Structural–Functional Units of Epidermis

The available data suggest that epidermis is organized as a system of discrete structural–functional units (SFUs) that reproduce both in vivo and in vitro. SFUs are formed in the culture of epidermal keratinocytes via self-organization of the developing cellular elements. SFUs are capable of self-maintenance and form a niche for stem cells. At the same time, due to the maintenance of asymmetric proliferation kinetics of the stem cells, SFUs serve as a barrier to their uncontrolled replication.     

Functional and Structural Effects of Amyloid-β Aggregate on Xenopus laevis Oocytes

Xenopus laevis oocytes exposed to amyloid-β aggregate generated oscillatory electric activity (blips) that was recorded by two-microelectrode voltage-clamp. The cells exhibited a series of “spontaneous” blips ranging in amplitude from 3.8 ± 0.9 nA at the beginning of the recordings to 6.8 ± 1.7 nA after 15 min of exposure to 1 μM aggregate. These blips were similar in amplitude to those induced by the channel-forming antimicrobial agents amphotericin B (7.8 ± 1.2 nA) and gramicidin (6.3 ± 1.1 nA). The amyloid aggregate-induced currents were abolished when extracellular Ca²⁺ was removed from the bathing solution, suggesting a central role for this cation in generating the spontaneous electric activity. The amyloid aggregate also affected the Ca²⁺-dependent Cl⁻ currents of oocytes, as shown by increased amplitude of the transient-outward chloride current (T_out) and the serum-activated, oscillatory Cl⁻ currents. Electron microcopy revealed that amyloid aggregate induced the dissociation of the follicular cells that surround the oocyte, thus leading to a failure in the electro-chemical communication between these cells. This was also evidenced by the suppression of the oscillatory Ca²⁺-dependent ATP-currents, which require proper coupling between oocytes and the follicular cell layer. These observations, made using the X. laevis oocytes as a versatile experimental model, may help to understand the effects of amyloid aggregate on cellular communication.     

Achondroplastic Dwarfism—Effects of Treatment with Human Growth Hormone

Two male patients with achondroplastic dwarfism aged 7-5/12 and 14½ years were treated with human growth hormone 5 mg daily. Both showed nitrogen retention on balance studies, the older second patient to a marked degree. In the younger patient, height increased from 95.4 to 106.3 cm on hgh 5 mg daily alone for 14 out of 24 months. The rate of growth approximately doubled during the first two treatment periods as compared with the pre-treatment rate. In the second older patient hgh was administered 5 mg daily intramuscularly for 21 out of 33 months. Growth from 129.6 cm to 137.8 cm occurred with the rate increasing following the addition of Na-1-thyroxine to the routine. This increased growth rate occurred during the post-puberty deceleration phase. Bone ages, interpreted from changes in the phalanges and metacarpals, increased from 4½ to 6 years during 16 months in Case 1, and from 13½ to 18 years in 33 months in Case 2. Transient adolescent gynecomastia appeared in Case 2. No local or general toxic effects were noted.These results are suggestive, but whether or not the eventual height of an achondroplastic dwarf can be significantly altered must await further studies.     

Structural—Functional Relationships between Terminal Deoxynucleotidyltransferase and 5′-Triphosphates of Nucleoside Analogs

Substrate properties of nucleoside 5′-triphosphate (NTP) analogs, namely, 5′-triphosphates of L- and D-arabinonucleosides (D-FIAUTP, D-FMAUTP, and L-FMAUTP), D- and L-enantiomers of ddCTP analogs (D-ddCTP, L-ddCTP, D-FOddCTP, L-OddCTP, and L-SddCTP), and acyclic guanosine analogs (acyclovir and penciclovir) towards terminal deoxynucleotidyltransferase (TdT, EC 2.7.7.31) were studied. TdT can polymerize 5′-triphosphates of arabinonucleoside analogs (D-FIAUTP and D-FMAUTP). In contrast, L-FMAUTP is not recognized by TdT as a substrate. Kinetic parameters of D- and L-enantiomers of ddCTP analogs and 5′-triphosphates of acyclic nucleosides were evaluated. It is shown that stereospecificity of dNTP analogs and structure of the furanose residue play crucial roles in the interaction with TdT: L-enantiomers are much less potent as substrates compared to their D-counterparts. 5′-Triphosphates of acyclovir (ACVTP) and penciclovir (PCVTP) are about two orders of magnitude less effective as substrates than nucleosides bearing furanose residues, with PCVTP being a better substrate than ACVTP. It can be assumed that the hydroxyl group of PCVTP mimics the 3′-hydroxyl group of the ribose residue and plays an important role in the interaction with TdT.__________Translated from Biokhimiya, Vol. 70, No. 8, 2005, pp. 1078–1085.Original Russian Text Copyright © 2005 by Kukhanova, Ivanov, Jasko.     

Structural–Functional Domains of the Eukaryotic Genome

It is well known that DNA folding in the eukaryotic cell nucleus is tightly coupled with the operation of epigenetic mechanisms defining the repertoires of the genes expressed in different types of cells. To understand these mechanisms, it is important to know how DNA is packaged in chromatin. About 30 years ago a hypothesis was formulated, according to which epigenetic mechanisms operate not at the level of individual genes, but rather groups of genes localized in structurally and functionally isolated genomic segments that were called structural and functional domains. The question of what exactly these domains constitute has been re-examined multiple times as our knowledge of principles of chromatin folding has changed. In this review, we discuss structural and functional genomic domains in light of the current model of interphase chromosome organization based on the results of analysis of spatial proximity between remote genomic elements.     

Acromegaly—The Effects of Various Steroid Hormones on the Insulin-Induced Growth Hormone Response

The availability of a sensitive assay for human growth hormone has made it possible to directly measure the effects of various agents purported to alter growth patterns. Acromegalic patients present a special problem both in early diagnosis and in therapy. Being able to measure growth hormone in these patients provides an accurate index of activity and a precise measure of therapeutic effectiveness.In an attempt to determine whether a pituitary block of growth hormone secretion is feasible in this condition, a study was made of the effects of estrogen, androgen and glucocorticoid administration on growth hormone response to a standard insulin tolerance test in a patient with active acromegaly. In the dosage schedules used in this study, it was not possible to suppress either basal growth hormone secretion or blunt its responsiveness to the normal physiologic stimulus of hypoglycemia.     

Effect of Trifluoroethanol on the Structural and Functional Properties of α-Crystallin

Alpha crystallin is an eye lens protein with a molecular weight of approximately 800 kDa. It belongs to the class of small heat shock proteins. Besides its structural role, it is known to prevent the aggregation of β- and γ-crystallins and several other proteins under denaturing conditions and is thus believed to play an important role in maintaining lens transparency. In this communication, we have investigated the effect of 2,2,2-trifluoroethanol (TFE) on the structural and functional features of the native α-crystallin and its two constituent subunits. A conformational change occurs from the characteristic β-sheet to the α-helix structure in both native α-crystallin and its subunits with the increase in TFE levels. Among the two subunits, αA-crystallin is relatively stable and upon preincubation prevents the characteristic aggregation of αB-crystallin at 20% and 30% (v/v) TFE. The hydrophobicity and chaperone-like activity of the crystallin subunits decrease on TFE treatment. The ability of αA-crystallin to bind and prevent the aggregation of αB-crystallin, despite a conformational change, could be important in protecting the lens from external stress. The loss in chaperone activity of αA-crystallin exposed to TFE and the inability of peptide chaperone—the functional site of αA-crystallin—to stabilize αB-crystallin at 20–30% TFE suggest that the site(s) involved in subunit interaction and chaperone-like function are quite distinct.     

Cross-validation of Non-linear Growth Functions for Modelling Tree Height–Diameter Relationships

Six non-linear growth functions were fitted to tree height–diameter data of ten conifer species collected in the inland Northwest of the United States. The data sets represented a wide range of tree sizes, especially large-sized trees. According to the model statistics, the six growth functions fitted the data equally well, but resulted in different asymptote estimates. The model prediction performance was evaluated using Monte Carlo cross-validation or data splitting for 25-cm diameter classes. All six growth functions yielded similar mean prediction errors for small- and middle-sized trees. For large-sized trees [e.g. DBH (diameter at breast height)>100 cm], however, five of the six growth functions (except the Gompertz function) overestimated tree heights for western white pine, western larch, Douglas-fir, subalpine fir, and ponderosa pine, but underestimated tree heights for western hemlock and Engelmann spruce. Among these five functions, the Korf/Lundqvist and Exponential functions produced larger overestimations. The Schnute, Weibull, and Richards functions were superior in prediction performance to others. The Gompertz function seemed always to underestimate tree heights for large-sized trees.     

The Mammalian β-Adrenergic Receptor: Structural and Functional Characterization of the Carbohydrate Moiety

Abstract

Mammalian β-adrenergic receptors are glycoproteins consisting of a single polypeptide chain of M_r ～64,000. Treatment of purified [¹²⁵I]-labeled hamster lung β-adrenergic receptor with α-mannosi-dase reveals two discrete populations of receptor consistent with previous studies using membrane bound photoaffinity-labeled receptor. Treatment of the [¹²⁵I]-labeled receptor with endo-glycosidase F results initially in the formation of a M_r ～57,000 peptide which is further converted to M_r ～49,000 suggesting that there are two N-linked carbohydrate chains per receptor polypeptide. Exoglycosidase treatments and lectin chromatography of the [¹²⁵I]-labeled receptor reveals the presence of two complex type carbohydrate chains (～10% of which are fucosylated) on ～45% of the receptors. The remaining ～55% of the receptors appear to contain a mixture of carbohydrate chains (possibly high mannose, hybrid and complex type chains). Deglycosylation of the receptor by endoglycosidase F does not appear to alter the binding affinity of the receptor for a variety of β-adrenergic agonists and antagonists. Moreover, the ability of control, α-mannosidase sensitive or insensitive (fractionated on immobilized wheat germ agglutinin) and neuraminidase, α-mannosidase or endoglycosidase F treated receptors to interact with the stimulatory guanine nucleo-tide regulatory protein in a reconstituted system were virtually identical. The deglycosylated receptor was also unaltered in its heat lability as well as its susceptibility to a variety of proteases. These findings demonstrate that the carbohydrate portion of the β-receptor does not contribute to determining either its specificity of ligand binding or coupling to the adenylate cyclase system.     

Structural and Functional Characterization of the α-Tubulin Acetyltransferase MEC-17

Tubulin protomers undergo an extensive array of post-translational modifications to tailor microtubules to specific tasks. One such modification, the acetylation of lysine 40 of α-tubulin, located in the lumen of microtubules, is associated with stable, long-living microtubule structures. MEC-17 was recently identified as the acetyltransferase that mediates this event. We have determined the crystal structure of the catalytic core of human MEC-17 in complex with its cofactor acetyl-CoA at 1.7 Å resolution. The structure reveals that the MEC-17 core adopts a canonical Gcn5-related N-acetyltransferase (GNAT) fold that is decorated with extensive surface loops. An enzymatic analysis of 33 MEC-17 surface mutants identifies hot-spot residues for catalysis and substrate recognition. A large, evolutionarily conserved hydrophobic surface patch that is critical for enzymatic activity is identified, suggesting that specificity is achieved by interactions with the α-tubulin substrate that extend outside of the modified surface loop. An analysis of MEC-17 mutants in Caenorhabditis elegans shows that enzymatic activity is dispensable for touch sensitivity.     

Growth Kinetics of Microbacterium lacticum and Nitrate-Dependent Degradation of Ethylbenzene under Anaerobic Conditions

A pure strain of Microbacterium lacticum DJ-1 capable of anaer-obic biodegradation of ethylbenzene was isolated from soil contaminated with gasoline. Growth of the strain and biodegradation of ethylbenzene in batch cultures led to stoichiometric reduction of nitrate. M. lacticum DJ-1 could degrade 100 mg L^?1 of ethylbenzene completely, with a maximum degradation rate of 15.02 ± 1.14 mg L^?1 day^?1. Increasing the initial concentration of ethy-lbenzene resulted in decreased degradative ability. The cell-specific growth rates on ethylbenzene conformed to the Haldane–Andrew model in the substrate level range of 10–150 mg L^?1. Kinetic parameters were determined by nonlinear regression on specific growth rates and various initial substrate concentrat-ions, and the values of the maximum specific growth rate, half saturation constant, and inhibition constant were 0.71 day^?1, 34.3 mg L^?1, and 183.5 mg L^?1, respectively. This is the first report of ethylbenzene biodegradation by a bacterium of Microbacterium lacticum under nitrate-reducing conditions.     

Promotive Effects of the Peptidyl Plant Growth Factor,Phytosulfokine-α, on the Growth and Chlorophyll Content of Arabidopsis Seedlings under High Night-time Temperature Conditions

In order to investigate the function of the peptidyl plant growth factor, phytosulfokine-α (PSK-α), in plants, we examined the effect of PSK-α on the growth and chlorophyll content of Arabidopsis seedlings under high night-time temperature conditions. Although exposure to high night-time temperatures markedly reduced the fresh weight and chlorophyll content of the seedlings, these parameters in the plants supplied with PSK-α remained at the same levels as those of non-treated controls. These effects were not apparent when [2-5]PSK, Tyr-SO₃H and kinetin were similarly supplied. The results suggest that PSK-α not only promotes cell proliferation, but may aid plants in their tolerance of heat stress.     

Food-Derived Carbohydrates — Structural Complexity and Functional Diversity

ABSTRACT:?

Carbohydrates are biomolecules abundantly available in nature. They are found in bewildering types ranging from simple sugars through oligo- and polysaccharides to glycoconjugates and saccharide complexes, each exhibiting characteristic bio-physiological and/or nutritional functions both in in vivo and in vitro systems. For example, their presence or inclusion in food dictates the texture (body) and gives desirable customer appeal (satisfaction), or their inclusion in the diet offers beneficial effects of great therapeutic value. Thus, carbohydrates are integrally involved in a multitude of biological functions such as regulation of the immune system, cellular signaling (communication), cell malignancy, antiinfection responses, host-pathogen interactions, etc. If starch is considered the major energy storage carbohydrate, the gums/mucilages and other non-starch carbohydrates are of structural significance. The most investigated properties of starch are its gelatinization and melting behavior, especially during food processing. This has led to the development of the food polymer science approach, which has enabled a new interpretive and experimental frame work for the study of the plasticizing influence of simple molecules such as water, sugars, etc. on food systems that are kinetically constrained. Starch, although considered fully digestible, has been challenged, and starch is found to be partly indigestible in the GI tract of humans. This fraction of starch-resisting digestion in vivo is known as resistant starch (RS). The latter, due to its excellent fermentative capacity in the gut, especially yielding butyric acid is considered a new tool for the creation of fiber-rich foods, which are of nutraceutical importance. By a careful control of the processing conditions the content of RS, a man-made fiber, can be increased to as high as 30%. Arabinoxylans are the major endospermic cell wall polysaccharides of cereals. In wheat they are found complexed with ferulic acid esters, which after oxidative coupling in vivo mediated by H₂O₂ and peroxidases or even by photochemical means give cross linked diferuloyl derivatives. The latter confer strength and extensibility to the cell wall and offer resistance for digestibility by ruminants. They also help blocking of the ingress of pathogens. The ester bound ferulic acid after oxidation in vivo generates reactive oxygen species that contribute to the fragmentation of non-starch polysaccharides (hemicelluloses), and thereby reduces the product viscosity, a property seen during long-term storage of rice. In plant tissues, the arabinogalactans are implicated in such diverse functions as cell-cell adhesion, nutrition of growing pollen tubes, response to microbial infections, and also as markers of identity expressed in the terminal sequences of saccharide chains.     

Structural and Functional Characterization of the Redβ Recombinase from Bacteriophage λ

The Red system of bacteriophage λ is responsible for the genetic rearrangements that contribute to its rapid evolution and has been successfully harnessed as a research tool for genome manipulation. The key recombination component is Redβ, a ring-shaped protein that facilitates annealing of complementary DNA strands. Redβ shares functional similarities with the human Rad52 single-stranded DNA (ssDNA) annealing protein although their evolutionary relatedness is not well established. Alignment of Rad52 and Redβ sequences shows an overall low level of homology, with 15% identity in the N-terminal core domains as well as important similarities with the Rad52 homolog Sak from phage ul36. Key conserved residues were chosen for mutagenesis and their impact on oligomer formation, ssDNA binding and annealing was probed. Two conserved regions were identified as sites important for binding ssDNA; a surface basic cluster and an intersubunit hydrophobic patch, consistent with findings for Rad52. Surprisingly, mutation of Redβ residues in the basic cluster that in Rad52 are involved in ssDNA binding disrupted both oligomer formation and ssDNA binding. Mutations in the equivalent of the intersubunit hydrophobic patch in Rad52 did not affect Redβ oligomerization but did impair DNA binding and annealing. We also identified a single amino acid substitution which had little effect on oligomerization and DNA binding but which inhibited DNA annealing, indicating that these two functions of Redβ can be separated. Taken together, the results provide fresh insights into the structural basis for Redβ function and the important role of quaternary structure.     

Structural and Functional Analysis of E. coli Cyclopropane Fatty Acid Synthase

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Bayesian and Maximum Likelihood Analyses of Rotifer–Acanthocephalan Relationships

Rotifera is composed of groups with unusual ultrastructural, physiological, and reproductive characters. Our ability to understand the evolution of these features is complicated by the fact that the phylogenetic relationships among the three traditional rotifer groups (Seisonidea, Monogononta, and Bdelloidea) and Acanthocephala remain unresolved. Here, I present maximum likelihood and Bayesian analyses of rotifer–acanthocephalan relationships using both the protein-coding gene hsp82 and a combined data set of hsp82 and ribosomal small subunit (SSU) DNA sequences, using nucleotide and codon based models of evolution. Statistical analysis of the phylogenetic support for any of the likely relationships among rotifer groups suggests that more than a combined hsp82 + SSU data set will be needed to resolve rotifer–acanthocephalan phylogeny with any degree of certainty.