH, and C16:0. The major isoprenoid quinone was Q-10 and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycophospholipid and an unidentified phospholipid. The genomic DNA G + C content was 67.9%. Based on the phenotypic and genotypic properties and phylogenetic inference, strain XMGL2T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas quercus sp. nov. is proposed. The type strain is XMGL2T (= JCM 34441 T = GDMCC 1.2153 T).

3D-visualization of amyloid-ß oligomer interactions with lipid membranes by cryo-electron tomography.

Amyloid-ß (Aß) assemblies have been shown to bind to lipid bilayers. This can disrupt membrane integrity and cause a loss of cellular homeostasis, that triggers a cascade of events leading to Alzheimer's disease. However, molecular mechanisms of Aß cytotoxicity and how the different assembly forms interact with the membrane remain enigmatic. Here we use cryo-electron tomography (cryoET) to obtain three-dimensional nano-scale images of various Aß assembly types and their interaction with liposomes. Aß oligomers and curvilinear protofibrils bind extensively to the lipid vesicles, inserting and carpeting the upper-leaflet of the bilayer. Aß oligomers concentrate at the interface of vesicles and form a network of Aß-linked liposomes, while crucially, monomeric and fibrillar Aß have relatively little impact on the membrane. Changes to lipid membrane composition highlight a significant role for GM1-ganglioside in promoting Aß-membrane interactions. The different effects of Aß assembly forms observed align with the highlighted cytotoxicity reported for Aß oligomers. The wide-scale incorporation of Aß oligomers and curvilinear protofibrils into the lipid bilayer suggests a mechanism by which membrane integrity is lost.