Bacteria-like structures in the endoplasm of Gregarina garnhami (Eugregarinida,Protozoa)

Summary An investigation of bacteria-like structures, which are found in large numbers in the endoplasm of the eugregarine, Gregarina garnhami, was carried out using light and electron microscopy. Gram staining indicates that these structures are gram negative; they show orange fluorescence when stained with acridine orange. Ultrastructural observations show that they resemble the endosymbiotic bacteria found in other protozoan species. Some of these structures appear to be dividing, and the possibility that these structures are in fact bacteria is discussed.     

An Anterior-Posterior Gradient of Refractive Index in the Ameba and Its Significance in Ameboid Movement

Sustained locomotion in Amoeba proteus and Amoeba dubia results in the establishment of a measureable gradient of refractive index along the anterior-posterior axis of the cell, provided thickness of the specimens is kept constant by even compression under a selected coverglass supported by quartz beams of uniform diameter. The tail region of the ameba develops a higher refractive index, indicative of from 6 to 40 per cent more organic matter (expressed as protein) there than present in the front. This gradient fades on cessation of movement. The average protein concentrations in the crystal-free tails and fronts of 15 A. proteus were 3.9 and 3.4 per cent, respectively. In individual experiments, the tail-front difference ranged from one to eight times the accuracy of the method. Since the gradient of refractive index was shown not to result from extraction of water from the tail by the contractile vacuole, it was interpreted as displacement of water toward the anterior part of the cell during movement. It is suggested that contraction of the ectoplasm drives forward a "tide" of syncretic fluid, the anterior border of which is visible as the hyaline cap, which contains less than 1 per cent protein. The movement of the granular endoplasm into the hyaline cap would then complete the cycle by imbibition of the fluid tide. The theoretical positions of Pantin and of Dellinger have been combined in the proposal that ameba cytoplasm consists of a network of a contractile phase which is able to expel (by syneresis) a highly mobile fluid phase. Some other possible interpretations are discussed.     

Prediction of tertiary structures in 'scorpion-toxin' type proteins.

In the three-dimensional architecture of macromolecules, the structural stability and proper folding manifest due to cooperative packing interaction of various segments. Hydrophobicity is the major factor stabilizing protein-protein associations. In the disulfide-containing proteins, S-S bonds are integral part of structural motifs and large part of the protein-folding problem can be reduced to identifying and understanding motifs and subdomains of these proteins. Identifying such a motif with S-S bonds in 'scorpion-toxin' type proteins, and from model-building studies, five tertiary structural models for these type of proteins can be proposed. These canonical structural models can be refined by regular minimum energy and computer simulation methods to arrive at the final tertiary structures. Such 'models' can be of considerable use i) in understanding the biochemical reaction mechanisms in the structure-function relationships, ii) structure determination by X-ray methods (molecular replacement method), iii) drug design etc.     

First description of the male of Cryptothele verrucosa L. Koch, 1872 (Araneae), the type species of the genus

The male of Cryptothele verrucosa L. Koch, 1872, the type species of Cryptothele L. Koch, 1872, known from Fiji and Samoa, is described for the first time. It is compared with the male of C. alluaudi Simon, 1893, the single properly described species of the genus.     

Movement behaviour of the pine weevil Hylobius abietis in relation to soil type: an arena experiment

Pine weevil, Hylobius abietis (L.) (Coleoptera: Curculionidae), movement behaviour on different substrates was studied in an indoor arena using a video camera and digital image processing technique. We analysed individual variation in movement characteristics, i.e. turning angles, movement directions, and distance moved per unit time on the bare and level arena surface which consisted of mineral soil (sand) and/or humus sections in various spatial configurations. Pine weevils on humus did not turn back when they came to the border with the sand. However, most individuals moved faster on sand than on humus. Thus, the results suggest that interactions between substrate differences and individual movement behaviour may to some extent explain why pine weevils have been observed to feed less frequently on coniferous seedlings planted on mineral soil than on those planted on humus.     

Branched structures in the intracellular DNA of herpes simplex virus type 1.

Herpes simplex virus type 1 (HSV-1) replication produces large intracellular DNA molecules that appear to be in a head-to-tail concatemeric arrangement. We have previously suggested (A. Severini, A.R. Morgan, D.R. Tovell, and D.L.J. Tyrrell, Virology 200:428-435, 1994) that these DNA species may have a complex branched structure. We now provide direct evidence for the presence of branches in the high-molecular-weight DNA produced during HSV-1 replication. On neutral agarose two-dimensional gel electrophoresis, a technique that allows separation of branched restriction fragments from linear fragments, intracellular HSV-1 DNA produces arches characteristic of Y junctions (such as replication forks) and X junctions (such as merging replication forks or recombination intermediates). Branched structures were resolved by T7 phage endonuclease I (gene 3 endonuclease), an enzyme that specifically linearizes Y and X structures. Resolution was detected by the disappearance of the arches on two-dimensional gel electrophoresis. Branched structures were also visualized by electron microscopy. Molecules with a single Y junction were observed, as well as large tangles containing two or more consecutive Y junctions. We had previously shown that a restriction enzyme which cuts the HSV-1 genome once does not resolve the large structure of HSV-1 intracellular DNA on pulsed-field gel electrophoresis. We have confirmed that result by using sucrose gradient sedimentation, in which both undigested and digested replicative intermediates sediment to the bottom of the gradient. Taken together, our experiments show that the intracellular HSV-1 DNA is held together in a large complex by frequent branches that create a network of replicating molecules. The fact that most of these branches are Y structures suggests that the network is held together by frequent replication forks and that it resembles the replicative intermediates of bacteriophage T4. Our findings add complexity to the simple model of rolling-circle DNA replication, and they pose interesting questions as to how the network is formed and how it is resolved for packaging into progeny virions.     

Comparison of crystal structures of human type 3 3alpha-hydroxysteroid dehydrogenase reveals an "induced-fit" mechanism and a conserved basic motif involved in the binding of androgen

The aldo-keto reductase (AKR) human type 3 3alpha-hydroxysteroid dehydrogenase (h3alpha-HSD3, AKR1C2) plays a crucial role in the regulation of the intracellular concentrations of testosterone and 5alpha-dihydrotestosterone (5alpha-DHT), two steroids directly linked to the etiology and the progression of many prostate diseases and cancer. This enzyme also binds many structurally different molecules such as 4-hydroxynonenal, polycyclic aromatic hydrocarbons, and indanone. To understand the mechanism underlying the plasticity of its substrate-binding site, we solved the binary complex structure of h3alpha-HSD3-NADP(H) at 1.9 A resolution. During the refinement process, we found acetate and citrate molecules deeply engulfed in the steroid-binding cavity. Superimposition of this structure with the h3alpha-HSD3-NADP(H)-testosterone/acetate ternary complex structure reveals that one of the mobile loops forming the binding cavity operates a slight contraction movement against the citrate molecule while the side chains of many residues undergo numerous conformational changes, probably to create an optimal binding site for the citrate. These structural changes, which altogether cause a reduction of the substrate-binding cavity volume (from 776 A(3) in the presence of testosterone/acetate to 704 A(3) in the acetate/citrate complex), are reminiscent of the "induced-fit" mechanism previously proposed for the aldose reductase, another member of the AKR superfamily. We also found that the replacement of residues Arg(301) and Arg(304), localized near the steroid-binding cavity, significantly affects the 3alpha-HSD activity of this enzyme toward 5alpha-DHT and completely abolishes its 17beta-HSD activity on 4-dione. All these results have thus been used to reevaluate the binding mode of this enzyme for androgens.     

Polyacrylamide gel electrophoretic analysis of herpes simplex virus type 1 immunoprecipitates obtained by quantitative immunoelectrophoresis in antibody-containing agarose gel.

Crossed immunoelectrophoresis was used to characterize herpes simplex virus type 1 (HSV-1) antigens produced by infected HEp-2 cells. We report on a method for analyzing the polypeptide content in individual antigen-antibody precipitates eluted from the second-dimensional agarose gel. Four glycoprotein antigens of HSV-1, Ag-8, Ag-11, Ag-6, and Ag-3, were isolated and analyzed for polypeptide content. The molecular weights of the polypeptides are presented.     

Dissipative structures in morphogenetic models of the Turing type

We investigate the general conditions for morphogenesis. It is found that not only the Turing condition shall be satisfied, but also that some other requirements must be fulfilled. Their physical meaning is that the system should have more than one stationary state. In biological terms this means that the competence of differentiation is necessary in order to finish the morphogenesic process. These ideas are illustrated by a simple mathematical model. For this model the bifurcation analysis and computer results are discussed. Furthermore the parametric regulation of the morphogenesis is considered in connection with the role played by the genetic information.     

真江蓠(Gracilaria verrucosa)对网箱养殖海区的生态修复及生态养殖匹配模式

2006年8～9月,在浙江象山港花鲈(Lateolabrax japonicus)养殖网箱中吊养真江蓠(Gracilaria verrucosa)对网箱养殖造成的水体富营养化进行生态修复研究.通过45d内的平面监测、定点跟踪监测和断面监测,结果表明:该网箱养殖区水体呈严重富营养化状态,营养状态指数(E)为32.00,其营养盐分布由高浓度的中心区向周围150m非养殖水域扩散;真江蓠对养殖区的富营养化海水具有较好的修复效果:江蓠生态修复区及其相邻网箱中水体PO4-P、NO2-N、NH4-N和NO3-N含量显著低于非修复区(P＜0.01),修复区海水PO4-P、NO2-N、NH4-N和NO3-N浓度比非修复区分别降低22%～58%、24%～48%、22%～61%和24%～47%.养殖真江蓠45d后,修复区水体DO浓度和透明度显著高于非修复区(P＜0.05),DO平均提高28%,透明度平均提高30%;而修复区水体Chl-a浓度显著低于非修复区(P＜0.05),平均降低49%.通过建立基于N平衡的鱼藻生态养殖模式,每收获1kg花鲈至少需要匹配江蓠4.7 kg wet wt才可实现对鱼类排放N的完全吸收.因此网箱内栽培江蓠的混合生态养殖模式,可平衡因经济动物养殖所带来的额外营养负荷,有利于实现动物养殖环境的自我修复.     

H3-rules: identification of CDR-H3 structures in antibodies.

For the third complementarity determining region of the antibody heavy chain (CDR-H3), we propose the 'H3-rules', which should identify the tertiary structure from the amino acid sequence of the CDR-H3 segment. A total of 100 CDR-H3 segments from well-determined crystal structures were analyzed. Distinctive relationships between the structures and the sequences were revealed from 55 segments, and the rules were examined for the other 45 segments and were verified. In some antibodies, basic residues at specific positions were revealed to be notable signals, with their ability to form salt bridges and to assume conformations inconsistent with the rules.     

Alterations in the U3 region of the long terminal repeat of an infectious thymotropic type B retrovirus.

We isolated and characterized a type B thymotropic retrovirus (DMBA-LV) which is highly related to mouse mammary tumor virus (MMTV) isolates and which induces T-cell thymomas with a high incidence and a very short latent period. Regions of nonhomology between the DMBA-LV genome and the MMTV genome were identified by heteroduplex mapping and nucleotide sequence studies. In the electron microscope heteroduplex mapping studies the EcoRI-generated 5' and 3' fragments of the DMBA-LV genome were compared with the corresponding fragments of the MMTV (C3H and GR) genome isolated from mammary tumors. The results indicated that DMBA-LV contained a region of nonhomologous nucleotide sequences in the 3' half of the U3 region of the long terminal repeat (LTR). Nucleotide sequence studies confirmed these results and showed that in this region 440 nucleotides of the MMTV (C3H) sequences were deleted and substituted with a segment of 122 nucleotides. This substituted segment in the form of a tandem repeat structure contained nucleotide sequences derived exclusively from sequences which flanked the substitution loop. The distal glucocorticoid regulatory element was unaltered, and two additional copies of the distal glucocorticoid regulatory element-binding site were present in the substituted region. The restriction endonuclease map of the reconstructed molecular clone of DMBA-LV was identical to that corresponding to unintegrated linear DMBA-LV DNA present in DMBA-LV-induced tumor cell lines. Since the nucleotide sequences of the LTRs present in four different DMBA-LV proviral copies isolated from a single thymoma were identical, we concluded that they were derived from the same parental virus and that this type B retrovirus containing an alteration in the U3 region of its LTR could induce thymic lymphomas. Thus, DMBA-LV represents the first example of a productively replicating type B retrovirus that contains an LTR modified in the U3 region and that has target cell and disease specificity for T cells.     

Expression of the Streptococcus pneumoniae type 3 synthase in Escherichia coli. Assembly of type 3 polysaccharide on a lipid primer.

Synthesis of the type 3 capsular polysaccharide of Streptococcus pneumoniae is catalyzed by the membrane-localized type 3 synthase, which utilizes UDP-Glc and UDP-GlcUA to form high molecular mass [3-beta-d-GlcUA-(1-->4)-beta-d-Glc-(1-->](n). Expression of the synthase in Escherichia coli resulted in synthesis of a 40-kDa protein that was reactive with antibody directed against the C terminus of the synthase and was the same size as the native enzyme. Membranes isolated from E. coli contained active synthase, as demonstrated by the ability to incorporate Glc and GlcUA into a high molecular mass polymer that could be degraded by type 3 polysaccharide-specific depolymerase. As in S. pneumoniae, the membrane-bound synthase from E. coli catalyzed a rapid release of enzyme-bound polysaccharide when incubated with either UDP-Glc or UDP-GlcUA alone. The recombinant enzyme expressed in E. coli was capable of releasing all of the polysaccharide from the enzyme, although the chains remained associated with the membrane. The recombinant enzyme was also able to reinitiate polysaccharide synthesis following polymer release by utilizing a lipid primer present in the membranes. At low concentrations of UDP-Glc and UDP-GlcUA (1 microm in the presence of Mg(2+) and 0.2 microm in Mn(2+)), novel glycolipids composed of repeating disaccharides with linkages consistent with type 3 polysaccharide were synthesized. As the concentration of the UDP-sugars was increased, there was a marked transition from glycolipid to polymer formation. At UDP-sugar concentrations of either 5 microm (with Mg(2+)) or 1.5 microm (with Mn(2+)), 80% of the incorporated sugar was in polymer form, and the size of the polymer increased dramatically as the concentration of UDP-sugars was increased. These results suggest a cooperative interaction between the UDP-precursor-binding site(s) and the nascent polysaccharide-binding site, resulting in a non-processive addition of sugars at the lower UDP-sugar concentrations and a processive reaction as the substrate concentrations increase.