Sequential folding of transfer RNA: A nuclear magnetic resonance study of successively longer tRNA fragments with a common 5′ end

Most folding studies on proteins and nucleic acids have been addressed to the transition between the folded and unfolded states of an intact molecule, where an entire residue sequence is present during the folding event. However, since these polymers are synthesized sequentially from one terminus to the other in vivo, their folding pathways may be influenced greatly by the sequential appearance of the residues as a function of time.The three-dimensional structure of yeast tRNA^Phe in the crystalline state is correlated with 360 MHz proton nuclear magnetic resonances from three fragments plus an intact molecule of the tRNA that share a common 5′ end and are in a solution condition similar to that of the crystal structure. This has allowed identification of folded structures present in the fragments and presumably present in the growing tRNA molecule as it is being synthesized from the 5′ end. The experiments show that only the correct stems are formed in the fragments; no additional or competing helical region is produced. This suggests that in the biosynthesis of this tRNA, correct folding of helical stems occurs before the entire molecule is formed. Further, some of the tertiary interactions (hydrogen bonds) found in the crystal structure are also probably present before the synthesis is completed. These findings are generalized to consider the precursor of the tRNA as well as other tRNAs.     

Evolution of concentration field in a membrane system

This paper deals with the evolution of concentration field at a single membrane system. Concentration field evolution is described by concentration effect of stable boundary layers, which originate in this system. The concentration effect of boundary layers (CBLE) is studied experimentally on the basis concentration profiles obtained from computer analysis of interferometric pictures of near-membrane regions. Besides experimental results, we also report theoretical investigations and numerical calculations of this effect for two models of membranes (an infinite thin wall and the wall of thickness l). Evolution of concentration field at different distances from membrane surface describes accurately the spatio-temporal structure of the concentration boundary layers (CBLs). Results have shown that their spatial structure is fully established and these layers develop diffusively.     

Oscheius tipulae, a widespread hermaphroditic soil nematode, displays a higher genetic diversity and geographical structure than Caenorhabditis elegans

The nematode Oscheius tipulae belongs to the same family (Rhabditidae) as the model species Caenorhabditis elegans . Both species reproduce through self-fertilizing hermaphrodites and facultative males. Recent studies have shown that the self-fertile C. elegans and C. briggsae displayed a 20-fold lower genetic diversity than the male–female species C. remanei . Several explanations have been put forward to account for this difference, including their mode of reproduction and dynamic population structure. Here, we present the results of extensive worldwide sampling of O. tipulae , which we previously used as a laboratory organism for developmental genetics. We found that O. tipulae is much more widespread and common in soil throughout the world than Caenorhabditis species. We analysed 63 O. tipulae isolates from several continents using amplified fragment length polymorphism (AFLP). We found that O. tipulae harbours a 5-fold higher genetic diversity than C. elegans and C. briggsae . As in C. elegans , a high proportion of this diversity was found locally. Yet, we detected significant geographical differentiation, both at the worldwide scale with a latitudinal structure and between three localities in France. In summary, O. tipulae exhibited significantly higher levels of genetic diversity and large-scale geographical structure than C. elegans , despite their shared mode of reproduction. This species difference in genetic diversity may be explained by a number of other differences, such as population size, distribution, migration and dynamics. Due to its widespread occurrence and relatively high genetic diversity, O. tipulae may be a promising study species for evolutionary studies.     

Structure of D-glyceraldehyde-3-phosphate dehydrogenase fromPalinurus versicolor in a tetragonal crystal form

D-glyceraldehyde-3-phosphate dehydrogenase (holo-GAPDH) from Palinurus versicolor was crystallized in a novel crystal form by the method of sitting-drop vapor diffusion. The crystals have space group P4212, cell parameters a=15.49 nm, c=8.03 nm and two subunits per asymmetric unit. The crystal structure at 0.34 nm was determined by the molecular replacement method. The final model has crystallographic Rfree and R factors of 0.274 and 0.262, and r.m.s. deviations of 0.002 nm for bond lengths and 2.33?for bond angles. The two subunits in asymmetric unit are similar to each other not only in the three-dimensional structure, but also in average temperature factors. This result demonstrates that the obvious difference in average temperature factors for the different subunits in C2 crystal form reported previously may be attributed to the different crystallographic environments of the subunits. This further supports that holo-GAPDH has a good 222 molecular symmetry.     

An experimental analysis of mate choice in the wren: a monomorphic, polygynous passerine

Male wrens (Troglodytes troglodytes) construct nests that areused in their display to females. Previous work has suggestedthat the number of vacant nests may be used as a mate choicecue. Correlational data from 1992 confirmed that females appearedto be assessing die number of vacant nests on a male's territoryand preferentially mating with males with more nests. Male taillengdi was also correlated widi mating success. In 1993 thenumbers of nests on territories was experimentally manipulated,the female setdement patterns confirmed that die number of vacantnests did mediate mate choice. Male tail length failed to explainadditional variance in mating success when die variance explainedby the experimental manipulation was removed, suggesting diatdie original correlation arose because both tail length andmating success were correlated widi a confounding variable.The structure of the vegetation in a male's territory influencedmating success. This appeared to be due to nests surviving betterin territories widi dense vegetation. Males on territories inwhich nests survive well had longer tails. Male-male competitionfor good territories may explain die observed effects of malemorphology on mating success. Furdier analysis of die nest choicedata showed diat all nests had an equal chance of being usedby a female. The fact diat all nests had an equal probabilityof being chosen by a female means diat each additional nestbuilt by a male wren results in die same increase in matingsuccess. This suggests diat die benefits to males of nest buildingincrease linearly. The number of nests on a territory will beaffected by various factors such as predation pressure, nestbuilding rate, and vegetation structure. The information diatfemales are getting by assessing such a signal is discussed.     

Three-dimensional structure of a cell wall glycoprotein

Electron microscopy and computer image analysis have been used to determine the three-dimensional structure of the crystalline glycoprotein cell wall layer of the alga Lobomonas piriformis. Images of negatively stained specimens, tilted through a range of angles up to 70 °, were combined to give a map of the molecular envelope to a resolution of 2.0 nm. The cell wall layer consists of crystalline plates the centres and edges of which display distinctly different but isomorphous structures. A comparison of three-dimensional reconstructions of the two areas shows the difference probably to be due to a conformational change of one of the glycoprotein subunits. The structure consists of two sets of dimers composed of rod-shaped subunits which lie with their long axes approximately in the plane of the crystal. The centre-edge transition may have significance in the pathway of accretion of new subunits during cell wall growth.     

Amelioration of mechanism-based inactivation of CYP3A4 by a H-PGDS inhibitor

This work describes the rational amelioration of mechanism-based inactivation (MBI) of Cytochrome P450 (CYP) 3A4 in a human hematopoietic prostaglandin D synthase (hH-PGDS) inhibitor (cpd 1). We utilized metabolism reports in order to check if patterns in the metabolism of 1 and similar compounds by CYP3A4 could be deciphered. Then we used structure based design, first modifying the CYP3A4 crystal structure (pdb code: 4NY4) by adding an oxyferryl moiety to the heme, followed by validating the modified structure to obtain the 1′ and 4 position oxidation products of midazolam and then recapitulating the metabolism patterns deciphered previously for 1 and analogs. We checked if the pattern deciphered could lead to a putative reactive moiety. Finally we used the docking pose of 1 into this model of the modified CYP3A4 crystal structure to guide transformation of 1 into MBI-free H-PGDS inhibitors.     

Salvifarin,x-ray structure determination of a cis neo-clerodane diterpenoid from salvia farinacea

The structure and absolute configuration of salvifarin, a neo-clerodane diterpenoid isolated from Salvia farinacea, have been established by X-ray diffraction analysis. This result modifies the structure previously assigned to this compound.     

Cannabinodiol: Conclusive identification and synthesis of a new cannabinoid from Cannabis sativa

A constituent of Lebanese hashish was shown to be 2,6-dihydroxy-6′-isopropenyl-3′-methyl-4-n-pentyl-biphenyl, the aromatic analogue of cannabidiol. Synthesis and acid catalyzed conversion into cannabinol confirmed the assignment. This structure, cannabinodiol, was earlier erroneously assigned by others to a different compound; a suggestion for the correct structure of the latter product is given.     

鲤鱼线粒体tRNA~(Cys)基因和轻链复制起始区的结构分析

我们测定了鲤鱼线粒体半胱氮酸tRNA 基因和轻链(L 链)复制起始区的核苷酸序列,绘制了半胱氨酸tRNA 三叶草形的二级结构以及L 链复制区的茎环结构。通过五种脊椎动物tRNA~(cya)基因的核苷酸序列分析发现,鲤鱼线粒体tRNA~(cya)基因有许多不同于细胞质tRNA~(cya)基因的不寻常的结构特点。鲤鱼线粒体L 链复制起始区含有36个碱基,复制起始区茎环结构中的茎含有11对碱基,而环则是由14个碱基组成。同其它10种脊椎动物L-链复制起始区的核苷酸序列比较发现,鲤鱼茎环结构中的茎序列是非常保守的,而环的序列及环的长度则变化较大。茎环结构可能在轻链复制中起着重要的作用。     

Arylsulfatase inactivation of slow reacting substance. Evidence for proteolysis as a major mechanism when ordinary commercial preparations of the enzyme are used

Type II B arylsulfatases are known to inactivate slow reacting substance (SRS), but the mechanism is unclear. In the present study, ordinary commercial preparations of Sigma limpet arylsulfatase largely inactivated the glutathionyl and cysteinyl-glycyl forms of SRS, but the cysteinyl form of SRS was largely resistant to the enzyme. Evidence is presented which established that a major mechanism for the inactivation of the glutathionyl and cysteinyl-glycyl SRS types, at least by the particular enzyme preparations we have studied, involves cleavage of the glycine moiety from the sulfur containing side chain. This was confirmed by digestion studies with glutathione itself. In addition, there is ome evidence to indicate that the enzyme may destabilize the double bond structure of the SRS molecule, contributing to the overall inactivation.     

香蕉枯萎病菌4号生理小种致病相关基因foABC1的分离

通过对香蕉枯萎病菌4号小种致病突变体B1233的进一步研究,分离了被突变的致病相关基因foABC1,同源性分析及保守结构预测该基因编码一类ABC转运蛋白,其功能可能同稻瘟病菌的ABC转运蛋白一样,负责真菌毒素的泵出,或是像其他真菌的ABC转运蛋白,在病原菌侵染寄主植物时能忍耐植物因防卫反应所释放的植保素或抗毒素类物质。     

Sativanine-g,a cyclopeptide alkaloid from Zizyphus sativa

In addition to the already described peptide alkaloids from the bark of Zizyphus sativa, a new compound of this class, sativanine-G, has been isolated and its structure elucidated. This alkaloid contains a 13-membered ring system and belongs to the nummularine-C class.     

Differential scanning calorimetry studies of some analogs for the lipid component of biological membranes

The melting behavior of members of newly synthesized series of rac-1,2-diglycerides with substituted phenyl groups or a benzyl group on the 3-position was investigated with differential scanning calorimetry (DSC). Solution crystallized samples had single melting temperatures, higher than those of the quenched or annealed specimens. Quenched samples exhibited polymorphic behavior; some melted and recrystallized during slow heating. This behavior is similar to that of lecithins and suggests that X-ray diffraction studies of the substituted diglycerides may be useful for understanding membrane structure and functions.     

Colony genetic structure in a facultatively eusocial hover wasp

The degree of genetic heterogeneity among the individuals inan animal society depends on the society's genetic structure.Genetic heterogeneity, in turn, means that group members willdiffer in their reproductive objectives and conflicts over reproductionmay arise. The resolution of these conflicts may be reflectedin the way that reproduction is partitioned between potentialreproductives. We used 5 microsatellite loci to investigategenetic structure and reproductive skew in 17 nests of the Malaysianhover wasp, Parischnogaster alternata. Parischnogaster alternatacolonies are small (1–10 females), and all adult colonymembers are capable of mating and producing offspring. We foundthat colonies tended to consist of closely related individualsand that at any one time the production of both female and maleoffspring was nearly always monopolized by a single dominantfemale, despite considerable variation between nests in parameterspredicted to affect skew. Subordinate females that remainedin their natal colonies obtained indirect fitness benefits byhelping to raise offspring to which they were related. Subordinatefemales also appeared to be positioned within an age-based queuefor inheritance of the dominant egg-laying position. We suggestthat the high skew in P. alternata may result from strong ecologicalconstraints on solitary nesting, high relatedness, and a relativelyhigh probability that subordinates will eventually inherit theposition of dominance.     

Nectar biodiversity: a short review

 Nectaries differ in many aspects but a common feature is some kind of advantage for the plant conferred by foraging of consumers which may defend the plant from predators in the case of extrafloral nectaries, or be agents of pollination in the case of floral nectaries. This minireview is concerned mainly with floral nectaries and examines the following characteristics: position in flower; nectary structure; origin of carbohydrates, aminoacids and proteins; manner of exposure of nectar; site of nectar presentation; volume and production of nectar in time; sexual expression of flower and nectary morphology; nectar composition and floral sexual expression; variability of nectar composition; fate of nectar; energy cost of nectar production. The species of certain large families, such as Brassicaceae, Lamiaceae and Asteraceae, resemble each other in nectary organisation; other families, such as Cucurbitaceae and Ranunculaceae, have various types of organisation. A scheme is presented to illustrate factors influencing nectary and nectar biodiversity. Received July 23, 2002; accepted September 18, 2002 Published online: June 2, 2003     

Docking of a single phage lambda to its membrane receptor maltoporin as a time-resolved event

We have been able to observe the first step in bacteriophage infection, the docking of phage lambda to its membrane receptor maltoporin, at the single-particle level. High-resolution conductance recording from a single trimeric maltoporin channel reconstituted into a planar lipid bilayer has allowed detection of the simultaneous and irreversible interaction of the phage tail with all three monomers of the receptor. The formation of a phage-maltoporin complex affects the channel transport properties. Our analysis demonstrates that phage attaches symmetrically to all three receptor monomers. The statistics of sugar binding to the phage-receptor complex on the side opposite to phage docking show that the monomers of maltoporin still bind sugar independently, with the kinetic constants expected from those of the phage-free receptor. This finding suggests that phage docking does not distort the structure of the receptor, and that the phage-binding regions are close to, but do not overlap with, the sugar-binding domains of the maltoporin monomers. However, ion fluxes through the pores of maltoporin in the phage-receptor complex share a new common pathway. We expect that the present study contributes to the current needs for structural information on the functional complexes involved in intercellular recognition.     

Anthropogenic effects on population structure of Acacia tortilis subsp. raddiana along a gradient of water availability in South Sinai,Egypt

Acacia trees in Sinai desert are suffering population decline. This study aims to explore this assumption and to determine the effects of grazing and urbanization on size structure of Acacia tortilis subsp. raddiana along a gradient of water availability in Wadi Feiran basin, South Sinai, Egypt. Size structure of 289 Acacia trees in thirteen isolated populations was analysed. Catchment area and lineament density as water availability indicators were calculated. Effects of grazing and urbanization on Acacia populations were evaluated. A strong positive correlation was recognized between tree height, crown diameter and trunk circumference. Acacia tree density and crown diameter are positively correlated with water availability indicators. Population structure of A. tortilis is characterized by absence of juveniles, clear reduction in numbers of small and large categories and increasing in medium categories. This pattern indicates very low recruitment and high mortality of small and large trees. The variation in water availability may have considerable effects on the structure of A. tortilis. Overgrazing, cutting and urbanization are the main causes of population decline of Acacia in Sinai desert. In addition, drought conditions and bruchid seed beetles aggravate the anthropogenic effect on recruitment of Acacia in South Sinai.     

Identification of an alternative form of caspase-9 in human gastric cancer cell lines: a role of a caspase-9 variant in apoptosis resistance

Overcoming apoptosis resistance to chemotherapy and radiation may lead to a reduction in gastric cancer death. We hypothesize that the apoptotic machinery in gastric cancer cells is dependent upon specific cellular conditions. In the course of our study of the expression of apoptosis-related genes in human gastric cancer cell lines, we have identified a cDNA clone which predicts an alternative form of caspase-9. The caspase-9 variant, which we designated as caspase-9 beta, retained a truncated structure of native caspase-9 without its catalytic domain and was expressed in seven cell lines from human gastric cancer. Among the cell lines examined, MKN-28 cells, which exhibited the most resistance against apoptotic stimuli, expressed the highest level of caspase-9 beta. The induction of apoptosis by staurosporine or actinomycin D was markedly suppressed in caspase-9 beta-transfected HeLa cells. These results are consistent with our hypothesis that the caspase-9 beta may be an endogenous dominant-negative molecule which attenuates apoptotic activity in human gastric cancer cells.