Trophic structure and species diversity

Equations derived from a contact pressure model of phyllotaxis are relevant to close packing of equal spheres on a cylindrical surface. They provide a general method of calculating the parameters for microscopic biological structures that are assembled in helical arrangements of protein monomers. In the triple-contact case of hexagonal packing, with km, kn and k(m+n) contact parastichies respectively, where m and n are relatively prime, the divergence angle d and the normalized internode distance r on the k fundamental spirals are completely determined by m, n and k, and formulas are given for calculating them. In the double-contact case of rhombic packing, with km and kn contact parastichies respectively, where m < n, d is a function of r, and the domain of r is the interval between the value of r determined for the triple-contact case of km, kn and k(m+n) parastichies and the value of r determined for the triple-contact case of k(n-m), km and kn parastichies. Here r and d can be determined from the measured ratio of the radius of the cylindrical surface to the radius of the spheres.     

CELLULAR BASIS FOR GROWTH AND TISSUE DIFFERENTIATION PATTERNS IN LINUM USITATISSIMUM (LINACEAE) STEMS: THE STEM UNIT

The stem unit is defined as the smallest portion of a stem that can duplicate the stem in toto through regular rotations and dilations over successive plastochrons. In stems exhibiting k(m, n) contact parastichy phyllotaxis, the stem unit is delimited vertically and tangentially by the boundaries of four successive leaf primordia along the m-, n-, and (m + n)- parastichies and radially by these boundaries extended to the centroid of the stem. With the stem unit concept, node refers only to the region of actual leaf insertion, rather than the entire transverse level of insertion. Many of the conflicting and complicating aspects of the traditional node-intemode subdivisions of stems are demonstrated, and the utility of the stem unit in circumventing these is illustrated. The stem unit is proposed as a more useful analytic subunit of the stem with which to examine stem growth and tissue differentiation processes than the more traditional node-intemode subdivisions of stems.     

A comparison of acylation, phosphorylation and binding in related substrates and inhibitors of serum cholinesterase

1. The K_m and catalytic-centre activities for human serum cholinesterase and methyl, ethyl, n-propyl and n-butyl butyrate substrates were determined and compared with the related inhibition constants of a similarly substituted organophosphate inhibitor series based on malaoxon. The results indicated that the catalytic-centre activities approximated to k_+2(a), the acylation rate constant, and that K_m approximated to the equilibrium binding constant. The inhibition constants measured were K_a, the equilibrium binding constant, and k_+2(p), the phosphorylation rate constant. 2. The effects of the alkyl substituents on k_+2(p) and k_+2(a) were closely parallel, and the decreasing order in each case was: n-butyl; methyl; n-propyl; ethyl. The Taft constants did not follow this order, suggesting that alkyl substituents did not primarily effect acylation or phosphorylation by electron induction. 3. For comparable homologues, the k_+2(a) values were on average 435 times the k_+2(p) values. The k_+2(p) values at 25° and pH7·6 ranged from 6·6min.⁻¹ for the diethyl member to 22·6min.⁻¹ for the di-n-butyl member. 4. The effect of the alkyl substituents on K_a and K_m were closely paralleled. The increasing order in each case was: n-butyl; n-propyl; ethyl; methyl. The K_a values were about 100 times less than the comparable K_m values. 5. Consideration of the binding energies suggested that only one of the two alkyl groups on the malaoxon homologues bound to the active site. 6. The possibility that malaoxon acted as a substrate as well as an inhibitor for cholinesterase was also investigated, but no evidence of a substrate reaction was found.     

Raman spectra and conformations of n-hexadecynoic fatty acids and their potassium salts

Raman spectra of n-hexadecynoic fatty acids, CH₃(CH₂)_m?2C  C(CH₂)_n?2COOH (with n = 4, 6, 7, 8 and 12, m + n = 16) and their potassium salts were recorded and assigned. The skeletal optical mode (SOM) regions were analysed on using the dispersion curve of the ν₄ (stretch) vibrations of saturated fatty acids. The localised vibrations of the carboxyl- and methyl-terminated sections of the hydrocarbon chains were assigned to the phase differences δ = kπ/m and kπ/n (k = 1, 2, …), respectively. Evidence for a ν₄ vibration with δ = π/2m was found. The materials were found to be resistant to chemical decomposition under laser illumination.     

The reversibility of adenosine triphosphate cleavage by myosin

For the simplest kinetic model the reverse rate constants (k₋₁ and k₋₂) associated with ATP binding and cleavage on purified heavy meromyosin and heavy meromyosin subfragment 1 from rabbit skeletal muscle in the presence of 5mm-MgCl₂, 50mm-KCl and 20mm-Tris–HCl buffer at pH8.0 and 22°C are: k₋₁<0.02s⁻¹ and k₋₁=16s⁻¹. Apparently, higher values of k₋₁ and k₋₂ are found with less-purified protein preparations. The values of k₋₁ and k₋₂ satisfy conditions required by previous ¹⁸O-incorporation studies of H₂¹⁸O into the P_i moiety on ATP hydrolysis and suggest that the cleavage step does involve hydrolysis of ATP or formation of an adduct between ATP and water. The equilibrium constant for the cleavage step at the myosin active site is 9. If the cycle of events during muscle contraction is described by the model proposed by Lymn & Taylor (1971), the fact that there is only a small negative standard free-energy change for the cleavage step is advantageous for efficient chemical to mechanical energy exchange during muscle contraction.     

Biodegradable Nasal Packings for Endoscopic Sinonasal Surgery: A Systematic Review and Meta-Analysis

Objectives

To assess biodegradable nasal packing effectiveness for improving postoperative symptoms and mucosal healing after endoscopic sinonasal surgery as compared with conventional/non-packing groups.

Methods

Relevant articles were searched on PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials. We included randomized controlled trials (RCTs) that compared biodegradable packings with conventional packings or no packing, reporting postoperative symptoms and/or mucosal healing outcomes.

Results

This review included 19 studies, of which 11 compared biodegradable packings with conventional packings. Meta-analysis found that biodegradable packings significantly improved postoperative symptoms: bleeding at removal, pain at removal, pain in situ, and nasal blockage. Mucosal healing outcomes were inconsistent within studies, with no data could be pooled. Eight studies compared biodegradable packings with non-packing group. Postoperative symptom data in this comparison could not be pooled: A protective or equal effect on postoperative bleeding was reported in different studies; no difference was reported in pain status and nasal blockage. As for mucosal healing, meta-analysis showed that two arms of comparison had similar effect on synechiae, edema, infection and granulation at each time point.

Conclusion

The limiting evidence suggests that biodegradable nasal packings are statistically better than conventional packings in postoperative symptoms, and probably comparable to non-packing group, as in this comparison we could not carry out meta-analysis. No beneficial or detrimental effect on postoperative mucosal healing could be determined based on existing evidence.     

Karyological and taxonomic observations onDracocephalum foetidum Bunge andKoenigia islandica L.

Chromosome numbers are reported for two Mongolian species,Dracocephalum foetidum Bunge (2n=12) andKoenigia islandica L. (2n=14). The relationship ofD. foetidum toD. moldavica L. (2n=10) and some patterns of phenotypic variation inK. islandica are briefly discussed. The following new combinations are proposed:K. cyanadra (Diels) Měsí?ek etSoják,K. forrestii (Diels) Měsí?ek etSoják,K. hubertii (Lingelsh.) Měsí?ek etSoják, andK. nummularifolia (Meisn.) Měsí?ek etSoják.     

A rapid assay for the binding of actinomycin to DNA.

The theory of countercurrent distribution (CCD) was reviewed and extended. The separation function for the fundamental distribution of CCD was presented in the form n = t²(αk₁+β)²/αk₁(β?1)² where n is the number of transfers, t the abscissa of the standard normal distribution, α = v_m/v₈ the phase ratio, β = k₁/k₂≥ 1 the separation factor, and k₁ the partition coefficient of the more radidly moving component; n was found to be minimal on the condition αk₁ = β. The separation function for the single withdrawal of CCD was obtained in the form N = u + 1 = t²{(αk₁ + 1)^1/2 + [β(αk₁ + β)]^1/2}²/(β ? 1)²+ 1, where N is the number of partition units. From this equation it appears that N is minimal when αk₁ = 0. Compared with the former separation functions presented in the literature, these separation functions have the advantage of giving directly the relationships among the phase ratio, the absolute partition coefficient, the separation factor, the resolution degree, and the number of transfers or partition units required. In addition, the dependencies of the elution volumes and the widths of the elution curves on α, β, and the partition coefficients were considered mathematically by means of differential calculus. The elution volumes were found to have minima at certain αk₁ values. The standard deviations, on the contrary, did not have minima in respect to αk₁. The theory presented can be used for selecting proper operating conditions while separating chemical compounds.     

Nitric-oxide Dioxygenase Function of Human Cytoglobin with Cellular Reductants and in Rat Hepatocytes

Cytoglobin (Cygb) was investigated for its capacity to function as a NO dioxygenase (NOD) in vitro and in hepatocytes. Ascorbate and cytochrome b₅ were found to support a high NOD activity. Cygb-NOD activity shows respective K_m values for ascorbate, cytochrome b₅, NO, and O₂ of 0.25 mm, 0.3 μm, 40 nm, and ∼20 μm and achieves a k_cat of 0.5 s⁻¹. Ascorbate and cytochrome b₅ reduce the oxidized Cygb-NOD intermediate with apparent second order rate constants of 1000 m⁻¹ s⁻¹ and 3 × 10⁶ m⁻¹ s⁻¹, respectively. In rat hepatocytes engineered to express human Cygb, Cygb-NOD activity shows a similar k_cat of 1.2 s⁻¹, a K_m(NO) of 40 nm, and a k_cat/K_m(NO) (k′_NOD) value of 3 × 10⁷ m⁻¹ s⁻¹, demonstrating the efficiency of catalysis. NO inhibits the activity at [NO]/[O₂] ratios >1:500 and limits catalytic turnover. The activity is competitively inhibited by CO, is slowly inactivated by cyanide, and is distinct from the microsomal NOD activity. Cygb-NOD provides protection to the NO-sensitive aconitase. The results define the NOD function of Cygb and demonstrate roles for ascorbate and cytochrome b₅ as reductants.     

Alpha-chymotrypsin: effects of bicyclic substrate geometry and hydrophobicity on reactivity

The α-chymotrypsin-catalyzed hydrolysis rates of p-nitrophenyl cyclopentane-carboxylate (I), p-nitrophenyl indan-2-carboxylate (II), and p-nitrophenyl spiro-[4.4]nonane-2-carboxylate (III) were measured at pH 8.1 in 20% methanol. After correction for variations in reactivity owing to stereoelectronic effects inherent to the substrates, the deacylation rate constants (k_c)_n of I and II are not significantly different. In $\text{(}\text{k}{}_{\mathrm{c}}\text{K}{}_{\mathrm{m}}\text{)}{}_{\mathrm{n}}$ II is 50 times more reactive than I, which demonstrates that the aromatic ring of the former substrate contributes significantly to its reactivity. The nearly equal reactivities of II and III indicate that the enzyme is rather insensitive to the geometry of the nonester-bearing ring of these compounds.     

Probabilistic Model of Microbial Cell Growth,Division, and Mortality

After a short time interval of length δt during microbial growth, an individual cell can be found to be divided with probability P_d(t)δt, dead with probability P_m(t)δt, or alive but undivided with the probability 1 − [P_d(t) + P_m(t)]δt, where t is time, P_d(t) expresses the probability of division for an individual cell per unit of time, and P_m(t) expresses the probability of mortality per unit of time. These probabilities may change with the state of the population and the habitat''s properties and are therefore functions of time. This scenario translates into a model that is presented in stochastic and deterministic versions. The first, a stochastic process model, monitors the fates of individual cells and determines cell numbers. It is particularly suitable for small populations such as those that may exist in the case of casual contamination of a food by a pathogen. The second, which can be regarded as a large-population limit of the stochastic model, is a continuous mathematical expression that describes the population''s size as a function of time. It is suitable for large microbial populations such as those present in unprocessed foods. Exponential or logistic growth with or without lag, inactivation with or without a “shoulder,” and transitions between growth and inactivation are all manifestations of the underlying probability structure of the model. With temperature-dependent parameters, the model can be used to simulate nonisothermal growth and inactivation patterns. The same concept applies to other factors that promote or inhibit microorganisms, such as pH and the presence of antimicrobials, etc. With P_d(t) and P_m(t) in the form of logistic functions, the model can simulate all commonly observed growth/mortality patterns. Estimates of the changing probability parameters can be obtained with both the stochastic and deterministic versions of the model, as demonstrated with simulated data.     

The mononuclear and dinuclear dimethoxyethane adducts of lanthanide trichlorides [LnCl3(DME)2]n, n=1 or 2, fundamental starting materials in lanthanide chemistry: preparation and structures

Some new dimethoxyethane (DME) adducts of lanthanide trichlorides of formula [LnCl₃(DME)₂]_n, n=1 or 2; (n=2, Ln=La, Ce, Pr, Nd; n=1, Ln=Eu, Tb, Ho, Tm, Lu) have been prepared by treating Ln₂O₃, or LnCl₃ · nH₂O, or Ln₂(CO₃)₃, in DME as medium, with thionyl chloride at room temperature, eventually in the presence of water in the case of Ln₂O₃ and Ln₂(CO₃)₃. The complexes from lanthanum to praseodymium included are chloro-bridged dimers. In the case of neodymium, the new results complement the literature data, showing that both the mononuclear and dinuclear species exist: neodymium can therefore be regarded as the turning element from dinuclear to mononuclear structures along the series. Only mononuclear complexes were isolated in the Eu-Lu sequence. The lanthanide contraction has been evaluated on the basis of the Ln-O and Ln-Cl bond distances on the isotypical series of the mononuclear complexes LnCl₃(DME)₂ covering a range of 12 atomic numbers.     

The Molecular Mechanism of Eukaryotic Elongation Factor 2 Kinase Activation

Calmodulin (CaM)-dependent eukaryotic elongation factor 2 kinase (eEF-2K) impedes protein synthesis through phosphorylation of eukaryotic elongation factor 2 (eEF-2). It is subject to complex regulation by multiple upstream signaling pathways, through poorly described mechanisms. Precise integration of these signals is critical for eEF-2K to appropriately regulate protein translation rates. Here, an allosteric mechanism comprising two sequential conformations is described for eEF-2K activation. First, Ca²⁺/CaM binds eEF-2K with high affinity (K_d(CaM)^app = 24 ± 5 nm) to enhance its ability to autophosphorylate Thr-348 in the regulatory loop (R-loop) by > 10⁴-fold (k_auto = 2.6 ± 0.3 s⁻¹). Subsequent binding of phospho-Thr-348 to a conserved basic pocket in the kinase domain potentially drives a conformational transition of the R-loop, which is essential for efficient substrate phosphorylation. Ca²⁺/CaM binding activates autophosphorylated eEF-2K by allosterically enhancing k_cat^app for peptide substrate phosphorylation by 10³-fold. Thr-348 autophosphorylation results in a 25-fold increase in the specificity constant (k_cat^app/K_m(Pep-S)^app), with equal contributions from k_cat^app and K_m(Pep-S)^app, suggesting that peptide substrate binding is partly impeded in the unphosphorylated enzyme. In cells, Thr-348 autophosphorylation appears to control the catalytic output of active eEF-2K, contributing more than 5-fold to its ability to promote eEF-2 phosphorylation. Fundamentally, eEF-2K activation appears to be analogous to an amplifier, where output volume may be controlled by either toggling the power switch (switching on the kinase) or altering the volume control (modulating stability of the active R-loop conformation). Because upstream signaling events have the potential to modulate either allosteric step, this mechanism allows for exquisite control of eEF-2K output.     

Asymptotic Distributions of Coalescence Times and Ancestral Lineage Numbers for Populations with Temporally Varying Size

The distributions of coalescence times and ancestral lineage numbers play an essential role in coalescent modeling and ancestral inference. Both exact distributions of coalescence times and ancestral lineage numbers are expressed as the sum of alternating series, and the terms in the series become numerically intractable for large samples. More computationally attractive are their asymptotic distributions, which were derived in Griffiths (1984) for populations with constant size. In this article, we derive the asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. For a sample of size n, denote by T_m the mth coalescent time, when m + 1 lineages coalesce into m lineages, and A_n(t) the number of ancestral lineages at time t back from the current generation. Similar to the results in Griffiths (1984), the number of ancestral lineages, A_n(t), and the coalescence times, T_m, are asymptotically normal, with the mean and variance of these distributions depending on the population size function, N(t). At the very early stage of the coalescent, when t → 0, the number of coalesced lineages n − A_n(t) follows a Poisson distribution, and as m → n, n(n ? 1)T_m/2N(0) follows a gamma distribution. We demonstrate the accuracy of the asymptotic approximations by comparing to both exact distributions and coalescent simulations. Several applications of the theoretical results are also shown: deriving statistics related to the properties of gene genealogies, such as the time to the most recent common ancestor (TMRCA) and the total branch length (TBL) of the genealogy, and deriving the allele frequency spectrum for large genealogies. With the advent of genomic-level sequencing data for large samples, the asymptotic distributions are expected to have wide applications in theoretical and methodological development for population genetic inference.     

Thermodynamics of base interaction in (A)n and (A.U)n

Using precision scanning microcalorimetry we studied (A)_n and (A·U)_n melting in highly diluted solutions (0.3 to 5.0 mm) with different Na⁺ activity. This permitted us to determine directly the thermodynamic functions of stacking interaction in (A)_n and base-pairing in (A·U)_n. For (A-A) stacking at (A)_n melting temperature we obtained ΔH^(A)n_m = 12.6 kJ mol^?1; ΔS^(A)n_m = 41 J K^?1 mol^?1. For A·U base-pairing at a standard temperature of 298 K and 0.1 m-Na⁺ we have: ΔH^(A·U) = 34 kJ mol^?1; ΔS^(A·U) = 102 J K^?1 mol^?1ΔG^(A·U) = ?3.5 kJ mol^?1.     

Novel 2,4-dichlorophenoxy acetic acid substituted thiazolidin-4-ones as anti-inflammatory agents: Design,synthesis and biological screening

A library of fourteen 2-imino-4-thiazolidinone derivatives (1a-1n) has been synthesized and evaluated for in vivo anti-inflammatory activity and effect on ex-vivo COX-2 and TNF–α expression. Compounds 1k (5-(2,4-dichloro-phenooxy)-acetic acid (3-benzyl-4-oxo-thiazolidin-2-ylidene)-hydrazide) and 1m (5-(2,4-dichloro-phenooxy)-acetic acid (3-cyclohexyl-4-oxo-thiazolidin-2-ylidene)-hydrazide) exhibited in vivo inhibition of 81.14% and 78.80% respectively after 5 h in comparison to indomethacin which showed 76.36% inhibition of inflammation without causing any damage to the stomach. Compound 1k showed a reduction of 68.32% in the level of COX-2 as compared to the indomethacin which exhibited 66.23% inhibition of COX-2. The selectivity index of compound 1k was found to be 29.00 in comparison to indomethacin showing selectivity index of 0.476. Compounds 1k and 1m were also found to significantly suppress TNF-α concentration to 70.10% and 68.43% in comparison to indomethacin which exhibited 66.45% suppression.     

Protein affinities for small molecules: conceptions and misconceptions.

There is much confusion and error in published treatments of data for multiple binding of ligands (e.g., substrates) by proteins (e.g., enzymes). There is a widespread impression that if the equilibrium binding, r, of ligand, A, by a protein with n sites can be fitted to an equation with two hyperbolic terms, i.e., $\text{r=}\text{n}{}_{\mathrm{\alpha }}\text{k}{}_{\mathrm{\alpha }}\text{(A)}\text{1+k}{}_{\mathrm{\alpha }}\text{(A)}\text{+}\text{n}{}_{\mathrm{\beta }}\text{k}{}_{\mathrm{\beta }}\text{(A)}\text{1+k}{}_{\mathrm{\beta }}\text{(A)}\text{(n}{}_{\mathrm{\alpha }}\text{+n}{}_{\mathrm{\beta }}\text{=n)}$ then k_β and k_β are always the intrinsic binding constants for two sets of sites. Such a conclusion is often incorrect. For example, in many cases, the protein is constituted of identical protomers with initially identical sites for binding ligands, and yet graphical representations of the binding data appear to behave as if the sites are partitioned between two classes. Although the use of a linear combination of hyperbolic terms to represent binding of ligands by macromolecules always yields empirical parameters k_α, k_β … k_λ, they cannot correspond to site binding constants when there are interactions between sites. In some circumstances their values may even be imaginary, complex numbers. On the other hand, stoichiometric binding constants can be assigned unambiguously without making any assumption regarding the nature of the interactions among binding sites. These principles are illustrated concretely by analyses of binding measurements for several different proteins containing two to six sites.     

Syntheses and crystal structures of three diorganoltin(IV) macrocycles

Three novel macrocyclic diorganotin(IV) compounds of the type: {[R₁₀(SnO)₃(SnOH)₂]H_nXO_m}₂ · L (n=1, m=4, R=PhCH₂, X=P, L=0, 1; n=0, m=4, R=PhCH₂, X=S, L=4H₂O, 2; n=0, m=3, R=n-Bu, X=N, L=0, 3) were synthesized by the reaction of (PhCH₂)₂SnCl₂ with Na₂H_nXO₄ (n=1, X=P; n=0, X=S) or (n-Bu)₂SnCl₂ with NaNO₃. All the compounds 1, 2 and 3 are characterized by elemental, IR and X-ray diffraction analyses. X-ray data reveal that a macrocyclic structure with two centrosymmetric ladders of hydrolysis exists in the crystals of the three compounds. The geometry about each tin atom involved is trigonal bipyramidal.     

Physiological effects of the addition of n-dodecane as an oxygen vector during steady-state Bacillus licheniformis thermophillic fermentations perturbed by a starvation period or a glucose pulse

The effect of the presence of n-dodecane as a potential oxygen vector during oxygen-limited continuous cultures of a Bacillus strain was studied, under extreme nutrient supply conditions: glucose excess, limitation and starvation. The addition of n-dodecane to the aqueous phase of a mechanically agitated and aerated fermentation increased the k_La by up to 35%. The n-dodecane additions to Bacillus licheniformis cells during starvation (oxygen limitation with concomitant glucose starvation) caused a severe detrimental progressive change in cell physiological state with respect to cytoplasmic membrane polarisation and permeability which was mitigated against by alleviating either the oxygen limitation (by increasing the mean energy dissipation rate or by the addition of n-dodecane as an oxygen vector) or by alleviating the carbon limitation (by resuming the carbon feed or by the addition of a glucose pulse). Further that during periods of excess glucose (glucose pulse) a much higher k_La was required to prevent the onset of anaerobic mixed acid fermentation than could be provided by the addition of n-dodecane alone. n-Dodecane can be used to increase the k_La when added in sufficient quantities to the aqueous phase of a mechanically agitated and aerated bioreactor but the magnitude of this increase is process and vessel geometry specific.