18S ribosomal RNA gene sequences of Cochliopodium (Himatismenida) and the phylogeny of Amoebozoa

Cochliopodium is a very distinctive genus of discoid amoebae covered by a dorsal tectum of carbohydrate microscales. Its phylogenetic position is unclear, since although sharing many features with naked "gymnamoebae", the tectum sets it apart. We sequenced 18S ribosomal RNA genes from three Cochliopodium species (minus, spiniferum and Cochliopodium sp., a new species resembling C. minutum). Phylogenetic analysis shows Cochliopodium as robustly holophyletic and within Amoebozoa, in full accord with morphological data. Cochliopodium is always one of the basal branches within Amoebozoa but its precise position is unstable. In Bayesian analysis it is sister to holophyletic Glycostylida, but distance trees mostly place it between Dermamoeba and a possibly artifactual long-branch cluster including Thecamoeba. These positions are poorly supported and basal amoebozoan branching ill-resolved, making it unclear whether Discosea (Glycostylida, Himatismenida, Dermamoebida) is holophyletic; however, Thecamoeba seems not specifically related to Dermamoeba. We also sequenced the small-subunit rRNA gene of Vannella persistens, which constantly grouped with other Vannella species, and two Hartmannella strains. Our trees suggest that Vexilliferidae, Variosea and Hartmannella are polyphyletic, confirming the existence of two very distinct Hartmannella clades: that comprising H. cantabrigiensis and another divergent species is sister to Glaeseria, whilst Hartmannella vermiformis branches more deeply.     

Structural elucidation of a novel fucogalactan that contains 3-O-methyl rhamnose isolated from the fruiting bodies of the fungus, Hericium erinaceus

A new heteropolysaccharide, HEPF3, was isolated from the fruiting bodies of Hericium erinaceus. HEPF3 has a molecular weight of 1.9 x 10(4) Da and is composed of fucose and galactose in a ratio of 1:4.12. Compositional analysis, methylation analysis, together with 1H and 13C NMR spectroscopy established that HEPF3 consists of a branched pentasaccharide repeating unit with the following structure: [structure: see text]. HEPF3 also contains a minor proportion of 3-O-methylrhamnose that is thought to terminate the polymer main chain.     

Mapping of the monoclonal antibody 80L5C4 epitope on the cell adhesion molecule gp80 of Dictyostelium discoideum

EDTA-resistant cell-cell binding sites are expressed on Dictyostelium discoideum cells at the aggregation stage of development. A cell surface glycoprotein of Mr 80,000 (gp80) has been found to mediate these binding sites via homophilic interaction. We have previously raised a monospecific monoclonal antibody 80L5C4 against gp80, which blocks the cell binding site of gp80 (Siu, C.-H., Lam, T.Y. and Choi, A.H.C. (1985) J. Biol. Chem. 260, 16030-16036). To map the 80L5C4 epitope, gp80 was digested with protease V8, and the smallest proteolytic fragment that retained immunoreactivity with 80L5C4 was about 27,000 Da, corresponding to the amino-terminal fragment predicted from the cleavage sites. In addition, cDNA fragments containing different gp80 coding regions were used to construct trpE/gp80 gene fusions in the expression vector pATH10. An analysis of these fusion proteins led to the mapping of the 80L5C4 epitope to a 51 amino-acid segment between residues 123 and 173.     

Multiplication of Legionella spp. in tap water containing Hartmannella vermiformis.

A model was developed to study the multiplication of various Legionella spp. in tap water containing Hartmannella vermiformis. Tap water cultures prepared with the following components were suitable for the multiplication studies: Legionella spp., 10(3) CFU/ml; H. vermiformis, 10(4.4) cysts per ml; and killed Pseudomonas paucimobilis, 10(9) cells per ml. Cocultures were incubated at 37 degrees C for at least 1 week. The following legionellae multiplied in tap water cocultures in each replicate experiment: L. bozemanii (WIGA strain), L. dumoffii (NY-23 and TX-KL strains), L. micdadei (two environmental strains), and L. pneumophila (six environmental strains and one clinical isolate). Growth yield values for these strains were 0.6 to 3.5 log CFU/ml. Legionellae which did not multiply in replicate cocultures included L. anisa (one strain), L. bozemanii (MI-15 strain), L. micdadei (a clinical isolate), L. longbeachae, (one strain), and L. pneumophila (Philadelphia 1 strain). L. gormanii and an environmental isolate of L. pneumophila multiplied in only one of three experiments. None of the legionellae multiplied in tap water containing only killed P. paucimobilis. The mean growth yield (+/- standard deviation) of H. vermiformis in the cocultures was 1.2 +/- 0.1 log units/ml. H. vermiformis supports multiplication of only particular strains of legionellae, some of which are from diverse origins.     

Multiplication of Legionella spp. in tap water containing Hartmannella vermiformis

A model was developed to study the multiplication of various Legionella spp. in tap water containing Hartmannella vermiformis. Tap water cultures prepared with the following components were suitable for the multiplication studies: Legionella spp., 10(3) CFU/ml; H. vermiformis, 10(4.4) cysts per ml; and killed Pseudomonas paucimobilis, 10(9) cells per ml. Cocultures were incubated at 37 degrees C for at least 1 week. The following legionellae multiplied in tap water cocultures in each replicate experiment: L. bozemanii (WIGA strain), L. dumoffii (NY-23 and TX-KL strains), L. micdadei (two environmental strains), and L. pneumophila (six environmental strains and one clinical isolate). Growth yield values for these strains were 0.6 to 3.5 log CFU/ml. Legionellae which did not multiply in replicate cocultures included L. anisa (one strain), L. bozemanii (MI-15 strain), L. micdadei (a clinical isolate), L. longbeachae, (one strain), and L. pneumophila (Philadelphia 1 strain). L. gormanii and an environmental isolate of L. pneumophila multiplied in only one of three experiments. None of the legionellae multiplied in tap water containing only killed P. paucimobilis. The mean growth yield (+/- standard deviation) of H. vermiformis in the cocultures was 1.2 +/- 0.1 log units/ml. H. vermiformis supports multiplication of only particular strains of legionellae, some of which are from diverse origins.     

毛木耳白色突变体的遗传规律及分子标记开发

2016年秋季,漳州一农户种植的褐色毛木耳Auricularia cornea品种“43012H”发生白色突变,有的菌袋同时长出褐色、白色、褐色与白色交杂的颜色嵌合体耳片,有的菌袋长出白色耳片,而有的菌袋出菇颜色正常。采集白色耳片、褐色耳片和嵌合体耳片进行组织分离,得到的菌种进行栽培试验,从褐色耳片（正常）分离获得的菌种（AC_B）,种植得到正常的毛木耳子实体;从白色耳片（突变）分离获得的菌种（AC_W）,种植得到纯白色子实体;从颜色嵌合体耳片分离获得的菌种（AC_R）,栽培后也只长白色子实体,没有出现嵌合体子实体。AC_B分别与AC_W、AC_R的菌种混合接种栽培,菌袋中同时长出白色、褐色和嵌合体耳片。再次进行组织分离与栽培试验,性状稳定。对AC_B和AC_W进行基因组测序,获得2个与本研究中所用菌株的耳片颜色相关的SNP位点,即SNP1和SNP2。上述组织分离得到的菌株中,褐色菌株的基因型为SNP1 A/G（杂合）、SNP2 A（纯合）,白色菌株的基因型为SNP1 G（纯合）、SNP2 A/C（杂合）。     

Pathogenic Naegleria sp.—Study of a Strain Isolated from Human Cerebrospinal Fluid

SYNOPSIS. Experimental observation of the pathogenicity of some strains of Hartmannella plus the observation of human meningo-encephalitis due to small amebas which had a structure compatible with that of Hartmannella in the tissues has suggested the concept of respiratory amebiasis followed by cerebral and other complications.
Until recently no cultural evidence was available to identify positively the amebas in the human cases. This report summarizes the isolation of Naegleria sp. (HB-1) from human spinal fluid by mouse inoculation followed by tissue culture of the infected mouse brain. C. Butt and his associates, who submitted this material to us, isolated the Naegleria on agar medium with Escherichia coli without antibiotics at 37 C.
The new isolate failed to grow on the medium previously suggested by us for Hartmannella. HB-1 is virulent for laboratory animals and has a structure in the tissues which more resembles the amebas in the human tissue than the amebas in experimental Hartmannella infections of mice.
Naegleria and Hartmannella are both potential pathogens for normal animals and man. A clinical laboratory method to detect Naegleria as well as Hartmannella is herein suggested.     

Structural elucidation of a 3-O-methyl-D-galactose-containing neutral polysaccharide from the fruiting bodies of Phellinus igniarius

PIP60-1, a novel heteropolysaccharide isolated from fruiting bodies of the medicinal fungus, Phellinus igniarius, has a molecular weight of 1.71 x 10(4)Da and is composed of L-fucose, D-glucose, D-mannose, D-galactose and 3-O-Me-D-galactose in a ratio of 1:1:1:2:1. A structural investigation of PIP60-1 carried out using sugar and methylation analyses, combined with (1)H and (13)C NMR spectroscopy, including COSY, TOCSY, NOESY, HSQC and HMBC experiments, established the repeating unit of the polysaccharide as the following: [structure: see text]     

Sequence variations in small-subunit ribosomal RNAs of Hartmannella vermiformis and their phylogenetic implications

Evidence of associations between free-living amoebas and human disease has been increasing in recent years. Knowledge about phylogenetic relationships that may be important for the understanding of pathogenicity in the genera involved is very limited at present. Consequently, we have begun to study these relationships and report here on the phylogeny of Hartmannella vermiformis, a free-living amoeba that can harbor the etiologic agent of Legionnaires' disease. Our analysis is based on studies of small-subunit ribosomal RNA genes (srDNA). Nucleotide sequences were determined for nuclear srDNA from three strains of H. vermiformis isolated from the United Kingdom, Germany, and the United States. These sequences then were compared with a sequence previously obtained for a North American isolate by J. H. Gunderson and M. L. Sogin. The four genes are 1,840 bp long, with an average GC content of 49.6%. Sequence differences among the strains range are 0.38%-0.76%. Variation occurs at 19 positions and includes 2 single-base indels plus 14 monotypic and 3 ditypic single-base substitutions. Variation is limited to eight helix/loop structures according to a current model for srRNA secondary structure. Parsimony, distance, and bootstrap analyses used to examine phylogenetic relationships between the srDNA sequences of H. vermiformis and other eukaryotes indicated that Hartmannella sequences were most closely related to those of Acanthamoeba and the alga Cryptomonas. All ditypic sites were consistent with a separation between European and North American strains of Hartmannella, but results of other tests of this relationship were statistically inconclusive.      

Collagen stimulates [3H]inositol trisphosphate formation in indomethacin-treated human platelets.

The present study investigates the pathway of metabolism of inositol phospholipids in human platelets exposed to collagen. Platelet activation by collagen was preceded by a lag phase usually lasting 10-20 s. Formation of [3H]inositol trisphosphate (IP3) was not observed during this period, but occurred in parallel with the onset of aggregation, release of ATP and phosphorylation of a 20 000 Da and a 40 000 Da protein. Indomethacin treatment partially inhibited all of these responses. Aggregation and ATP release, but not IP3 formation, were further inhibited in indomethacin-treated platelets loaded with the fluorescent Ca2+ indicator, quin2. Under these conditions there was no detectable mobilization of Ca2+. These results demonstrate that activation of platelets by collagen is associated with rapid hydrolysis of polyphosphoinositides by phospholipase C, thereby producing IP3. This observation is discussed in relation to IP3 as a possible Ca2+-mobilizing agent.     

A contemporary evaluation of the acrasids (Acrasidae, Heterolobosea, Excavata)

Sorocarpic protists are organisms that individually aggregate and work together to form a fungus-like fruiting body (sorocarp). The amoeboid forms are often colloquially referred to as "cellular slime molds" or "acrasids". We argue the latter term should be used only to refer to members of Acrasidae in Heterolobosea. Here we study the diversity of two Acrasidae genera, Acrasis and the closely similar Pocheina, using a combination of morphological characteristics and small subunit rRNA gene sequences. A total of eight isolates of Acrasis and an example of Pocheina were examined. Acrasis/Pocheina form a well-supported monophyletic group that is the highly supported sister to a clade containing Allovahlkampfia and several other amoebae. Four molecular lineages of Acrasis were resolved, each of which is characterized by a distinctive fruiting body morphology. Each lineage represents a species, two of which are novel, Acrasis kona n. sp. and Acrasis takarsan n. sp. An isolate identified as Pocheina rosea is nested within the clade containing isolates of the taxon Acrasis rosea, into which P. rosea is tentatively subsumed. One member of the tightly knit allovahlkampfid clade was induced to form a simple sorocarp, leading us to include this clade in Acrasidae.     

Comprehensive identification of novel post-translational modifications in cellular peroxiredoxin 6

Peroxiredoxin 6 (PRDX6), a 1-Cys peroxiredoxin, is a bifunctional enzyme acting both as a glutathione peroxidase and a phospholipase A2. However, the underlying mechanisms and their regulation mechanisms are not well understood. Because post-translational modifications (PTMs) have been shown to play important roles in the function of many proteins, we undertook, in this study, to identify the PTMs in PRDX6 utilizing proteomic tools including nanoUPLC-ESI-q-TOF MS/MS employing selectively excluded mass screening analysis (SEMSA) in conjunction with MOD(i) and MODmap algorithm. We chose PRDX6 obtained from liver tissues from two inbred mouse strains, C57BL/6J and C3H/HeJ, which vary in their susceptibility to high-fat diet-induced obesity and atherosclerosis, and a B16F10 melanoma cell line for this study. When PRDX6 protein samples were separated on 2D-PAGE based on pI, several PRDX6 spots appeared. They were purified and the low abundant PTMs in each PRDX6 spot were analyzed. Unexpected mass shifts (Δm = -34, +25, +64, +87, +103, +134, +150, +284 Da) observed at active site cysteine residue (Cys47) were quantified using precursor ion intensities. Mass differences of -34, +25, and +64 Da are presumed to reflect the conversion of cysteine to dehydroalanine, cyano, and Cys-SO(2) -SH, respectively. We also detected acrylamide adducts of sulfenic and sulfinic acids (+87 and +103 Da) as well as unknown modifications (+134, +150, +284 Da). Comprehensive analysis of these PTMs revealed that the PRDX6 exists as a heterogeneous mixture of molecules containing a multitude of PTMs. Several of these modifications occur at cysteine residue in the enzyme active site. Other modifications observed, in PRDX6 from mouse liver tissues included, among others, mono- and dioxidation at Trp and Met, acetylation at Lys, and deamidation at Asn and Gln. Comprehensive identification of the diverse PTMs occurring in this bifunctional PRDX6 enzyme should help understand how PRDX6 plays key roles in oxidative stresses.     

Interactions between metal ions and carbohydrates. The coordination behavior of neutral erythritol to neodymium ion

A single crystal of a coordinated complex of neutral erythritol (C4H10O4,E) with a neodymium ion, NdE(II), was synthesized and studied using FT-IR and X-ray diffraction analysis. In NdE(II) (NdCl3.2.5C4H10O4.C2H5OH) the Nd3+ coordinates with one chloride ion and eight OH groups from three erythritol molecules. There are two neodymium centers linked by one erythritol molecule with same coordination structure in the molecule. Two erythritol molecules provide 1,3,4-hydroxyl groups to coordinate with a neodymium ion; another erythritol molecule coordinates to two Nd ions via its 1,2-hydroxyl groups and 3,4-hydroxyl groups, respectively. The OH groups of erythritol act as ligand to coordinate to neodymium ions, and OH groups of erythritol form hydrogen bond networks that link chain and layer together to build three-dimensional structures. The ratio of metal to ligand is 1:2.5. The structure of NdE(II) is more complicated than the previously reported NdE(I), which is NdCl3.C4H10O4.6H2O; in NdE(I), Nd3+ is coordinated to four hydroxyl groups from two erythritol molecules, four water molecules and one chloride ion. The results indicate the complexity of metal-sugar interaction.     

THE EFFECTS OF LIGHT ON THE DEVELOPMENT OF THE CELLULAR SLIME MOLD ACRASIS ROSEA

No fruiting of the NC-18 isolate of Acrasis rosea occurs in cultures maintained in continuous light or in continuous dark. The use of different food organisms does not alter the aforementioned behavior. The time at which fruiting occurs in this isolate can be regulated by administering stimulatory light followed by a dark period. Mature sorocarps are formed approximately 14 hr after the termination of light and the start of darkness. Within this 14-hr interval aggregation and sorocarp development occur. After about 6 hr of dark incubation, NC-18 amebae, previously stimulated by light, form a few weak aggregation centers. After 8 hr of dark incubation there are numerous aggregation areas, large in size and deep rose in color. By 10 hr the aggregations are quite compact and firm in appearance, and between 12 and 14 hr late aggregations, sorogens and, finally, mature sorocarps are formed. The minimum dark period, i.e., the minimum time that is required in darkness (for cultures previously stimulated with light) to obtain at least some fruiting within the 14-hr developmental period, is 7–8 hr for NC-18 and 5–6 hr for Tu-26. Maximum numbers of sorocarps form when cultures are given 10–11 hr of uninterrupted dark. Light-stimulated cultures of NC-18 placed in darkness and interrupted by a 10- or 30-min exposure to wide-spectrum blue or cool white fluorescent light an hour prior to the minimal dark period exhibit a 4–5 hr-delay in fruiting when returned to darkness and inspected at intervals following the second irradiation. Growth and fruiting of NC-18 occurred with purified food sources of each of five different species of Chlorella and with the alga Stichococcus bacillaris. This is apparently the first report of the utilization of algae as food sources by a cellular slime mold. Fruiting of NC-18 was readily arrested by lowering the relative humidity to 40–45%. This change in the moisture content of the surrounding air induced microcyst formation. Growth on buffered medium occurred in the entire pH range tested, 3.5–7.6, but fruiting occurred only between pH 5.0 and 6.6.     

Relationship between immune system and gram-negative bacteria. IV. T lymphocytes from Lpsd mice possess binding site(s) for Rb Salmonella

We have previously shown that Salmonella minnesota R345 (Rb) spontaneously binds to 50 to 55% of human peripheral blood mononuclear cells (PBMC). In the present study, we have compared Rb cytoadherence to lymphoid cells from various tissues of lipopolysaccharide (LPS) hyporesponsive (Lpsd) and LPS responsive (Lpsn) mouse strains. A higher number of spleen cells from Lpsd mice (C3H/HeJ and C57BL/10ScN) bound Rb bacteria (22 to 30%) than cells from Lpsn mice (4 to 9%). Rb bound mainly to T cells, and cytoadherence occurred in both Lyt-1+ and Lyt-2+ T cell subsets. By contrast, purified splenic B cells from Lpsd and Lpsn mice gave less than 4% Rb cytoadherence. In both mouse strains, cytoadherence was mediated by the homologous LPS structure, because purified Rb-LPS blocked Rb Salmonella binding to T cells. On the other hand, smooth Salmonella typhimurium LT-2 LPS (S-LPS) and Salmonella R595 (Re) LPS (Re-LPS), which contain mainly lipid A, were without effect on Rb binding. Increased Rb binding was seen with T cells from Peyer's patches (PP), mesenteric lymph nodes (MLN), and peripheral blood than from spleen of C3H/HeN (Lpsn) mice; however, greater cytoadherence was always seen with T cells of these tissues from C3H/HeJ mice. Interestingly, treatment of whole spleen or purified T cells from C3H/HeN mice with neuraminidase enhanced cytoadherence to levels seen with C3H/HeJ cells. The observed Rb binding to PP, MLN, and PBMC cells in both mouse strains suggests that gut microbial environment may play an important role in Rb cytoadherence. This is also supported by the evidence that when spleen cells of germfree and conventional mice were tested for Rb binding, higher cytoadherence was observed in conventional mice only. Taken together, these results indicate that T cells of Lpsd mice express binding site(s) for Salmonella, whereas Lpsn mice have T cells with these structure(s) in a cryptic configuration.     

Mass spectrometric characterization of human histone H3: a bird's eye view

The modification of H3 in asynchronous HeLa cells was profiled using Top Down Mass Spectrometry. A broad distribution of species differing by 14 Da and containing less than 3% unmodified protein was observed for all three variants. Species of up to +168 Da were observed for H3.1, and fragmentation of all species by Electron Capture Dissociation (ECD) revealed approximately 5% methylation of K4 and approximately 50% dimethylation of K9. K14 and K23 were major sites of acetylation. H3.3 was slightly hypermodified with the apex of the distribution shifted by approximately +14 Da compared to H3.1. H3.1 (50% and 15%) from colchicine-treated cells was monophosphorylated and diphosphorylated, respectively, with equivalent modification of S10 and S28.     

Reductive damage in directly ionized DNA: saturation of the C5=C6 bond of cytosine in d(CGCG)(2) crystals

Electron paramagnetic resonance (EPR) was used to study an oligodeoxynucleotide duplex of d(CGCG)(2) that is known to crystallize in Z-form. After X irradiation at 4 K, EPR data were collected on single crystals and polycrystalline samples as a function of annealing temperature and dose. A radical produced by the net gain of a hydrogen atom at C6 and a proton at N3, Cyt(C6+H, N3+H(+))(+*), is identified. This radical had not been positively identified in polymeric DNA previously. The Cyt(C6+H, N3+H(+))(+*) makes up about 4% of the total radical population at 4 K, increasing to about 10-15% after the DNA is annealed to 240 K. There appears to be neither an increase nor a decrease in the absolute concentration of Cyt(C6+H, N3+H(+))(+*) upon annealing from 4 K to 240 K. Additionally, the presence of another radical, one due to the net gain of hydrogen at C5 of cytosine, the Cyt(C5+H)(*), is implicated. Together, these two radicals appear to account for 60-80% of the reduced species in DNA that has been irradiated at 4 K and annealed to 240 K.     

Purification and structural investigation of a water-soluble polysaccharide from Flammulina velutipes

A novel water-soluble heteropolysaccharide FVP60-B was extracted from the fruiting bodies of Flammulina velutipes with boiling water and purified by Sephacryl S-300 and S-400, which molecular weight was estimated to be 1.3 × 10⁴ Da by HPLC. It is composed of l-fucose, d-mannose, d-glucose and d-galactose in a ratio of 1.16:0.82:1.00:3.08. Sugar analysis, methylation analysis together with ¹H, ¹³C and 2D NMR spectroscopy disclosed that FVP60-B is consisted of a α-(1 → 6)-d-galactopyranan backbone with a terminal fucosyl, terminal glucosyl and α-(1 → 6)-d-mannopyranan units on O-2 of 2,6-O-substituted-d-galactosyl units.