Why are both ends of the polypeptide chain on the outside of proteins?

Protein folding starts before the whole polypeptide has been synthesized by the ribosome. No matter how long the polypeptide is or how intricate the fold, both ends of the chain always end up on the surface. From a topological point of view, this is surprising; one would have expected to find the starting (N-terminal) end inside the core of the folded protein, just as in a ball of yarn. We suggest here that the reason for this apparent paradox is that the first amino acid of the emerging polypeptide chain is gripped during protein synthesis, perhaps by the ribosome, and is not released until the whole polypeptide has been synthesized. This binding would greatly decrease the degrees of freedom for the protein-folding process and could also explain why knots are so rare in proteins. Gripping would also guarantee that the N-terminal is accessible on the protein surface as required for binding of ubiquitin, which regulates the natural degradation of proteins and avoids buildup of protein aggregates, such as those found in Huntington's, Alzheimer's, Parkinson's, and other neurodegenerative diseases.     

Why are Nitrogen Concentrations in Plant Tissues Lower under Elevated CO2? A Critical Examination of the Hypotheses

Plants grown under elevated atmospheric [CO2] typically have decreased tissue concentrations of N compared with plants grown under current ambient [CO2]. The physiological mechanisms responsible for this phenomenon have not been definitely established, although a considerable number of hypotheses have been advanced to account for it. In this review we discuss and critically evaluate these hypotheses. One contributing factor to the decreases in tissue N concentrations clearly is dilution of N by increased photosynthetic assimilation of C. In addition, studies on intact plants show strong evidence for a general decrease in the specific uptake rates (uptake per unit mass or length of root) of N by roots under elevated CO2. This decreased root uptake appears likely to be the result both of decreased N demand by shoots and of decreased ability of the soil-root system to supply N. The best-supported mechanism for decreased N supply is a decrease in transpiration-driven mass flow of N in soils due to decreased stomatal conductance at elevated CO2, although some evidence suggests that altered root system architecture may also play a role. There is also limited evidence suggesting that under elevated CO2, plants may exhibit increased rates of N loss through volatilization and/or root exudation, further contributing to lowering tissue N concentrations.     

Does the Gradualness of Leaf Shedding Govern Nutrient Resorption from Senescing Leaves in Mediterranean Woody Plants?

To reveal the environmental and substrate quality effects on decomposition process and enzyme activities, litterbag experiments containing Nuphar and Carex leaves, Nuphar rhizome, and Ranunculus shoot, were carried in five-subalpine marshes in Lake Tahoe basin, USA. Alkaline phosphatase, β-glucosidase, and β-xylosidase activities were determined by a fluorogenic method using methyumbelliferyl substrates. Carex leaves, Nuphar rhizome and leaves, and Ranunculus shoots lost, respectively, 33, 67, 82 and 93% of original dry weight over 268 days. Decay rates were different among substrates but not among marshes. Nitrogen and carbon contents increased during the first 58 days and subsequently remained stable. Phosphorus content was stable during the experimental period except for a decrease in the first 16 days in Nuphar shoots. Enzyme activities in decomposing Carex and Nuphar leaves in four marshes were not significantly affected by environmental conditions. β-glucosidase and β-xylosidase activities in decomposing Carex leaves increased with time, but in other plant tissue these enzyme activities remained stable during experimental period. Enzyme activities were significantly different among decomposing substrates. Alkaline phosphatase activity was highest in Nuphar leaves (ca. 1286 μ-mole h⁻¹ g DW −1) but lower and similar in other plant tissues (ca. 100 and 10 μ-mole h −1 g DW −1, respectively). This study showed differences in decay rates and enzyme activities rely on substrate and not the environment conditions of the study area. Decomposition rates in the early stage of decomposition were related to cumulative enzyme activities.     

Why are there about 5000 species of phytoplankton in the sea?

The relative abundances of phytoplankton taxa conform approximatelyto a finite geometric series in which there are 20–25species per decade of ranked abundance. Such series can contain160–400 species between the commonest (10²²–10²⁶cells) and the rarest (10¹⁰–10¹⁴ cells). Thus, between12 and 31 such series are needed to explain the observed diversity,5x10³ species, of marine phytoplankton. The number of seriesis similar to the number (20–25) of upper-ocean watermasses defined by dilution time scale of order 10¹–10²years. Interpretations of this coincidence are discussed.     

Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria

Identifying the traits that determine spatial distributions can be challenging when studying organisms, like bacteria, for which phenotypic information is limited or non‐existent. However, genomic data provide another means to infer traits and determine the ecological attributes that account for differences in distributions. We determined the spatial distributions of ~124 000 soil bacterial taxa across a 3.41 km² area to determine whether we could use phylogeny and/or genomic traits to explain differences in habitat breadth. We found that occupancy was strongly correlated with environmental range; taxa that were more ubiquitous were found across a broader range of soil conditions. Across the ~500 taxa for which genomic information was available, genomic traits were more useful than phylogeny alone in explaining the variation in habitat breadth; bacteria with larger genomes and more metabolic versatility were more likely to have larger environmental and geographical distributions. Just as trait‐based approaches have proven to be so useful for understanding the distributions of animals and plants, we demonstrate that we can use genomic information to infer microbial traits that are difficult to measure directly and build trait‐based predictions of the biogeographical patterns exhibited by microbes.     

Carbon of Chaillu forests based on a phytosociological analysis in Republic of Congo,more than meets the eye?

The objectives were to quantify aboveground, belowground and dead wood carbon pools near Mayoko in the Chaillu massif of Republic of Congo and explore relationships between carbon storage and plant diversity of all growth forms. A total of 190 plots (25 m by 25 m) were sampled (5072 stems, 211 species) and data analysed using recommended central-African forest allometric equations. Mean stem diameter at breast height was 33.6 cm, mean basal area 47.7 m² ha⁻¹ and mean density of individuals 407 ha⁻¹. Mean aboveground carbon (AGC) ranged from 13.93–412.66 Mg C ha⁻¹, belowground carbon from 2.86–96.97 Mg C ha⁻¹ and dead wood from 0.00–7.59 Mg C ha⁻¹. The maximum AGC value recorded in a plot was 916 Mg C ha⁻¹. The analysis performed using phytosociological association as basis rather than broad vegetation type is unique. AGC values for undisturbed terra firme forest sites featured among the highest recorded for African tropical forests. Considering only tree diversity, a weak, yet significant, relationship existed between AGC and species richness, Shannon-Wiener index of diversity and Fisher's alpha. However, if diversity of all plant growth forms is considered, no relationship between carbon and plant diversity existed.     

Why are flowers sweeter than fruits or buds? Variation in extrafloral nectar secretion throughout the floral ontogeny of a myrmecophile

Extrafloral nectar provision during floral ontogeny in ant‐plants has not been widely studied. Extrafloral nectar secretion differed between leaves associated with buds, flowers, and fruits, and peaked during anthesis when pollinators were present. This ontogenetic variation may result from mixed selective pressures involving strategies for defense and mutualist management.     

Testing 'Economy in Design' in Plants: are the Petioles and Rachises of Leaves 'Designed' According to the Principle of Uniform Strength?

Fifteen petioles and rachises from three dicotyledon species(Acer saccharum, A. negundo, and Aesculus hippocastanum), apalm (Chamaedorea erumpens), and a fern (Cyrtomium falcatum)were used to test the hypothesis of 'economy in design' in termsof the design principle of uniform strength, i.e. a beam inwhich the section modulus (Z) varies along beam-length (L) inthe same proportion as the bending moment (M). Such a beam is'economical' regarding the amount of material used in its 'construction'because each of its cross section has the minimum transversearea required to satisfy the conditions of strength. The extentto which the morphology of a petiole or rachis conformed withthis design principle was initially evaluated by normalizingZ (measured at a distance, x, from the tip of a petiole or rachis)with respect to the magnitude of Z measured at the base of thepetiole. The normalized values were plotted against normalizedpetiole-rachis length (x/L). The design principle was judgedto be demonstrated when such a plot was found to be isometric,i.e. when the plot had a slope of unity. This procedure wastested further by plotting M/Z vs. x/L for representative leavesof C. erumpens and A. saccharum, and judged adequate. The allometriesof all six simple/palmate leaves were found not agree with thedesign principle. The taperings of nine petioles and rachisesfrom pinnate leaves were consistent with the design principle.This was interpreted to provide circumstantial evidence for'economy in design' in the petioles of some pinnate leaves andevidence that the mechanical 'design' of the petioles of somesimple/palmate leaves differs substantially from that of pinnateleaves.Copyright 1993, 1999 Academic Press Leaf biomechanics, plant adaptation, petioles, rachises     

Role of PGF2α in luteolysis based on inhibition of PGF2α synthesis in the mare

The effects of inhibition of PGF2α synthesis on luteolysis in mares and on the incidence of prolonged luteal activity were studied in controls and in a group treated with flunixin meglumine (FM), a PGF2α inhibitor (n = 6/group). The FM was given every 8 hours (1.0 mg/kg) on each of Days 14.0 to 16.7. Concentration (pg/mL) of PGF2α metabolite averaged over 8 hours of hourly blood sampling at the beginning of each day, was lower in the FM group than in the controls on Day 14 after ovulation (6.7 ± 1.3 vs. 13.8 ± 2.9, P < 0.05), Day 15 (15.0 ± 3.9 vs. 35.2 ± 10.4, P < 0.10), and Day 16 (21.9 ± 5.7 vs. 54.7 ± 11.4, P < 0.03). Concentration (ng/mL) of progesterone (P4) was greater in the FM group than in the controls on Day 14 (10.1 ± 0.9 vs. 7.7 ± 0.9, P < 0.08), Day 15 (9.2 ± 1.0 vs. 4.3 ± 1.0, P < 0.008), and Day 16 (5.6 ± 1.6 vs. 1.2 ± 0.4, P < 0.02). The interval from ovulation to the beginning of a decrease in P4 and to the end of luteolysis (P4 < 1 ng/mL) was each delayed (P < 0.03) by ∼1 day in the FM group. Intervals involving the luteal phase were long (statistical outliers, P < 0.05) in two mares in the FM group, indicating prolonged luteal activity. Results supported the hypotheses that (1) inhibition of PGF2α synthesis interferes with luteolysis in mares and (2) inhibition of PGF2α at the expected time of luteolysis may lead to prolonged luteal activity.     

C4 photosynthetic carbon metabolism in the leaves of aromatic tropical grasses — I. Leaf anatomy,CO2 compensation point and CO2 assimilation

A few species of Cymbopogon and Vetiveria are potentially important tropical grasses producing essential oils. In the present study, we report on the leaf anatomy and photosynthetic carbon assimilation in five species of Cymbopogon and Vetiveria zizanioides. Kranz-type leaf anatomy with a centrifugal distribution of chloroplasts and exclusive localization of starch in the bundle sheath cells were common among the test plants. Besides the Kranz leaf anatomy, these grasses displayed other typical C₄ characteristics including a low (0–5 µl/l) CO₂ compensation point, lack of light saturation of CO₂ uptake at high photon flux densities, high temperature (35°C) optimum of net photosynthesis, high rates of net photosynthesis (55–67 mg CO₂ dm^-2 leaf area h^-1), little or no response of net photosynthesis to atmospheric levels of O₂ and high leaf ¹³C/¹²C ratios. The biochemical studies with ¹⁴CO₂ indicated that the leaves of the above plant species synthesize predominantly malate during short term (5 s) photosynthesis. In pulse-chase experiments it was shown that the synthesis of 3-phosphoglycerate proceeds at the expense of malate, the major first formed product of photosynthesis in these plant species.     

Why are hairy root clusters so abundant in the most nutrient-impoverished soils of Australia?

Rootlets, covered in long root hairs, are aggregated into distinct clusters in many groups of Australian plants. They are almost universal in the family Proteaceae, and some members of the Papilionaceae, Mimosaceae, Casuarinaceae, Cyperaceae, Restionaceae and Dasypogonaceae. These families have their centres of distribution in the oldest, most leached sands and laterites of the continent. Root clusters are almost confined to the uppermost 100 mm of the soil profile, often penetrating into the raw litter. These horizons are the major sources of mineral nutrients which are mobilized when these soils become moist. I argue that root clusters are an ideal solution for maximizing nutrient uptake in extremely impoverished soils, especially in seasonal climates.     

CO2 enrichment in a maturing pine forest: are CO2 exchange and water status in the canopy affected?

A _net, leaf net CO₂ assimilation
c_a, CO₂ concentration of air surrounding a leaf
c_i, leaf intercellular CO₂ concentration
Δ, ¹³C isotope discrimination
δ¹³C, relative stable carbon isotope content
?, ratio of A_net at c_a = 560μmol mol^–1 to A_net at c_a = 360 μmol mol^–1
FACE, free-air CO₂ enrichment
g_w, stomatal conductance to water vapour
Π_i, initial leaf osmotic potential
R_t, relative water content at incipient turgor loss
Ψ_l, xylem water potential of leaves
Ψ_m, soil matric potential

Elevated CO₂ is expected to reduce forest water use as a result of CO₂-induced stomatal closure, which has implications for ecosystem-scale phenomena controlled by water availability. Leaf-level CO₂ and H₂O exchange responses and plant and soil water relations were examined in a maturing loblolly pine (Pinus taeda L.) stand in a free-air CO₂ enrichment (FACE) experiment in North Carolina, USA to test if these parameters were affected by elevated CO₂. Current-year foliage in the canopy was continuously exposed to elevated CO₂ (ambient CO₂+200μmol mol^–1) in free-air during needle growth and development for up to 400 d. Photosynthesis in upper canopy foliage was stimulated by 50–60% by elevated CO₂ compared with ambient controls. This enhancement was similar in current-year, ambient-grown foliage temporarily measured at elevated CO₂ compared with long-term elevated CO₂ grown foliage. Significant photosynthetic enhancement by CO₂ was maintained over a range of conditions except during peak drought. There was no evidence of water savings in elevated CO₂ plots in FACE compared to ambient plots under drought and non-drought conditions. This was supported by evidence from three independent measures. First, stomatal conductance was not significantly different in elevated CO₂ versus ambient trees of P. taeda. Calculations of time-integrated c_i/c_a ratios from analysis of foliar δ¹³C showed that these ratios were maintained in foliage under elevated CO₂. Second, soil moisture was not significantly different between ambient and elevated CO₂ plots during drought. Third, pre-dawn and mid-day leaf water potentials were also unaffected by the seasonal CO₂ exposure, as were tissue osmotic potentials and turgor loss points. Together the results strongly support the hypothesis that maturing P. taeda trees have low stomatal responsiveness to elevated CO₂. Elevated CO₂ effects on water relations in loblolly pine-dominated forest ecosystems may be absent or small apart from those mediated by leaf area. Large photosynthetic enhancements in the upper canopy of P. taeda by elevated CO₂ indicate that this maturing forest may have a large carbon sequestration capacity with limiting water supply.     

More than the mean—A note on heterogeneity aspects in the assessment of water footprints

Water footprints for a crop produced in a specific country are often provided as mean values. However, mean values do not account for the spatial heterogeneity of water footprints within a country that is caused by heterogeneous climate conditions and production techniques. To sufficiently inform decision makers, the underlying heterogeneity should thus also be presented. We provide an illustrate example of seed cotton production in 19 regions in Brazil and China. Even though grey water footprints in Brazil are on average smaller, it also contains the highest possible grey water footprint across all regions. To avoid misleading inference on water footprint estimates, their spatial heterogeneity should be indicated. This will enable decision makers to consider trade-offs between average values and potential extremes.     

Why is the number of days required for induction of adult diapause in the linden bug Pyrrhocoris apterus fewer in the larval than in the adult stage?

Adult females of Pyrrhocoris apterus, programmed for diapause by short-day (SD) photoperiod and those programmed for reproduction by long-day (LD) retain photoperiodic information in continuous darkness (DD) until death. However, if the interruption of SD by DD is made in the course of diapause programming in adults, then the incidence of diapause depends on the number of SD cycles received before DD, with no evidence that the photoperiodic clock is free-running at DD to complete diapause induction. These results indicate that the photoperiodic clock is stopped after transfer to DD and the information accumulated before transfer to DD is maintained. Diapause programming in the adult stage requires 9–10 SD cycles to induce diapause in 80% of individuals. However, if the diapause programming starts after ecdysis of LD-larvae to the last instar, only 3 SD cycles before transfer to DD are required for diapause in 80% of individuals. Surprisingly, if the newly ecdysed last instar LD-larvae, sensitive to photoperiod, are transferred to DD (thus they did not experience any SD), diapause occurs in 40% of the individuals. Thus, diapause ‘information’ is present in LD-larvae and is responsible for a lower number of SD required for diapause induction in the larval than in the adult stage.     

Why is the force-velocity relationship in leg press tasks quasi-linear rather than hyperbolic?

Force-velocity relationships reported in the literature for functional tasks involving a combination of joint rotations tend to be quasi-linear. The purpose of this study was to explain why they are not hyperbolic, like Hill's relationship. For this purpose, a leg press task was simulated with a musculoskeletal model of the human leg, which had stimulation of knee extensor muscles as only independent input. In the task the ankles moved linearly, away from the hips, against an imposed external force that was reduced over contractions from 95 to 5% of the maximum isometric value. Contractions started at 70% of leg length, and force and velocity values were extracted when 80% of leg length was reached. It was shown that the relationship between leg extension velocity and external force was quasi-linear, while the relationship between leg extension velocity and muscle force was hyperbolic. The discrepancy was explained by the fact that segmental dynamics canceled more and more of the muscle force as the external force was further reduced and velocity became higher. External power output peaked when the imposed external force was ～50% of maximum, while muscle power output peaked when the imposed force was only ～15% of maximum; in the latter case ～70% of muscle power was buffered by the leg segments. According to the results of this study, there is no need to appeal to neural mechanisms to explain why, in leg press tasks, the force-velocity relationship is quasi-linear rather than hyperbolic.     

Why are cyclodisilazane rings more stable than cyclodisiloxanes? A qualitative molecular orbital approach to the bonding in cyclodisilazanes and cyclodisiloxanes

The approximate molecular orbitals of cyclic Si₂E₂ (E=nitrogen or oxygen) rings are discussed. It is shown that, due to high silicon 3p_z orbital contribution to the siloxane HOMO, the 3d orbitals can not strenghten the silicon-oxygen bond. In contrast, in the silazane ring considerable Si(3d_π)N(2pπ) bonding may occur. These additional π bonds are responsible for the relative stability of cyclodisilazane rings as compared with the isoelectronic cyclodisiloxane rings.     

Why are literature data for H2O2 contents so variable? A discussion of potential difficulties in the quantitative assay of leaf extracts

Leaf metabolism produces H₂O₂ at high rates, but current conceptssuggest that the potent signalling effects of this oxidant requirethat concentrations be controlled by a battery of antioxidativeenzymes. The extent to which H₂O₂ is allowed to accumulate remainsunclear. There is little consensus on leaf H₂O₂ values in theliterature and measured concentrations in unstressed conditionsrange from 50–5000 nmol g^–1 fresh weight, a differencethat probably reflects technical inaccuracies as much as biologicalvariability. This article uses new experimental and literaturedata to examine some of the difficulties in accurately measuringH₂O₂ in leaf extracts. Potential problems relate to sensitivity,interference from other redox-active compounds, and H₂O₂ stabilityduring sample preparation. Particular attention is drawn tothe influence of tissue mass/extraction volume in the quantitativeestimation of H₂O₂ contents, and the possibility that this factorcould contribute to the variability of literature data. Key words: Ascorbate, chemiluminescence, oxidative stress, redox signalling, xylenol orange Received 4 June 2007; Revised 18 June 2007 Accepted 23 June 2007