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PubMed2025

Large-scale Genome Analyses Provide Insights into Hymenoptera Evolution.

The order Hymenoptera includes a large number of species with diverse lifestyles and is known for its significant contributions to natural ecosystems. To better understand the evolution of this diverse order, we performed large-scale comparative genomics on 131 species from 13 superfamilies, covering most representative groups. We used these genomes to reveal an overall pattern of genomic change in terms of gene content and evolutionary rate throughout hymenopteran history. We identified genes that possibly contributed to the evolution of several key innovations, such as parasitoidism, wasp-waist, stinger, and secondary phytophagy. We also discovered the distinct genomic trajectories between the clade containing major parasitoid wasps (Parasitoida) and stinging species (Aculeata) since their divergence, which are involved in many aspects of genomic change, such as rapidly evolving gene families, gene gain and loss, and metabolic pathway evolution. In addition, we explored the genomic features accompanying the three independent evolution of secondary phytophagy. Our work provides insights for understanding genome evolution and the genomic basis of diversification in Hymenoptera.

Animals↗

PubMed1997

Technique for importing greater evolution resolution in multidimensional NMR spectrum.

A very simple and general procedure that extracts constant-evolution-frequency data from a truncated multidimensional (2D, 3D, 4D, etc.) FID is described, generalized, analyzed, and illustrated. The method replaces Fourier transformation of the evolution dimension with a linear model created from a separate, high-quality 1D FID. The equivalent of high resolution in the evolution dimension can be achieved without obtaining an extensive multidimensional FID. The analysis of the 1D FID can also be used to predict the signal to noise ratio of the extracted slices that will result from various evolution dimension sampling protocols, making it possible to develop a priori an optimal sampling strategy for the multidimensional FID. The evolution dimension need not be sampled periodically. The procedure has a potential signal-to-noise ratio advantage because it extracts usable information from a multidimensional FID at short evolution times before the magnetization has decayed significantly.

Data Interpretation, Statistical↗

PubMed1998

13C-NOESY-HSQC with Split Carbon Evolution for Increased Resolution with Uniformly Labeled Proteins.

Two new pulse sequences are presented for the recording of 2D 13C-HSQC and 3D 13C-NOESY-HSQC experiments, containing two consecutive carbon evolution periods. The two periods are separated by a z-filter which creates a clean CxHz-quantum state for evolution in the second period. Each period is incremented (in a non-constant-time fashion) only to the extent that the defocusing of carbon inphase magnetization through J-coupling with neighboring carbons remains insignificant. Therefore, 13C homonuclear J-couplings are rendered ineffective, reducing the loss of signal and peak splitting commonly associated with long 13C evolution times. The two periods are incremented according to a special acquisition protocol employing a 13C-13C gradient echo to yield a data set analogous to one obtained by evolution over the added duration of both periods. The spectra recorded with the new technique on uniformly 13C-labeled proteins at twice the evolution time of the standard 13C-HSQC experiment display a nearly twofold enhancement of resolution in the carbon domain, while maintaining a good sensitivity even in the case of large proteins. Applied to the IIAMan protein of E. coli (31 kDa), the 13C-HSQC experiment recorded with a carbon evolution time of 2 x 8 ms showed a 36% decrease in linewidths compared to the standard 13C-HSQC experiment, and the S/N ratio of representative cross-peaks was reduced to 40%. This reduction reflects mostly the typical loss of intensity observed when recording with an increased resolution. The 13C-NOESY-HSQC experiment derived from the 13C-HSQC experiment yielded additional NOE restraints between resonances which previously had been unresolved. Copyright 1998 Academic Press.

Journal Article↗

PubMed1996

Comparison of isotope exchange, H2 evolution, and H2 oxidation activities of Azotobacter vinelandii hydrogenase.

Azotobacter vinelandii hydrogenase was purified aerobically with a 35% yield. The purified enzyme catalyzed H2 oxidation at much greater velocity than H2 evolution. There was a large difference in activation energy for the two reactions. EA was 10 kcal/mol for H2 oxidation and 22 kcal/mol for evolution. This difference in activation energies between the two reactions means that the ratio of oxidation velocity to evolution velocity drops from 70 at 33 degrees C to 8 at 48 degrees C. With D2 and H2O as substrates, both membranes and purified enzyme produced only H2 and no HD in the isotope exchange reaction. The velocity of isotope exchange was equal to the velocity of H2 evolution from reduced methyl viologen, indicating that the two reactions share the same rate-limiting step. D2 and H2 inhibited H2 evolution, but D2 did not inhibit isotope exchange. We conclude that H2 and D2 do not inhibit H2 evolution by competing with H+ for the active site of the reduced enzyme. The Km for D2 in isotope exchange is 40-times greater than its Km in D2 oxidation. The difference in Km cannot be accounted for by differences in kcat. We propose that redox environment regulates hydrogenase's affinity for D2 (and likely H2 as well).

Aerobiosis↗

PubMed2005

Mathematical model for carbon dioxide evolution from the thermophilic composting of synthetic food wastes made of dog food.

The impacts of the aeration and the agitation on the composting process of synthetic food wastes made of dog food were studied in a laboratory-scale reactor. Two major peaks of CO(2) evolution rate were observed. Each peak represented an independent stage of composting associated with the activities of thermophilic bacteria. CO(2) evolutions known to correlate well with microbial activities and reactor temperatures were fitted successfully to a modified Gompertz equation, which incorporated three biokinetic parameters, namely, CO(2) evolution potential, specific CO(2) evolution rate, and lag phase time. No parameters that describe the impact of operating variables are involved. The model is only valid for the specified experimental conditions and may look different with others. The effects of operating parameters such as aeration and agitation were studied statistically with multivariate regression technique. Contour plots were constructed using regression equations for the examination of the dependence of CO(2) evolution potentials on aeration and agitation. In the first stage, a maximum CO(2) evolution potential was found when the aeration rate and the agitation parameter were set at 1.75 l/kg solids-min and 0.35, respectively. In the second stage, a maximum existed when the aeration rate and the agitation parameter were set at 1.8 l/kg solids-min and 0.5, respectively. The methods presented here can also be applied for the optimization of large-scale composting facilities that are operated differently and take longer time.

Animal Feed↗

PubMed1996

Effects of pH and thiocyanate on hydrogen peroxide-induced evolution of molecular oxygen in human mixed saliva.

Hydrogen peroxide-induced evolution of molecular oxygen was measured with a Clark-type electrode in a buffered reaction mixture containing mixed whole or dialysed saliva. The optimum pH for oxygen evolution in mixed whole saliva was around 8. Oxygen evolution was also observed in dialysed saliva, suggesting that free SCN- is not essential. The optimum pH was around pH 6. Sodium thiocyanate inhibited the oxygen evolution under acidic conditions in dialysed saliva, increasing the K(m) of hydrogen peroxide and decreasing the Vmax. Ferric chloride (1 mM), a chelator of SCN-, also inhibited oxygen evolution in dialysed saliva; activity was completely restored by 10 mM sodium citrate. Under alkaline conditions, NaSCN slightly enhanced the oxygen evolution without affecting the K(m) of hydrogen peroxide but increasing the Vmax. Hydrogen peroxide-induced oxidation of SCN- in dialysed saliva was much faster at pH 5 than pH 8. These findings suggest that a function of peroxidase in stimulated saliva where the pH is typically between 7 and 8 is the scavenging of hydrogen peroxide to produce molecular oxygen but without producing OSCN- plus HOSCN.

Chelating Agents↗

PubMed1988

Evolution of aphasia in the first year post-onset.

Evolution of aphasia was studied in the first year of recovery in 43 patients sustaining left hemisphere strokes with language impairment. Observations were made daily during acute hospitalization and subsequently at approximately one, two, three, four-to-six and seven-to-twelve month intervals post-stroke. Aphasias were classified according to standard criteria. A significantly larger percentage of the sample (59%) exhibited evolution of aphasia than in previous studies. This was attributed to earlier and more intensive patient observations in this investigation. Most changes occurred within the first two weeks of recovery. Two patterns of evolution were clearly present in the sample, one being early rapid change and the other a more gradual evolution. An expansion and integration of Gloning and Quatember's (1964) model of evolution is proposed on the basis of combined results from several studies. Also, the influence of aging, evolution of aphasia and the emergence of dementia post-stroke are discussed.

Adult↗

PubMed2001

How enzymes adapt: lessons from directed evolution.

Enzymes that are adapted to widely different temperature niches are being used to investigate the molecular basis of protein stability and enzyme function. However, natural evolution is complex: random noise, historical accidents and ignorance of the selection pressures at work during adaptation all cloud comparative studies. Here, we review how adaptation in the laboratory by directed evolution can complement studies of natural enzymes in the effort to understand stability and function. Laboratory evolution experiments can attempt to mimic natural evolution and identify different adaptive mechanisms. However, laboratory evolution might make its biggest contribution in explorations of nonnatural functions, by allowing us to distinguish the properties nutured by evolution from those dictated by the laws of physical chemistry.

Algorithms↗

PubMed2003

The function of the chloride ion in photosynthetic oxygen evolution.

The involvement of Cl(-) and several other monovalent anions in photosynthetic oxygen evolution was studied using photosystem II membranes depleted of Cl(-) by dialysis. The results of these studies differ significantly from results obtained using other depletion methods. Binding studies with glycerol as a cryoprotectant confirm our previous observations with sucrose of two interconvertible binding states of photosystem II with similar activities and with slow or fast exchange, respectively, of the bound ion. With glycerol, Cl(-) depletion decreased the oxygen evolution rate to 55% of that with Cl(-) present without decreasing the quantum efficiency of the reaction, supporting our previous conclusion that oxygen evolution can proceed at high rates in the absence of Cl(-). Further, after Cl(-) depletion the S(2) state multiline signal displayed the same periodic appearance with the same signal yield after consecutive laser flashes as with Cl(-) present. Br(-), I(-), and NO(3)(-), although with different capacities to reactivate oxygen evolution, also showed two binding modes. I(-) inhibited when bound in the low-affinity, fast-exchange mode but activated in the high-affinity mode. A comparison of the EPR properties of the S(2) state with these anions suggests that the nature of the ion or the binding mode only has a minor influence on the environment of the manganese. In contrast, F(-) completely inhibited oxygen evolution by preventing the S(2) to S(3) transition and shifted the equilibrium between the g = 4.1 and multiline S(2) forms toward the former, which suggests a considerable perturbation of the manganese cluster. To explain these and earlier observations, we propose that the role of chloride in the water-splitting mechanism is to participate together with charged amino acid side chains in a proton-relay network, which facilitates proton transfer from the manganese cluster to the medium. The structural requirements likely to be involved may explain the sensitivity of oxygen evolution to Cl(-) depletion or other perturbations.

Anions↗

PubMed1976

Hydrogen evolution: A major factor affecting the efficiency of nitrogen fixation in nodulated symbionts.

Nitrogenase-dependent hydrogen evolution from detached legume nodules and from reaction mixtures containing cell-free nitrogenase has been well established, but the overall effect of hydrogen evolution on the efficiency of nitrogen fixation in vivo has not been critically assessed. This paper describes a survey which revealed that hydrogen evolution is a general phenomenon associated with nitrogen fixation by many nodulated nitrogen-fixing symbionts. An evaluation of the magnitude of energy loss in terms of the efficiency of electron transfer to nitrogen, via nitrogenase, in excised nodules suggested that hydrogen production may severely reduce nitrogen fixation in many legumes where photosynthate supply is a factor limiting fixation. With most symbionts, including soybeans, only 40-60% of the electron flow to nitrogenase was transferred to nitrogen. The remainder was lost through hydrogen evolution. In situ measurements of hydrogen evolution and acetylene reduction by nodulated soybeans confirmed the results obtained with excised nodules. In an atmosphere of air, a major portion of the total electron flux available for the reduction of atmospheric nitrogen by either excised nodules or intact nodulated plants was utilized in the production of hydrogen gas. Some non-leguminous symbionts, such as Alnus rubra, and a few legumes (i.e., Vigna sinensis) apparently have evolved mechanisms of minimizing net hydrogen production, thus increasing their efficiency of electron transfer to nitrogen. Our results indicate that the extent of hydrogen evolution during nitrogen reduction is a major factor affecting the efficiency of nitrogen fixation by many agronomically important legumes.

Journal Article↗

PubMed2001

Evolutive pattern in Crohn's disease: a simplified index using clinical parameters predicts obstructive behaviour.

BACKGROUND: Two clearly differentiated evolutive patterns of Crohn's disease, obstructive and fistulizing, exist, but the early clinical parameters which can predict the evolution are unknown. AIM: To evaluate whether clinical variables, present at the time of diagnosis, may help in predicting a subsequent evolutive behaviour. PATIENTS AND METHODS: Ninety out of 140 evaluable patients were included. After a median of 50.2 months since diagnosis, 64 patients (71%) followed an obstructive pattern while 26 patients (28.9%) had a fistulizing form. Clinical variables were analysed as predictors of outcome. Logistic regression was carried out in order to obtain a mathematical model that would predict the evolution. The individual ability of the mathematical model to predict evolution was assessed using relative receiver operating characteristic (ROC) curves. RESULTS: The variables which were retained in the model were duration of disease before diagnosis (DD), onset of symptoms (OS), presence of anal disease (AD) and the presence of abdominal mass (AM). The equation z = -9.49 + 2.2643 (AD) - 0.0066 (DD) + 2.5282 (AM) + 1.3433 (OS) was obtained. The probability of evolution towards an obstructive form was P = 1/(1 + e(-Z)). This model can predict 96.88% of obstructive forms but only 53.85% of fistulizing forms. The mathematical point section (ROC curve) corresponds to a probability of 45.2%. Considering an obstructive pattern when the probabilities are above this point, the sensitivity is 98% and the specificity is 50%. CONCLUSIONS: The prediction of an obstructive pattern is feasible using simple clinical variables. The mathematical model obtained is useful for predicting this but not the fistulizing pattern.

Adolescent↗

PubMed1992

On the Mechanism of Resistance to Paraquat in Hordeum glaucum and H. leporinum: Delayed Inhibition of Photosynthetic O(2) Evolution after Paraquat Application.

The mechanism of resistance to paraquat was investigated in biotypes of Hordeum glaucum Steud. and H. leporinum Link. with high levels of resistance. Inhibition of photosynthetic O(2) evolution after herbicide application was used to monitor the presence of paraquat at the active site. Inhibition of photosynthetic O(2) evolution after paraquat application was delayed in both resistant biotypes compared with the susceptible biotypes; however, this differential was more pronounced in the case of H. glaucum than in H. leporinum. Similar results could be obtained with the related herbicide diquat. Examination of the concentration dependence of paraquat-induced inhibition of O(2) evolution showed that the resistant H. glaucum biotype was less affected by herbicide compared with the susceptible biotype 3 h after treatment at most rates. The resistant H. leporinum biotype, in contrast, was as inhibited as the susceptible biotype except at the higher rates. In all cases photosynthetic O(2) evolution was dramatically inhibited 24 h after treatment. Measurement of the amount of paraquat transported to the young tissue of these plants 24 h after treatment showed 57% and 53% reductions in the amount of herbicide transported in the case of the resistant H. glaucum and H. leporinum biotypes, respectively, compared with the susceptible biotypes. This was associated with 62% and 66% decreases in photosynthetic O(2) evolution of young leaves in the susceptible H. glaucum and H. leporinum biotypes, respectively, a 39% decrease in activity for the resistant H. leporinum biotype, but no change in the resistant H. glaucum biotype. Photosynthetic O(2) evolution of leaf slices from resistant H. glaucum was not as inhibited by paraquat compared with the susceptible biotype; however, those of resistant and susceptible biotypes of H. leporinum were equally inhibited by paraquat. Paraquat resistance in these two biotypes appears to be a consequence of reduced movement of the herbicide in the resistant plants; however, the mechanism involved is not the same in H. glaucum as in H. leporinum.

Journal Article↗

PubMed1995

Chilling-Induced Heat Evolution in Plants.

Increases in respiration, particularly via the alternative pathway, are observed in response to chilling. These increases result in increased heat evolution. We have measured increases in heat evolution in response to chilling in a number of plant species using a microcalorimeter. After 8 h of exposure to 8[deg]C, heat evolution in a variety of chilling-sensitive species increased 47 to 98%. No increase in heat evolution was seen with the extremely chilling-sensitive ornamental Episcia cupreata Hook. Heat evolution increased only 7 to 22% in the chilling-resistant species. Increases in heat evolution were observed when plants were chilled in constant light or in the dark, but not when plants were chilled at high humidity. Increased capacity to produce respiratory heat after exposure to chilling temperatures may contribute to the cold-acclimation process.

Journal Article↗

PubMed1976

Water deficit and ethylene evolution by young cotton bolls.

Ethylene evolution and abscission of young cotton (Gossypium hirsutum L.) bolls were shown, in earlier papers, to increase when plants were subjected to conditions that decreased photosynthesis and sugar content of bolls (dim light, long warm nights). Moisture stress also increased ethylene evolution by young bolls, but it did not decrease their concentrations of fructose, glucose, or sucrose. When detached bolls were incubated for 16 or 24 hours at high or low humidity, their rate of ethylene evolution increased markedly at low humidity and slightly at high humidity. These results suggest that water deficit stimulates ethylene evolution by young bolls directly through partial desiccation, but do not exclude the possibility of a stimulus from moisture-stressed plants. Although attached and detached bolls both lost only a small percentage of their water content, detached bolls lost more for a given rate of ethylene evolution than bolls on moisture-stressed plants. The increased rate of ethylene evolution by young cotton bolls on plants subjected to a water deficit is probably adequate, in many cases, to cause their abscission.

Journal Article↗

PubMed1977

Patterns of Ethylene and Carbon Dioxide Evolution during Cotton Explant Abscission.

The relationship between abscission and the evolution of ethylene and CO(2) was examined in explants and explant segments of cotton seedlings (Gossypium hirsutum L. cv. Acala SJ-1) under both static and flow system conditions, and in the presence and absence of mercuric perchlorate. Explant excision was immediately followed by increased ethylene evolution (wound ethylene); senescence was also accompanied by increased ethylene evolution (senescence ethylene). One or two ethylene peaks were found to interrupt the low background rate of ethylene evolution during the period between excision and senescence. The first intermediate ethylene peak coincided with a rise in CO(2) evolution; however, precedence could not be established. No statistical correlations were discovered between either intermediate ethylene peak and abscission. The best statistical correlation was found between wound ethylene and abscission at 12 hr after excision. No positive correlations were found between senescence ethylene and abscission. Implications of these results for the understanding of the role of ethylene in explant abscission are discussed.Relationships between a number of different explant treatments and ethylene evolution were also examined. Ethylene production in response to indoleacetic acid applications, abscisic acid applications, and different types of wounding is summarized. It was concluded that the results of the standard abscission bioassay (conducted in Petri dishes) have not been influenced by unnatural ethylene accumulations.

Journal Article↗

PubMed1981

Evolution of Nitrogen Oxide(s) during In Vivo Nitrate Reductase Assay of Soybean Leaves.

Studies were conducted to quantitate the evolution of nitrogen oxides (NO((x))) from soybean [Glycine max (L.) Merr.] leaves during in vivo nitrate reductase (NR) assays with aerobic and anaerobic gas purging. Anaerobic gas purging (N(2) and argon) consistently resulted in greater NO((x)) evolution than did aerobic gas purging (air and O(2)). The evolution of NO((x)) was dependent on gas flow rate and on NO(2) (-) formation in the assay medium; although a threshold level of NO(2) (-) appeared to exist beyond which the rate of NO((x)) evolution did not increase further.The loss of NO((x)) from in vivo NR assays under gas purging explains partially, but not stoichiometrically, the decrease in NO(2) (-) accumulation in in vivo NR assay medium with young soybean leaves. The lack of stoichiometry between NO((x)) evolution and apparent NO(2) (-) loss suggests that other mechanisms are also involved in loss of NO(2) (-) or inhibition of formation of NO(2) (-) during anaerobic and aerobic incubation conditions imposed on the in vivo NR assay of soybean. The mechanism of NO((x)) evolution under the assay conditions imposed and the relevance of this phenomenon to intact plants remains unclear.

Journal Article↗

PubMed1983

Characterization of dicarboxylate stimulation of ammonia, glutamine, and 2-oxoglutarate-dependent o(2) evolution in isolated pea chloroplasts.

Intact isolated chloroplasts from pea (Pisum sativum) leaves carried out light-dependent (NH(3), 2-oxoglutarate) and (glutamine, 2-oxoglutarate)-dependent O(2) evolution at rates of 3.3 +/- 0.7 (n = 7) and 6.0 +/- 0.4 (n = 5) micromoles per milligram chlorophyll per hour, respectively. Malate stimulated the rate of (NH(3), 2-oxoglutarate)-dependent O(2) evolution 2.1 +/- 0.5 (n = 7)-fold in the absence of glutamine, and 3.3 +/- 0.4 (n = 11)-fold in the presence of glutamine. Malate also stimulated (glutamine, 2-oxoglutarate)-dependent O(2) evolution in the presence of high concentrations of glutamine. The affinity (K(1/2)) of (NH(3), glutamine, 2-oxoglutarate)-dependent O(2) evolution for 2-oxoglutarate was estimated at 200 to 250 micromolar in the absence of malate and 50 to 80 micromolar when malate (0.5 millimolar) was present. In contrast to malate and various other dicarboxylates, aspartate, glutarate, and glutamate did not stimulate (NH(3), glutamine, 2-oxoglutarate)-dependent O(2) evolution in isolated pea chloroplasts. Using both in vitro assays and reconstituted chloroplast systems, malate was shown to have no effect on the activities of either glutamine synthetase or glutamate synthase.The concentration of malate required for maximal stimulation of O(2) evolution was dependent on the concentration of 2-oxoglutarate present. However, the small extent of the competition between malate and 2-oxoglutarate for uptake was not consistent with that predicted by the current ;single carrier' model proposed for the uptake of dicarboxylates into chloroplasts.

Journal Article↗

PubMed1984

Inhibition of 3-Phosphoglycerate-Dependent O(2) Evolution by Phosphoenolpyruvate in C(4) Mesophyll Chloroplasts of Digitaria sanguinalis (L.) Scop.

The effects of phosphoenolpyruvate (PEP), inorganic phosphate (Pi), and ATP on 3-phosphoglycerate (PGA)-dependent O(2) evolution by chloroplasts of Digitaria sanguinalis (L.) Scop. (crabgrass) were evaluated relative to possible mechanisms of PEP transport by the C(4) mesophyll chloroplast. Crude and Percoll purified chloroplast preparations exhibited rates of PGA-dependent O(2) evolution in the range of 90 to 135 micromoles O(2) per milligram chlorophyll per hour, and up to 180 micromoles O(2) per milligram chlorophyll per hour at optimal Pi concentrations (approximately 0.2 millimolar at 9 millimolar PGA). Higher concentrations of Pi were inhibitory. PEP inhibited O(2) evolution (up to 70%) in both chloroplast preparations when the PEP to PGA ratio was high (i.e. 9 millimolar PEP to 0.36 millimolar PGA). Usually no inhibition was seen when the PEP to PGA ratio was less than 2. PEP acted as a competitive inhibitor and, at a concentration of 9 millimolar, increased the apparent K(m) (PGA) from 0.15 to 0.53 millimolar in Percoll purified chloroplasts. A low concentration of PGA and high ratio of PEP to PGA, which are considered unphysiological, were required to detect any inhibition of O(2) evolution by PEP. Similar results were obtained from crude versus Percoll purified preparations. Neither the addition of Pi nor ATP could overcome PEP inhibition. As PEP inhibition was competitive with respect to PGA concentration, and as addition of ATP or Pi could not prevent PEP inhibition of PGA-dependent O(2) evolution, the inhibition was not due to PEP exchange of adenylates or Pi out of the chloroplast. Analysis of the effect of Pi and PEP, separately and in combination, on PGA-dependent O(2) evolution suggests interactions between PEP, Pi, and PGA on the same translocator in the C(4) mesophyll chloroplast. C(3) spinach chloroplasts were also found to be sensitive to PEP, but to a lesser extent than crabgrass chloroplasts. The apparent K(i) values (PEP) were 3 and 21 millimolar for crabgrass and spinach, respectively.

Journal Article↗