Overexpression of myoglobin and assignment of its amide,Cα and Cβ resonances

Summary Sperm whale apomyoglobin was expressed to high levels on minimal media and isotopically labeled with ¹³C and ¹⁵N nuclei. The isotopically labeled apoprotein was purified to homogeneity in a single step by reversed-phase chromatography and reconstituted with hemin and carbon monoxide gas for NMR analysis. Sequence-specific backbone ¹H^N, ¹⁵N and ¹³C as well as side-chain ¹³C resonance assignments have been made for over 90% of the amino acids in the carbon monoxide complex of the protein. Resonance assignments were made by analysis of a series of 3D triple resonance spectra measured on the uniformly labeled sample. These assignments will provide the basis for analyzing the effects of point site mutations on the structure, stability and dynamics of the protein in solution.     

Molecular properties of phosphoenolpyruvate carboxylase from C3, C3−C4 intermediate,and C4 Flaveria species

Phosphoenolpyruvate carboxylase (PEPCase; EC 4.1.1.31) from Flaveria trinervia Mohr (C₄), F. floridana Johnston (C₃–C₄), and F. cronquistii Powell (C₃) leaves were compared by electrotransfer blotting/enzyme-linked immunoassay (Western-blot analysis), mobility of the native enzyme in polyacrylamide gels and in isoelectric focusing (IEF) gels, peptide mapping, and in-vitro translation of RNA isolated from each plant. The PEPCases from the C₃ and C₃–C₄ plants were very similar to each other in terms of electrophoretic mobilities on gels and isoenzyme patterns on IEF gels, and identical in peptide mapping. Quantitative differences were noted, however, in that the C₃–C₄ intermediate plant contained more PEPCase overall and that the relative activity of individual isoenzymes shifted between the C₃ and C₃–C₄ intermediate PEPCases. The PEPCase from the C₄ plant had a different isoenzyme pattern, a different peptide map, and was far more abundant than the other two enzymes. Western blot analysis demonstrated the cross-reactivity of PEPCases from all three Flaveria species with antibody raised against maize PEPCase. The results provide evidence, at the molecular level, that supports the view of C₃–C₄ intermediate species as C₃-like plants with some C₄-like photosynthetic characteristics, but there are differences from the C₃ plant in the quantity and properties of the PEPCase from the C₃–C₄ intermediate plant.Abbreviations IEF isoelectric focusing - kDa kilodalton - PEPCase phosphoenolpyruvate carboxylase - Rubisco Ribulose-1,5-bisphosphate carboxylase/oxygenase     

In-situ immunofluorescent localization of phosphoenolpyruvate and ribulose 1,5-bisphosphate carboxylases in leaves of C3, C4, and C3−C4 intermediatePanicum species

The in-situ inter- and intracellular localization patterns of phosphoenolpyruvate (PEP) and ribulose 1,5-bisphosphate (RuBP) carboxylases in green leaves of severalPanicum species were investigated using an indirect immunofluorescence technique. Four species were examined and compared:P. miliaceum (C₄),P. bisulcatum (C₃), andP. decipiens andP. milioides (C₃–C₄ intermediates which have Kranz-like leaf anatomy and reduced photorespiration). In the C₄ Panicum, PEP carboxylase was located in the cytosol of the mesophyll cells and RuBP carboxylase was restricted to the bundle-sheath chloroplasts. In contrast, in the C₃ Panicum species, PEP carboxylase was found throughout the leaf chlorenchyma, in both the cytosol and chloroplasts, and RuBP carboxylase was located in the chloroplasts. For the C₃–C₄ intermediate plants, the patterns depended on the species examined. ForP. decipiens, the in-situ localization of both carboxylases was similar to that described forP. bisulcatum and other C₃ plants. However, inP. milioides, PEP carboxylase was found exclusively in the cytosol of the mesophyll cells, as inP. miliaceum and other C₄ species, whereas RuBP carboxylase was distributed in both the mesophyll and bundle-sheath chloroplasts.Abbreviations PEP phosphoenolpyruvate - RuBP ribulose 1,5-bisphosphate     

Phylodynamics of hepatitis C virus subtype 2c in the province of Córdoba, Argentina

The Hepatitis C Virus Genotype 2 subtype 2c (HCV-2c) is detected as a low prevalence subtype in many countries, except in Southern Europe and Western Africa. The current epidemiology of HCV in Argentina, a low-prevalence country, shows the expected low prevalence for this subtype. However, this subtype is the most prevalent in the central province of Córdoba. Cruz del Eje (CdE), a small rural city of this province, shows a prevalence for HCV infections of 5%, being 90% of the samples classified as HCV-2c. In other locations of Córdoba Province (OLC) with lower prevalence for HCV, HCV-2c was recorded in about 50% of the samples. The phylogenetic analysis of samples from Córdoba Province consistently conformed a monophyletic group with HCV-2c sequences from all the countries where HCV-2c has been sequenced. The phylogeographic analysis showed an overall association between geographical traits and phylogeny, being these associations significant (α = 0.05) for Italy, France, Argentina (places other than Córdoba), Martinique, CdE and OLC. The coalescence analysis for samples from CdE, OLC and France yielded a Time for the Most Common Recent Ancestor of about 140 years, whereas its demographic reconstruction showed a “lag” phase in the viral population until 1880 and then an exponential growth until 1940. These results were also obtained when each geographical area was analyzed separately, suggesting that HCV-2c came into Córdoba province during the migration process, mainly from Europe, which is compatible with the history of Argentina of the early 20th century. This also suggests that the spread of HCV-2c occurred in Europe and South America almost simultaneously, possibly as a result of the advances in medicine technology of the first half of the 20th century.     

Determination of HN,Hα and HN,C′ coupling constants in 13C, 15N-labeled proteins

Summary Sensitive three-dimensional NMR experiments, based on the E.COSY principle, are presented for the measurement of the ³J(H^N,H) and ³J(H^N,C) coupling constants in uniformly ¹³C- and ¹⁵N-labeled proteins. They employ gradient coherence selection in combination with the sensitivity enhancement method in HSQC-type spectra (Cavanagh et al., 1991; Palmer et al., 1991). In most cases, the two measured coupling constants unambiguously define the -angle for protein structure determination. The method is applied to uniformly ¹³C, ¹⁵N-labeled ribonuclease T₁.     

Effects of low atmospheric CO2 and elevated temperature during growth on the gas exchange responses of C3, C3–C4 intermediate, and C4 species from three evolutionary lineages of C4 photosynthesis

This study evaluates acclimation of photosynthesis and stomatal conductance in three evolutionary lineages of C(3), C(3)-C(4) intermediate, and C(4) species grown in the low CO(2) and hot conditions proposed to favo r the evolution of C(4) photosynthesis. Closely related C(3), C(3)-C(4), and C(4) species in the genera Flaveria, Heliotropium, and Alternanthera were grown near 380 and 180 μmol CO(2) mol(-1) air and day/night temperatures of 37/29°C. Growth CO(2) had no effect on photosynthetic capacity or nitrogen allocation to Rubisco and electron transport in any of the species. There was also no effect of growth CO(2) on photosynthetic and stomatal responses to intercellular CO(2) concentration. These results demonstrate little ability to acclimate to low CO(2) growth conditions in closely related C(3) and C(3)-C(4) species, indicating that, during past episodes of low CO(2), individual C(3) plants had little ability to adjust their photosynthetic physiology to compensate for carbon starvation. This deficiency could have favored selection for more efficient modes of carbon assimilation, such as C(3)-C(4) intermediacy. The C(3)-C(4) species had approximately 50% greater rates of net CO(2) assimilation than the C(3) species when measured at the growth conditions of 180 μmol mol(-1) and 37°C, demonstrating the superiority of the C(3)-C(4) pathway in low atmospheric CO(2) and hot climates of recent geological time.     

Molecular analysis of complement component C8β and C9 cDNAs of Japanese flounder, Paralichthys olivaceus

 The amino acid sequences of the human terminal complement components show extensive structural similarity to each other. In this study the C8β and C9 cDNAs of Japanese flounder, Paralichthys olivaceus, were cloned and analyzed. The derived deduced amino acid sequences of the two terminal components were homologous to those of humans, in that the sequences of both species contained LDL receptor, EGF precursor, and two thrombospondin domains. Japanese flounder C9 was found to have a second thrombospondin region in the C-terminus, similar to that reported for rainbow trout and pufferfish. Moreover, these two complement component cDNAs of Japanese flounder had partial similarity to human perforin. These findings show that Japanese flounder C8β and C9 have similar structures, which supports the hypothesis that the terminal complement genes originated from the same ancestral gene. Collectively, these features emphasize the strong similarity among the members of the terminal complement family. Received: 23 March 1999 / Revised: 1 June 1999     

Kinetics and characteristics of 70 °C, VFA-grown, UASB granular sludge

We studied in batch reactors the kinetics and characterization of 70 °C, volatile fatty acids (VFAs)-grown, upflow anaerobic sludge blanket granular sludge with 55 and 35 °C sludge as reference. The half-saturation constant (K _s), the inhibition constant (K _i), the maximum specific methane production rate (μ_CH4max), and the inhibition response coefficient (n) of the 70 °C sludge were 6.15 mM, 48.2 mM, 0.132 h⁻¹, and 2.48, respectively, while no inhibition occurred at 55 and 35 °C, where the K _s was 3.67 and 3.82 mM, respectively. At 70 °C, the highest initial specific methanogenic activity (ISMA, 0.311 gCH₄-COD per gram volatile solids per day) on VFAs was about 12–15% lower than that on acetate and three to four times less than the ISMA for the 55 and 35 °C sludge. In the acetate conversion study, residual acetate (79 mg l⁻¹) at 70 °C was three to five times higher than that at 55 and 35 °C. Further, the methane produced as percentage of the acetate consumed at 70 °C (89%) was lower than that at 55 (95%) and 35 °C (97%). At 70 °C, 10% of the ISMA remained after 15 days of starvation as compared to 26% (55 °C) and 92% (35 °C) after 30 days of starvation. Thus, the kinetics of the 70 °C granular sludge seem to differ from those at 55 and 35 °C. Received: 1 February 1999 / Accepted: 20 March 1999     

Ecological Partitioning of Cercopithecus campbelli, C. petaurista, and C. diana in the Taï Forest

I determined the degree of ecological partitioning among 3 species of guenons (Cercopithecus campbelli, C. petaurista, and C. diana) in the Taï Forest, Côte d’Ivoire and used the partitioning data to understand competitive relationships among them. Over a 13-mo period, I measured ecological partitioning in terms of food and canopy stratum use for 2 habituated groups of each guenon species and also collected data on food availability. I found that the study species diverged primarily in food items consumed and vertical strata occupied. Cercopithecus petaurista ate much more foliage than the other species did and used mostly the middle strata (5–20 m). Cercopithecus diana ate primarily fruit and used mostly the upper strata (>20 m). Cercopithecus campbelli ate mostly fruit together with large amounts of animal matter and primarily occupied the ground and low strata (<5 m). Of the specific pairs, the diets of Cercopithecus campbelli/C. diana overlapped the most overall and decreased during the season of low fruit availability. Cercopithecus campbelli and C. diana age/sex classes also overlapped more than the age/sex classes of other species pairs. The results suggest that the potential for competition was more intense for Cercopithecus campbelli/C.diana relations than it is for other species pairs. I compare my results from Taï with those from other primate and guenon communities and demonstrate that dietary overlaps and seasonal dietary divergence are lower in Taï than in most other guenon communities.     

Kinetics of Avibactam Inhibition against Class A,C, and D β-Lactamases

Avibactam is a non-β-lactam β-lactamase inhibitor with a spectrum of activity that includes β-lactamase enzymes of classes A, C, and selected D examples. In this work acylation and deacylation rates were measured against the clinically important enzymes CTX-M-15, KPC-2, Enterobacter cloacae AmpC, Pseudomonas aeruginosa AmpC, OXA-10, and OXA-48. The efficiency of acylation (k₂/K_i) varied across the enzyme spectrum, from 1.1 × 10¹ m⁻¹s⁻¹ for OXA-10 to 1.0 × 10⁵ for CTX-M-15. Inhibition of OXA-10 was shown to follow the covalent reversible mechanism, and the acylated OXA-10 displayed the longest residence time for deacylation, with a half-life of greater than 5 days. Across multiple enzymes, acyl enzyme stability was assessed by mass spectrometry. These inhibited enzyme forms were stable to rearrangement or hydrolysis, with the exception of KPC-2. KPC-2 displayed a slow hydrolytic route that involved fragmentation of the acyl-avibactam complex. The identity of released degradation products was investigated, and a possible mechanism for the slow deacylation from KPC-2 is proposed.     

Synthesis of [¹¹C]uric acid, using [¹¹C]phosgene, as a possible biomarker in PET imaging for diagnosis of gout

The synthesis and in vivo evaluation of (11)C -labeled uric acid ([(11)C]1), a potential imaging agent for the diagnosis of urate-related life-style diseases, was performed using positron emission tomography (PET) image analysis. First, the synthesis of [(11)C]1 was achieved by reacting 5,6-diaminouracil (2) with (11)C-labeled phosgene ([(11)C]COCl(2)). The radiochemical yield of [(11)C]1 was 37±7% (decay-corrected based on [(11)C]COCl(2)) with specific radioactivities of 96-152GBq/μmol at the end of synthesis (n=6). The average time of radiosynthesis from the end of bombardment, including formulation, was about 30min with >98% radiochemical purity. Second, the synthetic approach to [(11)C]1 was optimized using 5,6-diaminouracil sulfate (3) with [(11)C]COCl(2) in the presence of 1,8-bis(dimethylamino)naphthalene. [(11)C]1 was synthesized in 36±6% radiochemical yield, 89-142GBq/μmol of specific radioactivities, and 98% radiochemical purity by this method (n=5). This allowed the synthesis of [(11)C]1 to be carried out repeatedly and the radiochemical yield, specific radioactivities, average time of synthesis, and radiochemical purity of [(11)C]1 were similar to those obtained using 2. PET studies in rats showed large differences in the accumulation of radioligand in the limbs under normal and hyperuricemic conditions. Thus, an efficient and convenient automated synthesis of [(11)C]1 has been developed, and preliminary PET evaluation of [(11)C]1 confirmed the increased accumulation of radioactivity in the limbs of a rat model of hyperuricemia.     

The future of C4 research--maize, Flaveria or Cleome?

C4 photosynthesis has evolved multiple times among the angiosperms: the spatial rearrangement of the photosynthetic apparatus, combined with alterations to the leaf structure, allows CO2 to be concentrated around Rubisco. Higher CO2 concentrations at Rubisco decrease the rate of oxygenation and therefore reduce the amount of energy lost through photorespiration. C4 plants are particularly prevalent in tropical and subtropical regions because they can sustain higher rates of net photosynthesis; they also represent some of our most productive crops. To date, most progress in identifying genes crucial for C4 photosynthesis has been made using maize and Flaveria. We propose that Cleome, the most closely related genus containing C4 species to the C3 model Arabidopsis, be used together with Arabidopsis resources to accelerate our progress in elucidating the genetic basis of C4 photosynthesis.     

Microbial metabolism of C1 and C2 compounds. The role of acetate during growth of Pseudomonas AM1 on C1 compounds, ethanol and β-hydroxybutyrate

Pseudomonas AM1 grows on beta-hydroxybutyrate and methanol at similar rates. beta-Hydroxybutyrate is not metabolized by way of the glyoxylate bypass, but is assimilated by the novel route (with acetate as an intermediate) that operates during growth of this organism on ethanol. Evidence from short-term labelling experiments indicates that acetate, which is a possible intermediate in the assimilation of C(1) compounds, is rapidly metabolized to glycine during growth of Pseudomonas AM1 on methanol.     

Spawning Season Variations of Female Nile Tilapia, Oreochromis niloticuss, From Man-made Lakes of Côte D'Ivoire

The spawning season of Oreochromis niloticus females was studied over two annual cycles in 6 small agropastoral and 2 large hydroelectric reservoirs of Côte d'Ivoire (Ayamé and Kossou), situated between 5 and 10°N of latitude. Reproduction occurred during a marked season in the agropastoral reservoirs and in Lake Ayamé, whereas it was continuous in Lake Kossou. Spawning season differed between reservoirs and among years within the same reservoir. Seasonal changes in temperature, rainfall, day length, chlorophyll a concentration and water level often corresponded with changes in the annual spawning cycle. However, annual periodicity of O. niloticus reproduction was more likely influenced by the ephemerides cycle.     

Sleep-Wake Cycle of Adolescents in Côte d'Ivoire: Influence of Age,Gender, Religion and Occupation

The human sleep-wake cycle is characterized by significant individual differences. Those differences in the sleep-wake cycle are partially heritable but are also influenced by environmental factors like the light/dark cycle or social habits. In this study we analyse for the first time the sleep-wake rhythm of adolescent pupils and working adolescents in a less industrialised country in West Africa near the equator. The aim of this study was to explore the sleep wake cycle in this geographical region, using Côte d'Ivoire as an example. Data collection took place between 2nd of March and 10th of June 2009. 588 adolescents (338 girls, 250 boys) between 10 and 15 years (mean?±?SD: 12.72?±?1.63) participated in this study. We collected data on the religion of the participants (Christian (N?=?159), Muslim (N?=?352), other/no religion (N?=?77)) and their occupation. Participants were either pupils attending school (N?=?336) or adolescents that were already working (N?=?252) and not attending school. The interviewer filled in the questionnaire. We found significant effects of age (p?<?0.001), gender (p?<?0.001), occupation (p?=?0.002), religion (p?<?0.001) and region (p?<?0.001). The midpoint of sleep was on average 1:26 (SD: 00:30) on weekdays and 1:37 (SD: 00:42) on weekend days. There are significant differences between weekdays and weekend days, but these were only small. Sleep duration suggests that adolescents in Côte d'Ivoire may gain sufficient sleep during week and weekend days, and thus, may live more in accordance with their own biological clock than adolescents in the northern hemisphere. In contrast, the data can be interpreted that adolescents live in a permanent ‘jetlag’. Factors may be the more continuous light/dark cycle in the tropics, low amount of ambient light and less electricity.     

Mössbauer, EPR, and MCD studies of the C9S and C42S variants of Clostridium pasteurianum rubredoxin and MCD studies of the wild-type protein

Rubredoxins contain a mononuclear iron tetrahedrally coordinated by four cysteinyl sulfurs. We have studied the wild-type protein from Clostridium pasteurianum and two mutated forms, C9S and C42S, in the oxidized and reduced states, with Mössbauer, integer-spin EPR, and magnetic circular dichroism (MCD) spectroscopies. The Mössbauer spectra of the ferric C42S and C9S mutant forms yielded zero-field splittings, D=1.2?cm^?1, that are about 40% smaller than the D-value of the wild-type protein. The ⁵⁷Fe hyperfine coupling constants were found to be ca. 8% larger than those of the wild-type proteins. The present study also revealed that the ferric wild-type protein has δ=0.24±0.01?mm/s at 4.2?K rather than δ=0.32?mm/s as reported in the literature. The Mössbauer spectra of both dithionite-reduced mutant proteins revealed the presence of two ferrous forms, A and B. These forms have isomer shifts δ=0.79?mm/s at 4.2?K, consistent with tetrahedral Fe²⁺(Cys)₃(O-R) coordination. The zero-field splittings of the two forms differ substantially; we found D=?7±1?cm^?1, E/D=0.09 for form A and D=+6.2±1.3?cm^?1, E/D=0.15 for form B. Form A exhibits a well-defined integer-spin EPR signal; from studies at X- and Q-band we obtained g _z =2.08±0.01, which is the first measured g-value for any ferrous rubredoxin. It is known from X-ray crystallographic studies that ferric C42S rubredoxin is coordinated by a serine oxygen. We achieved 75% reduction of C42S rubredoxin by irradiating an oxidized sample at 77?K with synchrotron X-rays; the radiolytic reduction produced exclusively form A, suggesting that this form represents a serine-bound Fe²⁺ site. Studies in different buffers in the pH?6–9 range showed that the A:B ratios, but not the spectral parameters of A and B, are buffer dependent, but no systematic variation of the ratio of the two forms with pH was observed. The presence of glycerol (30–50% v/v) was found to favor the B form. Previous absorption and circular dichroism studies of reduced wild-type rubredoxin have suggested d-d bands at 7400, 6000, and 3700?cm^?1. Our low-temperature MCD measurements place the two high-energy transitions at ca. 5900 and 6300?cm^?1; a third d-d transition, if present, must occur with energy lower than 3300?cm^?1. The mutant proteins have d-d transitions at slightly lower energy, namely 5730, 6100?cm^?1 in form A and 5350, 6380?cm^?1 in form B.