β-Amino acid residues: Conformational characterization of an N- and C-protected homo-β-(S)-leucine

Summary An N- and C-protected derivative ofhomo-β-leucine, Fmoc-homo-β-(S)-leucine methyl ester, synthesized from the corresponding proteinogenic parent α-amino acid in enantiopure form has been fully characterized in the solid state by X-ray diffraction analysis. The crystal conformation of this new residue indicates and extended conformation for thishomo-β-residue, with the ϕ torsion angle being more constrained than the μ and ψ angles.     

A fundamental form for the differential equation of colonial and organism growth

When total cell number is used as the basic parameter of growth, rational equations which describe colonial and organism growth under varying circumstances have been derived from a single differential form. These equations result from making specific, but reasonable assumptions about two additive factors, ϕ and θ which determine community growth. The first factor (ϕ) is assumed to arise from conditions within the growing cell itself, while the second factor (θ) arises from interactions between the growing cells of the community. If it is further assumed that the cells of a community are homogeneous with respect to density and volume, it has been shown that the mathematical expressions commonly used to describe growth data may be rationally derived from the general form. Clerical assistance in the preparation of these materials was furnished by the personnel of Work Projects Administration, Official Project No. 65-1-08-62, Unit A-8.     

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between ¹³C, ¹⁵N and ¹H chemical shifts and backbone torsion angles ϕ and ψ (Cornilescu et al. J Biomol NMR 13 289–302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted ϕ and ψ angles, equals ±13°. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Contributions to the theory of imitative behavior

The imitation effects in a social group depend both on the size of the group and on the distribution of a certain psychobiological quantity ϕ which measures the tendency of an individual towards a given behavior. The distribution function of ϕ determines the ratio μ of the individuals in the society who adopt a given behavior. When the size of the social group is not too large, the actual distribution of ϕ will deviate from the most probable one, and therefore communities of the same size and having the same parameters may have different values of μ. Approximate equations are developed which give the probability of a given μ for a group of a given size. Possible effects of interactions of communities of different sizes are briefly discussed. A generalization of the theory of imitative behavior to any number of mutually exclusive behaviors is given, and its possible sociological implications are discussed.     

Isolation and characterization of two types of actinophage infectingStreptomyces scabies

Two types of actinophages, ϕS and ϕL, were isolated from soil samples by usingStreptomyces scabies, a potato scab pathogen, as indicator strain. The phages were partially characterized according to their physicochemical properties, plaques and particles morphology, and their host range; this varied from narrow (for ϕS) to wide (for ϕL). The adsorption rate constants of the ϕS and ϕL were 3.44 and 3.18 pL/min, and their burst sizes were 1.61 and 3.75 virions per mL, respectively. One-step growth indicated that ϕS and ϕL have a latent period of 1/2 h followed by a rise period of 1/2 h. The temperate character of these phages was tested in other isolates ofStreptomyces. Four of the phages (ϕSS3, ϕSS12, ϕSS13 and ϕSS17) were identified as temperate phages, since they were able to lysogenize SS3, SS12, SS13 and SS17. ϕSS3, ϕSS12 and ϕSS13 were homoimmune, and they were heteroimmune with respect to ϕSS17. The restriction barriers of lysogenic isolates (SS12, SS13 and SS17) interfered with the blockage of plaque formation by phages (ϕSS12, ϕSS13 or ϕSS17) propagated on them, about 75% of lysogenic isolates had restriction systems. The exposure of the lysogenic isolates (SS12, SS13 and SS17) to UV-irradiation prevented the possible restriction barriers of these isolates so that these barriers could be overcome.     

Thermocouple psychrometer for measurements of water potential in plant tissues by isopiestic method

The paper describes a thermocouple psychrometer for measurements of water potential (ψ_w) and its components—osmotic potential (ψ_{s + m}) and turgor pressure (ψ_p)—in biological objects. The isopiestic method applied in this work does not require preliminary scarification of plant material for eliminating cuticular resistance to diffusion of water vapors. The device is reliable and simple in operation owing to an original design of replaceable plungers carrying the thermocouples. A modified construction of the lid for a thermocouple chamber and the application of a cryoholder excluded the necessity of removing the sample from the chamber after ψ_w measurements prior to its freezing in liquid nitrogen and subsequent thawing for determination of ψ_{s +m}. This feature improves the accuracy of determining ψ_p, which is calculated as ψ_w − ψ_{s + m}. The device can operate with minimal quantities of plant material and allows determination of all three components (ψ_w, ψ_{s + m}, ψ_p) for the same sample.     

Age and Detection of Retroprocessed Pseudogenes in Murine Rodents

Retroprocessed pseudogenes, calmodulin II (ψ₁, ψ₂, and ψ₃ CALMII), ψα-tubulin, π-glutathione S-transferase (ψπ-GST) from rat, lactic acid dehydrogenase (ψ LDH) from mouse, and heat shock protein 60 chaperonin (ψ HSP60) from Chinese hamster, were examined for their presence in these species by polymerase chain reaction (PCR). Pseudogenes of these murine rodents were detected by PCR only in those species in which the genes were originally identified, suggesting that the selected pseudogene of one species arose too recently to be detected in the genomes of the other rodent species. The calculated ages of the rodent pseudogenes ranged from 1.7 Myr (ψα-tubulin) to 7.5 Myr (ψ₃ CALMII) when employing a homologous functional gene of the taxon as a reference in the relative rate test with the mouse or rat as the outgroup. Given the high rate of divergence of the genes of rodents relative to other species, selection of an outgroup with similar mutation rates seems warranted. To justify further the conclusion that the selected pseudogenes were indeed retroprocessed after these three taxa diverged, the presence of the pseudogenes in the genome of different rat species was examined. The existence of ψ₃ CALMII and ψα-tubulin pseudogenes of Rattus norvegicus among species belonging to Rattus sensu stricto is evidence for the common ancestry of this group. Received: 23 May 2001 / Accepted: 31 May 2001     

The occurrence of protein kinase C ϕ and λ isoforms in retina of different species

The localization and immunochemical identification of the novel protein kinase C ϕ (nPKC ϕ) and the atypical protein kinase C λ (aPKC λ) isoforms in retinas of different species were analyzed by immunohistochemistry and SDS-PAGE/Western blotting. nPKC ϕ immunoreactivity is associated with bipolar cells of mammalian (rabbit, rat and guinea pig) retinas but not the non-mammalian goldfish retina which has a lower concentration of nPKC ϕ. However, SDS-PAGE and Western blotting data indicate the antigen recognized by the nPKC ϕ monoclonal antibody in the retina is of a lower molecular weight than that expected for nPKC ϕ. This would suggest nPKC ϕ is more susceptible to degradation/breakdown than other PKC isoforms found in the retina or that the nPKC ϕ antibody may be recognizing an unknown retinal antigen. A comparison of nPKC ϕ and nPKC ϕ is present in the developing retina at an earlier stage than cPKC α. The typical ‘transport’ of cPKC α toward axonal terminals by phorbol-12,13-dibutyrate does not occur for nPKC ϕ yet both are translocated from the cytosolic to membrane compartments. The inner plexiform layer and the inner nuclear layer (putative horizontal cells) of all species examined (rabbit, rat, guinea pig and goldfish) exhibited positive immunoreactivity for aPKC λ as confirmed by SDS-PAGE/Western blotting. Special issue dedicated to Dr. Kinya Kuriyama.     

Molecular and crystal structure of Nα-(9-fluorenyl)- methoxycarbonyl-L-ornithine hydrochloride diethyl ether solvate

Summary The solid-state conformation of the first N-protected ornithine derivative has been established by X-ray analysis. The hydrochloride of N^α-(9-fluorenyl)methoxycarbonyl-l-ornithine crystallises as diethyl ether solvate. The backbone (ω₀ ϕ, ψ χ¹) torsion angles are (174.9°,–84.0°, 145.9°,–171.0°). The conformation of the urethane amide bonds istrans. The ornithine aliphatic side chain adopts preferred fully extended conformation which is stabilised by the hydrogen bonding of the-NH ₃ ⁺ group to the diethyl ether molecule, carboxyl group and Cl⁻ anions.     

Times of measurement optimalization in the investigation of leaf water potential daily course

Using the statistical analysis of leaf wator potential (ψ daily course of forest tree species (Quercus cerris, Acer campestre andCarpinus betulus) we have determined the optimal times of ψ measurement (i.e. at 08.00, 10.00 and 16.00) making possible the calculation of the ψ daily course resp. ψ-value at any time. The accuracy of the calculation does not deviate much from the errors of ψ measurement. The probable error of a single ψ-measurement was forQ. cerris 0.06 MPa and for bothA. campestre andC. betulus it was 0.05 MPa.     

Mathematical biology of social behavior: IV. Imitation effects as a function of distance

In previous publications, social groups have been studied in which each individual has a preference for one of two possible mutually exclusive activities. This preference is measured by a quantity ϕ. The value ϕ=0 corresponds to no preference; a preference for one activity is measured by a positive ϕ, the preference for the other by a negative ϕ. The quantity ϕ varies from individual to individual. It has been shown previously that, owing to effects of imitation, even when the average ϕ for the group is zero, one of the two behaviours will be chosen by the majority of the group. Whereas in previous studies the imitation effect was considered as independent of the distance between the imitating and imitated individuals, in the present study the case is considered in which the effect of imitation decreases with the distance between the individuals. It is found that under certain conditions a greater percentage near the center of the area occupied by the group, rather than near the periphery, exhibits the chosen behavior. The possible sociological meaning of this gradient of behavior is discussed.     

Water potential and gas exchange did not reflect performance of Pinus radiata D. Don in an agroforestry system under conditions of soil-water deficit in a temperate environment

In order to understand how radiata pines respond to declining supply of soil-water in agroforestry systems, we monitored water potential in xylem (ψ _x ), osmotic potential (ψ) and relative water content (q) for fascicles at pre-dawn and at mid-day for 3-year-old trees that were raised from either seedlings (Seedling) or from tissue culture (TC3 and TC4), and grown either alone (Control) or over lucerne (Medicago sativa) pasture (Lucerne). Water relations at dawn were mostly similar for all the pines, except late in the season when ψ was lower, bulk turgor pressure (P), deduced as the difference between ψ _x and ψ, was higher, for TC3 than for the other two pines. At mid-day, Seedling often had higher ψ _x and ψ, but because of its poor osmotic adjustment (OA) had lower P, than either TC3 or TC4. The cell walls were more elastic in Seedling with modulus of elasticity (e) of 6.5 MPa compared with 8.1 MPa for both TC3 and TC4, while loss of turgor was estimated to occur at ψ _x of −1.45 MPa for Seedling, −1.38 MPa for TC3 and −1.35 MPa for TC4. All trees irrespective of their origin had higher ψ _x , P, CO₂ assimilation (A), and stomatal conductance (g _s ), but lower ψ, in Control than in Lucerne in which the soil profile was consistently drier. The trends in ψ _x , ψ, q and A did not reflect the known differences in dry weight of trees, P was in the order TC3 > TC4 > Seedling, consistent with previously reported tree weights. Both TC3 and TC4 had higher P, due to their larger OA, than Seedling, although the latter had higher A. Thus ψ _x and A that are routinely measured may not always adequately explain differences in growth amongst pines; it is advisable that ψ be determined to allow deductions of P be made when using water relations to analyse plant growth.     

The root–soil system of Norway spruce subjected to turning moment: resistance as a function of rotation

The reactions of trees to wind, rockfall, and snow and debris flow depend largely on how strong and deformable their anchorage in the soil is. Here, the resistive turning moment M of the root–soil system as a function of the rotation ϕ at the stem base plays the major role. M(ϕ) describes the behavior of the root–soil system when subject to rotational moment, with the maximum M(ϕ) indicating the anchorage strength M _a of the tree. We assessed M(ϕ) of 66 Norway spruce (Picea abies L. Karst) by pulling them over with a winch. These 45- to 170-year-old trees grew at sites of low and high elevation, with a diameter at breast height DBH = 14–69 cm and a height H = 9–42 m. M(ϕ) displayed a strong nonlinear behavior. M _a was reached at a lower ϕ for large trees than for small trees. Thus overhanging tree weight contributed less to M _a for the large trees. Overturning also occurred at a lower ϕ for the large trees. These observations show that the rotational ductility of the root–soil system is higher for small trees. M _a could be described by four monovariate linear regression equations of tree weight, stem weight, stem volume and DBH ² ·H (0.80 < R ² < 0.95), and ϕ at M _a, ϕ _a, by a power law of DBH²·H (R ² = 0.85). We found significantly higher M _a for the low-elevation spruces than for the high-elevation spruces, which were more shallowly anchored, but no significant difference in ϕ _a. The 66 curves of M(ϕ), normalized (_n) by M _a in M-direction and by ϕ _a in ϕ-direction, yielded one characteristic average curve: . Using and the predictions of M _a and ϕ _a, it is shown that M(ϕ) and the curves associated with M(ϕ) can be predicted with a relative standard error ≤25%. The parameterization of M(ϕ) by tree size and weight is novel and provides useful information for predicting with finite-element computer models how trees will react to natural hazards.     

Macrophages from lupus-prone MRL mice have a conditional signaling abnormality that leads to dysregulated expression of numerous genes

Macrophages (mϕ) from pre-diseased mice of the major murine inbred models of spontaneous autoimmunity (AI), including multiple lupus-prone strains and the type I diabetes-prone NOD (non-obese diabetic) strain, have identical apoptotic target-dependent abnormalities. This characteristic feature of mϕ from AI-prone mice suggests that abnormal signaling events induced within mϕ following their interaction with apoptotic targets may predispose to AI. Such signaling abnormalities would affect predominantly the processing and presentation of self-antigen (i.e., derived from apoptotic targets), while sparing the processing and presentation of foreign antigen (i.e., derived from non-apoptotic sources). Here, we used DNA microarrays to test the hypothesis that mϕ from AI-prone mice (MRL/MpJ [MRL/+] or MRL/MpJ-Tnfrsf6 ^lpr [MRL/lpr]) differentially express multiple genes in comparison to non-AI mϕ (BALB/c), but do so in a largely apoptotic cell-dependent manner. Mϕ were stimulated with lipopolysaccharide, a potent innate stimulus, in the presence or absence of serum (an experimental surrogate for apoptotic targets). In accord with our hypothesis, the number of genes differentially expressed by MRL mϕ was significantly increased in the presence vs. the absence of serum, the apoptotic target surrogate (n = 401 vs. n = 201). Notably, for genes differentially expressed by MRL mϕ in the presence of serum, serum-free culture normalized their expression to a level statistically indistinguishable from that by non-AI mϕ. Comparisons of mϕ from AI-prone NOD and non-AI C57BL/6 mice corroborated these findings. Together, these data support the hypothesis that mϕ from MRL and other AI-prone mice are characterized by a conditional abnormality elicited by serum lipids or apoptotic targets.     

Changes in the water status and rheological characteristics of pea seedling axillary buds during their transitions growth-dormancy-growth in apical dominance

The technique of isopiestic thermocouple psychrometry was used for the analysis of bud transition from dormancy to growth and back in 8-18-day-old pea (Pisum sativum L.) seedlings. We monitored changes in the water (ψ_w) and osmotic (ψ_{s + m}) potentials and also turgor pressure (ψ_p) in dormant buds and threshold turgor (Y) in growing buds, the latter being one of the cell-wall rheological characteristics. Seedling decapitation resulted in a decrease of Y in the bud, which coincided with the start of its outgrowth. The replacement of terminal shoot with exogenous auxin (IAA or NAA) retarded bud outgrowth and maintained the high level of Y, which argues for the auxin control of this parameter. When growth of the first axillary bud was inhibited by the second one, positioned higher and remained on the plant, the beginning of Y increase preceded visible correlative growth suppression; this makes this rheological index an early marker of bud transition from growth to dormancy. The effects of the terminal shoot part and auxin application on the bud osmotic status differed substantially. In fact, bud transition to dormancy in the presence of the terminal shoot, the main or developing from the second axillary bud, was accompanied by the rise in ψ_{s + m}, whereas, in the case of the replacement of the second bud with exogenous auxin, the first bud growth suppression occurred with the decrease in ψ_{s + m}. The low value of the bud ψ_{s + m} is a factor for creating a considerable gradient of the water potential between the stem and bud supporting water transport to the bud, which was much more active than in plants with a terminal shoot. It seems likely that this is the reason for the absence of complete growth suppression observed by us and other researchers even after application of high auxin concentrations. Immediately after seedling decapitation, ψ_{s + m} in the buds reduced; however, this was not the result of trophic metabolite redistribution due to the loss of their active sink because ψ_{s + m} reduced also in experiments with complete isolation of the bud releasing from dormancy in the chamber at 100% humidity. Auxin application to the cut surface of decapitated seedlings did not affect the ψ_{s + m} decrease. Like decapitation, cotyledon removal resulted in the increase in the bud turgor pressure. However, in this case, water stress did not change the bud osmotic status. Thus, the induction of osmotica accumulation in the bud after the removal of the terminal shoot is evidently related to neither trophic, nor auxin, nor hydraulic signal. The data obtained allowed us to conclude that both components of the bud water potential—ψ_{s + m} and Y—play an important role in the control of bud growth at apical dominance. Auxin produced in the shoot apex is involved in the control of Y, whereas the nature of the signal controlling the ψ_{s + m} level is unclear.     

Novel mitochondrial alcohol metabolizing enzymes of <Emphasis Type="Italic">Euglena gracilis</Emphasis>

Ethanol is one of the most efficient carbon sources for Euglena gracilis. Thus, an in-depth investigation of the distribution of ethanol metabolizing enzymes in this organism was conducted. Cellular fractionation indicated localization of the ethanol metabolizing enzymes in both cytosol and mitochondria. Isolated mitochondria were able to generate a transmembrane electrical gradient (Δψ) after the addition of ethanol. However, upon the addition of acetaldehyde no Δψ was formed. Furthermore, acetaldehyde collapsed Δψ generated by ethanol or malate but not by D-lactate. Pyrazole, a specific inhibitor of alcohol dehydrogenase (ADH), abolished the effect of acetaldehyde on Δψ, suggesting that the mitochondrial ADH, by actively consuming NADH to reduce acetaldehyde to ethanol, was able to collapse Δψ. When mitochondria were fractionated, 27% and 60% of ADH and aldehyde dehydrogenase (ALDH) activities were found in the inner membrane fraction. ADH activity showed two kinetic components, suggesting the presence of two isozymes in the membrane fraction, while ALDH kinetics was monotonic. The ADH Km values were 0.64–6.5 mM for ethanol, and 0.16–0.88 mM for NAD⁺, while the ALDH Km values were 1.7–5.3 μM for acetaldehyde and 33–47 μM for NAD⁺. These novel enzymes were also able to use aliphatic substrates of different chain length and could be involved in the metabolism of fatty alcohol and aldehydes released from wax esters stored by this microorganism.     

Site-specific integration of transgene targeting an endogenous <Emphasis Type="Italic">lox-</Emphasis>like site in early mouse embryos

Functional lox-like sequences have been identified within the yeast and mammalian genome. These hetero-specific lox sites also allow Cre recombinase to specifically target efficient integration of exogenous DNA into the endogenous pseudo-lox (ψlox) sequences that occur naturally in the host genome using a Cre/loxP integrative recombination system. We investigated whether the Cre/ψlox system is useful for site-specific integration of transgenes and for improving the production efficiency of transgenic animals. This is the first report on Cre-mediated integrative recombination targeting an endogenous lox-like sequence termed pseudo-loxm5 (ψloxm5) in early mouse embryos. We characterized the Cre/ψloxm5 system in embryonic environment. Cre-expressing plasmid and a transgene (CMV/LacZ gene) flanked by ψloxm5 and ψloxcorem5 sites were co-microinjected into the pronucleus of fertilized mouse oocytes. The injected eggs were transferred into foster mothers, and the recombination products were investigated. The results show that the ψloxm5 site is an active substrate for Cre-mediated recombination in the mouse embryonic environment. The transgenesis efficiency was up to 27% (6/22). The site-specific integration of the transgene into the endogenous ψloxm5 site was found in 50 % of the transgenic pups. Our findings demonstrated that the Cre/ψloxm5 integrative recombination system is an efficient and simple strategy for targeting an endogenous lox-like site in mammalian embryos.     

Drought Stress Response on Some Key Enzymes of Cowpea (<Emphasis Type="Italic">Vigna unguiculata</Emphasis> L. Walp.) Nodule Metabolism

A greenhouse experiment was carried out aiming to evaluate the response to drought stress of cowpea nodule enzymatic activities during different plant developmental stages leading to biological N₂ fixation. Stress was applied by controlling soil’s water-potential through a porous cup. Cowpea plants cv IPA 205 were grown in pots with yellow latosol soil under three different matric potential (ψ_m) treatments. Even with high evaporative demand and limited soil water availability, cowpea could not induce an extremely low leaf water potential (ψ_w). Sap ureides concentration in cowpea declined during the drought stress period. There was a decline in enzyme activity in the metabolic pathways concerned with N₂ fixation: NADH-dependent glutamate synthase (EC 1.4.1.14), glutamine synthetase (EC 6.3.1.2) and phosphoenolpyruvate carboxylase (EC 4.1.1.31). In contrast, an increase in glutamate dehydrogenase (EC 1.4.1.4) was observed as the ψ_m declined. Metabolism associated with N₂ assimilation was impaired every time that the ψ_w was reduced below −0.73 MPa as had happened in the stressed treatments. The stress applied by the porous cup was gradual and the plant recovered its turgor, avoiding permanent deleterious alterations in the cellular metabolism, even from a limited cowpea-growth ψ_m.     

A novel structural motif and structural trees for proteins containing it

In the present study, a novel structural motif that can be represented as a combination of the known βαβ-unit and ψ-motif is described and analyzed. In theory, there are four possible combinations of the motifs since each of them can exist in two forms, left-handed and right-handed. For this study, we have selected 140 nonhomologous proteins in which 158 combinations of such types have been found. The combination of the right-handed ψ-motif and the right-handed βαβ-unit has been shown to occur most often (87 cases out of 158) and the combination of the left-handed βαβ-unit and the left-handed ψ-motif does not occur at all. Three novel structural trees in which the commonly occurring combinations are taken as the root structures have been constructed.     

Silk moth chorion pseudogenes: Hallmarks of genomic evolution by sequence duplication and gene conversion

The part of the genetic locus of the domesticated silk moth,Bombyx mori, in which high cysteine (Hc) chorion genes of late developmental specificity reside contains regions encompassing genelike sequences which exhibit properties distinct from those of functional Hc genes. One of these regions has been characterized and shown to contain a chorion pseudogene, ψHcB.15, which shares pronounced similarities with a transcribed chorion pseudogene, ψHcB.12/13, which was characterized previously. Both pseudogenes are homologous to HcB chorion genes but bear multiple single nucleotide substitutions and short segmental mutations (insertions and deletions) which introduce translational frame shifts and termination codons in the coding regions. Structural characteristics unique to the two pseudogenes suggest that ψHcB.15 was generated first from a functional HcB gene and gave rise subsequently to ψHcB 12/13 as a result of a sequence duplication event. The two pseudogenes can be distinguished from each other by the presence of distinct regions of similarity to the consensus sequence of functional HcB genes which appear to have arisen from gene-conversionmediated correctional events. These findings lend support to the hypothesis that chorion pseudogene sequences represent reservoirs of genetic information that participates in the evolution of the chorion locus rather than relics of inactivated genes passively awaiting extinction. Presented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992