Alkaline Bohr effect of bird hemoglobins: the case of the flamingo

The hemoglobin (Hb) substitution His-->Gln at position alpha89, very common in avian Hbs, is considered to be responsible for the weak Bohr effect of avian Hbs. Phoenicopterus ruber ruber is one of the few avian Hbs that possesses His at alpha89, but it has not been functionally characterized yet. In the present study the Hb system of the greater flamingo (P. ruber roseus), a bird that lives in Mediterranean areas, has been investigated to obtain further insight into the role played by the alpha89 residue in determining the strong reduction of the Bohr effect. Functional analysis of the two purified Hb components (HbA and HbD) of P. ruber roseus showed that both are characterized by high oxygen affinity in the absence of organic phosphates, a strong modulating effect of inositol hexaphosphate, and a reduced Bohr effect. Indeed, in spite of the close phylogenetic relationship between the two flamingo species, structural analysis based on tandem mass spectrometry of the alpha(A) chain of P. ruber roseus Hb showed that a Gln residue is present at position alpha89.     

Gender determination by body weight and linear measurements in American and Chilean flamingos,previously surgically sexed: Within-sex comparison to greater flamingo measurements

Gender was determined by laparoscopic visualization of the gonads for 38 adult American flamingos (Phoenicopterus ruber ruber L.) and 36 adult Chilean flamingos (P. chilensis L.). Concomitant body weight (kg) and linear measurements (mm) of the culmen (bill), tarsus (tarsometatarsus), middle toe, and wing were taken. Statistical comparisons of body weight and linear measurements for male vs. female were made for each species. Also, the same-sex statistical comparisons were made between these two species, and between each of these two species and with data for greater flamingos (P. r. roseas L.) from a previous publication. As previously published for greater flamingos, an overlap between sexes existed in all measurements with males on average larger than females for both American and Chilean flamingos. However, Students' t-test indicated a significant sexual difference for all measurements between males and females of each species except for culmen length in Chilean flamingos. Students' t-test also indicated a significant difference when species were compared (Chilean vs. greater, and American vs. Chilean) and subspecies (American vs. greater) were compared for most of the 5 measurements. Thus, despite limitations imposed by between-sex overlap, weights and linear measurements, especially tarsus, middle toe, and wing length, appear to be useful in determining an individual's gender when species or subspecies identification is considered.     

Comparative ultrastructure of coxal glands in unfed larvae of Leptotrombidium orientale (Schluger, 1948) (Trombiculidae) and Hydryphantes ruber (de Geer, 1778) (Hydryphantidae)

Coxal glands of unfed larvae Leptotrombidium orientale (Schluger, 1948) (Trombiculidae), a terrestrial mite parasitizing vertebrates, and Hydryphantes ruber (de Geer, 1778) (Hydryphantidae), a water mite parasitizing insects were studied using transmission electron microscopy. In both species, the coxal glands are represented by a paired tubular organ extending on the sides of the brain from the mouthparts to the frontal midgut wall and are formed of the cells arranged around the central lumen. As in other Parasitengona, the coxal glands are devoid of a proximal sacculus. The excretory duct, joining with ducts of the prosomal salivary glands constitutes the common podocephalic duct, opening into the subcheliceral space. The coxal glands of L. orientale are composed of a distal tubule with a basal labyrinth, an intermediate segment without labyrinth, and a proximal tubule bearing tight microvilli on the apical cell surface and coiled around the intermediate segment. The coxal glands of H. ruber mainly consist of the uniformly organized proximal tubule with apical microvilli of the cells lacking the basal labyrinth. This tubule shows several loops running backward and forward in a vertical plane on the side of the brain. In contrast to L. orientale , larvae of H. ruber reveal a terminal cuticular sac/bladder for accumulation of secreted fluids. Organization of the coxal glands depends on the ecological conditions of mites. Larvae of terrestrial L. orientale possess distal tubule functioning in re‐absorption of ions and water. Conversely, water mite larvae H. ruber need to evacuate of the water excess, so the filtrating proximal tubule is prominent.     

Species-specific oocyte proteins as molecular markers for Lineus taxonomy

The yolk proteins from the eggs of five species of thenemertean genus Lineus were analysed and theresulting data were used to define L. longissimus, L. sanguineus, L. lacteus, L. ruber, and L. viridis as distinct taxa (species to date). All fivespecies have at least one large (80–60 kDa) and onemedium sized (45–30 kDa) vitellin subunit, but thereare significant differences in the number and sizes ofthe molecular subunits. The large and medium sizedvitellin components of all the species areglycosylated, except for the 145 kDa protein of L. sanguineus. Rabbit antibodies to the L. lacteus vitellin subunits cross-reacted withthe vitellin subunits in the eggs of the otherspecies. The vitellin components of these five speciesof nemertean are very similar. Two species, L.ruber and L. viridis, lay their eggsin gelatinous masses, and the electrophoretic patternsof the jelly proteins show that the physicalconsistency of the jelly depends on molecular weightsof the components. The egg mass of L. viridis contains smaller proteins than the egg massof L. ruber. The repeatablespecies-specific patterns of vitellin componentsprovide a useful complement to the usual taxonomiccriteria.     

红色红曲菌蛋白质组双向凝胶电泳体系的建立

红曲菌是一种具有较高食用和药用价值的丝状真菌,能够产生红曲色素、莫纳可林K等多种生理活性物质。通过分析比较培养基、蛋白质裂解液组成以及水化上样条件对双向电泳结果的影响,建立了红色红曲菌蛋白质组的双向凝胶电泳体系,为从蛋白质水平研究红曲菌及其次级代谢产物的生物合成提供依据。结果表明：用YES培养基培养红色红曲菌6 d,TCA 丙酮法提取菌体总蛋白质,蛋白质裂解液组分为8mol/L尿素,2mol/L硫脲,4 % CHAPS,1 % DTT和2 % Bio-lyte,可获得蛋白质样点数量多,清晰度高的双向电泳图像,为进一步研究红曲菌蛋白质组奠定了基础。     

Species-specific oocyte proteins as molecular markers for Lineus taxonomy

The yolk proteins from the eggs of five species of thenemertean genus Lineus were analysed and theresulting data were used to define L. longissimus, L. sanguineus, L. lacteus, L. ruber, and L. viridis as distinct taxa (species to date). All fivespecies have at least one large (80–60 kDa) and onemedium sized (45–30 kDa) vitellin subunit, but thereare significant differences in the number and sizes ofthe molecular subunits. The large and medium sizedvitellin components of all the species areglycosylated, except for the 145 kDa protein of L. sanguineus. Rabbit antibodies to the L. lacteus vitellin subunits cross-reacted withthe vitellin subunits in the eggs of the otherspecies. The vitellin components of these five speciesof nemertean are very similar. Two species, L.ruber and L. viridis, lay their eggsin gelatinous masses, and the electrophoretic patternsof the jelly proteins show that the physicalconsistency of the jelly depends on molecular weightsof the components. The egg mass of L. viridis contains smaller proteins than the egg massof L. ruber. The repeatablespecies-specific patterns of vitellin componentsprovide a useful complement to the usual taxonomiccriteria.     

Genetic characterization in four sciaenid species from the Arabian Sea

Four sciaenid species Johnieops dussumieri, Kathala axillaris, Pennahia macropthalmus and Otolithes ruber were analysed electrophoretically for genetic variation at 18 loci (16 in P. macropthalmus and O. ruber ). Twelve loci were polymorphic in J. dussumieri , 10 in K. axillaris , three in P. macropthalmus and 12 in O. ruber ( P <0·99). Average heterozygosity ranged from 0·033 ± 0·100 to 0·070 ± 0·122. The allele frequencies of 14 loci were used to estimate Nei's genetic distance (). The values ranged from 0·334 to 0·612. Three isozyme loci ( LDH-B*, MDH-2* and G3PDH-1* ) were found to be the most reliable species-specific markers.     

红色红曲霉Mr-1的次级代谢产物生物活性成分分析

【背景】红曲霉(Monascus)是一种重要的药食同源性真菌,其自身产生的次级代谢产物具有多种生理活性功能,然而红曲霉中的生物活性成分却鲜有报道。利用红曲霉发酵液进行药效物质成分追溯,对了解红曲霉药效物质基础具有十分重要的意义。【目的】对红色红曲霉(M.ruber)Mr-1次级代谢产物中的生物活性成分和生物学功能进行研究。【方法】采用硅胶柱、SephadexLH-20凝胶柱等色谱技术对活性成分进行分离纯化,通过核磁共振和高分辨质谱技术对化合物结构进行解析;对鉴定的化合物进行体外抗氧化、抑菌和酶活性测定。【结果】从红色红曲霉Mr-1次级代谢产物中分离得到4个活性化合物,鉴定为3个黄酮类化合物Luteolin(1)、Hesperetin(2)、Glycitein(3)和1个萜类化合物Ursolic acid(4)。化合物1、2、4为首次从红曲菌科中分离得到。在抗氧化试验中,化合物1对ABTS⁺、DPPH和OH^-自由基具有较强的清除能力,IC₅₀分别为13.36、8.74和32.75μg/mL;在抑菌试验中,化合物4对金黄色葡萄球菌(Staphylococcus aureus)和李斯特菌(Listeria monocytogenes)表现出中等强度的抑菌能力,抑菌圈直径分别为13.4 mm和11.9 mm;在α-葡萄糖苷酶抑制活性试验中,化合物4表现出很强的抑制能力,IC₅₀为21.34μg/mL。【结论】红色红曲霉Mr-1是宝贵的微生物种质资源,其产生的次级代谢产物生物活性成分多样,具有开发成功能性食品原料的潜能。     

The titanium binding protein of Rhodococcus ruber GIN1 (NCIMB 40340) is a cell-surface homolog of the cytosolic enzyme dihydrolipoamide dehydrogenase

Rhodococcus ruber GIN1 (formally Rh. strain GIN1) was previously isolated on the basis of its strong adherence to coal fly ash (CFA) and titanium dioxide particles from CFA sedimentation ponds of an electrical power plant in Israel. The interaction of the bacterium with oxides has been shown to be mediated by a cell surface protein designated TiBP (titanium binding protein) involving primarily strong, non-electrostatic forces. In this work, we set forward to identify this unique exocellular protein. Sequence analysis of the purified protein by mass spectrometry (LC/MS/MS) following trypsinization revealed 11 peptides. All of them showed >90% amino acid residues identity with sequences of one of the orthologs (dldh1) of the cytosolic enzyme dihydrolipoamide dehydrogenase (DLDH), based on the genome sequence of Rhodococcus strain RHA1. This genome was selected as a reference since currently it is the only sequenced Rhodococcal genome. Altogether, these peptides covered over 25% of the 52 kDa protein molecule. N- and C-termini primers were prepared and used to sequence the paralog gene from Rh. ruber GIN1 after polymerase chain reaction (PCR) amplification. All 11 peptides showed 100% identity with the sequence of this gene. The homology of TiBP with the supposedly cytosolic DLDH raised the question of whether the exocellular TiBP possesses DLDH activity. Indeed, intact late logarithmic phase Rh. ruber GIN1 cells, previously shown to express TiBP, were found to possess such activity, while very low activity was associated with stationary phase cells which possess diminished TiBP expression on their surface. Further evidence for the exocellular location of TiBP/DLDH was achieved using specific anti-TiBP polyclonal antibodies by whole cell and protein enzyme-linked immunosorbent assay (ELISA), showing high reactivity of the logarithmic phase cell surface and substantially lower reactivity with the stationary phase cells. As expected, logarithmic phase spheroplasts were not recognized by these antibodies. Similar results were obtained by fluorescence and scanning electron microscopy. Our postulation that DLDH is located on the surface of Rh. ruber GIN1, serving as a TiO2 binding protein, is in accordance with literary evidence on DLDH in other organisms, Bacteria, Archea, and Eukaryots that suggests it is associated with the outer membranes or cell surfaces. As an exocellular protein DLDH assumes various tasks which are not related to its classical role as a 2-oxoacid dehydrogenase, including serving as an adhesion/binding protein in certain bacteria.     

Preparative isolation of lipid inclusions from Rhodococcus opacus and Rhodococcus ruber and identification of granule-associated proteins

Triacylglycerol granules synthesized and accumulated by Rhodococcus opacus and Rhodococcus ruber were isolated by glycerol density gradient centrifugation. Whereas only one type of granule could be isolated from R. opacus, two types of granules with different specific densities were isolated from R. ruber. Both types of R. ruber granules showed a similar content of triacylglycerols and poly(3-hydroxybutyrate- co-3-hydroxyvalerate), but the protein profiles of both types were significantly different. The granules with the lower specific density were colorless; the granules with the higher specific density had a deep orange pigmentation. Solubilization studies revealed three different groups of granule-associated proteins: (1) unspecifically bound proteins, (2) relatively weakly associated proteins, and (3) proteins that resisted solubilization by treatment with 2 M NaCl, 2% (w/v) Triton X-114, 6 M guanidinium hydrochloride, up to 8% (w/v) SDS, and proteolytic digestion. The strong association of proteins of the last group suggested that these may play a specific role in the synthesis or mobilization of storage lipids or in the structure of the granules. The N-terminal amino acid sequences of the most tightly bound proteins were obtained. Proteins of low molecular weight with striking sequence similarity to the ribosomal protein L7 from various actinomycetes were always copurified with the granules.     

North-south regional variation in phospholipase A activity in the venom of Crotalus ruber.

1. Twenty-seven individual venoms from the rattlesnake species Crotalus ruber from different regions were comparatively analyzed by reverse-phase HPLC and analyzed for phospholipase A (PLA) content using a polarographic assay. 2. Two fractions containing PLA activity were detected by HPLC in the venoms of all the C. ruber specimens from southern Baja, Mexico, but specimens from southern California, U.S.A., were lacking corresponding fractions and were extremely low or lacking in PLA activity in their venoms. 3. The north-south regional variation in PLA content in C. ruber venom does not correlate with the north-south ranges (based on external morphology) of the subspecies C. ruber ruber and C. ruber lucasensis.     

Form of Vitamin B(12) and Its Role in a Methanol-Utilizing Bacterium Protaminobacter ruber

A methanol-utilizing bacterium, Protaminobacter ruber, produced a large amount of vitamin B(12). The compounds were isolated from the cells and identified as methylcobalamin (methyl-B(12)) and adenosylcobalamin (adenosyl-B(12)) by various tests. The variation in the form of B(12) during cultivation was examined by bioautography with cellulose acetate membrane electrophoresis. Methyl-B(12) and adenosyl-B(12) were the two main B(12) compounds produced in the various phases of bacterial growth. The ratio of the amount of methyl-B(12) to total B(12) compounds was higher during the earlier phases of growth. After the logarithmic phase, adenosyl-B(12) was the predominant form. The existence of N-methyltetrahydrofolate:homocysteine transmethylase and methyl-B(12):homocysteine transmethylase was demonstrated in cell-free extracts of Protaminobacter ruber. Methyl-B(12) in P. ruber seems to function mainly in the B(12)-dependent methionine synthetase system.     

Modelling the combined effect of temperature,pH and aw on the growth rate of Monascus ruber,a heat-resistant fungus isolated from green table olives

AIMS: Growth modes predicting the effect of pH (3.5-5.0), NaCl (2-10%), i.e. aw (0.937-0.970) and temperature (20-40 degrees C) on the colony growth rate of Monascus ruber, a fungus isolated from thermally-processed olives of the Conservolea variety, were developed on a solid culture medium. METHODS AND RESULTS: Fungal growth was measured as colony diameter on a daily basis. The primary predictive model of Baranyi was used to fit the growth data and estimate the maximum specific growth rates. Combined secondary predictive models were developed and comparatively evaluated based on polynomial, Davey, gamma concept and Rosso equations. The data-set was fitted successfully in all models. However, models with biological interpretable parameters (gamma concept and Rosso equation) were highly rated compared with the polynomial equation and Davey model and gave realistic cardinal pHs, temperatures and aw. CONCLUSIONS: The combined effect of temperature, pH and aw on growth responses of M. ruber could be satisfactorily predicted under the current experimental conditions, and the models examined could serve as tools for this purpose. SIGNIFICANCE AND IMPACT OF THE STUDY: The results can be successfully employed by the industry to predict the extent of fungal growth on table olives.     

Isolation and identification of a thermophilic strain producing trehalose synthase from geothermal water in China

A slightly thermophilic strain, CBS-01, producing trehalose synthase (TreS), was isolated from geothermal water in this study. According to the phenotypic characteristics and phylogenetic analysis of the 16s rRNA gene sequence, it was identified as Meiothermus ruber. The trehalose synthase gene of Meiothermus ruber CBS-01 was cloned by polymerase chain reaction and sequenced. The TreS gene consisted of 2,895 nucleotides, which specified a 964-amino-acid protein. This novel TreS catalyzed reversible interconversion of maltose and trehalose.     

Phosphodiesterase from the venom of Crotalus ruber ruber

Phosphodiesterase was isolated from the venom of Crotalus ruber ruber from the U.S.A. using the gel filtration on a Sephadex G-75 column, followed by anion or cation exchange chromatography. Phosphodiesterase was homogeneous as established by a single band on acrylamide gel electrophoresis and isoelectric focusing electrophoresis. Phosphodiesterase activity was inhibited by ethylenediamine tetraacetic acid (EDTA), o-phenanthroline, thioglycolic acid or p-chloromercuribenzoate (PCMB), but not by soybean trypsin inhibitor (SBTI) or benzamidine. The molecular weight of this enzyme was determined to be approx. 98,000 and the isoelectric point was found to be pH 10.5 by isoelectric focusing with carrier ampholyte. This enzyme contained 1.04 mol zinc per mol. The Michaelis constant (Km) of this enzyme for p-nitrophenyl thymidine-5'-phosphate and inhibition constant (Ki) for PCMB were found to be 8.3 X 10(-3) and 1.2 X 10(-2) M, respectively.     

Production and partial characterization of antibody to cord factor (trehalose 6,6'-dimycolate) in mice.

Antibody production against the trehalose 6,6'-dimycolate (TDM, cord factor) of Rhodococcus ruber, a non-pathogenic species of the Actinomycetales group, was investigated in mice by repeated intraperitoneal injection of TDM in water-in-oil-in-water micelles without carrier protein. The antigenic TDM was isolated and purified chromatographically from the chloroform-methanol extractable lipids of R. ruber. The hydrophobic moiety of this TDM was composed of two molecules of monoenoic or dienoic alpha-mycolic acids with a carbon chain length ranging from C44 to C48 centering at C46. To detect the antibody, an enzyme-linked immunosorbent assay (ELISA) system was employed using plastic plates coated with TDM. The antibody reacted against the TDM of R. ruber. The antibody was reactive in similar fashion against glycosyl monomycolates differing in the carbohydrate moiety, such as that of glucose mycolate (GM) and mannose mycolate (MM), obtained from R. ruber. Moreover, the antibody reacted against mycolic acid methyl ester itself when it was used as the antigen in ELISA, and trehalose did not absorb the antibody to TDM or inhibit the reaction. These results indicate that the epitope of TDM recognized by the antibody is mycolic acid, an extremely hydrophobic part of the molecule. Next, we prepared monoclonal anti-TDM antibody (moAb) in mice myeloma cells to examine its biological activities and the role of humoral immunity in mycobacterial infection. MoAb reacted against the TDM, glycosyl mycolate, and mycolic acid methyl ester in ELISA in the same manner as our polyclonal antibody did. The administration of moAb suppressed granuloma formation in the lungs, spleen, and liver induced by TDM and inhibited the production of interleukin-1 (IL-1) and chemotactic factor, which is reported to precede granuloma formation.     

笼头菌属一新种

本文报道了采白海南岛南部地区笼头菌属(Clathrus Mich：Pers．)一个新种,即：海南笼头菌Clathrus hainanensis X．L Wu sp．nov.。文中对新种的形态特征作了拉丁文和汉文的描述,附有新种担子果和孢子(扫描电镜)照片,并讨论了新种与本属其他种的区别。主模式标本保存于贵州科学院真菌标本室(HGAS),副模式标本保存于中国科学院昆明植物研究所隐花植物标本馆(HKAS)。     

Identification and characterization of a Hsp70 (DnaK) chaperone system from<Emphasis Type="Italic"> Meiothermus ruber</Emphasis>

We have cloned the genes encoding the chaperones of Meiothermus ruber, Hsp70 (Mru.Hsp70), Hsp40 (Mru.Hsp40) and Hsp22 (Mru.Hsp22). The genes hsp70, hsp22 and hsp40 of M. ruber are organized into an operon. The amino acid sequences of the three M. ruber chaperones show strong similarity with the heat shock proteins of Thermus thermophilus. Both Mru.Hsp40 and its homolog from T. thermophilus lack a cysteine-rich region. However, recombinant Mru.Hsp70 and Mru.Hsp40 associate in an ATP-dependent manner, and assemble into a complex in the absence of other proteins, unlike their counterparts from T. thermophilus, which require DafA for assembly. The analysis revealed that Mru.Hsp70 and Mru.Hsp40 assemble as monomers into the complex, although their homologs from T. thermophilus enter the complex as trimers. The Mru.Hsp70 and Mru.Hsp40 complex increases the spontaneous rate of refolding of denatured mitochondrial malate dehydrogenase by tenfold.     

Purification and characterization of a 14-kilodalton protein that is bound to the surface of polyhydroxyalkanoic acid granules in Rhodococcus ruber.

The N-terminal amino acid sequence of the polyhydroxyalkanoic acid (PHA) granule-associated M(r)-15,500 protein of Rhodococcus ruber (the GA14 protein) was analyzed. The sequence revealed that the corresponding structural gene is represented by open reading frame 3, encoding a protein with a calculated M(r) of 14,175 which was recently localized downstream of the PHA synthase gene (U. Pieper and A. Steinbüchel, FEMS Microbiol. Lett. 96:73-80, 1992). A recombinant strain of Escherichia coli XL1-Blue carrying the hybrid plasmid (pSKXA10*) with open reading frame 3 overexpressed the GA14 protein. The GA14 protein was subsequently purified in a three-step procedure including chromatography on DEAE-Sephacel, phenyl-Sepharose CL-4B, and Superose 12. Determination of the molecular weight by gel filtration as well as electron microscopic studies indicates that a tetrameric structure of the recombinant, native GA14 protein is most likely. Immunoelectron microscopy demonstrated a localization of the GA14 protein at the periphery of PHA granules as well as close to the cell membrane in R. ruber. Investigations of PHA-leaky and PHA-negative mutants of R. ruber indicated that expression of the GA14 protein depended strongly on PHA synthesis.     

Molecular data confirm the validity of the Portuguese blenny (Parablennius ruber, Valenciennes, 1836) and its presence in Western Europe

DNA sequence analysis confirms the distinction between Parablennius ruber and Parablennius gattorugine , simultaneously validating the presence of the former species in Western Europe where it has been reported for >150 years. A possible scenario involving speciation of P. ruber at the Azores and subsequent transport of larvae to Europe, a process that may be still occurring nowadays, could explain this pattern of occurrence.