Noise yields order--auxin, actin, and polar patterning

Plant patterns have to integrate environmental cues and to cope with a high level of noise in the sensory outputs of individual cells. In the first part of this review, we demonstrate that local self-amplification linked to lateral inhibition can meet this requirement. In the second part, we describe the search for candidates for such self-amplification loops in the context of auxin-dependent cell growth using Graminean coleoptiles as a model. Auxin-dependent reorganization of actin microfilaments interfered with the auxin sensitivity of growth. Auxin might control the intracellular transport of factors important for auxin sensing via the actomyosin system. By means of a rice mutant with elevated auxin responsiveness, we identified an auxin response factor (OSARF1), whose expression is upregulated by auxin as a second candidate for a self-amplification loop. We studied the cross-talk between auxin signalling and environmental cues in the rice mutant hebiba, where the photoinhibition of growth is impaired. We found that jasmonate plays a central role in this cross-talk correlated to a downregulation of auxin responsiveness. To obtain an insight into auxin-dependent coordination, we analyzed a tobacco cell line with axial cell divisions. By a combination of modelling and physiological manipulation, we could demonstrate that auxin synchronizes the divisions of adjacent cells on the background of strong heterogeneity of individual cells. We conclude that self-amplification of auxin signalling coupled to mutual competition for available auxin provides a versatile tool to fulfill the special requirements posed by patterning in plants.     

Reaction pattern of a novel thermostable α-amylase

A novel thermostable α-amylase, D45 was studied for its reaction pattern on starch hydrolysis. Fine structures of the dextrins and oligosaccharides produced by D45 were determined and compared with those produced by other thermostable α-amylases, Termamyl^®LC (LC) and Termamyl^®SC (SC). Waxy maize starch dispersion was hydrolyzed with LC, SC and D45 at different concentrations to obtain hydrolysates with the same dextrose equivalent value (DE). At DE 13, molecular weight distribution of dextrins produced by D45 displayed a mono-distribution with a peak centered at degree of polymerization (DP) of 7, whereas LC and SC hydrolysates displayed a bimodal-distribution of the molecular weight profiles with one peak centered at DP 5 and the other at DP 34. Thin-layer chromatograms (TLC) showed that DP 2, 3, 5, 6 and 7 were the primary oligosaccharides produced in LC hydrolysate, DP 4–7 in SC hydrolysate, and DP 6–9 in D45 hydrolysate. Comparison of the decrease in the blue color of amylose-iodine complex at 620 nm (blue value) with the increase in reducing value for the hydrolysis of amylose by LC, SC and D45 showed that for an equivalent decrease in blue value, LC and SC produced a higher percentage of reducing sugar than did D45. The results suggest that D45 has a greater degree of random attack (multichain) reaction, whereas LC and SC have more multiple-attack reactions.     

Regulation of ventilation in the caiman (Caiman latirostris): effects of inspired CO2 on pulmonary and upper airway chemoreceptors

In order to study the relative roles of receptors in the upper airways, lungs and systemic circulation in modulating the ventilatory response of caiman (Caiman latirostris) to inhaled CO₂, gas mixtures of varying concentrations of CO₂ were administered to animals breathing through an intact respiratory system, via a tracheal cannula by-passing the upper airways (before and after vagotomy), or via a cannula delivering gas to the upper airways alone. While increasing levels of hypercarbia led to a progressive increase in tidal volume in animals with intact respiratory systems (Series I), breathing frequency did not change until the CO₂ level reached 7%, at which time it decreased. Despite this, at the higher levels of hypercarbia, the net effect was a large and progressive increase in total ventilation. There were no associated changes in heart rate or arterial blood pressure. On return to air, there was an immediate change in breathing pattern; breathing frequency increased above air-breathing values, roughly to the same maximum level regardless of the level of CO₂ the animal had been previously breathing, and tidal volume returned rapidly toward resting (baseline) values. Total ventilation slowly returned to air breathing values. Administration of CO₂ via different routes indicated that inhaled CO₂ acted at both upper airway and pulmonary CO₂-sensitive receptors to modify breathing pattern without inhibiting breathing overall. Our data suggest that in caiman, high levels of inspired CO₂ promote slow, deep breathing. This will decrease dead-space ventilation and may reduce stratification in the saccular portions of the lung.     

Uncovering conserved patterns in bioactive peptides in Metazoa

Bioactive (neuro)peptides play critical roles in regulating most biological processes in animals. Peptides belonging to the same family are characterized by a typical sequence pattern that is conserved among the family's peptide members. Such a conserved pattern or motif usually corresponds to the functionally important part of the biologically active peptide. In this paper, all known bioactive (neuro)peptides annotated in Swiss-Prot and TrEMBL protein databases are collected, and the pattern searching program Pratt is used to search these unaligned peptide sequences for conserved patterns. The obtained patterns are then refined by combining the information on amino acids at important functional sites collected from the literature. All the identified patterns are further tested by scanning them against Swiss-Prot and TrEMBL protein databases. The diagnostic power of each pattern is validated by the fact that any annotated protein from Swiss-Prot and TrEMBL that contains one of the established patterns, is indeed a known (neuro)peptide precursor. We discovered 155 novel peptide patterns in addition to the 56 established ones in the PROSITE database. All the patterns cover 110 peptide families. Fifty-five of these families are not characterized by the PROSITE signatures, and 12 are also not identified by other existing motif databases, such as Pfam and SMART. Using the newly identified peptide signatures as a search tool, we predicted 95 hypothetical proteins as putative peptide precursors.     

Nanosecond pulsed electric field generators for the study of subcellular effects

Modeling and experimental studies have shown that pulsed electric fields of nanosecond duration and megavolt per meter amplitude affect subcellular structures but do not lead to the formation of large pores in the outer membrane. This "intracellular electromanipulation" requires the use of pulse generators which provide extremely high power but low energy pulses. In this study, we describe the concept of the required pulsed power sources, their design, operation, and the necessary diagnostics. Two types of pulse generators based on the Blumlein line principle have been developed and are described here. One system is designed to treat a large number of cells in cuvettes holding volumes from 0.1 to 0.8 ml. Pulses of up to 40 kV amplitude, with a duration of 10 ns and a rise time close to 1 ns can be applied to the cuvette. For an electrode gap of 1 mm this voltage corresponds to an average electric field of 40 MV/m. The second system allows for real time observation of individual cells under a microscope. It generates pulses of 10-300 ns duration with a rise time of 3.5 ns and voltage amplitudes up to 1 kV. Connected to a microreactor with an electrode gap of 100 microm, electric fields up to 10 MV/m are applied.     

A multi-species assessment of post-dispersal seed predation in the central Chilean Andes

BACKGROUND AND AIMS: Post-dispersal seed predation in alpine communities has received little attention despite evidence that seeds removed by granivores can decrease plant recruitment into ecosystems. Moreover, few studies have assessed the effects of removal of seeds of a range of species after dispersal on the seeds remaining in ecosystems. A comparison was made of the magnitude of seed removal by ants and birds of nine different shrubby-, herbaceous- and cushion-plant species in the central Chilean Andes in order to assess the interactions between birds, ants and wind, and the types of seeds. METHODS: A total of 324 soil-covered plates, each containing 50 seeds of one species, were placed in the field at an altitude of 2700 m and assigned to one of four treatments: control, exclusion of ants, birds, and both. The design also allowed the effects of wind to be assessed. Seed removal from plates was monitored over 20 d. KEY RESULTS: Mean accumulative seed removal by granivores averaged over all nine species combined was 25%. However, large differences between species were evident, with limited seed removal (3-11%) in three herbaceous species (Alstroemeria pallida, Sisyrinchium arenarium, Pozoa coriacea), moderate (18-33%) in five species, including a shrub (Chuquiraga oppositifolia), two herbs (Taraxacum officinale, Rhodophiala rhodolirion), and two cushion-plants (Laretia acaulis, Azorella monantha), and substantial (78%) in the shrub Anarthrophyllum cumingii. The magnitudes of losses caused by birds compared with ants did not differ for the majority of species, although removal by birds was greater than by ants in A. cumingii, and smaller for C. oppositifolia. CONCLUSIONS: Post-dispersal seed removal is shown to be an important cause of decreased potential plant species recruitment into alpine ecosystems. The substantial differences in the magnitude of seed losses to ants and birds demonstrate the need for evaluation of seed removal on a wide range of species in any given ecosystem.     

An 'unconditional-like' structure for the conditional estimator of odds ratio from 2 x 2 tables

In the estimation of the odds ratio (OR), the conditional maximum-likelihood estimate (cMLE) is preferred to the more readily computed unconditional one (uMLE). However, the exact cMLE does not have a closed form to help divine it from the uMLE or to understand in what circumstances the difference between the two is appreciable. Here, the cMLE is shown to have the same 'ratio of cross-products' structure as its unconditional counterpart, but with two of the cell frequencies augmented, so as to shrink the unconditional estimator towards unity. The augmentation involves a factor, similar to the finite population correction, derived from the minimum of the marginal totals.     

Respiratory pattern of captive Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis)

Cetacean respiration usually happen in bouts. The most widely applied quantitative method used to analyze the structure of these bouts is the log_e-survivorship analysis, based on the assumption that the respiratory intervals are distributed as negative exponentials. However, for the data collected from three captive Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis), we failed to obtain a convergent result with the application of log_e-survivorship analysis. However, the two-Gaussian model, which was recently proposed to analyze the feeding behavior of cows, was successfully fitted to the data. According to the fitting results, the overall respiratory pattern of the captive Yangtze finless porpoises can be described as a dive with a mean duration of around 30–40 s, followed by two or three ventilations with a mean interval of approximately 9 s. The average intra-bout intervals during both active and inactive periods are constant at 7.7–9.9 s for all individuals. However, when shifting from active to inactive states, the adult male and female decrease their mean numbers of respirations per bout and average length of inter-bout respiratory intervals, while the estimates of both parameters increase for the juvenile female. It was pointed out that the two-Gaussian model might be more adequate for cetacean respiratory-bout structure analyses than the log_e-survivorship technique.     

Cloning of a novel human NHEDC1 (Na+/H+ exchanger like domain containing 1) gene expressed specifically in testis

The Na⁺/H⁺ exchangers (NHEs) catalyze the transport of Na⁺ in exchange for H⁺ across membranes in organisms and are required for numerous physiological processes. Here we report the cloning and characterization of a novel human NHEDC1 (Na⁺/H⁺ exchanger like domain containing 1) gene, which was mapped to human chromosome 4p24. This cDNA is 1859 bp in length, encoding a putative protein of 515 amino acids. The NHEDC1 proteins are highly conserved in mammals including human, mouse, rat, and Macaca fascicularis. One remarkable characteristic of human NHEDC1 gene is that it is exclusively expressed in the testis by RT-PCR analysis. Western blot analysis showed that the molecular weight of NHEDC1 is about 56 KDa. Guangming Ye and Cong Chen contributed equally to this work.     

The flexible evolutionary anchorage-dependent Pardee's restriction point of mammalian cells. How its deregulation may lead to cancer

Living cells oscillate between the two states of quiescence and division that stand poles apart in terms of energy requirements, macromolecular composition and structural organization and in which they fulfill dichotomous activities. Division is a highly dynamic and energy-consuming process that needs be carefully orchestrated to ensure the faithful transmission of the mother genotype to daughter cells. Quiescence is a low-energy state in which a cell may still have to struggle hard to maintain its homeostasis in the face of adversity while waiting sometimes for long periods before finding a propitious niche to reproduce. Thus, the perpetuation of single cells rests upon their ability to elaborate robust quiescent and dividing states. This led yeast and mammalian cells to evolve rigorous Start [L.H. Hartwell, J. Culotti, J. Pringle, B.J. Reid, Genetic control of the cell division cycle in yeast, Science 183 (1974) 46–51] and restriction (R) points [A.B. Pardee, A restriction point for control of normal animal cell proliferation, Proc. Natl. Acad. Sci. U. S. A. 71 (1974) 1286–1290], respectively, that reduce deadly interferences between the two states by enforcing their temporal insulation though still enabling a rapid transition from one to the other upon an unpredictable change in their environment. The constitutive cells of multicelled organisms are extremely sensitive in addition to the nature of their adhering support that fluctuates depending on developmental stage and tissue specificity. Metazoan evolution has entailed, therefore, the need for exceedingly flexible anchorage-dependent R points empowered to assist cells in switching between quiescence and division at various times, places and conditions in the same organism. Programmed cell death may have evolved concurrently in specific contexts unfit for the operation of a stringent R point that increase the risk of deadly interferences between the two states (as it happens notably during development). But, because of their innate flexibility, anchorage-dependent R points have also the ability to readily adjust to a changing structural context so as to give mutated cells a chance to reproduce, thereby encouraging tumor genesis. The Rb and p53 proteins, which are regulated by the two products of the Ink4a-Arf locus [C.J. Sherr, The INK4a/ARF network in tumor suppression, Nat. Rev., Mol. Cell Biol. 2 (2001) 731–737], govern separable though interconnected pathways that cooperate to restrain cyclin D- and cyclin E-dependent kinases from precipitating untimely R point transit. The expression levels of the Ink4a and Arf proteins are especially sensitive to changes in cellular shape and adhesion that entirely remodel at the time when cells shift between quiescence and division. The Arf proteins further display an extremely high translational sensitivity and can activate the p53 pathway to delay R point transit, but, only when released from the nucleolus, ‘an organelle formed by the act of building a ribosome’ [T. Mélèse, Z. Xue, The nucleolus: an organelle formed by the act of building a ribosome, Curr. Opin. Cell Biol. 7 (1995) 319–324]. In this way, the Ink4a/Rb and Arf/p53 pathways emerge as key regulators of anchorage-dependent R point transit in mammalian cells and their deregulation is, indeed, a rule in human cancers. Thus, by selecting the nucleolus to mitigate cell cycle control by the Arf proteins, mammalian cells succeeded in forging a highly flexible R point enabling them to match cell division with a growth rate imposed by factors controlling nucleolar assembling, such as nutrients and adhesion. It is noteworthy that nutrient control of critical size at Start in budding yeast has been shown recently to be governed by a nucleolar protein interaction network [P. Jorgensen, J.L. Nishikawa, B.-J. Breitkreutz, M. Tyers, Systematic identification of pathways that couple cell growth and division in yeast, Science 297 (2002) 395–400].