Structural similarities and evolutionary relationships in chloride-dependent alpha-amylases

The alpha-amylase sequences contained in databanks were screened for the presence of amino acid residues Arg195, Asn298 and Arg/Lys337 forming the chloride-binding site of several specialized alpha-amylases allosterically activated by this anion. This search provides 38 alpha-amylases potentially binding a chloride ion. All belong to animals, including mammals, birds, insects, acari, nematodes, molluscs, crustaceans and are also found in three extremophilic Gram-negative bacteria. An evolutionary distance tree based on complete amino acid sequences was constructed, revealing four distinct clusters of species. On the basis of multiple sequence alignment and homology modeling, invariable structural elements were defined, corresponding to the active site, the substrate binding site, the accessory binding sites, the Ca(2+) and Cl(-) binding sites, a protease-like catalytic triad and disulfide bonds. The sequence variations within functional elements allowed engineering strategies to be proposed, aimed at identifying and modifying the specificity, activity and stability of chloride-dependent alpha-amylases.     

The value of preoperative Doppler sonography for planning free perforator flaps

The individual perforating vessels have a high degree of anatomical variation, therefore it is desirable to conduct a careful examination of them before undertaking a perforator flap operation. Because locating the vessels beforehand makes performing the operative procedure much easier, the aim of the present study was to assess the value of using simple acoustic Doppler sonography to plan a perforator flap operation. The vessel examinations were carried out before taking 46 free microvascular flaps from either the lower abdominal wall or the buttock for reconstructive breast surgery. The perforating vessels located were marked, and their position relative to the umbilicus or the most cranial point of the rima ani recorded using a coordinate system. In 40 patients, a perforator flap operation (deep inferior epigastric perforator flap, n = 32; superior gluteal artery perforator flap, n = 8) was actually carried out; in six of these patients, a myocutaneous flap was used because of the insufficient availability of perforating vessels. Before the operation, perforating vessels were marked for each patient, with an average of 7.3 for the deep inferior epigastric perforator flap and 6.5 for the superior gluteal artery perforator flap. Out of 286 vessels marked for later perforator flaps, 162 were identified during the operation. A preoperatively marked vessel was used in 37 of 40 patients. In the remaining patients, a vessel was used that had not been previously marked. The vertical and horizontal distance between the perforating vessels identified during the operation and the preoperative marks averaged 0.8 cm. The results show preoperative Doppler sonography to be useful for locating the position of individual perforating vessels, making it much easier to find them during the operation.     

Effects of forest age and disturbance on population persistence in the understory herb,Arisaema triphyllum (Araceae)

Long-lived understory herbs experience a highly dynamic forest over space and time, yet can persist for more than a century. To understand how these populations persist, we examined effects of forest age and disturbance on potential sexual reproduction and clonal growth in the sexually labile perennial, Arisaema triphyllum. Potential sexual reproduction (female:male ratio) was significantly greater in the Young and Old-Gap forest states compared with Old, closed-canopy sites, where it was virtually absent. In contrast, clonal growth (estimated by cormlet production) did not differ significantly among the three forest states. Of seven environmental variables measured, only light (positively) and plant density (negatively) contributed significantly to the variation in potential sexual reproduction, while no measured variables contributed significantly to the variation in number of cormlets. The larger sexual reproductive effort (flower+stalk biomass/total biomass) for males in the undisturbed, 100 yr old forest may explain the absence of females in these sites, while the invariant vegetative reproductive effort (cormlet biomass/total biomass) may explain the similarity in average number of cormlets per individual per season across forest states. These results suggest that potential sexual reproduction is resource-limited, while clonal growth may be resource-independent. By maintaining ramet production during unfavorable periods, A. triphyllum populations disperse temporally, waiting for conditions under which sexual reproduction may resume.     

Long-Distance Transport of Alkali Metals in Maturing Wheat

The alkali metals cesium, rubidium, lithium and sodium were introduced together with strontium via flaps into leaf laminas or into the stem of maturing, intact winter wheat (Triticum aestivum L. cv. Arina) grown in a field. Long-distance transport of these elements and the influence of the application date and of different application positions were investigated. The phloem-immobile Sr served as a marker for the distribution of the xylem sap in the plants. Dry matter accumulation in the grains and the transpiration per shoot were not markedly affected by the treatments as compared to control plants. The phloem mobility was rather high for Cs and Rb. Li was almost immobile in the phloem (similarly to Sr). An application into the cut stem xylem below the second leaf node contributed more to the contents in the grains than an application into the flag leaf. An earlier feeding date led to a higher accumulation in the grains. The marked losses of the elements applied during maturation (most pronounced for Li) can be explained by leakage in the rain.     

Cell-penetrating SH3 domain blocker peptides inhibit proliferation of primary blast cells from CML patients.

Bcr-Abl contributes prominently to the development of most chronic myeloid leukemias (CMLs). Prior work has identified the adapter protein CRKL as a major substrate of the Bcr-Abl tyrosine kinase. CRKL can also bind via its first SH3 domain [SH3(1)] to specific sequences in Bcr-Abl. Cell-penetrating peptides were developed that bind with high affinity and selectivity to the SH3(1) domain of CRKL. They disrupt Bcr-Abl-CRKL complexes and strongly reduce the proliferation of primary CML blast cells and cell lines established from Bcr-Abl-positive patients. Activation-specific antibodies against phosphorylated MAP kinase (MAPK) showed that MAPK activity is down-regulated in blast cells treated with the CRKLSH3(1) blocker peptides. We conclude that the Bcr-Abl-CRKL complexes are largely dependent on the CRKLSH3(1) domain, that the central mitogenic cascade is down-regulated as a consequence of the disruption of CRKLSH3(1) interactions, and that CRKL therefore contributes to the proliferation of CML blast cells.     

CO2 efflux from cleared mangrove peat

Background

CO₂ emissions from cleared mangrove areas may be substantial, increasing the costs of continued losses of these ecosystems, particularly in mangroves that have highly organic soils.

Methodology/Principal Findings

We measured CO₂ efflux from mangrove soils that had been cleared for up to 20 years on the islands of Twin Cays, Belize. We also disturbed these cleared peat soils to assess what disturbance of soils after clearing may have on CO₂ efflux. CO₂ efflux from soils declines from time of clearing from ∼10 600 tonnes km⁻² year⁻¹ in the first year to 3000 tonnes km² year⁻¹ after 20 years since clearing. Disturbing peat leads to short term increases in CO₂ efflux (27 umol m⁻² s⁻¹), but this had returned to baseline levels within 2 days.

Conclusions/Significance

Deforesting mangroves that grow on peat soils results in CO₂ emissions that are comparable to rates estimated for peat collapse in other tropical ecosystems. Preventing deforestation presents an opportunity for countries to benefit from carbon payments for preservation of threatened carbon stocks.     

Stepwise adaptations to low temperature as revealed by multiple mutants of psychrophilic α-amylase from Antarctic Bacterium

The mutants Mut5 and Mut5CC from a psychrophilic α-amylase bear representative stabilizing interactions found in the heat-stable porcine pancreatic α-amylase but lacking in the cold-active enzyme from an Antarctic bacterium. From an evolutionary perspective, these mutants can be regarded as structural intermediates between the psychrophilic and the mesophilic enzymes. We found that these engineered interactions improve all the investigated parameters related to protein stability as follows: compactness; kinetically driven stability; thermodynamic stability; resistance toward chemical denaturation, and the kinetics of unfolding/refolding. Concomitantly to this improved stability, both mutants have lost the kinetic optimization to low temperature activity displayed by the parent psychrophilic enzyme. These results provide strong experimental support to the hypothesis assuming that the disappearance of stabilizing interactions in psychrophilic enzymes increases the amplitude of concerted motions required by catalysis and the dynamics of active site residues at low temperature, leading to a higher activity.     

Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125

The psychrophilic model bacterium Pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, of P. haloplanktis strain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacterium P. haloplanktis in its natural environments.